US 2012O178642A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2012/0178642 A1 Salomon et al. (43) Pub. Date: Jul. 12, 2012

(54) GENE EXPRESSION PROFILES ASSOCATED Related U.S. Application Data WITH CHRONICALLOGRAFT (60) Provisional application No. 61/224.328, filed on Jul.9. NEPHROPATHY 2009, provisional application No. 61/224.317, filed on Jul. 9, 2009. (75) Inventors: Daniel Salomon, San Diego, CA (US); Sunil M. Kurian, Ssan Publication Classification Diego, CA (US); Steven R. Head, (51) Int. Cl. Lakeside, CA (US) C40B 30/04 (2006.01) C40B 40/06 (2006.01) (73) Assignee: The Scripps Research Institute, (52) U.S. Cl...... 506/9; 506/16 La Jolla, CA (US) (57) ABSTRACT (21) Appl. No.: 13/261,130 By a genome-wide gene analysis of expression profiles of over 50,000 known or putative gene sequences in peripheral (22) PCT Fled: Jul. 9, 2010 blood, the present inventors have identified a consensus set of gene expression-based molecular biomarkers associated with (86) PCT NO.: PCT/US2O10/041598 chronic allograft nephropathy and/or interstitial fibrosis and tubular atrophy CAN/IFTA and subtypes thereof. These S371 (c)(1), genes sets are useful for diagnosis, prognosis, monitoring (2), (4) Date: Mar. 20, 2012 and/or subtyping of CAN/IFTA. Patent Application Publication Jul. 12, 2012 Sheet 1 of 2 US 2012/0178642 A1

Top 50 Mild CAN genes 1.0 ------0.9 ------0.8 -- 0.7 ----- Top 50 Mild CAN genes 0.6 -

0.5 79%. 82% 0.4 82% 79%

O.O O.2 0.4 O.6 O.8 1.O FIG. 1 Patent Application Publication Jul. 12, 2012 Sheet 2 of 2 US 2012/0178642 A1

Top 50 ModeratelSevere CAN Genes

'll ------0.85 / ----- Top 50 Moderate/Severe CAN Genes 0.65

0.45 Banff 2,3

FIG. 2 US 2012/0178642 A1 Jul. 12, 2012

GENE EXPRESSION PROFILES ASSOCATED genes that are differentially expressed at the mRNA level in WITH CHRONICALLOGRAFT kidney biopsies in the presence of CAN/IFTA16.20.21. The NEPHROPATHY limitation of these studies is that they require an invasive transplant biopsy. Others have reported analyzing urine and CROSS-REFERENCE TO RELATED peripheral blood using RT-qPCR or proteomics to identify APPLICATIONS small numbers of potential biomarkers for CAN/IFTA, 0001. The present application is a nonprovisional and though none is validated for clinical use22.23. claims the benefit of U.S. Ser. No. 61/224,328 and 61/224, 317 each filed Jul. 9, 2009, and incorporated by reference in BRIEF SUMMARY OF THE INVENTION its entirety for all purposes. 0006. The invention provides methods of prognosing, diagnosing or monitoring chronic allograft nephropathy and/ STATEMENT AS TO RIGHTS TO INVENTIONS or interstitial fibrosis and tubular atrophy (CAN/IFTA). The MADE UNDER FEDERALLY SPONSORED methods entail (a) determining expression levels in a subject RESEARCH ORDEVELOPMENT of at least 5 genes selected from the genes in Table A, B, C, D, E, F, G, H, I and/or J.; and (b) prognosing diagnosing or 0002 The invention was made in part with funding pro monitoring CAN/IFTA in a subject from the expression lev vided by NIH grant U19A1063603. The US Government has els. Optionally, for each of the at least five genes, step (b) certain rights in the invention. comprises comparing the expression level of the gene in the Subject to one or more reference expression levels of the gene BACKGROUND OF THE INVENTION associated with CAN/IFTA or lack of CAN/IFTA. Option 0003 Kidney transplantation offers a significant improve ally, step (b) further comprises for each of the at least five ment in life expectancy and quality of life for patients with genes assigning the expression level of the gene in the Subject end stage renal disease 1. Unfortunately, a chronic, progres a value or other designation providing an indication whether sive allograft dysfunction of uncertain etiology continues to the subject has or is at risk of CAN/IFTA. Optionally, the be a primary cause of graft loss2.3. There has been some expression level of each of the at least five genes is assigned evolution of terminology for describing the histological basis a value on a normalized scale of values associated with a of this chronic, progressive nephropathy, which is still com range of expression levels in kidney transplant patients with monly referred to as chronic allograft nephropathy (CAN) and without CAN/IFTA. Optionally, the expression level of and more recently as interstitial fibrosis and tubular atrophy each of the at least five genes is assigned a value or other (IFTA)4-6. In current practice CAN refers to a clinical designation providing an indication that the Subject has is at entity of a chronic progressive loss of kidney transplant func risk of CAN/IFTA, lacks and is not at risk of CAN/IFTA, or tion associated with a rising serum creatinine and a falling that the expression level is uninformative. Optionally, step (b) creatinine clearance. In current practice, IFTA refers to the further comprises, combining the values or designations for histological findings based on review of a kidney transplant each of the genes to provide a combined value or designation biopsy. Immunologic factors linked to CAN/IFTA are acute, providing an indication whether the Subject has or is at risk of sub-clinical and CAN/IFTA, HLA mismatching and circulat CAN/IFTA. Optionally, the method is repeated at different ing donor-specific anti-HLA antibodies7.8). Non-immuno times on the Subject. logic factors include hypertension, chronic toxicity of cal 0007. In some methods, the subject is receiving a drug, and cineurin inhibitors, hyperfiltration and diabetes mellitus 9 a change in the combined value or designation over time 12. The unifying mechanism is thought to be a progressive provides an indication of the effectiveness of the drug. cycle of vascular and tissue injury, incomplete repair, com Optionally, the Subject has undergone a kidney transplant pensatory hypertrophy, progressive interstitial fibrosis and within 1-10 years of performing step (a). Optionally, step (a) nephron loss 13. Moreover, increasing evidence is Suggest is performed on a blood sample of the subject. Optionally, the ing that the primary mechanism of CAN/IFTA is a chronic blood sample is a plasma sample. Optionally, step (a) is immunological injury mediated by a combination of T cell performed on at least ten, 20, 40, or 100 genes from Table A, and antibody-mediated immunity, in other words, chronic B, C, D, E, F, G, H, I and/or J. rejection. 0008. Some methods further comprise changing the treat 0004 As early as two years post kidney transplant, proto ment regime of the patient responsive to the prognosing, col biopsies have shown that more than 50% of recipients diagnosing or monitoring step. In some methods, the Subject have mild CAN/IFTA2,15,16 and by 10 years over 50% of has received a drug before performing the methods, and the kidney transplant recipients have severe CAN/IFTA that is change comprises administering an additional drug or admin associated with diminishing graft function2. Traditional istering a higher dose of the same drug. Some methods, fur kidney function measurements like serum creatinine and ther comprise performing an additional procedure, such as a glomerular filtration rates used to predict CAN/IFTA have kidney biopsy, to detect CAN/IFTA or risk thereof if the poor predictive values 17 and a diagnosis requires a trans determining step provides an indication the Subject has or is at plant biopsy 18, 19. Predicting graft outcomes strictly based risk of CANAIFTA. on the kidney biopsy is difficult and this invasive procedure In some methods, the at least five genes are from Table A, B, has significant costs and risks for patients. Thus, there is a C and/or D expression levels are determined at the mRNA pressing medical need to identify minimally invasive biom level. In some methods, the at least five genes are from Tables arkers that are able to identify early stages of CAN/IFTA at a E, F, G, H, I, and/or J and expression levels are determined at time that changes in therapy may alter outcomes. the protein level. In some methods, step (b) is performed by a 0005 Rapidly evolving technologies for genomics have computer. In some methods, the at least five genes are created new opportunities to develop minimally invasive selected from Tables C and D. In some methods, the at least biomarkers. Recent studies, including our own, have reported five genes are selected from Table C. In some methods, the at US 2012/0178642 A1 Jul. 12, 2012

least five genes are selected from Table D. In some methods, reference expression levels of the gene associated with the the at least five genes are selected from Table E and For Hand subtype of CAN/IFTA or lack of CAN/IFTA. Some methods I and expression levels are determined at the protein level. further comprise for each of the at least five genes assigning 0009. The invention further provides an array, comprising the expression level of the gene in the subject a value or other a Support or Supports bearing a plurality of nucleic acid designation providing an indication whether the Subject has probes complementary to a plurality of mRNAs fewer than or is at risk of the subtype of CAN/IFTA. In some methods, 5000 in number, wherein the plurality of mRNAs includes the expression level of each of the at least five genes is mRNAs expressed by at least five genes selected from Tables assigned a value on a normalized scale of values associated A, B, C, D. Optionally, the plurality of mRNAs are fewer than with a range of expression levels in kidney transplant patients 1000, or 100 in number. Optionally a plurality of nucleic acid with the subtype and without CAN/IFTA. In some methods, probes are attached to a planar Support or to beads. Option the expression level of each of the at least five genes is ally, the at least five genes are selected from Table C and D. assigned a value or other designation providing an indication Optionally, the at least five genes are selected from Table C. that the subject has or is at risk of the subtype of CAN/IFTA, Optionally, the at least five genes are selected from Table D. lacks and is not at risk of the subtype of CAN/IFTA, or that the 0010. The invention further provides an array, comprising expression level is uninformative. In some methods, step (b) a Support or Supports bearing a plurality of ligands that spe further comprises, combining the values or designations for cifically bind to a plurality of proteins fewer than 5000 in each of the genes to provide a combined value or designation number, wherein the plurality of proteins includes at least five providing an indication whether the Subject has or is at risk of proteins selected from Tables E, F, G, H, I and/or J. Option the subtype of CAN/IFTA. Some methods are repeated at ally, the plurality of proteins are fewer than 1000 or 100 in different times on the subject. In some methods, the subject is number. Optionally, the plurality of ligands are attached to a receiving a drug, and a change in the combined value or planar Support or to beads. Optionally, the at least five pro designation over time provides an indication of the effective teins are selected from Tables E and F and/or I and J. Option ness of the drug. In some methods, the Subject has undergone ally, the ligands are different antibodies, wherein the different a kidney transplant within 1-10 years of performing step (a). antibodies bind to different proteins of the plurality of pro Some methods are performed on a blood sample of the sub teins. ject, Such as a plasma or whole blood sample. Some methods 0011. The invention further provides a method of expres are performed on at least ten, 20, 40 or 100 genes selected sion analysis, comprising determining expression levels of up from Tables A, B, C, D, E, F, G, H, I and/or J. Some methods to 5000 genes in a sample from a subject having a kidney further comprise changing the treatment regime of the patient transplant, wherein the genes include at least 5 genes selected responsive to the whether the subtype is present. In some from Table A, B, C, D, E, F, G, H, I and/or J. Optionally, the methods, the Subject has received a drug before performing expression levels of up to 1000 or 100 genes are determined. the methods, and the change comprises administering an The expression levels can be determined at the mRNA or additional drug or administering a higher dose of the same protein level. The levels can be determined by, for example, drug. Some methods further comprise performing an addi quantitative PCR or hybridization to an array. tional procedure, such as a kidney biopsy, to detect CAN/ 0012. The invention further provides methods of screen IFTA or risk thereof if the determining step provides an indi ing a compound for activity in inhibiting or treating CAN/ cation the subject has or is at risk of the subtype of CAN/ IFTA. The methods entail (a) administering the compound to IFTA. Expression levels can be determined at the mRNA or a subject having or at risk of CAN/IFTA; (b) determining protein level. In some methods, step (b) is performed by a expression levels of at least five genes in the Subject selected computer. In some methods, the at least five genes are from Table A, B, C, D, E, F, G, H, I, and/or J and species selected from Table C. In some methods, the at least five variants thereof before and after administering the drug to the genes are selected from Table D. In some methods, the at least Subject, and (c) determining whether the compound has activ five genes are selected from Table E and expression levels are ity in inhibiting or treating CAN/IFTA from a change in determined at the protein level. In some methods, the at least expression levels of the genes after administering the com five genes are selected from Table F and the expression levels pound. Optionally, step (c) comprises for each of the at least are determined at the protein level. In some methods, the at five changes assigning a value or designation depending on least five genes are selected from Table H and the expression whether the change in the expression level of the gene relative levels are determined at the protein level. In some methods, to one or more reference levels indicating presence or absence the at least five genes are selected from Table I and the of CAN/IFTA. Optionally, the method further comprises expression levels are determined at the protein level. determining a combined value or designation for the at least five genes from the values or designations determined for BRIEF DESCRIPTION OF THE DRAWINGS each gene. Optionally, the Subject is human or a nonhuman 0014 FIG. 1: Class prediction analysis of Banff 0 vs. animal model of CAN/IFTA. Banff 1 (mild CAN/IFTA) based on Diagonal Linear Dis 0013 The invention further provides methods of subtyp criminant Analysis for the top 50 Banff0 vs. Banff 1 consen ing CAN/IFTA. The methods entail (a) determining expres SuS genes ranked by p values. A) depicts the Receiver Oper sion levels in a subject of at least 5 genes selected from the ating Characteristic (ROC) curves and provides the genes in Tables A, B, C, D, E, F, G, H, I and/or J.; and (b) Sensitivity, Specificity, Positive Predictive Value (PPV) and determining a subtype of CAN/IFTA from the expression Negative Predictive Value (NPV): levels. The Subtype can be selected from the group consisting (0015 FIG. 2: Class prediction analysis of Banff 0 vs. of stage 0, 1, 2, or 3 of CAN/IFTA. Optionally, the subtype is Banff 2.3 (moderate to severe CAN/IFTA) based on Diagonal stage 0, stage 1 or stage 2 and/or 3. In some methods for each Linear Discriminant Analysis for the top 50 Banff0 vs. Banff of the at least five genes, step (b) comprises comparing the 2.3 consensus genes ranked by p values. A) depicts the expression level of the gene in the Subject to one or more Receiver Operating Characteristic (ROC) curves and pro US 2012/0178642 A1 Jul. 12, 2012

vides the Sensitivity, Specificity, Positive Predictive Value dition. This includes persons with no defined illness who are (PPV) and Negative Predictive Value (NPV); B) depicts the being investigated for signs of pathology. heat map classifying Banff 0 vs. Banff 2.3 using the top 50 0023 Diagnosis refers to methods of estimating or deter consensus genes where (red) is up-regulated and (green) is mining whether or not a patient is Suffering from a given down-regulated. disease or condition or severity of the condition. Diagnosis does not require ability to determine the presence or absence DEFINITIONS of a particular disease with 100% accuracy, or even that a given course or outcome is more likely to occur than not. 0016. The term Chronic Allograft Nephropathy/Intersti Instead, the “diagnosis' refers to an increased probability that tial Fibrosis and Tubular Atrophy (CAN/IFTA) refers to a a certain disease or condition is present in the Subject com progressive, chronic, kidney tissue injury that eventually pared to the probability before the diagnostic test was per causes a progressive, chronic deterioration of kidney trans formed. plant function. The histological changes of CAN/IFTA can be 0024. Similarly, a prognosis signals an increased probabil found in protocol kidney transplant biopsies as early as 6 ity that a given course or outcome will occur in a patient months post transplant and frequently the clinical changes of relative to the probability before the prognostic test. progressive kidney transplant dysfunction evolve Subse 0025. A probe or polynucleotide probe is an nucleic acid quently over the next year or several years (e.g., six months to capable of binding to a target nucleic acid of complementary ten years). CAN/IFTA is usually a consequence of combined sequence through one or more types of chemical bonds, usu immunological injury (e.g. chronic rejection) and non-immu ally through complementary base pairing, usually through nological damage (e.g. hypertensive nephrosclerosis, or hydrogen bond formation, thus forming a duplex structure. nephrotoxicity of immunosuppressants like cyclosporine A), The probe binds or hybridizes to a “probe binding site. A taking place months or years after transplantation and ulti probe can include natural (i.e., A, G, C, or T) or modified mately leading to histologically detectable fibrosis and scle bases (e.g., 7-deazaguanosine, inosine.). A probe can be an rosis of the transplant and progressive loss of kidney function. oligonucleotide which is a single-stranded DNA. Polynucle Chronic rejection of a transplanted kidney is increasingly otide probes can be synthesized or produced from naturally thought to be the major mechanism of CAN/IFTA mediated occurring polynucleotides. In addition, the bases in a probe through both T cell mediated immunity and antibodies can be joined by a linkage other than a phosphodiester bond, directed at antigens expressed in the kidney transplant. The so long as it does not interfere with hybridization. Thus, hybrid term, CAN/IFTA includes histological changes and/or probes can include, for example, peptide nucleic acids in functional deterioration of the kidneys or both. In some which the constituent bases are joined by peptide bonds rather patients, the present methods can provide an indication of than phosphodiesterlinkages (see, e.g., Nielsen et al., Science histological changes before detectable functional deteriora 254, 1497-1500 (1991)). Some probes can have leading and/ tion of the kidneys has occurred, thereby allowing early thera or trailing sequences of noncomplementarity flanking a peutic intervention. region of complementarity. 0017 Transplantation is the transfer of tissues, cells oran 0026. A perfectly matched probe has a sequence perfectly organ from a donor into a recipient. If the donorand recipient complementary to a particular target sequence. The probe is as the same person, the graft is referred to as an autograft and typically perfectly complementary to a portion (Subsequence) as is usually the case between different individuals of the of a target sequence. The term “mismatch probe' refer to same species an allograft. Transfer of tissue between species probes whose sequence is deliberately selected not to be is referred to as a Xenograft. perfectly complementary to a particular target sequence. 0018. A biopsy is a specimen obtained from a living (0027. The term “isolated,” “purified” or “substantially patient for diagnostic evaluation. Kidney biopsies can be pure” means an object species (e.g., a nucleic acid sequence obtained with a needle. described herein or a polypeptide encoded thereby) has been 0019. An average value can refer to any of a mean, median at least partially separated from the components with which it or mode. is naturally associated. 0020. A gene expression level is associated with a particu 0028. Differential expression refers to a statistically sig lar phenotype e.g., presence of CAN/IFTA or a subtype nificant difference in expression levels of a gene between two thereof if the gene is differentially expressed in a patient populations of samples (e.g., Samples with and without CAN/ having the phenotype relative to a patient lacking the pheno IFTA). The expression levels can differ for example by at least type to a statistically significant extent. Unless otherwise a factor of 1.5 or 2 between such populations of samples. apparent from the context a gene expression level can be Differential expression includes genes that are expressed in measured at the mRNA and/or protein level. one population and are not expressed (at least at detectable 0021. A target nucleic acids is a nucleic acid (often derived levels) in the other populations. Unique expression refers to from a biological sample), to which a polynucleotide probe is detectable expression in one population and undetectable designed to specifically hybridize. The probe can detect pres expression (i.e., insignificantly different from background) in ence, absence and/or amount of the target. The term can refer the other population using the same technique (e.g., as in the to the specific Subsequence of a larger nucleic acid to which present example for detection). the probe is directed or to the overall sequence (e.g., cDNA or 0029 Control populations for comparison with popula mRNA) whose expression level it is desired to detect. tions undergoing CAN/IFTA are usually referred to as being 0022. The term subject or patient can include human or without CAN/IFTA. Unless otherwise indicated, such a con non-human animals. Thus, the methods and described herein trol population also means Subjects without acute kidney are applicable to both human and Veterinary disease and rejection. animal models. Preferred subjects are “patients, i.e., living 0030 Hybridization reactions are preferably performed humans that are receiving medical care for a disease or con understringent conditions in which probes or primers hybrid US 2012/0178642 A1 Jul. 12, 2012 ize to their intended target with which they have perfect provides similar information to Table E for 28 genes uniquely complementarity and not to or at least to a reduced extent to expressed in kidney transplant patients not undergoing CAN/ other targets. An example of stringent hybridization condi ITFA and not at detectable levels in patients undergoing tions are hybridization in 6x sodium chloride/sodium citrate CAN/IFTA level 2 or 3. Table I provides similar information (SSC) at about 45° C., followed by one or more washes in to Table F for 510 proteins uniquely expressed in CAN/IFTA 0.2xSSC, 0.1% SDS at 50° C., 55° C., 60° C., and even more level 2 or 3 and not detectable in kidney transplant patients not or 65° C. undergoing CAN/IFTA. Table J provides similar information 0031 Statistical significance means p-0.05 or <0.01 or to Table G for 284 proteins differentially expressed between even <0.001 level. kidney transplant patients at CAN/IFTA level 0 versus level 2 or 3. If a gene symbol or gene name is not available, the DETAILED DESCRIPTION OF THE INVENTION protein symbol should be understood as referring to both the genes. I. General 0035. The genes referred to in the above tables are human 0032. By a genome-wide gene analysis of expression pro genes. In some methods, species variants or homologs of files of over 50,000 known or putative gene sequences in these genes are used in a non-human animal model. Species peripheral blood, the present inventors have identified con variants are the genes in different species having greatest sensus sets of gene expression-based molecular biomarkers sequence identity and similarity in functional properties to associated with CAN/IFTA. A set of 393 genes has differen one another. Many species variants of the above human genes tial expression levels between mild chronic allograft nephr are listed in the Swiss-Prot database. opathy (CAN/IFTA) and non-rejected transplants. A set of 63 0036 Raw gene expression levels are comparable genes have differential expression between moderate or between different genes in the same sample but not necessar severe CAN/IFTA and non-rejected transplants. Additional ily between different samples. As noted above, values given set of protein markers showing differential or unique expres for gene expression levels can be normalized so that values sion between CAN/IFTA and nonrejected transplants are also for particular genes are comparable within and between the provided. populations being analyzed. The normalization eliminates or at least reduces to acceptable levels any sample to sample II. Genes in Profiles differences arising from factors other than CAN/IFTA (e.g. 0033 Table A lists 393 genes whose expression changes differences in overall transcription levels of patients due to significantly between kidney transplant patients undergoing general state of health and differences in sample preparation mild CAN/IFTA, Banff stage 1 compared with patients not or nucleic acid amplification between samples). The normal undergoing Such rejection (Banffstage 0) one year post trans ization effectively applies a correction factor to the measured plant. The columns in the table have the following meanings: expression levels from a given array Such that a profile of column 1 is a number assigned to a gene, column 2 is a many expression levels in the array are the same between measure of the statistical significance of change in gene different patient samples. Software for normalizing overall expression between the above populations, column 3 is a expression patterns between different samples is both com mean expression level of a gene in kidney transplant patients mercially and publically available (e.g., XRAY from Biotique undergoing chronic rejection (normalized as described Systems or BRB ArrayTools from the National Cancer Insti below), column 4 is mean expression level of the gene in tute). After applying appropriate normalizing factors to the kidney transplant patients not undergoing CAN/IFTA (simi measured expression value of a particular gene in different larly normalized), column 5 is a ratio of the expression levels, samples, an average value of the expression level is deter column 6 is an Affymetrix number indicating a set of probes mined for the samples in a population. The average values Suitable for measuring expression of the gene, column 7 is a between different populations are then compared to deter gene name (recognized names of HUGO or similar bodies are mine whether expression level has changed significantly used when available), and column 8 is a further description of between the populations. The changes in expression level the gene. Table B provides similar information for 62 genes indicated for a given gene represent the relative expression that show differential expression between kidney transplant level of that gene in Samples from a population of individuals patients undergoing moderate or severe CAN/IFTA (Banff with a defined condition (e.g., transplant patients with CAN/ stage 2 or 3) with kidney transplant patients not undergoing IFTA of specified Banff stage) relative to samples from a CAN/IFTA. Tables C and D provide subsets of 50 preferred control population (kidney transplant patients not undergoing genes from Tables A and B respectively. CAN/IFTA). Similar principles apply in normalizing gene 0034 Table E provides 117 genes and corresponding pro expression levels at the mRNA and protein levels. Compari teins for which the proteins is uniquely expressed in patients Sons between populations are made at the same level (e.g., not undergoing CAN/IFTA and not at detectable levels in mRNA levels in one population are compared with mRNA patients undergoing CAN/IFTA level 1. Column 1 is a levels in another population or protein levels in one popula sequential number for a gene/protein, column 2 is a protein tion with protein levels in another population). symbol, column 3 is a gene symbol, and column 4 is a gene III. Subject Population name. Table F provides similar information about 143 pro teins uniquely expressed in patients undergoing CAN/IFTA 0037. The methods are particularly useful on human sub and not at detectable levels in kidney transplant patients with jects who have undergone a kidney transplant although can out CAN/IFTA. Table G provides similar information regard also be used on Subjects who have gone other types of trans ing 188 proteins that are differentially expressed between plant (e.g., heart, liver, lungs, stem cell) or on non-humans CAN/IFTA levels 0 and 1. The right hand column of the table who have undergone kidney or other transplant. Gene expres indicates the degree of differential expression with positive sion levels in Such subjects can be measured, for example, numbers being upregulated in Banffstage 1 patients. Table H within, three months, six months, one year, two years, five US 2012/0178642 A1 Jul. 12, 2012 years or ten years after a kidney transplant. In some methods, 0041) A variety of approaches are available for determin gene expression levels are determined at regular intervals, ing mRNA levels including probe arrays and quantitative e.g., every 3 months, 6 months or every year posttransplant, PCR. A number of distinct array formats are available. Some either indefinitely, or until evidence of CAN/IFTA is arrays, such as an Affymetrix GeneChip(R) array, have differ observed, in which case the frequency of monitoring is some ent probes occupying discrete known areas of a contiguous times increased. In some methods, baseline values of expres Support. Other arrays, such as arrays from Illumina, have sion levels are determined in a subject before a kidney trans different probes attached to different particles or beads. In plant in combination with determining expression levels at such arrays, the identity of which probe is attached to which one or more time points thereafter. In other methods, a mea particle or beads is usually determinable from an encoding Surement is initiated responsive to some other indication of system. The probes can be oligonucleotides. In such case, potential kidney impairment, such as a rise in levels of crea typically several match probes are included with perfect tinine or BUN or a decrease in glomerular filtration rate. complementarity to a given target mRNA together, optionally Similar methods can be practiced in non-human species, in together with mismatch probes differing from the match which cases, the expression levels measured are the species probes area known number of oligonucleotides (Lockhart, et equivalent of the human genes referenced above. al., Nature Biotechnology 14:1675-1680 (1996); and Lips chutz, et al., Nature Genetics Supplement 21:20-24, 1999). IV. Chronic Allograft Nephropathy (Can/IFTA) and its Sub Other arrays including full length cDNA sequences with per types fect or near perfect complementarity to a particular cDNA 0038. The methods are particularly useful for detecting (Schena et al. (Science 270:467-470 (1995); and DeRisi et al. CAN/IFTA. CAN/IFTA can be further classified by histologi (Nature Genetics 14:457-460 (1996)). Such arrays can also cal analysis of kidney transplant biopsies based on the Banff include various control probes, such as a probe complemen 2007 schema and the following four subtypes or stages are tarity with a housekeeping gene likely to be expressed in most recognized indicating severity: 0 (no CAN/IFTA), 1 (mild samples. Regardless of the specifics of array design, an array CAN/IFTA), 2 (moderate CAN/IFTA) and 3 (severe CAN/ contains one or more probes either perfectly complementary IFTA)4. An alternative and complementary histology grad to a particular target mRNA or sufficiently complementarity ing schema is the Chronic Allograft Damage Index (CADI) to the target mRNA to distinguish it from other mRNAs in the score and this score is often provided by pathologists with the sample, and the presence of Such a target mRNA can be Banff classification score as Supplemental information (for determined from the hybridization signal of such probes, example, see Yilmaz et al., JAm Soc Nephrol 2003 14: 773 optionally by comparison with mismatch or other control 779). There is also a Banff 2007 classification for acute rejec probes included in the array. Typically, the target bears a tion 4. Acute rejection is characterized histologically by an fluorescent label, in which case hybridization intensity can be active, inflammatory/immune cell infiltration comprised of determined by, for example, a scanning confocal microscope various numbers of T cells and B cells as well as sometimes in photon counting mode. Appropriate scanning devices are plasma cells, eosinophils, neutrophils and macrophages. described by e.g., U.S. Pat. No. 5,578,832, and U.S. Pat. No. 5,631,734. The intensity of labeling of probes hybridizing to V. Methods of Measuring Profiles aparticular mRNA or its amplification product provides a raw measure of expression level. 0039. The preferred sample type for analysis is a blood 0042. In other methods, expression levels are determined sample, which refers to whole blood or fractions thereof, such by so-called “real time amplification' methods also known as as plasma, or lymphocytes. Other samples that can be ana quantitative PCR or Taqman (see, e.g., U.S. Pat. Nos. 5,210, lyzed include urine, feces, saliva, and a kidney biopsy. The 015 to Gelfand, 5,538,848 to Livak, et al., and 5,863,736 to samples are typically isolated from a Subject, particularly as a Haaland, as well as Heid, C. A., et al., Genome Research, peripheral blood sample, and not returned to the subject. The 6:986-994 (1996); Gibson, U. E. M. et al., Genome Research analytes of interests in the samples can be analyzed with or 6:995-1001 (1996); Holland, P. M., et al., Proc. Natl. Acad. without further processing of the sample, Such as purification Sci. USA 88:7276-7280, (1991); and Livak, K.J., et al., PCR and amplification. Samples not requiring biopsy to obtain, Methods and Applications 357-362 (1995)). The basis for this particularly peripheral blood, are preferred. method of monitoring the formation of amplification product 0040 Expression profiles are preferably measured at the is to measure continuously PCR product accumulation using nucleic acid level, meaning that levels of mRNA or nucleic a dual-labeled fluorogenic oligonucleotide probe. The probe acid derived therefrom (e.g., cDNA or cRNA). An expression used in Such assays is typically a short (ca. 20-25 bases) profile refers to the expression levels of a plurality of genes in polynucleotide that is labeled with two different fluorescent a sample. A nucleic derived from mRNA means a nucleic acid dyes. The 5' terminus of the probe is typically attached to a synthesized using mRNA as a template. Methods of isolation reporter dye and the 3' terminus is attached to a quenching dye and amplification of mRNA are well known as described for The probe is designed to have at least Substantial sequence example WO97/10365, WO 97/27317, Chapter 3 of Labora complementarity with a site on the target mRNA or nucleic tory Techniques in Biochemistry and Molecular Biology acid derived from. Upstream and downstream PCR primers Hybridization With Nucleic Acid Probes, Part I. Theory and that bind to flanking regions of the locus are also added to the Nucleic Acid Preparation, (P. Tijssen, ed.) Elsevier, N.Y. reaction mixture. When the probe is intact, energy transfer (1993). If mRNA or a nucleic acid therefrom is amplified, the between the two fluorophors occurs and the quencher amplification is performed under conditions that approxi quenches emission from the reporter. During the extension mately preserve the relative proportions of mRNA in the phase of PCR, the probe is cleaved by the 5' nuclease activity original samples, such that the levels of the amplified nucleic of a nucleic acid polymerase Such as Taq polymerase, thereby acids can be used to establish phenotypic associations repre releasing the reporter from the polynucleotide-quencher and sentative of the mRNAs. resulting in an increase of reporter emission intensity which US 2012/0178642 A1 Jul. 12, 2012

can be measured by an appropriate detector. The recorded from several different pathways are represented (e.g., at least values can then be used to calculate the increase in normal one gene from at least 2, 3, 5, or 10 pathways, such as those ized reporter emission intensity on a continuous basis and described in the Examples). The genes within a pathway tend ultimately quantify the amount of the mRNA being amplified. to be expressed in a co-ordinated expression whereas genes mRNA levels can also be measured without amplification by from different pathways tend to be expressed more indepen hybridization to a probe, for example, using a branched dently. Thus, changes in expression based on the aggregate nucleic acid probe, such as a QuantiGene R. Reagent System changes of genes from different pathways can have greater from Panomics. Statistical significance than aggregate changes of genes 0043 Alternatively or additionally, expression levels of within a pathway. genes can be determined at the protein level, meaning that 0045. In some methods, expression levels of at least 2, 3, 4, levels of proteins encoded by the genes discussed above are 5, 10, 20, 25, 50, 100, or 150 proteins or corresponding genes measured. Several methods and devices are well known for shown in any of Tables E, F, G, H, I and/or Jare determined. determining levels of proteins including immunoassays Such In some methods, expression levels of at least 2,3,4, 5, 10, 20, as described in e.g., U.S. Pat. Nos. 6,143,576; 6,113,855: 25, 50, 100, 150 or all proteins or genes shown in Table E, F, 6,019,944; 5,985,579; 5,947,124; 5,939,272; 5,922,615; and/or G are determined and/or expression levels of 2, 3, 4, 5, 5,885,527; 5,851,776; 5,824,799; 5,679,526; 5,525,524; and 10, 20, 25, 50 or all proteins or genes shown in Tables H, I 5,480,792. These assays include various sandwich, competi and/or Jare determined. In some methods, proteins or genes tive, or non-competitive assay formats, to generate a signal are selected from the same table (e.g., proteins uniquely that is related to the presence or amount of an protein analyte expressed in Banffstage 1, or corresponding genes). In some of interest. Any Suitable immunoassay may be utilized, for methods, proteins or genes are selected from two tables (e.g., example, lateral flow, enzyme-linked immunoassays proteins uniquely expressed in Banff stage 0 (or correspond (ELISA), radioimmunoassays (RIAS), competitive binding ing genes) and proteins uniquely expressed in Banff Stage 1 assays, and the like. Numerous formats for antibody arrays (or corresponding genes). In some methods, proteins or genes have been described proposed employing antibodies. Such are selected from three tables (e.g., proteins uniquely arrays typically include different antibodies having specific expressed in Banff Stage 0 or corresponding genes, proteins ity for different proteins intended to be detected. For example, uniquely expressed in Banffstage 1 and corresponding genes, usually at least one hundred different antibodies are used to and proteins differentially expressed between Banffstages 1 detect one hundred different protein targets, each antibody and 0. Analogous selections of proteins can be made from being specific for one target. Other ligands having specificity Tables H-J for purposes of distinguishing Banff stages 0 and for a particular protein target can also be used, such as the 2/3. In some methods, proteins or corresponding genes are synthetic antibodies disclosed in WO/2008/048970. Other selected such that proteins from several different pathways compounds with a desired binding specificity can be selected are represented (e.g., at least one gene from at least 2, 3, 5, or from random libraries of peptides or small molecules. U.S. 10 pathways, such as those described in the Examples). Pat. No. 5,922,615 describes a device that utilizes multiple 0046 Expression levels of the present genes and/or pro discrete Zones of immobilized antibodies on membranes to teins can be combined with or without determination of detect multiple target antigens in an array. U.S. Pat. Nos. expression levels of any other genes or proteins of interest 5,458,852, 6,019,944, U.S. Pat. No. 6,143,576. Microtiter (e.g., genes or proteins associated with rejection of kidneys or plates or automation can be used to facilitate detection of other organs in WO 2007/104537, WO 2009/060035), Angli large numbers of different proteins. Protein levels can also be cheau et al., PNAS 106,5330-5335 (2009)) and references, determined by mass spectrometry as described in the 16, 20, 21, 22, 23, 25, 26, 37 and 39. In some methods, the examples. gene is not DPYD or IRS2 or the method includes determin 0044) The selection of genes for determination of expres ing the expression level of at least 5, 10, 25 or 50 genes other sion levels depends on the particular application (e.g., analy than DPYD and IRS2. sis of CAN/IFTA in general or one of the subtypes described 0047 Regardless of the format adopted, the present meth above). In general, the genes are selected from one of the ods can (but need not) be practiced by detection expression tables indicated above as appropriate for the application. In levels of a relatively small number of genes or proteins com some methods, expression levels of at least 2, 3, 4, 5, 10, 20, pared with the whole genome level expression analysis 25, 50, 100, 150, 250 (e.g. 100-250) genes shown in any of described in the Examples. In some methods, the total num Table A, B, C or Dare determined. In some methods, expres ber of genes whose expression levels are determined is less sion levels of at least 2, 3, 4, 5, 10, 20, 25, 50, 100, 150, 250 than 5000, 1000, 500, 200, 100, 50, 25, 10, 5 or 3. In some or all genes shown in Table A are determined and/or expres methods, the total number of genes whose expression level is sion levels of 2, 3, 4, 5, 10, 20, 25, 50 or all genes shown in determined is 100-1500, 100-250, 500-1500 or 750-1250. In Table B are determined. In some methods, expression levels Some methods, the total number of proteins whose expression of at least 2, 3, 4, 5, 10, 20, 25, or all 50 genes in Table C and levels are determined is less than 5000, 1000, 500, 200, 100, at least 2, 3, 4, 5, 10, 20, 25, or all 50 genes in Table Dare 50, 25, 10, 5 or 3. In some methods, the total number of determined. In some methods, expression levels of 2, 3, 4, 5, proteins whose expression level is determined is 100-1500, 10, 20, 25, 50 or all genes shown in Tables 2, 3, 4, 5 and/or 6 100-250, 500-1500 or 750-1250. Correspondingly, when an are determined (genes for which both mRNAs and proteins array form is used for detection of expression levels, the array are differentially expressed). In some methods, all genes are includes probes or probes sets for less than 5000, 1000, 500, from the same table (i.e., all genes with differential expres 200, 100, 50, 25, 10, 5 or 3 genes. Thus, for example, an sion associated with mild CAN/IFTA). In some methods, Affymetrix GeneChip(R) expression monitoring array con genes from different tables (i.e., including genes associated tains a set if about 20-50 oligonucleotide probes (half match with mild CAN/IFTA and moderate/severe CAN/IFTA) are and half-mismatch) for monitoring each gene of interest. tested. In some methods, genes are selected Such that genes Such an array design would include less than 5000, 1000, US 2012/0178642 A1 Jul. 12, 2012

500, 200, 100, 50, 25, 10, 5 or 3 such probes sets for detecting or at least minimize changes in expression level unrelated to less than 5000, 1000, 500, 200, 100, 50, 25, 10, 5 or 3 genes. CAN/IFTA (e.g., from differences in overall health of the By further example, an alternative array including one cDNA patient or sample preparation). Normalization can be per for each gene whose expression level is to be detected would formed by determining what factor is needed to equalize a contain less than 5000, 1000, 500, 200, 100, 50, 25, 10, 5 or 3 profile of expression levels measured from different genes in such cDNAs for analyzing less than 5000, 1000, 500, 200, a sample with expression levels of these genes in a set of 100, 50, 25, 10, 5 or 3 genes. By further example, an array reference samples from which the reference levels were containing a different antibody for each protein to be detected determined. Commercial software is available for performing would containing less than 5000, 1000, 500, 200, 100, 50, 25, such normalizations between different sets of expression lev 10, 5 or 3 different antibodies for analyzing less than 5000, els. 1000, 500, 200, 100, 50, 25, 10, 5 or 3 gene products. 0.052 Comparison of the measured expression level of a gene with one or more of the above reference points provides VI. Analysis of Expression Levels a value (i.e., numerical) or other designation (e.g., symbol or 0048 Analysis of expression levels initially provides a word(s)) of presence or susceptibility to CAN/IFTA. In some measurement of the expression level of each of several indi methods, a binary system is used; that is a measured expres vidual genes. The expression level can be absolute in terms of sion level of a gene is assigned a value or other designation a concentration of an expression product, or relative in terms indicating presence or susceptibility to CAN/IFTA or lack ofa relative concentration of an expression product of interest thereof without regard to degree. For example, the expression to another expression product in the sample. For example, level can be assigned a value of 1 to indicate presence or relative expression levels of genes can be expressed with susceptibility to CAN/IFTA and -1 to indicate absence or respect to the expression level of a house-keeping gene in the lack of susceptibility to CAN/IFTA. Such assignment can be sample. Relative expression levels can also be determined by based on whether the measured expression level is closer to an simultaneously analyzing differentially labeled samples average level in kidney transplant patients having or not hav hybridized to the same array. Expression levels can also be ing CAN/IFTA. In other methods, a ternary system is used in expressed in arbitrary units, for example, related to signal which an expression level is assigned a value or other desig intensity. nation indicating presence or susceptibility to CAN/IFTA or 0049. The individual expression levels, whether absolute lack thereof or that the expression level is uninformative. or relative, can be converted into values or other designations Such assignment can be based on whether the expression providing an indication of presence or risk of CAN/IFTA by level is closer to the average level in kidney transplant patient comparison with one or more reference points. The principles undergoing CAN/IFTA, closer to an average level in kidney are first discussed with respect to CAN/IFTA without regard transplant patients lacking CAN/IFTA or intermediate ing to Subtype. However, the same principles apply for analy between such levels. For example, the expression level can be sis of subtypes except that the gene sets used may be different. assigned a value of +1, -1 or 0 depending on whether it is For example, mild CAN/IFTA can be determined using genes closer to the average level inpatients undergoing CAN/IFTA, or proteins from Tables A, C, E, F and/or G. Mid to severe is closer to the average level in patients not undergoing CAN/ CAN/IFTA can be determine using genes or proteins from IFTA or is intermediate. In other methods, aparticular expres Tables B, D, H, I and/or J. Genes or proteins from any of the sion level is assigned a value on a scale, where the upper level tables can be used in analyzing CAN/IFTA without regard to is a measure of the highest expression level found in kidney subtype. Preferably, genes in both Tables A/C and B/D or transplant patients and the lowest level of the scale is a mea proteins occurring in at least one of Tables E-G and at least sure of the lowest expression level found in kidney transplant one of Tables H-J are used for such analysis. Genes or pro patients at a defined time point at which patients may be teins are found in both Banff 1 and Banff 2,3 CAN/IFTA but susceptible to CAN/IFTA (e.g., one year post transplant). not found in Banff 0 are also useful in distinguishing the Preferably, such a scale is normalized scale (e.g., from 0-1) presence of CAN/IFTA in a patient. A combination of genes Such that the same scale can be used for different genes. and/or proteins associated with mild CAN/IFTA and genes Optionally, the value of a measured expression level on Such and/or proteins associated with mid to severe CAN/IFTA can a scale is indicated as being positive or negative depending on be used. whether the upper level of the scale associates with presence 0050. The reference points can include a measure of an or susceptibility to CAN/IFTA or lack thereof. It does not average expression level of a gene in Subjects having had a matter whether a positive or negative sign is used for chronic kidney transplant without CAN/IFTA, and/or an average ejection or lack thereofas long as the usage is consistent for value of expression levels in Subjects having had a kidney different genes. transplant with CAN/IFTA. The reference points can also 0053 Values or other designation can also be assigned include a scale of values found in kidney transplant patients based on a change in expression level of a gene relative to a including patients having and not having CAN/IFTA. The previous measurement of the expression level of gene in the reference points can also or alternatively include a reference same patient. Here as elsewhere expression level of agene can value in the subject before kidney transplant, or a reference be measured at the protein or nucleic acid level. Such a value in a population of a patients who have not undergone change can be characterized as being toward, away from or kidney transplant. Such reference points can be expressed in neutral with respect to average expression levels of the gene terms of absolute or relative concentrations of gene products in kidney transplant patients undergoing or not undergoing as for measured values in a sample. CAN/IFTA. For example, a gene whose expression level 0051. For comparison between a measured expression changes toward an average expression level in kidney trans level and reference level(s), the measured level sometimes plant patients undergoing CAN/IFTA can be assigned a value needs to be normalized for comparison with the reference of 1 and a gene whose express level changes way from an level(s) or vice versa. The normalization serves to eliminate average expression level in kidney transplant patients under US 2012/0178642 A1 Jul. 12, 2012 going CAN/IFTA and toward an average expression level in plant patients undergoing CAN/IFTA of a different subtype, kidney transplant patients not undergoing CAN/IFTA can be or an earlier measurement of expression level of the gene in assigned a value -1. Ofcourse, more Sophisticated systems of the same patient. assigning values are possible based on the magnitude of 0057. If subtyping is performed for both mild CAN/IFTA changes in expression of a gene in a patient. and moderate/severe CAN/IFTA, the aggregate of the results 0054 Having determined values or other designations of also indicates overall CAN/IFTA. For example, if the patient expression levels of individual genes providing an indication is assigned a value or other designation indicating absence or of presence or Susceptibility to chronic ejection or lack relatively low risk of developing mild CAN/IFTA and a value thereof, the values or designations are combined to provide an or other designation indicating absence or relatively low risk aggregate value for all of the genes being analyzed. If each of developing moderate/severe CAN/IFTA, then the patient is gene is assigned a score of +1 if its expression level indicates also indicated as having absence of overall CAN/IFTA and/or presence or susceptibility to CAN/IFTA and -1 if its expres a relatively low risk of developing the same. Conversely, if the sion level indicates absence or lack of susceptibility to CAN/ patient is assigned a value or other designation indicating IFTA and optionally Zero if uninformative, the different val presence or enhanced risk to either mild CAN/IFTA or mid/ ues can be combined by addition. The same approach can be severe CAN/IFTA, or both, the patients is also indicated as used if each gene is assigned a value on the same normalized having presence or enhanced risk of overall CAN/IFTA. scale and assigned as being positive or negative depending whether the upperpoint of the scale is associate with presence VIII. Diagnosis, Prognosis and Monitoring or susceptibility to CAN/IFTA or lack thereof. Other methods 0058. The above described methods can provide a value or of combining values for individual markers of disease into a other designation for a patient which indicates whether the composite value that can be used as a single marker are aggregate measured expression levels in a patient is more like described in US2004O126767 and WO/2004/059293. kidney transplant patients with or without CAN/IFTA or a VII. Subtyping subtype thereof. Such a value provides an indication that the patient either has or is at enhanced risk of CAN/IFTA or a 0055 CAN/IFTA can be classified into three subtypes, subtype thereof, or conversely does not have or is at reduced mild, mid and severe by the Banff scheme. These subtypes risk of CAN/IFTA or a subtype thereof. Risk is a relative term differ by histology and severity. The subtypes can be distin in which risk of one patient is compared with risk of other guished by the same principles and strategy as just discussed patients either qualitatively or quantitatively. For example, for presence or absence of CAN/IFTA, except that the set of the a value of one patient can be compared with a scale of genes whose expression levels is determined may be different values for a population of patients having undergone kidney for presence and absence of CAN/IFTA overall and each of transplant to determine whether the patient's risk relative to the Subtypes as indicated above. In some methods, one first that of other patients. In general, diagnosis is the determina analyzes CAN/IFTA independent of subtype and then looks tion of the present condition of a patient (e.g., presence or at profiles of one or more sets of genes characteristic of one of absence of CAN/IFTA) and prognosis is developing future the above subtypes. In some methods, detection of CAN/ course of the patient (e.g., risk of developing CAN/IFTA in IFTA and subtypes are performed simultaneously, for the future or likelihood of improvement in response to treat example, by including probes for the sets of genes required ment); however, the analyses contemplated by these terms for each analysis on the same array. In other methods, analysis may overlap or even be the same. For example, the present of multiple Subtypes is performed sequentially or simulta methods alone do not necessarily distinguish between pres neously and analysis of overall CAN/IFTA is performed by ence and enhanced risk of CAN/IFTA or a subtype thereof. aggregating the results from the different Subtypes. However, these possibilities can be distinguished by addi 0056. The principles for subtyping are closely analogous tional testing. to those for analyzing CAN/IFTA independent of subtype. 0059. If a patient is indicated as having or being at For example, to analyze whether mild CAN/IFTA is present, enhanced risk of CAN/IFTA or a subtype thereof, the physi one determines expression levels of a set of genes whose cian can Subject the patient to additional testing including expression levels are characterized of this subtype (Tables A, performing a kidney biopsy or performing other analyses C, E, F and/or G). The measured expression levels are then such as creatinine, BUN or glomerular filtration rate at compared with one or more reference levels of the genes. The increased frequency. Additionally or alternatively, the physi reference levels can, for example, represent an average cian can change the treatment regime being administered to expression level of a gene in kidney transplant patients under the patient. A change in treatment regime can include admin going mild CAN/IFTA with borderline phenotype and an istering an additional or different drug, or administering a average expression level of the gene in kidney transplant higher dosage or frequency of a drug already being adminis patients not undergoing any kidney rejection, an average tered to the patient. Many different drugs are available for expression level of the gene in kidney transplant patients treating rejection, such as immunosuppressive drugs used to undergoing CAN/IFTA of a different subtype, or an earlier treat transplant rejection calcineurin inhibitors (e.g., measurement of expression level of the gene in the same cyclosporine, tacrolimus), mTOR inhibitors (e.g., sirolimus patient. The same principles are used for analyzing combined and everolimus), anti-proliferatives (e.g., azathioprine, moderate/severe CAN/IFTA except that the set of genes is mycophenolic acid), corticosteroids (e.g., prednisolone and selected from Tables B, D, H, I and/or J and the reference hydrocortisone) and antibodies (e.g., basiliximab, dacli levels represent an average expression level of a gene in Zumab, Orthoclone, anti-thymocyte globulin and anti-lym transplant patients undergoing CAN/IFTA with Banff sub phocyte globulin). Conversely, if the value or other designa type 2 or 3, an average expression level of the gene in kidney tion of aggregate expression levels of a patient indicates the transplant patients not undergoing kidney rejection of any patient does not have or is at reduced risk of CAN/IFTA, the kind, an average expression level of the gene in kidney trans physician need not order further diagnostic procedures, par US 2012/0178642 A1 Jul. 12, 2012 ticularly not invasive ones such as biopsy. Further, the physi control populations compared. Average changes in the cian can continue an existing treatment regime, or even expression levels of genes can then be compared between the decrease the dose or frequency of an administered drug. two populations. 0060. In some methods, expression levels are determined at intervals in a particular patient (i.e., monitoring). Such X. Computer Implemented Methods methods can provide a series of values changing over time 0065 Expression levels can be analyzed and associated indicating whether the aggregate expression levels in a par with status of a Subject (e.g., presence or Susceptibility to ticular patient are more like the expression levels in patients chronic kidney infection) in a digital computer. Optionally, undergoing CAN/IFTA or not undergoing CAN/IFTA. Such a computer is directly linked to a scanner or the like Movement in value toward or away from CAN/IFTA or a receiving experimentally determined signals related to Subtype can provide an indication whether an existing immu expression levels. Alternatively, expression levels can be nosuppressive regime is working, whether the immunosup input by other means. The computer can be programmed to pressive regime should be changed or whether a biopsy or convert raw signals into expression levels (absolute or rela increased monitoring by markers such as creatinine or glom tive), compare measured expression levels with one or more erular filtration rate should be performed. reference expression levels, or a scale of Such values, as 0061 Information from subtyping analysis can provide described above. The computer can also be programmed to further guidance in whether to perform additional diagnostic assign values or other designations to expression levels based measures and/or change the immunosuppressive regime on the comparison with one or more reference expression administered to a Subject. For example, presence or risk of levels, and to aggregate Such values or designations for mul Subtype 2 or 3 is more suggestive of performing an additional tiple genes in an expression profile. The computer can also be diagnostic procedure (e.g., biopsy) and/or increasing the programmed to output a value or other designation providing rigor of an immunosuppressive regime that is the presence or an indication of presence or susceptibility to CAN/IFTA as risk of subtype 1. well as any of the raw or intermediate data used in determin ing Such a value or designation. IX. Drug Screening 0066. A typically computer (see U.S. Pat. No. 6,785,613 FIGS. 4 and 5) includes a bus which interconnects major 0062. The expression profiles associated with CAN/IFTA Subsystems such as a central processor, a system memory, an (including subtypes) or lack thereofprovided by the invention input/output controller, an external device Such as a printer are useful in screening drugs, either in clinical trials or in via a parallel port, a display Screen via a display adapter, a animal models of CAN/IFTA. A clinical trial can be per serial port, a keyboard, a fixed disk drive and a floppy disk formed on a drug in similar fashion to the monitoring of a drive operative to receive a floppy disk. Many other devices individual patient described above, except that drug is admin can be connected Such as a scanner via I/O controller, amouse istered in parallel to a population of kidney transplant connected to serial port or a network interface. The computer patients, usually in comparison with a control population contains computer readable media holding codes to allow the administered a placebo. computer to perform a variety of functions. These functions 0063. The changes in expression levels of genes can be include controlling automated apparatus, receiving input and analyzed in individual patients and across a treated or control delivering output as described above. The automated appara population. Analysis at the level of an individual patient pro tus can include a robotic arm for delivering reagents for vides an indication of the overall status of the patient at the determining expression levels, as well as Small vessels, e.g., end of the trial (i.e., whether gene expression profile indicates microtiter wells for performing the expression analysis. presence or enhanced susceptibility to CAN/IFTA) and/or an indication whether that profile has changed toward or away EXAMPLES from such indication in the course of the trial. Results for individual patients can be aggregated for a population allow Materials and Methods: ing comparison between treated and control population. 0067 Patient Populations: Test Set 1 comprised 42 kidney 0064. Similar trials can be performed in non-human ani transplant patients randomized to either cyclosporine or de mal models of chronic kidney disease, e.g., the mouse model novo rapamycin at the Cleveland Clinic, whose clinical of Mannon et al., Kidney International (1999)55, 1935-1944 courses have been previously, described 15, 16.24. Density In this case, the expression levels of genes detected are the gradient-purified peripheral blood lymphocytes (PBL) were species variants or homologs of the human genes referenced collected at the time of protocol two-year biopsies. Test Set 2 above in whatever species of non-human animal on which comprised 35 patients from 3 clinical centers (St. Vincent's tests are being conducted. Although the average expression Medical Center, Scripps Clinic, and Cleveland Clinic). All levels of human genes determined in human kidney transplant patients were on FK506. Whole blood was collected directly patients undergoing or not undergoing CAN/IFTA are not into PaxGene Tubes (PreAnalytix) at the time of biopsies for necessarily directly comparable to those of homologgenes in suspected CAN/IFTA or protocol one-year biopsies. All the an animal model, the human values can nevertheless be used studies in this manuscript were covered by Human Subjects to provide an indication whether a change in expression level Research Protocols approved by each Center's Institutional of a non-human homolog is in a direction toward or away Review Board and by the IRB of The Scripps Research Insti from CAN/IFTA or susceptibility thereto. The expression tute as the parent institution. Informed consent was obtained profile of individual animals in a trial can provide an indica from all study subjects in the study. tion of the status of the animal at the end of the trial with 0068 Pathology: Banff IF/TA grades based on tubuloint respect to presence or susceptibility to CAN/IFTA and/or erstitial features were determined for all patients by kidney change in Such status during the trial. Results from individual biopsies: grade 0 (no evidence CAN/IFTA), 1 (mild CAN/ animals can be aggregated across a population and treated and IFTA), and 2 (moderate CAN/IFTA) and 3 (severe CAN/ US 2012/0178642 A1 Jul. 12, 2012

IFTA). We merged patients with Banff2 and Banff3 IF/TA to serum creatinine compared to the Banff0, thus, renal function increase numbers. Diagnosis was done first by local patholo levels perse were not a major determinant of the gene pro gists and reviewed inablinded fashion. C4d staining was only files. The higher creatinine levels in the Banff 2.3 group of available in the more recently acquired Test Set 2. Test Set 2 most likely reflect the fact that this group was 0069 Gene expression profiling and analysis: RNA was “biopsy for cause whereas Test Set 1 were all protocol extracted from Test Set 1 using Trizol (Invitrogen) and in Test biopsies done regardless of any renal function change. How Set 2 using Paxgene Blood RNA system (PreAnalytix) and ever, by design, the two Test Sets differed significantly in globin transcripts were reduced using GlobinClear (Am recipientage, HLA mismatch, induction therapy, clinical cen bion). Biotinylated cRNA was prepared using Ambion Mes ter, immunosuppression, serum creatinines, and time to sage Amp Biotin II (Ambion) and hybridized to Affymetrix biopsy. Human Genome U133 Plus 2.0 GeneChips. Normalized sig nals that were generated using a quantile normalization strat Gene Expression Profiling of Mild CAN/IFTA egy (RMAExpress25) were used for class comparisons 0072 We performed ANOVA-based class comparisons (ANOVA) and class predictions (BRB Array Tools; linus.nci. between Banff 0 (nohistological evidence of CAN/IFTA) and nih.gov/BRB-ArrayTools.html). We chose the Diagonal Lin Banff 1 (mild CAN/IFTA). At p-values.<0.005, 1066 genes ear Discriminant Analysis (DLDA) method for class predic (1307 probe sets) were differentially expressed. Annotation tions, which is based on maximum likelihood discriminant of function by Gene Ontology (GO) shows 8 categories com rules that give consistently good results with our data set and prised of >25 genes each including 58 genes linked to immu others26. Receiver Operating Characteristics (ROC) analy nity and inflammation. The percentage of genes in each cat sis was done using JROCFIT (rad.jhmi.edu/eng/javarad/roc/ egory was immune/inflammatory 5%, apoptosis, 4%, cell JROCFITi.html). Heatmaps were generated using Cluster adhesion 3%, signal transduction 5%, regulation of transcrip and Treeview27 and functional analysis was performed tion 6%, protein phosphorylation 3%, cell cycle 3%, metabo using Gene Ontology (GO) (geneontology.org/) and Ingenu lism 11%, other functions 40%, unknown functions 20%. IPA ity Pathway Analysis (IPA). Consensus analysis was designed shows that these 1066 genes fall into 27 networks with >15 to identify true classifiers in the two independently collected genes per network. The top network was immune response data sets. Variability between the two test sets within each and two additional networks in the top 10 were also immune class (i.e. Banff 1/Test Set 1 vs. Banff 1/Test Set 2) was response with 27 and 22 focus genes, respectively. The top eliminated by removing all genes with a Student's t-test canonical pathway was Toll-like Receptor Signaling fol p-value of <0.05 after which the remaining genes were used to lowed by SAPKJJNK, Apoptosis, Notch and Death Receptor identify consensus candidates by class comparisons. All the and Interferon Signaling. Finding 1066 significantly differ microarray data for this study is available for review at the entially expressed genes is a first indication that PBL tran private GEO accession site ncbi.nlm.nih.gov/geo/query/acc. Script profiling is capable of classifying Subjects defined by cgi?token-vbgvzkwuggqiqpy&acc=GSE 12187. CAN/IFTA biopsy histology. Class prediction using DLDA 0070 Shotgun LC/MS/MS proteomics: All protein demonstrates 90% mean correct classification32.33). Super samples were prepared from density gradient-purified PBL. vised hierarchical clustering shows misclassification of only Individual patient samples were pooled within each Test Set 2 samples. (3 samples/pool) based on Banff classifications and pools 0073 Based on gene expression profiles of the whole were run in triplicates. Total protein was proteolytically blood samples in Test Set 2, there were 1429 genes (1591 digested with trypsin and samples run using Multidimen probe sets) differentially expressed at p-values.<0.005. GO sional Protein Identification Tool (MudPIT) protocol as pre annotation of gene functions revealed the same groups as viously described28 using an LTQ XL mass spectrometer PBL including 50 immune response genes. The percentage of (ThermoEisher). Raw data were searched against the EBI genes in each category was immune/inflammatory 4%, apo IPI human 12 01 2006 database supplemented with a ptosis, 2%, cell adhesion 2%, signal transduction 8%, regu decoy database where each entry of the original protein con lation of transcription 6%, protein phosphorylation 1%, cell tains its reversed sequence. Database searching used cycle 1%, metabolism 4%, other functions 35%, unknown SEQUEST (v27)|29 and outcomes were filtered using DTA functions 37%. IPA reveals 30 networks with 215 genes per Select30. Relative quantifications were done using spectral network. The top canonical pathways were: B Cell Receptor, counts nothialized to the median of the total spectral counts Toll-like Receptor, Death Receptor, Chemokine, Glucocorti 31. Pair-wise comparisons between CAN/IFTA biopsy coid Receptor, and IL-4Signaling. DLDA demonstrates 88% classes were done by differentially expressed proteins (Stu mean correct classification. Supervised hierarchical cluster dent's t-test, p<0.05) and as all-or-none/unique events. ing shows misclassification of only 1 sample. 0074. A consensus analysis for Banff 0 vs. Banff 1 was Results: performed with these two independently collected data sets Study Population by a class comparison at p-values<0.005 and identified 393 genes (424 probe sets) significantly differentially expressed 0071 Recipients in both Test Sets were sex and age in both data sets. This “consensus’ gene list represents the matched (Table 1). The only significant differences in Test Set intersection of these two significantly different test sets clas 1 were Donorage between Banff 0 and Banff 1 groups. In Test sifying mild CAN/IFTA by blood transcription profiling. We Set 2 there were significant differences in induction therapy then combined all the samples of both Test Sets (n=55) and between Banff 0 and Banff 1 and between Banff 0 and the performed class predictions using the top 50 differentially Banff 2,3; time to biopsy between Banff 0 and Banff 1 and expressed, consensus genes ranked by p values to obtain a between Banff 0 and the Banff 2,3; and steroid use between class prediction accuracy of 80% depicted as a ROC curve Banff 0 and Banff 1 and between Banff0 and Banff 2.3. Only (FIG. 1). A heat map classifying Banff0 vs. Banff 1 using the the Banff 2.3 group in Test Set 2 had a significantly higher 50 genes shows there are large “blocks” of up- or down US 2012/0178642 A1 Jul. 12, 2012 regulated genes that classify the Banff 0 vs. Banff 1 (mild apoptosis, NK cell and PTEN signaling for moderate/severe CAN/IFTA). However, signatures of multiple genes are CAN/IFTA). In other cases, such as signaling via T and B cell advantageous to achieve high class predictive accuracies in receptors, IL4 and JAK/STAT, the same canonical pathways heterogeneous clinical populations that are the reality of were found but different unique proteins were identified. transplantation medicine. We took the top 10 and top 3 genes 0078. Using only the differentially expressed proteins, from our consensus set for mild CAN/IFTA and performed DLDA obtained a 64% mean correct classification of mild class prediction using the DLDA method. The top 10 had a CAN/IFTA and an 83% correct classification for moderate? predictive accuracy of 80%, sensitivity of 85% and specificity severe CAN/IFTA. In contrast, the unique proteins identified of 77%, whereas the top 3 genes had a predictive accuracy of only in the blood of patients with biopsy-documented mild 80%, sensitivity of 74% and specificity of 86%. (n=135) or moderate/severe CAN/IFTA (n=322), represent candidate biomarkers with a 100% class prediction value in Gene Expression Profiling of Moderate/Severe CAN/IFTA this data set. 0079 We compiled the matches between proteins identi 0075 Class comparisons between Banff 0 and Banff 2.3 fied by mass spectrometry and mRNA transcripts identified identified genes differentially expressed between patients using microarrays. The premise is that protein/transcript without CAN/IFTA and those with moderate to severe CAN/ matches are a form of candidate biomarker validation based IFTA. In Test Set 1, 172 genes were differentially expressed on two independent technologies. There were 11 matches for (p<0.005) and classified the samples by DLDA with 78% the 393 consensus genes for mild CAN/IFTA, 32 matches for accuracy. In Test Set 2 there were 545 differentially expressed the 1066 genes for mild CAN/IFTA in Test Set 1 and 40 genes. DLDA classified 95% of the samples accurately. The matches for the 1429 genes for mild CAN/IFTA in Test Set 2. percentage of genes in each category for sets 1 and 2 was There were no matches for the 62 consensus genes for mod immune/inflammatory 4%. 3%, apoptosis, 2%. 3%, cell erate/severe CAN/IFTA but 9 matches in the 172 genes for adhesion 2%. 3%, signal transduction 8%, 7%, regulation of moderate? severe CAN/IFTA in Test Set 1 and 9 matches in the transcription 6%, 8%, protein phosphorylation 1%. 3%, cell 545 genes for moderate/severe CAN/IFTA in Test Set 2. All cycle 1%, 1%, metabolism 4%, 6% other functions 33%, protein/transcript matches are listed in Tables 2-6. 30%, unknown functions 37%, 36%. A consensus analysis was done as already described to yield 62 differentially DISCUSSION expressed genes (p<0.005) shared for both Test Sets of mod erate/severe CAN/IFTA (n=49). The ROC curve for the top 0080. The primary objective of this study (also reported as 50 genes from this consensus gene set shows a class predic 40) was the discovery of biomarkers in the peripheral blood tion accuracy of 92% (FIG. 2). of kidney transplant patients with biopsy-documented inter stitial fibrosis and tubular atrophy (IF/TA) and no known Proteomic Expression of Mild and Moderate/Severe CAN/ cause, which we refer to here as Chronic Allograft Nephropa IFTA thy (CAN/IFTA) 14. To this end, we integrated the results of two, independently collected sets of patient samples that were 0076. To investigate using proteomics to define blood cell significantly different in multiple clinical elements. Thus, the biomarkers for CAN/IFTA, we performed shotgun tandem selection of biomarker candidates was not significantly influ mass spectrometry. All samples represented purified PBL enced by the time of biopsy (ranging from 1 to 6 years post obtained at the same time as biopsies. We did not use the transplant), the specific immunosuppressive protocols (use of whole blood samples from Test Set 2 because high quality different calcineurin inhibitors vs. sirolimus) or the technol protein preparations cannot be obtained from PaxGene tubes. ogy used to purify the mRNA transcripts (density gradient Differential protein expression was performed using a rela separated cells vs. whole blood). This experimental design tive quantification strategy based on normalized spectral was chosen for its advantages in defining a consensus set of counts 31. We identified 206 differentially expressed pro robust candidate biomarkers for CAN/IFTA suitable for clini teins (p<0.05) for Banff 0 vs. Banff 1 (mild CAN/IFTA). In cal use. addition, we identified 135 proteins unique to Banff 0 and 167 I0081. Using more closely matched sets of patient samples, proteins unique to Banff 1. Class comparisons for Banff0 vs. for example, patients only 2 years post-transplant or only one Banff 2.3 (moderate/severe CAN/IFTA) yielded 282 differ source of blood cell RNA such as the PaxGene tubes might entially expressed proteins (p<0.05) and 509 proteins unique have resulted in higher total numbers of differentially to Banff 2.3. We found 95 proteins differentially expressed in expressed candidate mRNA transcripts and proteins. How mild and moderate/severe CAN/IFTA as compared to Banff ever, classifications for CAN/IFTA based on the consensus 0, representing candidate protein markers for any stage of mRNA candidates described here for these otherwise very CAN/IFTA. In parallel, 94 proteins were differentially heterogeneous clinical data sets are 80% for mild CAN/IFTA expressed only in mild CAN/IFTA and these were linked to and 92% for moderate/severe CAN/IFTA. By contrast, the cell death, cell signaling, and post-translational protein modi widely used prostate specific antigen (PSA) biomarker, tested fications. The 168 proteins differentially expressed only in in an equally heterogenous human population, was originally moderate/severe CAN/IFTA were linked to cellular morphol introduced with a predictive value of 28-35%34 because ogy, growth and proliferation and signaling via ERK/MAPK, there was no other minimally invasive option for early detec acute phase responses, IGF1 and PPARa/RXRa. tion of prostate cancer at that time, which is true for CAN/ 0077. There were 135 proteins unique to mild CAN/IFTA IFTA today. and 322 proteins unique to moderate/severe CAN/IFTA. Both I0082 We obtain very reasonable predictive accuracy, sen mild and moderate? severe CAN/IFTA had immune and sitivity and specificity with 150, 100 and 50 total genes per inflammation related proteins (20 and 37, respectively) but signature. There are now several technology platforms per many of these proteins are not mapped to the same functional fectly suitable for point of clinical service implementation pathways (e.g. calcium signaling in mild CAN/IFTA and that can measure 100 genes or more cost effectively and US 2012/0178642 A1 Jul. 12, 2012 within hours. In clinical practice, the differentially expressed porated by reference in their entirety for all purposes to the genes and proteins can be used for serial, prospective mea same extent as if each individual publication, patent and surements of the signature at regular intervals for the life of patent application was specifically and individually indicated the kidney transplant. The absence of a positive CAN/IFTA to be incorporated by reference in its entirety for all purposes. signature at any point in time will indicate adequate immu In the event of any variance in sequences associated with nosuppression or over-immunosuppression. Careful reduc Genbank, Unigene, International Protein Index, Entrez, Uni tions in immunosuppressive drug doses can then be used with ProtKB/Swiss-Prot accession numbers and the like, the appli repeat monitoring of the signature to establish the optimal cation refers to the sequences associated with the cited acces drug combination and level for each patient to prevent CAN/ sion numbers as of Jul. 9, 2009. IFTA and ensure the long term safety of the therapy. 0083 Biomarker discovery has been reported using REFERENCES peripheral blood profiling for acute rejection in heart trans I0088 1. Meier-Kriesche (2001) J Am Soc Nephrol 12: plantation35.36. Peripheral blood studies of kidney trans 1293-1296. plant patients with "operational tolerance included 22 I0089 2. Nankivell (2003) N Engl J Med 349: 2326-2333. patients with biopsy-documented CAN/IFTA37. Two of the 0090. 3. Pascual (2002) N Engl J Med 346: 580-590. genes (DPYD, IRS2) reported to distinguish “operational (0091. 4. Solez (2008) Am J Transplant 8:753-760. tolerance' are identified in our consensus sets. Our earlier 0092 5. Racusen (1999) Kidney Int 55: 713-723. study of 42 kidney biopsies showed that gene expression (0093. 6. Solez K, (2007) Am J Transplant 7:518-526. profiles of CAN/IFTA had significant up-regulation of (0094 7. Banasik M. Klinger M(2006) Ann Transplant 11: immune/inflammation, fibrosis and tissue remodeling genes 7-10. 16. However, only 5 genes from these CAN/IFTA biopsies (0095 8. Yates (2006) Transpl Immunol 16: 148-157. were identified in the current peripheral blood consensus sets. 0096 9. Caine (1978) Lancet 2: 1323-1327. A study of 11 CAN/IFTA biopsies identified 3 genes linked to 0097 10. de Mattos (2000) Am J Kidney Dis35:333-346. immunity and fibrosis that were tested by quantitative PCR in (0098 11. Jevnikar (2008) ClinJ AmSoc. Nephrol 3 Suppl urine and peripheral blood with good correlations in urine but 2: S56-67. none in peripheral blood38. Therefore, gene biomarkers (0099 12. Pascual. (1998) Immunol Today 19:514-519. identified in peripheral blood are mostly distinct from those 0100 13. Nankivell (2006) Transplantation 81: 643-654. identified in tissue. 0101. 14. Colvin RB (2003) N Engl J Med 349: 2288 0084. Although practice of the invention is not dependent 229O. on an understanding of mechanism, we propose that the 0102) 15. Flechner (2007) Transplantation 83: 883-892. peripheral blood represents a fully functional and distinct (0103 16. Flechner (2004) Am J Transplant 4: 1776-1785. compartment of the immune system that actively serves to 0104 17. Yilmaz (2007) Transpl Int 20:608-615. traffic and modulate all the components of effector immunity. 0105. 18. Lachenbruch (2004) Am J Transplant 4: 451 Although the tissue injury that causes the progression of 457. CAN/IFTA is occurring in the kidney, we believe that a sig 0106. 19. Pascual (1999) Transplantation 67: 737-741. nificant determinant of the phenotype of the host immune 0107 20. Kurian (2005) Current Opinion in Organ Trans response, either acceptance of the graft or CAN/IFTA, is plantation 10: 193-197. actually established and Subsequently regulated within the 0108. 21. Kurian (2007) Int Immunopharmacol 7: 1948 peripheral blood compartment, lymph nodes and spleen. 1960. 0085 Urine based proteomics have been used to report 0109 22. Oetting (2006) Am J Kidney Dis 47: 898-904. biomarkers for acute rejection using SELDI-TOF mass spec 0110 23. Schaub (2005) Am J Transplant 5: 729-738. troscopy23.39 but to our knowledge this is the first study to 0111 24. Flechner (2004) Am J Transplant 4: 1475-1489. identify blood cell-based proteomic markers for transplanta 0112) 25. Bolstad (2003) Bioinformatics 19:185-193. tion using tandem mass spectroscopy. We have identified 0113. 26. Dudoit (2002) Journal of the American Statisti several hundred proteins that are significantly differentially cal Association 97: 77-87. expressed in peripheral blood of patients with CAN/IFTA as 0114 27. Eisen (1998) Proc Natl Acad Sci USA 95: a function of histology grade, mild to moderate? severe. The 14863-14868. group of uniquely identified proteins potentially represents 0115 28. Washburn (2001) Nat Biotechnol 19: 242-247. the highest value biomarker candidates giving 100% accu 0116. 29. Sady.gov (2002) J Proteome Res 1: 211-215. racy in our tests. Integrating proteomics with gene expres 0117 30. Tabb (2002) J Proteome Res 1: 21-26. sion, we identified over 80 protein/transcript matches for 0118. 31. Liu (2004) Anal Chem 76: 4193-4201. CAN/IFTA providing candidate validation based on two 0119) 32. Guo (2007) Biostatistics 8: 86-100. independent technologies. However, genes in which differen I0120 33. Huang (2006) Pediatr Blood Cancer 46: 728 tial expression is found only at the gene or protein level but 738. not both also allow accurate analyses. 0121 34. Woolf (1995) N Engl J Med 333: 1401-1405. I0086 Although the invention has been described with ref (0.122 35. Deng (2006) Am J Transplant 6: 150-160. erence to the presently preferred embodiments, it should be (0123. 36. Horwitz (2004) Circulation 110: 3815-3821. understood that various modifications can be made without (0.124 37. Brouard (2007) Proc Natl Acad Sci USA 104: departing from the invention. Unless otherwise apparent from 15448-15453. the context any step, element, embodiment, feature or aspect (0.125) 38. Mas (2007) Transplantation 83: 448-457. of the invention can be used with any other. (0.126 39. Clarke (2003) Ann Surg. 237: 660-664; discus 0087 All publications (including GenBank Accession sion 664-665. numbers, UniProtKB/Swiss-Prot accession numbers and the (O127 40. Kurian et al., PLoS One. 2009 Jul. 10; 4(7): like), patents and patent applications cited are herein incor e6212 US 2012/0178642 A1 Jul. 12, 2012 13

TABLE 1.

Clinical Characteristics of the Study Populations.

Test Set 1 WS. Test Set 1 Test Set 2 Test Set 2

Signifi- Signifi- Signifi Banff0 Banff 1 Banff 2, 3 cance Banff0 Banff 1 Banff 2, 3 cance C8CC.

Number 18 15 9 NA 8 14 13 NA NS Recipientage 42.61 - 12.8 48.47 11.6 45.67 - 17.5 NS 56.88 12.2 51.36 - 12.6 49.08 - 12.9 NS Banff) = O.O1 Recipient 38.9 2O 44.4 NS 62.5 35.7 53.8 NS NS gender (% female) Recipient race 22.22 13.33 11.11 NS O 14.3 7.7 NS NS African American Pretx diabetes 16.7 26.7 22.2 NS 25 14.3 7.7 NS NS PRA >20% (%) S.6 6.7 11.1 NS 12.5 7.1 15.4 NS NS HLA mismatch 3.06 - 1.7 2.66 - 1.6 2.67 - 22 NS 3.43 + 2.4 4.33 + 1.4 3.58 - 16 NS Banffl = O.OO8 Deceased donor 55.6 73.3 77.8 NS 75 71.4 46.2 NS NS % re-transplant O O O O 14.3 15.4 NS NS Donor age 32.39:15.7 42.33 - 11.8 37.11 - 12.1 Banff) vs. 31.25 + 19.3 41.54 - 17.7 44.62. 13.4 NS NS Banffl p = 0.05 Donor gender SO 53.3 33.3 NS 12.5 57 53.8 NS NS emale Donor race 16.7 13.3 11.1 NS O 7.1 7.7 NS NS African American induction 100 1OO 100 NS 75 21.4 23.1 Banff) wS. Banffl = Ban O.OOO1 p = 0.026; Banff2, 3 = Banff) wS. O.OOOS Banff2, 3 b = 0.032 Serum 1.32 0.38 1.45 - O.S1 1840.77 NS 1.70 - 1.3 2.41 + 0.7 3.09 - 12 Banff) wS. Banffl = Creatinine Banff2, 3 O.OOO2 b = 0.025 Banff2, 3 = O.007 Time to Biopsy 7SS 101 710 109 659 133 NS 42O309 1664 - 1364 2398 - 1120 Banff) wS. Banff) = Ban O.OS p = 0.005; Banff 1 = Banff) wS. O.O2 Banff2, 3 Banff2, 3 = b = OOOOO2 O.OOO1 CNI 38.9 60 77.8 NS 1OO 100 846 NS Banff) = O.007 MMF 100 93.3 88.9 NS 75 78.6 76.9 NS NS Steroids 100 1OO 100 NS 37.5 100 92.3 Banff) vs. Banffl = Banff O.OOO9 p = 0.0002: Banff) vs. Banff2, 3 b = OOO22 C4d+ staining ND ND ND NA NA 2 3 NS NA

NTD. Not Done NA-Not Applicable NS-Not Significant US 2012/0178642 A1 Jul. 12, 2012 14

TABLE A Differentially expressed consensus genes for mild CAN for both Test Mild CAN = CAN Banff Class 1: No evidence of CAN = CAN Banff Class 0 Probesets with positive fold changes are upregulated in mild CAN

Geom Geom mean mean of of intensities intensities Parametric in class 1: in class 2: Fold p-value Banff0 Banff 1 Change Probe Set ID Gene Symbol Gene Title 1 O.OOOOO2 27.9 19.3 -1.45 203796 s at BCL7A B-cell CLL/lymphoma 7A 2.1E-O6 11.6 16.7 44 233650 a CEP63 centrosomal protein 63 kDa 3 3.2E-06 50.5 40.1 -1.26 1552892 at TNFRSF13C tumor necrosis factor receptor Superfamily, member 13C 4 5.9E-06 19.2 33.6 .75 1565597 at EST1 Homo sapiens, clone IMAGE: 4275461, mRNA S 8.3E-06 15.1 23.5 .56 24.1752 a SLC8A1 Solute carrier family 8 (sodium calcium exchanger), member 1 6 1.2SE-OS 8O3.7 1OS.O.S 31 213702 X at ASAH1 N-acylsphingosine amidohydrolase (acid ceramidase) 1 7 1.61E-OS 224.8 174.8 -1.29 223259 a ORMDL3 ORM1-like 3 (S. cerevisiae) 8, 184E-05 1354 189.9 40 204054 a PTEN phosphatase and tensin homolog (mutated in multiple advanced cancers 1) 9 186E-OS 26 46 .77 239012 a BRDC2 IBR domain containing 2 10 2.39E-OS 1182 1724.7 .46 200975 a. PPT1 Palmitoyl-protein thioesterase 1 (ceroid-lipofuscinosis, neuronal 1, infantile) 11 O.OOOO24 1743 363.5 2.09 206584 a LY96 Lymphocyte antigen 96 12 3.3SE-OS 9 7.6 -1.18 228044 a C13orf21 Chromosome 13 open reading frame 21 13 4.41E-OS 2SO.1 327.6 31 225492 a. EST2 14 4.53E-OS 7828 1066O2 36 202917 s at S100A8 S100 calcium binding protein A8 15 O.OOOO47 374.1 724.5 .94 2235O1 a TNFSF13B Tumor necrosis factor (ligand) Superfamily, member 13b 16 4.7SE-OS 112.7 204 .81 222496 s at FLJ20273 RNA-binding protein 17 S.11E-OS 22.4 38.8 .73 224996 a EST3 CDNA FLI39064 fis, clone NT2RP7014.583 18 S.13E-OS 21.6 17.5 -1.23 244863 a EST4 Transcribed locus 19 O.OOOOS2 7.5 9 20 238791 a ZNF100 Zinc finger protein 100 20 S.66E-OS 85.2 123.8 .45 218.177 a CHMP1B Chromatin modifying protein 1B 21 S.67E-OS 2O3.3 336.4 .65 2262.08 a ZSWIM6 Zinc finger, SWIM-type containing 6 22 7.26E-OS 180.8 237.2 31 203778 a MANBA Mannosidase, beta A, lysosomal 23 O.OOOO89 86.6 1234 42 238903 a LOC137886 Hypothetical protein LOC137886 24 OOOOO94 19.7 14.5 -1.36 214308 s at HGD Homogentisate 1,2-dioxygenase (homogentisate oxidase) 25 O.OOO 103 492.9 744.6 .51 21 1368 is at CASP1 Caspase 1, apoptosis-related cysteine peptidase (interleukin 1, beta, convertase) 26 O.OOO 103 132.8 1848 39 227017 at ERICH1 Glutamate-rich 1 27 O.OOO107 10.3 15.5 .50 228624 at TMEM144 Transmembrane protein 144 28 O.OOO108 128.7 1702 .32 232149 s at NSMAF Neutral sphingomyelinase (N-SMase) activation associated factor 29 O.OOO112 26.4 35.2 .33 243287 s at OSTM1 Osteopetrosis associated transmembrane protein 1 3O O.OOO116 59.5 134.7 2.26 1552773 at CLEC4D C-type lectin domain family 4, member D 31 O.OOO121 2887.4 3972.4 .38 202902 s at CTSS Cathepsin S 32 O.OOO12S 142.4 229 .61 211744 s at CD58 CD58 molecule 33 O.OOO133 35.6 26.9 -1.32 24.3507 is at C20orf196 Chromosome 20 open reading frame 196 34 O.OOO137 101.9 77.4 -1.32 228832 a FLJ20O21 Hypothetical LOC90024 3S O.OOO149 1057.6 1433.5 36 202727 s at IFNGR1 Interferon gamma receptor 1 36 O.OOO169 4O.S 55.5 37 21395.2 s at ALOX5 Arachidonate 5-lipoxygenase 37 O.OOO174 364.6 288.1 -1.27 219045 a. RHOF Ras homolog gene family, member F (in filopodia) 38 O.OOO175 666 974.1 .46 212268 a SERPINB1 Serpin peptidase inhibitor, clade B (ovalbumin), member 1 39 O.OOO18 80.3 119.4 .49 203276 a LMNB1 Lamin B1 40 OOOO19 347.2 814.1 2.34 219666 a MS4A6A Membrane-spanning 4-domains, subfamily A, member 6A 41 O.OOO2O4 S4.9 110.9 2.02 204860 s at NAIP if NLR family, apoptosis inhibitory protein if neuronal NAIP1B apoptosis inhibitory protein (centromeric) 42 O.OOO212 3.8124 4958.6 1.30 202388 a RGS2 Regulator of G-protein signaling 2, 24 kDa 43 O.OOO226 24.5 43.9 1.79 1553514 a at VNN3 Vanin 3 44 O.OOO239 84.6 108.3 1.28 218364 a LRRFIP2 Leucine rich repeat (in FLII) interacting protein 2 45 O.OOO242 15.5 21.5 1.39 218888 is at NETO2 Neuropilin (NRP) and tolloid (TLL)-like 2 46 O.OOO258 64.6 87.8 1.36 204108 a NFYA Nuclear transcription factorY., alpha 47 O.OOO273 35.6 SO.1 1.41 213935 a. ABHDS Abhydrolase domain containing 5 48 0.000278 S4 75.5 1.40 208883 a UBRS Ubiquitin protein ligase E3 component n-recognin 5 49 O.OOO282 334.9 425 1.27 222148 s at RHOT1 Ras homolog gene family, member T1 SO 0.000284 564.8 712.6 1.26 227266 s at FYB FYN binding protein (FYB-120/130) S1 O.OOO287 75.4 138.6 1.84 204714 S at FS Coagulation factor V (proaccelerin, labile factor) S2 O.OOO3O2 6.3 5.6 -1.13 229777 a CLRN3 Clarin 3 S3 O.OOO3O2 16.9 19.2 1.14 241073 a EST5 Transcribed locus S4 O.OOO309 29.8 52.7 1.77 1558,549 s at VNN1 Vanin 1 US 2012/0178642 A1 Jul. 12, 2012 15

TABLE A-continued Differentially expressed consensus genes for mild CAN for both Test Mild CAN = CAN Banff Class 1: No evidence of CAN = CAN Banff Class 0 Probesets with positive fold changes are upregulated in mild CAN

Geom Geom mean mean of of intensities intensities Parametric in class 1: in class 2: Fold p-value Banff0 Banff 1 Change Probe Set ID Gene Symbol Gene Title SS O.OOO319 S84.3 710 .22 201007 a HADHB Hydroxyacyl-Coenzyme A dehydrogenase, 2-ketoacyl Coenzyme A thiolase? enoyl-Coenzyme A hydratase (trifunctional protein), beta subunit S6 O.OOO323 9 7.8 -1.15 241171 a EST6 Transcribed locus S7 O.OOO328 18.4 33.5 .82 239759 a EST7 Transcribed locus S8 O.OOO368 44.5 76.4 .72 209684 a RIN2 Ras and Rab interactor 2 S9 O.OOO369 22.6 18.4 -1.23 240654 a EST8 Transcribed locus 6O O.OOO37 356 693 .95 217738 a PBEF1 Pre-B-cell colony enhancing factor 1 61 O.OOO377 48.8 73.7 .51 228.540 a QK Quaking homolog, KH domain RNA binding (mouse) 62 O.OOO386 24.1 2O -1.21 221261 x at MAGED4 Melanoma antigen family D, 4B, melanoma antigen MAGED4B amily D, 4 63 O.OOO393 8.3 9.9 .19 1562458 at UBE2W Ubiquitin-conjugating enzyme E2W (putative) 64 O.OOO399 28.9 40.2 39 227403 a PIGX Phosphatidylinositol glycan anchor biosynthesis, class X 6S O.OOO4O6 21.6 27.6 .28 226827 a TMEM16S Transmembrane protein 165 66 O.OOO418 61.4 54.1 -1.13 1568691 at EST9 CDNA clone IMAGE: 3613441 67 O.OOO444 31 S1.9 .67 230343 a EST 10 Transcribed locus 68 O.OOO445 10.3 8.2 -1.26 212650 a EHBP1 EH domain binding protein 1 69 O.OOO448 168.6 306.1 .82 238.066 a RBP7 Retinol binding protein 7, cellular 7O O.OOO4S1 69.6 97.7 40 213292 S at SNX13 Sorting nexin 13 71 O.OOO463 38.7 63.7 .65 228.362 s at FAM26F Family with sequence similarity 26, member F 72 0.000477 30 23.6 -1.27 236139 a EST11 Transcribed locus 73 O.OOO486 15.4 2O2 31 2207 75 s at UEVLD UEV and lactate/malate dehydrogenase domains 74 O.OOO493 55.2 46.9 -1.18 221189 sat TARS2 Threonyl-tRNA synthetase 2, mitochondrial (putative) 7S O.OOO497 24.5 2O -1.23 21 O150 s at LAMA5 Laminin, alpha 5 76 O.OOOSO9 49.3 41.2 -1.2O 211304 x at KCNJS Potassium inwardly-rectifying channel, Subfamily J, member 5 77 O.OOOS24 5.4 4.7 -1.15 233609 at PTPRK Protein tyrosine phosphatase, receptor type, K 78 O.OOOS38 12.2 17.6 .44 202422 s at ACSLA Acyl-CoA synthetase long-chain family member 4 79 0.000539 360.3 442.2 .23 225284 at DNAJC3 DnaJ (Hsp40) homolog, Subfamily C, member LOC144871 3///hypothetical protein LOC144871 80 O.OOOS49 10.4 8.7 -1.20 204983 s at GPC4 Glypican 4 81 O.OOOSSS 15.5 13.4 -1.16 231318 at C15orf51 Chromosome 15 open reading frame 51 82 O.OOOS64 59.4 83.9 41 20815.8 s at OSBPL1A Oxysterol binding protein-like 1A 83 0.000571 9.2 8.1 -1.14 205542 at STEAP1 Six transmembrane epithelial antigen of the prostate 1 84 O.OOOS73 186.9 235.8 .26 2.18905 at NTS8 integrator complex subunit 8 85 O.OOOS88 100.3 177.5 .77 212820 at DMXL2 Dmx-like 2 86 0.000594 16O.S 341.8 2.13 215049 X at CD163 CD163 molecule 87 0.000595 20.8 34.4 .65 206674 at FLT3 Fms-related tyrosine kinase 3 88 O.OOO595 52.3 40.2 -1.30 233487 s at LRRC8A Leucine rich repeat containing 8 family, member A 89 O.OOO607 7.5 21.1 .21 33197 at YO7A Myosin VIIA 90 O.OOO642 26.5 23.5 -1.13 203793 X at PCGF2 Polycomb group ring finger 2 91 O.OOO648 9.1 8.2 -1.11 1566935 at TYRO3P TYRO3P protein tyrosine kinase pseudogene 92 O.OOO663 O.8 5.2 41 203767 s at STS Steroid sulfatase (microsomal), isozyme S 93 O.OOO668 303.5 421.8 39 226136 at GLIPR1 GLI pathogenesis-related 1 (glioma) 94 O.OOO67 S2.1 81.1 .56 216252 x at FAS Fas (TNF receptor Superfamily, member 6) 95 O.OOO694 244.7 42O.S .72 221724 S at CLEC4A C-type lectin domain family 4, member A 96 O.OOO696 1.6 3.1 13 230419 at FLJ37644 Hypothetical gene Supported by AKO94963 97 O.OOO701 26.8 33.2 .24 225778 at FUT1 Fucosyltransferase (galactoside 2-alpha-L- lucosyltransferase, H blood group) 98 O.OOO702 4.8 O.3 -1.44 216063 at HBBP1 Hemoglobin, beta pseudogene 1 99 O.OOO745 6.9 6.2 -1.11 207516 at CHRNB4 Cholinergic receptor, nicotinic, beta 4 1OO O.OOO749 21.8 7.3 -1.26 216910 at XPNPEP2 X-prolylaminopeptidase (aminopeptidase P) 2, membrane-bound 101 O.OOO75 4.7 2.5 -1.18 1555655 at OR1OA4 Olfactory receptor, family 10, subfamily A, member 4 102 O.OOO7SS 266.1 339 .27 225606 at BCL2L11 BCL2-like 11 (apoptosis facilitator) 103 O.OOO768 7 4.8 -1.15 207967 at VPS45 Vacuolar protein sorting 45 homolog (S. cerevisiae) 104 O.OOO775 2S3.9 336.8 .33 219079 at CYB5R4 Cytochrome b5 reductase 4 1 OS O.OOO803 94.6 1341 .42 222498 at AZI2 5-azacytidine induced 2 106 O.OOO81 570.4 686.2 20 210817 s at CALCOCO2 Calcium binding and coiled-coil domain 2 107 O.OOO82 344.4 494.4 .44 211404 S at APLP2 Amyloid beta (A4) precursor-like protein 2 108 O.OOO824 9.6 6.4 .71 1562481 at EST12 109 O.OOO834 78.3 105.7 35 203693 s at E2F3 E2F transcription factor 3 110 O.OOO84 23.2 33.6 .45 205841 at JAK2 Janus kinase 3 (a protein tyrosine kinase) 111 O.OOO847 10.2 9.1 -1.12 1553504 at MRGPRX4 MAS-related GPR, member X4 112 O.OOO85 140.6 212.9 .51 2031.39 at DAPK1 Death-associated protein kinase 1 113 O.OOO864 186.1 235.2 .26 226850 at SUMF1 Sulfatase modifying factor 1 US 2012/0178642 A1 Jul. 12, 2012 16

TABLE A-continued Differentially expressed consensus genes for mild CAN for both Test Mild CAN = CAN Banff Class 1: No evidence of CAN = CAN Banff Class 0 Probesets with positive fold changes are upregulated in mild CAN

Geom Geom mean mean of of intensities intensities Parametric in class 1: in class 2: Fold p-value Banff0 Banff 1 Change Probe Set ID Gene Symbol Gene Title 14 O.OOO896 4.9 5.4 10 230684 a GTPBP10 GTP-binding protein 10 (putative) 15 O.OOO907 34.8 21.7 -1.60 228802 a RBPMS2 RNA binding protein with multiple splicing 2 16 O.OOO969 7.6 6.8 -1.12 204596 s at STC1 Stanniocalcin 1 17 O.OOO972 45.3 57 .26 228061 a CCDC126 Coiled-coil domain containing 126 18 O.OOO979 31.4 22.6 -1.39 244876 a EST13 19 O.OOO992 12.4 10.7 -1.16 233015 a. MBNL1 Muscleblind-like (Drosophila) 2O O.OO1033 21.6 14.5 -1.49 234284 a GNG8 Guanine nucleotide binding protein (G protein), gamma 8 21 O.OO1036 38.2 24.8 -1.54 156O262 at EST14 Homo sapiens, clone IMAGE: 5751523, mRNA 22 O.OO1037 5.4 4.8 -1.13 1562902 at EST15 Homo sapiens, clone IMAGE: 5176738, mRNA 23 O.OO1045 1215.1 2O849 .72 205863 a S100A12 S100 calcium binding protein A12 24 O.OO1057 37.8 31.9 -1.18 2223O2 a EST16 25 O.OO1065 44.9 S1.1 .14 212932 a RAB3GAP1 RAB3 GTPase activating protein subunit 1 (catalytic) 26 O.OO1066 36.3 49.6 37 233924 S at EXOC6 Exocyst complex component 6 27 O.OO1087 34.5 41.5 20 230209 a EST17 CDNA FLI36477 fis, clone THYMU2017158 28 O.OO1103 498.4 4193 -1.19 41047 at C9orf16 Chromosome 9 open reading frame 16 29 O.OO1136 57.1 40.8 -1.40 200884 a CKB Creatine kinase, brain 3O O.OO1137 177 245.9 39 219157 a KLHL2 Kelch-like 2, Mayven (Drosophila) 31 O.OO1153 7.3 6.4 -1.14 207818 S at HTR7 5-hydroxytryptamine (serotonin) receptor 7 (adenylate cyclase-coupled) 32 O.OO1162 13.3 16.1 .21 234977 a ZADH2 Zinc binding alcohol dehydrogenase, domain containing 2 33 O.OO1164 4.6 4.3 -1.07 238391 a EST18 Transcribed locus 34 O.OO1173 125.2 1603 .28 222759 a SUV42OH1 Suppressor of variegation 4–20 homolog 1 (Drosophila) 3S O.OO1197 16.5 13.5 -1.22 233962 a. C20orf120 Chromosome 20 open reading frame 120 36 O.OO1212 183 2SO.9 37 204526 is at TBC1D8 TBC1 domain family, member 8 (with GRAM domain) 37 O.OO1214 39.9 31.5 -1.27 235417 a SPOCD1 SPOC domain containing 1 38 O.OO1228 67.2 87.8 31, 1552472 a. at CENTB2 Centaurin, beta 2 39 O.OO1232 423 S13.3 .21 200768 is at MAT2A Methionine adenosyltransferase II, alpha 40 O.OO1246 7 14.7 -1.16 229536 a REC8 REC8 homolog (yeast) 41 O.OO1283 1790.8 2281.3 .27 204220 a GMFG Glia maturation factor, gamma 42 O.OO1291 41.6 35.4 -1.18 234958 a EST19 Clone HQ0352 PROO352 43 O.OO1294 1519.9 1803 19 207168. S. at H2AFY H2A histone family, member Y 44 O.OO1329 9.9 8.3 -1.19 1557235 at EST20 CDNA FLI44051 fis, clone TESTI4033433 45 O.OO1329 7.7 6.8 -1.13 207120 a ZNF667 Zinc finger protein 667 46 (O.OO1348 2 15.3 .28 226688 a C3orf23 Chromosome 3 open reading frame 23 47 O.OO1363 2016 3.11.2 .54 224374 S at EMILIN2 Elastin microfibril interfacer 2 48 0.OO1364 79.4 48.9 -1.62 244523 a MMD Monocyte to macrophage differentiation-associated 49 O.OO1415 0.4 9.1 -1.14 226,533 a HINT3 Histidine triad nucleotide binding protein 3 SO O.OO1421 505.7 358.5 -1.41 202074 s at OPTN Optineurin S1 O.OO1438 O.9 9.6 -1.14 234372 a LOC644728 Similar to Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) (38 kDa 8FA-dependent ADP ribosylation substrate) (BARS-38) 52 O.OO1448 239.8 331.7 .38 202192 s a GAS7 Growth arrest-specific 7 S3 O.OO1464 6.6 20.7 .25 1559052 S at PAK2 p21 (CDKN1A)-activated kinase 2 S4 O.OO1472 32.5 47.6 46 223304 a SLC37A3 Solute carrier family 37 (glycerol-3-phosphate transporter), member 3 SS O.OO1491 43.1 58.5 36 213582 a. ATP11A ATPase, Class VI, type 11A S6 O.OO1507 6.5 5.8 -1.12 233770 a EST21 CDNA FLI12077 fis, clone HEMBB10O2453 57 0.001515 14.1 12.7 -1.11 234627 a FL21408 Hypothetical gene Supported by AKO25061 S8 O.OO152 815.3 1047.6 .28 209007 s at C1orf63 Chromosome 1 open reading frame 63 S9 O.OO153 15.6 11.2 -1.39 214502 a HIST1H2BJ Histone cluster 1, H2b 6O O.OO1533 206.6 140.7 -1.47 202124 S at TRAK2 Trafficking protein, kinesin binding 2 61 O.OO1538 16.1 12.9 -1.25 223709 S at WNT10A Wingless-type MMTV integration site family, member OA 62 O.OO1544 1431 1943 36 219132 a PELI2 Pellino homolog 2 (Drosophila) 63 O.OO1561 556.9 684.6 .23 217492 s at LOC731292 Phosphatase and tensin homolog (mutated in multiple PTEN advanced cancers 1) phosphatase and tensin PTENP1 homolog (mutated in multiple advanced cancers 1), pseudogene 1///similar to Phosphatidylinositol-3,4,5- Erisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN (Phosphatase and tensin homolog) (Mutated in multiple advanced cancers1) 164 O.OO1562 7.4 6.7 -1.10 241226 at EST22 Transcribed locus 16S O.OO1565 12.1 10.6 -1.14 231965 at FAM113A Family with sequence similarity 113, member A 166 O.OO157 39.4 69.3 1.76 2076.05 x at ZNF117 Zinc finger protein 117 US 2012/0178642 A1 Jul. 12, 2012 17

TABLE A-continued Differentially expressed consensus genes for mild CAN for both Test Mild CAN = CAN Banff Class 1: No evidence of CAN = CAN Banff Class 0 Probesets with positive fold changes are upregulated in mild CAN

Geom Geom mean mean of of intensities intensities Parametric in class 1: in class 2: Fold p-value Banff0 Banff 1 Change Probe Set ID Gene Symbol Gene Title 67 O.OO16O2 22.4 19.4 -1.15 232249 a FMNL3 Formin-like 3 68 O.OO1612 81.2 116 43 205698 is at MAP2K6 Mitogen-activated protein kinase kinase 6 69 O.OO1613 110.4 1403 .27 229798 is at EST23 7O O.OO162 21 17.7 -1.19 219554 a RHCG Rh family, C glycoprotein 71 O.OO1625 7 6.1 -1.15 244690 a EST24 Transcribed locus 72 O.OO163 343.7 4974 45 225919 is at C9orf72 Chromosome 9 open reading frame 72 73 O.OO1642 74.3 101.7 37 213792 is at INSR Insulin receptor 74 O.OO1677 23.1 26.8 .16 208328 s at MEF2A Myocyte enhancer factor 2A 7S O.OO168 6.9 6.2 -1.11 207362 a SLC30A4 Solute carrier family 30 (zinc transporter), member 4 76 O.OO1709 17.5 15.4 -1.14 206521 S at GTF2A1 General transcription factor IIA, 1, 19/37 kDa 77 0.001735 10O2 142 42 218027 a MRPL15 Mitochondrial ribosomal protein L15 78 O.OO1737 19.6 22.8 .16 2241.98 a ELA1 Elastase 1, pancreatic 79 0.001741 69.6 97.1 40 212572 a. STK38L Serine/threonine kinase 38 like 80 O.OO1743 22.3 18.6 -1.20 206993 a ATP5S ATP synthase, H+ transporting, mitochondrial FO complex, Subunits (factor B) 81 O.OO1788 45.4 36.5 -1.24 203479 is at OTUD4 OTU domain containing 4 82 O.OO1835 13.4 11 -1.22 232820 s at FAM112A Family with sequence similarity 112, member A 83 O.OO1854 7.2 6.6 -1.09 1558621 at CABLES1 CdkS and Ablenzyme substrate 1 84 O.OO1854 59.1 49.6 -1.19 220765 S at LIMS2 LIM and Senescent cell antigen-like domains 2 85 O.OO1859 24.3 2O6 -1.18 205477 s at AMBP Alpha-1-microglobulinibikunin precursor 86 O.OO189 102.8 59 0.57 2078.26 s a ID3 Inhibitor of DNA binding 3, dominant negative helix loop-helix protein 87 O.OO1892 1O.S 17.8 .70 209992 at PFKFB2 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 2 88 O.OO1928 2O7.8 151.9 -1.37 201841 is at HSPB1 Heat shock 27 kDa protein 1 89 O.OO1936 61.4 83.5 36 210768 x at TMCO1 Transmembrane and coiled-coil domains 1 90 O.OO1951 43.1 63.6 48 242794 at MAML3 Mastermind-like 3 (Drosophila) 91 O.OO1976 58.7 79.2 35 213379 at COQ2 Coenzyme Q2 homolog, prenyltransferase (yeast) 92 O.OO1983 425.9 6SO.8 .53 202446 s at PLSCR1 Phospholipid scramblase 1 93 O.OO1984 24.7 28.7 .16 204210 S at PCYT1A Phosphate cytidylyltransferase 1, choline, alpha 94 O.OO1993 31.8 58.3 83 236898 at EST25 Transcribed locus. Strongly similar to XP 0011011634.1 similar to tripartite motif-containing 25 (Macaca mulatta) 95 O.OO2 8.8 7.4 -1.19 2426.61 x at ALS2CR12 Amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 12 96 O.OO2013 19.4 15.4 -1.26 1558773 s at RANBP10 RAN binding protein 10 97 O.OO2O32 63.6 79.5 .25 218896 s at C17orf&S Chromosome 17 open reading frame 85 98 O.OO2O33 27.8 37.2 .34 220865 S at PDSS1 Prenyl (decaprenyl) diphosphate synthase, subunit 1 99 O.OO2O38 214.1 2824 .32 224.51.1 s a TXNDC17 Thioredoxin domain containing 17 2OO O.OO2O45 7.6 6.4 -1.19 243347 a EST26 2O1 O.OO2O54 8.1 7 -1.16 236336 a EST 27 CDNA clone IMAGE: 4796690 202 0.002098 153.9 205.6 .34 224983 a SCARB2 Scavenger receptor class B, member 2 2O3 O.OO2099 30.1 26 -1.16 1569144 a at LOC653325 Similar to RIKEN cDNA 231000215 gene??/hypothetical LOC653325 MGC5993.7 204 O.OO2104 15.9 13.7 -1.16 234511 a C20orf&6 Chromosome 20 open reading frame 86 2O5 O.OO2106 20.3 17.2 -1.18 237254 a SLC5A11 Solute carrier family 5 (sodium glucose cotransporter), member 11 2O6 O.OO2112 9.3 1O.S 13 231310 a EST28 Transcribed locus 2O7 O.OO2171 15.7 13 -1.21 244226 s at EST29 2O8 O.OO22 13.3 11.4 -1.17 230957 a PCDHB19F Protocadherin beta 19 pseudogene 209 O.OO2206 10.8 9.5 -1.14 232321 a MUC17 Mucin 17, cell Surface associated 21 O O.OO221 27.4 19.8 -1.38 2355.57 a LOC1SO763 Hypothetical protein LOC150763 211 O.OO2.218 11251.4 8508.5 -1.32 214414 x at HBA2 Hemoglobin, alpha 2 212 0.00222 16.1 13.8 -1.17 1558118 at DGCRS DiGeorge syndrome critical region gene 5 (non-coding) 213 O.OO2223 18.1 15.9 -1.14 231994 a CHDH Choline dehydrogenase 214 O.OO2229 29.1 34.7 19 212710 a CAMSAP1 Calmodulin regulated spectrin-associated protein 1 215 O.OO2253 94.3 73.7 -1.28 243579 a MSI2 Musashi homolog 2 (Drosophila) 216 O.OO2256 446.2 305.3 -1.46 200702 s at DDX24 DEAD (Asp-Glu-Ala-Asp) box polypeptide 24 217 O.OO2266 94.9 124.4 31 227046 a SLC39A11 Solute carrier family 39 (Metal ion transporter), member 11 218 O.OO2294 36 31.2 -1.15 40020 at CELSR3 Cadherin, EGF LAG seven-pass G-type receptor 3 (flamingo homolog, Drosophila) 219 O.OO2303 27.6 22.9 -1.21 218903 s at OBFC2B Oligonucleotidefoligosaccharide-binding fold containing 2B US 2012/0178642 A1 Jul. 12, 2012 18

TABLE A-continued Differentially expressed consensus genes for mild CAN for both Test Mild CAN = CAN Banff Class 1: No evidence of CAN = CAN Banff Class 0 Probesets with positive fold changes are upregulated in mild CAN

Geom Geom mean mean of of intensities intensities Parametric in class 1: in class 2: Fold p-value Banff0 Banff 1 Change Probe Set ID Gene Symbol Gene Title 22O O.OO2329 5.5 6.7 .22 223861 a HORMAD1 HORMA domain containing 1 221 O.OO2348 508.5 692.2 36 201926 s at CD55 CD55 molecule, decay accelerating factor for complement (Cromer blood group) 222 O.OO23S 1265.9 1098.5 -1.15 209075 is a SCU Iron-sulfur cluster scaffold homolog (E. coli) 223 O.OO23S1 7.1 6 -1.18 231721 a AM3 Junctional adhesion molecule 3 224 O.OO23S4 8.2 7.4 -1.11 237505 a EST30 Transcribed locus 225 O.OO2368 67.4 100.4 49 201952 a ALCAM Activated leukocyte cell adhesion molecule 226 O.OO2389 10 8.7 -1.15 211896 s at DCN Decorin 227 O.OO2394 40.2 31.8 -1.26 216080 s at FADS3 Fatty acid desaturase 3 228 O.OO2427 252.5 326.4 .29 202277 a SPTLC1 Serine palmitoyltransferase, long chain base subunit 1 229 O.OO2435 37.7 56.3 49 208488 is at CR1 Complement component (3b.f4b) receptor 1 (Knops blood group) 230 O.OO2437 100.3 135.1 35 21386.8 s at DHRS7 Deydrogenase/reductase (SDR family) member 7 231 O.OO2443 314.9 419.1 .33 225921 a NIN Ninein (GSK3B interacting protein) 232 O.OO2447 56.7 82.8 46 233329 s at KRCC1 Lysine-rich coiled-coil 1 233 O.OO2472 28.3 24.6 -1.15 232663 s at LOC390595 Similar to ubiquitin-associated protein 1 (predicted) 234 O.OO2474 88.9 143.5 .61 204150 a STAB1 Stabilin 1 23S O.OO2S11 O 11.5 .15 219831 a CDKL3 Cyclin-dependent kinase-like 3 236 O.OO2S28 69.8 101.9 46 216202 s at SPTLC2 Serine palmitoyltransferase, long chain base subunit 2 237 O.OO2S36 28.7 24.3 -1.18 233381 a RUFY1 RUN and FYVE domain containing 1 238 O.OO2S52 67.7 84 .24 222842 a EIF2C4 Eukaryotic translation initiation factor 2C, 4 239 O.OO2S66 3.7 10.6 -1.29 1554413 s at RUNDC2B / RUN domain containing 2B///RUN domain containing RUNDC2C 2C 24O O.OO2598 3.9 12.2 -1.14 2024.03 s at COL1A2 Collagen, type 1, alpha 2 241 O.OO2603 531.4 440.6 -1.21 210950 s at FDFT1 Farnesyl-diposphate farnesyltransferase 1 242 O.OO26OS O.1 8.5 -1.19 215742 at EST31 CDNA FLI12157 fis, clone MAMMA1000500 243 O.OO2672 35.9 42.2 18 221567 at NOL3 Nucleolar protein 3 (apoptosis repressor with CARD domain) 244 O.OO2691 6 12 -1.33 203151 at MAP1A Microtubule-associated protein 1A 245 O.OO2693 4O6.6 S4O.S .33 208864 S at TXN Thioredoxin 246 O.OO27O6 83 62.3 -1.33 201072 s at SMARCC1 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, Subfamily c, member 1 247 O.OO271S 777 63.5 -1.22 211358 s at CIZ1 CDKN1A interacting zinc finger protein 1 248 0.002724 1.1 13.7 .23 205416 s at ATXN3 Ataxin 3 249 O.OO2731 27 23.9 -1.13 244694 a LOC4O266S hCG1651476 2SO O.OO2731 94.6 135.6 .43 212511 a PICALM Phosphatidylinositol binding clathrin assembly protein 251 O.OO2736 81.1 112.4 39 223978 is at CRLS1 Cardiolipin synthase 1 252 O.OO2737 2.1 10.7 -1.13 210923 a SLC1A7 Solute carrier family 1 (glutamate transporter), member 7 2S3 O.OO2738 S.6 S.1 -1.10 204320 a COL11A1 Collagen, type XI, alpha 1 254 O.OO2739 61 83.3 37 209666 s at CHUK Conserved helix-loop-helix ubiquitous kinase 255 0.002747 29.9 24.5 -1.22 238097 a EST32 2S6 O.OO2749 O.1 8.6 -1.17 205295 a CKMT2 Creatine kinase, mitochondrial 2 (sarcomeric) 257 0.002773 24O1 331.4 38 1555797 a. at ARPC5 Actin related protein 2/3 complex, subunit 5, 16 kDa 258 O.OO2776 32.5 28.1 -1.16 23:54.02 a C11orf66 Chromosome 11 open reading frame 66 259 O.OO2793 30.8 25.5 -1.21 216562 a EST33 26O O.OO28.23 9.6 17.1 -1.15 1553967 at ADAT3 Adenosine deaminase, tRNA-specific 3, TAD3 homolog (S. cerevisiae) 261 O.OO2831 883.8 1069.3 .21 226525 a. EST34 Transcribed locus 262 O.OO2853 65.1 109.4 .68 220034 a IRAK3 Interleukin-1 receptor-associated kinase 3 263 O.OO2856 7.7 7.1 -1.08 1563656 at EST35 MRNA, cDNA DKFZp586H1217 (from clone DKFZp586H1217) 264 O.OO2859 6O.S 53.8 -1.12 233235 X at EST36 CDNA: FLI21443 fis, clone COLO4430 26S O.OO2876 5 5.5 10 1558.640 a. at LOC7284.11 Similar to Beta-glucuronidase precursor 266 O.OO288 143.4 216.8 .51 204646 at DPYD Dihydropyrimidine dehydrogenase 267 O.OO2888 52.8 83.6 58. 207719 x at CEP170 Centrosomal protein 170 kDa 268 O.OO289 41.3 SO.9 .23 228791 at C15orf58 Chromosome 15 open reading frame 38 269 O.OO2915 17.6 15 -1.17 240705 at CYP19A1 Cytochrome P450, family 19, subfamily A, polypeptide 1 27O O.OO2927 50.7 42.9 -1.18 218725 at SLC25A22 Solute carrier family 25 (mitochondrial carrier:glutamate), member 22 271 O.OO2996 105.1 1634 .55 201328 at ETS2 v-ets erythroblastosis virus E26 oncogene homolog 2 (avian) 272 O.OO2997 13.9 16.3 .17 239332 at EST37 Homo sapiens, clone IMAGE: 3897 156, mRNA 273 O.OO3O2 14 16.9 .21 240394 at EST38 Transcribed locus 274 O.OO3O49 60.3 51.8 -1.16 1556900 at LOC149773 Hypothetical protein LOC149773 275 O.OO3057 43.4 33.4 -1.30 220588 at BCAS4 Breast carcinoma amplified sequence 4 US 2012/0178642 A1 Jul. 12, 2012 19

TABLE A-continued Differentially expressed consensus genes for mild CAN for both Test Mild CAN = CAN Banff Class 1: No evidence of CAN = CAN Banff Class 0 Probesets with positive fold changes are upregulated in mild CAN

Geom Geom mean mean of of intensities intensities Parametric in class 1: in class 2: Fold p-value Banff0 Banff 1 Change Probe Set ID Gene Symbol Gene Title 276 O.OO3O67 O.1 8.4 -1.20 2101.27 at RAB6B RAB6B, member RAS oncogene family 277 O.OO3O68 5.5 4.9 -1.12 1559450 at EST39 CDNA clone IMAGE: 5286225 278 O.OO3109 22 36.6 66 1558920 at EST40 CDNA FLI43417 fis, clone OCBBF2026025 279 0.003116 9.2 8.2 -1.12 206847 s at HOXA7 Homeobox A7 280 O.OO3117 2.9 11.3 -1.14 216303 s at MTMR1 Myotubularin related protein 1 281 O.OO3131 4 12.3 -1.14 216799 a EST41 MRNA, cDNA DKFZp547GO44 (from clone DKFZp547GO44) 282 O.OO3131 5.8 5.3 -1.09 242130 a. EST42 Transcribed locus 283 O.OO3145 O6 9.4 -1.13 1562106 at EST43 Homo sapiens, clone IMAGE: 5240933, mRNA 284 O.OO3147 40.2 46.9 .17 224416 s at MED28 Mediator complex subunit 28 28S O.OO3153 441.7 716.5 .62 203799 a CD3O2 CD302 molecule 286 O.OO318 23.2 9.5 -1.19 243062 a FLCN Folliculin 287 O.OO3188 S.1 9.7 30 239574 a EST44 Transcribed locus 288 O.OO31.89 5.7 5.2 -1.10 1559518 at HSD17B12 Hydroxysteroid (17-beta) dehydrogenase 12 289 O.OO32 27.3 38.8 42 207601 a SULT1B1 Sulfotransferase family, cytosolic, 1B, member 1 290 O.OO3219 4.6 3 -1.12 219576 a MAP7D3 MAP7 domain containing 3 291 O.OO3229 98.4 127.1 .29 209234 a KIF1B Kinesin family member 1B 292 O.OO3234 1514 100.7 -1.50 225775 a. TSPAN33 Tetraspanin 33 293 O.OO32SS O.8 2.9 19 238921 a LOC641767 Hypothetical protein LOC641767/7/hypothetical LOC644794 LOC644794 294 O.OO3276 5.2 5.8 12 236262 a MMRN2 Multimerin 2 295 O.OO3296 20.4 6.2 -1.26 215526 a EST45 MRNA, cDNA DKFZp586C2020 (from clone DKFZp586C2020) 296 O.OO3296 14.9 3.2 -1.13 236914 a EST46 Transcribed locus, moderately similar to XP 001137307.1 hypothetical protein (Pan troglodytes) 297 O.OO3306 43.6 58.4 .34 236465 a RNF175 Ring finger protein 175 298. O.OO334 106.2 210.1 .98 204619 is at WCAN Versican 299 O.OO336S 15.3 2.5 -1.22 243365 is at AUTS2 Autism Susceptibility candidate 2 3OO O.OO3378 165.7 146 -1.13 201618 x at GPAA1 Glycosylphosphatidylinositol anchor attachment protein 1 homolog (yeast) 301 O.OO3383 82.2 97.6 19 209445 X at C7orfA4 Chromosome 7 open reading frame 44 3O2 O.OO3388 66.1 101.4 .53 1552485 at LACTB Lactamase, beta 3O3 O.OO3393 6 5.5 -1.09 1558O10 s. at SLC1A2 Solute carrier family 1 (glial high affinity glutamate transporter), member 2 3O4 O.OO3404 8 11 .38 225008 at EST47 CDNA FLI39064 fis, clone NT2RP7014.583 3OS O.OO3412 13.5 11.3 -1.19 156O108 at EST48 CDNA FLI30757 fis, clone FEBRA2000468 306 0.003423 29.3 27.2 -1.08 244055 at EST49 Transcribed locus 307 O.OO3447 16.6 2O 20 233750 S at C1orf25 Chromosome 1 open reading frame 25 3O8 O.OO346 5.4 5 -1.08 220361 at QCH IQ motif containing H 309 O.003472 110 1812 .65 222303 at EST50 31 O O.OO3SO2 58.3 80.3 .38 23.0937 at LOC28S835 Hypothetical protein LOC285.835 311 O.OO3S35 39.4 52 32 207627 s at TFCP2 Transcription factor CP2 312 O.OO3S39 20.3 17.5 -1.16 1555752 at STH Saitohin 313 O.OO3S42 3O88.2 3805.3 .23 212501 at CEBPB CCAAT?enhancer binding protein (C/EBP), beta 314 O.OO3SS1 6.2 5.7 -1.09 244675 at RGS8 Regulator of G-protein signaling 8 315 0.003571 12.7 11.2 -1.13 208.275 X at UTF1 Undifferentiated embryonic cell transcription factor 1 316 O.OO3S72 3974 524.7 .32 210951 X at RAB27A RAB27A, member RAS oncogene family 317 O.OO3S82 7.8 6.7 -1.16 21984.0 s at TCL6 T-cell leukemia/lymphoma 6 318 O.OO3626 124.1 166.3 .34 219256 S at SH3TC1 SH3 domain and tetratricopeptide repeats 1 319 O.OO3657 5.3 4.8 -1.10 1558778. S. at MKL2 MKL/myocardin-like 2 32O O.OO366 32.1 27.1 -1.18 218480 at AGBLS ATP/GTP binding protein-like 5 321 O.OO3672 118 176.7 .50 204099 at SMARCD3 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, Subfamily d, member 3 322 O.OO3678 480.1 579 21 225750 at EST51 CDNA FLI14162 fis, clone NT2RM4002.504 323 O.OO371S 50.7 43.5 -1.17 214253 S at DTNB Dystrobrevin, beta 324 O.OO3718 12.1 10.8 -1.12 243048 at CECR7 Cat eye syndrome chromosome region, candidate 7 325 O.OO3757 9 7.9 -1.14 1556O12 at KLHDC7A Kelch domain containing 7A 326 O.OO3773 17.6 23.4 .33 215285 s at PHTF1 Putative homeodomain transcription factor 1 327 O.OO378 64.4 81.7 .27 231321 S at PHCA Phytoceramidase, alkaline 328 O.OO3783 5.4 4.9 -1.10 238901 at EST52 Full length insert cDNA clone ZEO1A04 329 O.OO3793 25.4 21.4 -1.19 214595 at KCNG1 Potassium voltage-gated channel, Subfamily G, member 1 US 2012/0178642 A1 Jul. 12, 2012 20

TABLE A-continued Differentially expressed consensus genes for mild CAN for both Test Mild CAN = CAN Banff Class 1: No evidence of CAN = CAN Banff Class 0 Probesets with positive fold changes are upregulated in mild CAN

Geom Geom mean mean of of intensities intensities Parametric in class 1: in class 2: Fold p-value Banff0 Banff 1 Change Probe Set ID Gene Symbol Gene Title 330 O.OO38 1O.S 9.4 -1.12 21.6470 X at PRSS1 Protease, serine, 1 (trypsin1), protease, serine, 2 PRSS2 (trypsin2). protease, serine, 3 (mesotrypsin) PRSS3 trypsinogen 3 TRY6 331 O.OO3819 36.6 59.4 .62 204787 at WSIG4 V-set and immunoglobulin domain containing 4 332 O.OO3841 11.7 102 -1.15 216101 at EST53 Full length insert cDNA clone YR67C11 333 O.OO384.5 51 75.1 47 224862 at GNAQ Guanine nucleotide binding protein (G protein), q polypeptide 334 O.OO3873 17.6 23.6 .34 234664 at LOC2847O1 Hypothetical protein LOC284701 33S O.OO3878 16.8 14 -1.20 202796 at SYNPO Synaptopodin 336 O.OO3884 11.4 10 -1.14 2.38217 at EST54 Transcribed locus 337 O.OO390S 559.2 823.8 47 20918.4 S at IRS2 insulin receptor Substrate 2 338 O.OO390S S.6 5.2 -1.08 1565578 at EST55 CDNA FLI34486 fis, clone HLUNG2004217 339 O.OO3909 2O2.6 269.2 .33 217823 s at UBE21 Ubiquitin-conjugating enzyme E2, J1 (UBC6 homolog, yeast) 340 O.OO3952 7 6.2 -1.13 240873 X at DAB2 Disabled homolog2, mitogen-responsive phosphoprotein (Drosophila) 341 O.OO3967 206.9 281.1 36 212795 a KIAA1033 KIAA1033 342 O.OO3968 36 48.9 36 239085 a EST56 Transcribed locus 343 O.OO3972 110.8 171.2 .55 223423 a GPR160 G protein-coupled receptor 160 344 O.OO3992 12.3 10.8 -1.14 238917 s at MGC24039 Hypothetical protein MGC24039 345 O.OO3999 36.9 48.4 31 226395 a LOC286170 Hypothetical protein LOC286170 346 (O.OO4021 155.6 222.8 .43 215000s at FEZ2 Fasciculation and elongation protein zeta 2 (Zygin II) 347 O.OO4032 196.3 235.6 20 203605 a SRPS4 Signal recognition particle 54 kDa 348 O.OO4054 7.7 6.6 -1.17 2428OS a EST57 349 O.OO4085 SO4 66.2 31 204043 a TCN2 Transcobalamin II; macrocytic anemia 3SO O.OO4142 9.8 11.4 .16 237845 a. EST58 Transcribed locus, moderately similar to XP 001103240.1 similar to kinesin family member 27 (Macaca mitiatta) 351 O.OO4144 28S 22.5 -1.27 1569499 at EST59 CDNA clone IMAGE: 384.0913 352 O.OO4179 21.1 18.5 -1.14 217876 a GTF3C5 General transcription factor IIIC, polypeptide 5, 63 kDa 353 O.OO418S 9.9 15.3 .55 223660 a ADORA3 Adenosine A3 receptor 3S4 O.OO4186 5.8 6.3 .09 231160 a EST60 Transcribed locus 3SS O.OO419 9.7 15.7 .62 236901 a EST61 Transcribed locus 356 O.OO42 20.9 18 -1.16 215979 s at SLC7A1 Solute carrier family 7 (cationic amino acid transporter, y- system), member 1 357 O.OO4234 1525.2 1779.3 .17 208736 a ARPC3 Actin related protein 2/3 complex, subunit 3, 21 kDa 358 O.OO4238 82.6 123.2 .49 229383 a EST62 CDNA FLI34016 fis, clone FCBBF2002541 359 O.OO426S 32 27.2 -1.18 32137 at AG2 Jagged 2 360 O.OO4278 7.6 6.9 -1.1O 213249 a FBXL7 F-box and leucine-rich repeat protein 7 361 O.OO4288 2770.3 3252 .17 2028.03 s a TGB2 Integrin, beta 2 (complement component 3 receptor 3 and 4 subunit) 362 0.004321 119 159.5 .34 203310 a STXBP3 Syntaxin binding protein 3 363 0.00433S 798.5 1181 .48 202295 s at CTSH Cathespin H 364 O.OO4354 10.4 9.1 -1.14 220994 S at STXBP6 Syntaxin binding protein 6 (amisyn) 365 0.0043SS 49 90.4 .84 212224 a ALDH1A1 Aldehyde dehydrogenase 1 family, member A1 366 0.004381 208.3 260.9 .25 212120 a RHOQ Ras homolog gene family, member Q 367 O.OO443S 32.8 29.9 -1.10 37586 at ZNF142 Zinc finger protein 142 368 O.OO4453 285.1 404.8 42 219356 S at CHMP5 Chromatin modifying protein 5 369 O.OO4.458 118.6 152.6 .29 241370 a LOC286052 Hypothetical protein LOC286052 37O O.OO446S 13.1 11.4 -1.15 1558476 at C1orf16S Chromosome 1 open reading frame 165 371 O.OO448S 5.5 6.2 13 206533 a CHRNAS Cholinergic receptor, nicotinic, alpha 5 372 O.OO4489 33.2 28.8 -1.15 229979 x a EST63 Transcribed locus 373 O.OO4526 66.2 83.5 .26 200764 S at CTNNA1 Catenin (cadherin-associated protein), alpha 1, 102 kDa 374 O.OO4SS6 7.3 6.5 -1.12 240874 a EST64 Transcribed locus 375 O.OO4558 20.4 17.2 -1.19 1556672 a. at RBM6 RNA binding motif protein 6 376 O.OO4S59 13.6 10.9 -1.25 236268 a SEC22C SEC22 vesicle trafficking protein homolog C (S. cerevisiae) 377 O.OO4594 68.3 57 -1.20 220968 is at TSPAN9 Tetraspanin 9 378 O.OO4616 363.3 284.7 -1.28 223042 s at FUNDC2 FUN14 domain containing 2 379 O.OO4683 6.9 9.4 36 226311 a EST65 CDNA clone IMAGE: 30924414 380 O.OO4699 5 4.7 -1.06 1570482 at EST66 Pp14356 381 O.OO476 5.9 6.6 .12 1562274 at EST67 MRNA, cDNA DKFZp 313IO929 (from clone DKFZp313IO929) 382 O.OO4769 4O.S 32.8 -1.23 201792 a AEBP1 AE binding protein 1 US 2012/0178642 A1 Jul. 12, 2012 21

TABLE A-continued Differentially expressed consensus genes for mild CAN for both Test Mild CAN = CAN Banff Class 1: No evidence of CAN = CAN Banff Class 0 Probesets with positive fold changes are upregulated in mild CAN

Geom Geom mean mean of of intensities intensities Parametric in class 1: in class 2: Fold p-value Banff0 Banff 1 Change Probe Set ID Gene Symbol Gene Title 383 O.OO4776 11.7 13.7 1.17 229671 S. at C21orfA5 Chromosome 21 open reading frame 45 384 O.OO4783 23 15.8 -1.46 208501 a GFI1B Growth factor independent 1B (potential regulator of CDKN1A, translocated in CML) 385 O.OO4788 6.6 5.9 -1.12 206142 a. ZNF135 Zing finger protein 135 386 O.OO4813 6.9 6.4 -1.08 233594 a EST68 CDNA clone IMAGE: 4823221 387 O.OO4845 9 8 -1.13 1565.407 at LHX9 LIM homeobox 9 388 O.OO4861 7.1 6.3 -1.13 1559634 at CHRM3 Cholinergic receptor, muscarinic 3 389 O.004927 23.8 36.5 1.53 236297 a EST 69 CDNA FLI45742 fis, clone KIDNE2016327 390 O.OO4932 29.6 33.1 1.12 215930 S. at CTAGES CTAGE family, member 5 391 O.OO4946 101.1 128.9 1.27 2094.63 s at TAF12 TAF12 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 20 kDa 392 O.OO4975 26.4 18.6 -1.42 206759 a FCER2 Fc fragment of IgE, low affinity II, receptor for (CD23) 393 O.OO4988 14.3 12.3 -1.16 230950 a EST70 Transcribed locus

TABLE B Differentially expressed consensus genes for moderate, severe CANIFTA for both Test Sets Moderate/Severe CAN/IFTA = CAN/IFTA Banff Class 2, 3: No evidence of CAN/IFTA = CAN/IFTA Banff Class 0 Probesets with positive fold changes are upregulated in moderate/severe CAN

Geom Geom mean of mean of intensities intensities Ratio of Parametric in class 1: in class 2: geom p-value Banff0 Banff 2, 3 (8S Probe Set ID Gene Symbol Gene Title O.OOO1775 11.1 9 -1.23 1566879 at EST1 ATP/GTP binding protein-like 1 O.OOO3852 4.9 4.5 241139 a EST2 OOOO4281 5.5 6.1 231591 a BHMT anthrax toxin receptor 2 O.OOO4852 2O.S 26.2 242619 x a EST3 O.OOOST16 20.8 34.5 206674 a FLT3 LIM homeobox 9 O.OOOS983 S.6 4.9 204005 s a PAWR O.OOO6361 23 39.6 22O112 a ANKRDSS OOOO6841 6.6 5.9 239312 a EST4 Phospholipase C epsilon O.OOO7962 21.4 28.1 205977 s a EPHA1 1 O.OOO8868 9.3 8.1 210412 a GRIN2B olfactory receptor, family 8, Subfamily G, member 1 O.OOO8881 5 4.5 216089 a MCFD2L O.OOO9531 10 8.5 226211 a MEG3 PRKC, apoptosis, WT1, regulator O.OO1086 58.7 72.7 226856 a MUSTN1 CUG triplet repeat, RNA binding protein 1 O.OO11S6 11.7 4.7 229671 s a C21orfA5 PBX knotted 1 homeobox. 1 O.OO1212 10 1.6 219831 a CDKL3 cleavage stimulation factor, 3' pre-RNA, subunit 2, 64 kDa O.OO13123 8.7 O 233429 a FLJ23577 matrix metallopeptidase 1 (interstitial collagenase) O.OO13489 14 9 210896 s a ASPH IKAROS family Zinc finger 1 (Ikaros) O.OO14846 9.7 5 236901 a EST5 EPH receptor A1 O.OO15437 7.7 6.8 213994 s a SPON1 fms-related tyrosine kinase 3 O.OO15498 11 9.5 242417 a LOC283278 cytochrome P450, family 4, Subfamily B, polypeptide 1 O.OO15652 6.3 S.6 229777 a CLRN3 glutamate receptor, ionotropic, N-methyl D-aspartate 2B O.OO1688S 3.11.3 218.7 205039 s a KZF1 aspartate beta-hydroxylase O.OO17597 18.8 22.5 204113 a CUGBP1 nuclear factor of kappa light polypeptide gene enhancer in B-cells 2 (p49, p100) 24 O.OO19344 11.6 4.8 28 233650 a CEP63 met proto-oncogene (hepatocyte growth factor receptor) 25 O.OO19513 42.8 57 .33 236832 a. LOC221442 spondin 1, extracellular matrix protein 26 O.OO19757 21.9 8.6 228721 a C3orfA1 27 O.OO2O356 6.9 8.9 29 226311 a EST6 Secretogranin III 28 0.0020555 5.5 4.6 -1.20 1566428 at EST7 cyclin-dependent kinase-like 3 29 O.OO2O848 18.7 5 -1.25 229532 a. ZNF502 ankyrin repeat domain 55 30 O.OO21794 10.6 2 13 1554615 at EST8 heparan-alpha-glucosaminide N-acetyltransferase 31 O.OO22636 5.9 5.4 -1.09 230650 a EST9 family with sequence similarity 135, member A 32 0.0022797 76.1 624 -1.22 204459 a CSTF2 maternally expressed 3 (non-protein coding) 33 O.OO238O8 5.3 4.8 -1.10 1570.050 at EST 10 34 O.OO238SS 4.7 4.3 -1.09 1566096 X at EST11 musculoskeletal, embryonic nuclear protein 1 35 O.OO2S531 9 8 -1.13 1565.407 at LHX9 hexokinase domain containing 1 36 O.OO2S848 S.1 S.6 1O 232770 a TUSC3 US 2012/0178642 A1 Jul. 12, 2012 22

TABLE B-continued Differentially expressed consensus genes for moderate, severe CANIFTA for both Test Sets Moderate/Severe CAN/IFTA = CAN/IFTA Banff Class 2, 3: No evidence of CAN/IFTA = CAN/IFTA Banff Class 0 Probesets with positive fold changes are upregulated in moderate/severe CAN

Geom Geom mean of mean of intensities intensities Ratio of Parametric in class 1: in class 2: 9. (Oil p-value Banff0 Banff 2, 3 Probe Set ID Gene Symbol Gene Title 37 O.OO26131 6.4 S.6 204475 a MMP1 hypothetical protein LOC90784 38 O.OO26527 11.3 14.3 27 243349 a KIAA1324 thyroid hormone receptor, beta (erythroblastic leukemia viral (v-erb-a) oncogene homolog2, avian) 39 0.0027257 5.7 S.1 240604 a EXOD1 chromosome 3 open reading frame 41 40 O.OO27342 6 S.6 210096 a CYP4B1 RNA binding protein with multiple splicing 2 41 O.OO27896 39.3 22 228390 a EST12 hypothetical protein LOC729680 42 O.OO27907 6.3 6.9 228977 a LOCA2968O nuclear receptor Subfamily 2, group F, member 2 43 O.OO28215 9.5 10.6 213807 x at MET Zinc finger protein 502 44 O.OO28343 7.9 6.7 228716 a THRB CDNA FU90800 fis, clone Y79AA1000 127 45 O.OO291OS 6.1 10.7 1560800 at EST13 clarin 3 46 O.OO31196 12.6 14.3 1567060 at OR8G1 47 O.OO33408 24.1 19.6 223497 a FAM13SA Betaine:homocysteine methyltransferase 48 O.OO39416 5.3 5.9 211524 a NFKB2 tumor Suppressor candidate 3 49 O.OO39539 14.2 12.3 241261 x at EST14 sperm flagellar 2 50 O.OO3958 12.1 1O.S 243048 a CECR7 centrosomal protein 63 kDa 51 34.8 22.1 228802 a RBPMS2 52 4.7 4.4 219196 a SCG3 hypothetical LOC221442 53 O.OO41033 18.9 24.7 227614 a HKDC1 S4 O.OO41799 39.2 46 204195 S at PKNOX1 55 O.OO42431 25 30.2 228515 a. LOC90784 exoribonuclease 2 56 O.OO42468 9.7 8.7 1566.739 at PLCE1 57 O.OO43315 27.7 33.5 222491 a HGSNAT S8 O.OO44839 7.3 8.1 1553447 at AGBL1 59 O.OO45669 6.7 6.2 229092 a EST15 hypothetical protein LOC283278 60 O.OO47554 9.7 11.1 233993 a EST16 61 0.004775 17.7 21 242264 a EST17 cat eye syndrome chromosome region, candidate 7 62 O.OO48752 34.1 38.1 1555536 at ANTXR2 KIAA1324

TABLE C Differentially expressed consensus genes for mild CANIFTA for both Test Sets Mild CAN/IFTA = CAN/IFTA Banff Class 1: No evidence of CAN/IFTA = CAN/IFTA Banff Class 0 Probesets with positive fold changes are upregulated in mild CAN

Geom Geom mean of mean of intensities intensities Parametric in class 1: in class 2: Fold p-value Banff0 Banff1 Change Probe Set ID Gene Symbol Gene Title OOOOOO2 27.9 19.3 45 203796 s at BCL7A B-cell CLL/lymphoma 7A 21E-06 11.6 16.7 .44 233650 a CEP63 centrosomal protein 63 kDa 3.2E-06 50.5 40.1 26 1552892 at TNFRSF13C tumor necrosis factor receptor Superfamily, member 13C 5.9E-06 19.2 33.6 .75 1565597 at EST1 Homo sapiens, clone IMAGE: 4275461, mRNA 8.3E-O6 15.1 23.5 S6 24.1752 a. SLC8A1 Solute carrier family 8 (sodium calcium exchanger), member 1 6 1.25 8O3.7 1OS.O.S 31 213702 x at ASAH1 N-acylsphingosine amidohydrolase (acid ceramidase) 1 1.61 224.8 174.8 29 223259 a ORMDL3 ORM1-like 3 (S. cerevisiae) 1.84 E-E-E- o 135.4 189.9 40 204054 a PTEN phosphatase and tensin homolog (mutated in multiple advanced cancers 1) 1.86 26 46 77 239012 a BRDC2 IBR domain containing 2 2.39 1182 1724.7 46 200975 a. PPT1 palmitoyl-protein thioesterase 1 (ceroid-lipofuscinosis, neuronal 1, infantile) 11 OOOOO24 1743 363.5 2.09 206584 a LY96 lymphocyte antigen 96 12 3.35E-OS 9 7.6 18 228044 a C13orf21 chromosome 13 open reading frame 21 13 4.41 2SO.1 327.6 31 225492 a. EST2 14 4.53 - g 7828 1066O2 36 202917 s at S1 OOA8 S100 calcium binding protein A8 15 OOOOO47 374.1 724.5 .94 2235.01 a TNFSF13B tumor necrosis factor (ligand) Superfamily, member 13b 16 4.7SE-OS 112.7 204 81 222496 s at FLJ2O273 RNA-binding protein 17 S.11 22.4 38.8 73 224996 a EST3 CDNA FLJ39064 fis, clone NT2RP7014.583 18 S.13 - g 21.6 17.5 23 244863 a EST4 Transcribed locus 19 OOOOOS2 7.5 9 2O 238791 a ZNF100 Zinc finger protein 100 2O S.66E-OS 85.2 123.8 45 218177 a CHMP1B chromatin modifying protein 1B US 2012/0178642 A1 Jul. 12, 2012 23

TABLE C-continued Differentially expressed consensus genes for mild CANIFTA for both Test Sets Mild CAN/IFTA = CAN/IFTA Banff Class 1: No evidence of CAN/IFTA = CAN/IFTA Banff Class 0 Probesets with positive fold changes are upregulated in mild CAN

Geom Geom mean of mean of intensities intensities Parametric in class 1: in class 2: Fold p-value Banff0 Banff1 Change Probe Set ID Gene Symbol Gene Title 21 S-67E-OS 2O3.3 336.4 .65 2262.08 at ZSWIM6 Zinc finger, SWIM-type containing 6 22 7.26E-OS 180.8 237.2 31 203778 at MANBA mannosidase, beta A, lysosomal 23 O.OOOO89 86.6 123.4 42 238903 at LOC137886 hypothetical protein LOC137886 24 OOOOO94 19.7 14.5 -1.36 214308 s at HGD homogentisate 1,2-dioxygenase (homogentisate oxidase) 25 O.OOO 103 492.9 744.6 .51 21 1368 s at CASP1 caspase 1, apoptosis-related cysteine peptidase (interleukin 1, beta, convertase) 26 OOOO103 132.8 1848 39 227017 at ERICH1 glutamate-rich 1 27 O.OOO107 10.3 15.5 .50 228624 at TMEM144 transmembrane protein 144 28 OOOO108 128.7 170.2 32 232149 s at NSMAF neutral sphingomyelinase (N-SMase) activation associated factor 29 O.OOO112 26.4 35.2 .33 243287 s at OSTM1 osteopetrosis associated transmembrane protein 1 30 OOOO116 59.5 134.7 2.26 1552773 at CLEC4D C-type lectin domain family 4, member D 31 O.OOO121 2887.4 3972.4 .38 202902 s at CTSS cathepsin S 32 O.OOO12S 142.4 229 .61. 211744 S at CD58 CD58 molecule 33 O.OOO133 35.6 26.9 -1.32 24.3507 is at C20orf196 chromosome 20 open reading frame 196 34 OOOO137 101.9 77.4 -1.32 228832 a FLJ20021 hypothetical LOC90024 3S O.OOO149 1057.6 1433.5 36 202727 s at FNGR1 interferon gamma receptor 1 36 OOOO169 40.5 55.5 37 213952 S at ALOX5 Arachidonate 5-lipoxygenase 37 O.OOO174 364.6 288.1 -1.27 219045 a. RHOF ras homolog gene family, member F (in filopodia) 38 OOOO175 666 974.1 46 212268 a SERPINB1 serpin peptidase inhibitor, clade B (ovalbumin), member 1 39 O.OOO18 80.3 119.4 49 203276 a LMNB1 lamin B1 40 OOOO19 347.2 8141 2.34 219666 a MS4A6A membrane-spanning 4-domains, subfamily A, member 6A 41 O.OOO2O)4 54.9 110.9 2.02 204860s at NAIP NLR family, apoptosis inhibitory protein if neuronal NAIP1B apoptosis inhibitory protein (centromeric) 42 O.OOO212 3812.4 4958.6 30 202388 a RGS2 regulator of G-protein signaling 2, 24 kDa 43 O.OOO226 24.5 43.9 .79 1553514 a at VNN3 wanin 3 44 OOOO239 846 108.3 .28 218364 a LRRFIP2 leucine rich repeat (in FLII) interacting protein 2 45 O.OOO242 15.5 21.5 39 218888. S. at NETO2 neuropilin (NRP) and tolloid (TLL)-like 2 46 O.OOO258 64.6 87.8 36 204108 a NFYA nuclear transcription factor Y, alpha 47 O.OOO273 35.6 SO.1 41 213935 a. ABHDS abhydrolase domain containing 5 48 0.000278 S4 75.5 40 208883 a UBRS ubiquitin protein ligase E3 component n-recognin 5 49 O.OOO282 334.9 425 .27 222148 S. at RHOT1 ras homolog gene family, member T1 SO O.OOO284 564.8 712.6 26 227266 s at FYB FYN binding protein (FYB-120/130)

TABLED Top 50 Differentially expressed consensus genes for moderatefsevere CAN/IFTA for both Test Sets Moderatef Severe CANIFTA = CANIFTA Banff Class 2,3: No evidence of CANIFTA = CANIFTA Banff Class 0

Geom Geom mean of mean of intensities intensities Ratio of Parametric in class 1: in class 2: geom p-value Banff0 Banff 2, 3 means Probe Set ID Gene Symbol Gene Title 1 O.OOO178 11.1 9 -1.23 1566879 at EST1 ATP/GTP binding protein-like 1 2 O.OOO385 4.9 4.5 -1.09 241139 a EST2 3 O.OOO428 5.5 6.1 .11 231591 a BHMT anthrax toxin receptor 2 4 O.OOO485 2O.S 26.2 .28 242619 x at EST3 5 0.000572 20.8 34.5 .66 206674 a FLT3 LIM homeobox 9 6 O.OOOS98 S.6 4.9 -1.14 204005 s at PAWR 7 O.OOO636 23 39.6 .72 220112 a ANKRDSS 8 O.OOO684 6.6 5.9 -1.12 239312 a EST4 Phospholipase C epsilon 9 O.OOO796 21.4 28.1 31 205977 s at EPHA1 10 O.OOO887 9.3 8.1 -1.15 210412 a GRIN2B olfactory receptor, family 8, Subfamily G, member 1 11 O.OOO888 5 4.5 -1.11 216089 a MCFD2L 12 O.OOO953 10 8.5 -1.18 226211 a MEG3 PRKC, apoptosis, WT1, regulator 13 O.OO1086 58.7 72.7 24 226856 a MUSTN1 CUG triplet repeat, RNA binding protein 1 14 O.OO1156 11.7 14.7 26 229671 S. at C21orfA5 PBX knotted 1 homeobox. 1 15 O.OO1212 10 11.6 16 219831 a CDKL3 cleavage stimulation factor, 3' pre-RNA, subunit 2, 64 kDa 16 O.OO1312 8.7 10 .15 233429 a FLJ23577 matrix metallopeptidase 1 (interstitial collagenase) 17 O.OO1349 14 19 36 210896 S. at ASPH IKAROS family Zinc finger 1 (Ikaros) 18 O.OO1485 9.7 15 .55 236901 a EST5 EPH receptor A1 US 2012/0178642 A1 Jul. 12, 2012 24

TABLE D-continued Top 50 Differentially expressed consensus genes for moderatefsevere CAN/IFTA for both Test Sets Moderatef Severe CANIFTA = CANIFTA Banff Class 2,3: No evidence of CANIFTA = CANIFTA Banff Class 0

Geom Geom mean of mean of intensities intensities Ratio of Parametric in class 1: in class 2: geom p-value Banff0 Banff 2, 3 means Probe Set ID Gene Symbol Gene Title 19 O.OO1544 7.7 6.8 -1.13 213994 S at SPON1 fms-related tyrosine kinase 3 2O O.OO15S 11 9.5 -1.16 242417 a LOC283278 cytochrome P450, family 4, Subfamily B, polypeptide 1 21 O.OO1565 6.3 S.6 -1.13 229777 a CLRN3 glutamate receptor, ionotropic, N-methyl D-aspartate 2B 22 O.OO1689 3.11.3 218.7 -142 205039 S at IKZF1 aspartate beta-hydroxylase 23 O.OO176 18.8 22.5 .20 204113 a CUGBP1 nuclear factor of kappa light polypeptide gene enhancer in B-cells 2 (p49, p100) 24 11.6 14.8 .28 233650 a CEP63 met proto-oncogene (hepatocyte growth factor receptor) 25 42.8 57 .33 236832 a LOC221442 spondin 1, extracellular matrix protein 26 21.9 18.6 -1.18 228721 a C3orfA1 27 6.9 8.9 29 226311 a EST6 Secretogranin III 28 5.5 4.6 -1.20 1566428 at EST7 cyclin-dependent kinase-like 3 29 18.7 15 -1.25 229532 a ZNF502 ankyrin repeat domain 55 30 10.6 12 .13 1554615 at EST8 heparan-alpha-glucosaminide N-acetyltransferase 31 5.9 5.4 -1.09 23.0650 a EST9 family with sequence similarity 135, member A 32 76.1 624 -1.22 204459 a CSTF2 maternally expressed 3 (non-protein coding) 33 5.3 4.8 -1.10 1570050 at EST 10 34 4.7 4.3 -1.09 1566096 X at EST11 musculoskeletal, embryonic nuclear protein 1 35 9 8 -1.13 1565.407 at LHX9 hexokinase domain containing 1 36 S.1 S.6 10 232770 a TUSC3 37 6.4 S.6 -1.14 204475 a MMP1 hypothetical protein LOC90784 38 11.3 14.3 .27 243349 a KIAA1324 thyroid hormone receptor, beta (erythroblastic leukemia viral (v-erb-a) oncogene homolog2, avian) 39 O.OO2726 5.7 S.1 -1.12 240604 a EXOD1 chromosome 3 open reading frame 41 40 O.OO2734 6 5.6 -1.07 210096 a CYP4B1 RNA binding protein with multiple splicing 2 41 O.OO279 39.3 22 -1.79 228390 a EST12 hypothetical protein LOC729680 42 O.OO2791 6.3 6.9 10 228977 a LOCA2968O nuclear receptor Subfamily 2, group F, member 2 43 O.OO2822 9.5 10.6 12 213807 x at MET Zinc finger protein 502 44 O.OO2834 7.9 6.7 -1.18 228716 a THRB CDNA FLJ90800 fis, clone Y79AA1000127 45 O.OO2911 6.1 10.7 .75 1560800 at EST13 clarin 3 46 O.OO312 12.6 14.3 .13 1567060 at OR8G1 47 O.OO3341 24.1 19.6 -1.23 223497 a FAM13SA Betaine:homocysteine methyltransferase 48 O.OO3942 5.3 5.9 .11 211524 a NFKB2 tumor Suppressor candidate 3 49 O.OO3954 14.2 12.3 -1.15 241261 x at EST14 sperm flagellar 2 50 O.OO3958 12.1 1O.S -1.15 243048 a CECR7 centrosomal protein 63 kDa

TABLE E

international Pro ein index/UniGene Symbol Entrez Gene Name O3854 DOK1 docking pro ein 1, 62 kDa (downstream of tyrosine kinase 1) O9752 C6ORF108 chromosome 6 open reading frame 108 10675 APOC1 apolipoprotein C-I 16459 MAN2A2 mannosidase, alpha, class 2A, member 2 17331 TREML.1 triggering receptor expressed on myeloid cells-like 1 19177 ARF3 ADP-ribosy ation factor 3 23198 MYO9B myosin IXB 34084 M6PR mannose-6-phosphate receptor (cation dependent) 51135 FN3K ructosamine 3 kinase 59509 SERPINF2 Serpin pepti ase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 2 S.190334 RAP1A RAP1A, member of RAS oncogene family S.191215 CYTH1 cytohesin 1 S.202 TSPO translocator protein (18 kDa) S.2O3637 PLS1 plastin 1 (I isoform) S.226007 RDH11 retinol dehy rogenase 11 (all-trans 9-cis, 11-cis) S.241.78 EML2 echinoderm microtubule associated protein like 2 S.24258 GUCY1A3 guanylate cyclase 1, Soluble, alpha 3 S.24889 FMN2 ormin 2 S.26O7SO SNX12 Sorting nexin 12 S.277624 ZZEF1 Zinc finger, ZZ-type with EF-hand domain 1 S.287714 RAB32 RAB32, member RAS oncogene family S.3O1412 UFC1 ubiquitin-fold modifier conjugating enzyme 1 US 2012/0178642 A1 Jul. 12, 2012 25

TABLE E-continued

international Protein index/UniGene Symbol Entrez Gene Name 23 S.306327 RAB3GAP1 RAB3 GTPase activating protein subunit 1 (catalytic) 24 S.3275.27 SMARCA4 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4 25 S.363396 CFEH complement factor H 26 S.368.078 DNAJA2 DnaJ (Hsp40) homolog, subfamily A, member 2 27 S.368527 TOLLIP toll interacting protein 28 S.368626 RTN1 reticulon 1 29 S.369840 NID2 nidogen 2 (osteonidogen) 30 S.376.933 GUK1 guanylate kinase 1 31 S.38449 SERPINE2 Serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 2 32 S.390S67 FYN FYN oncogene related to SRC, FGR, YES 33 S.390667 GSTK1 glutathione S-transferase kappa 34 S.411312 TGA2B integrin, alpha2b (platelet glycoprotein IIb of IIb.IIIa complex, antigen CD41) (includes EG: 3674) 35 S.414.795 SERPINE1 Serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1 36 S.416848 CTSW cathepsin W 37 S.42O529 UBE2V1 ubiquitin-conjugating enzyme E.2 variant 1 38 S.429608 REEP5 receptor accessory protein 5 39 S.433068 PRKAR2B protein kinase, cAMP-dependent, regulatory, type II, beta 40 S.435291 ARHGAP6 Rho GTPase activating protein 6 41 S.435512 PPP3CA protein phosphatase 3 (formerly 2B), catalytic Subunit, alpha isoform 42 S.438906 C22ORF30 chromosome 22 open reading frame 30 43 S.443976 CEP250 centrosomal protein 250 kDa 44 S.458917 SCAMP2 Secretory carrier membrane protein 2 45 S.46O109 MYH11 myosin, heavy chain 11, Smooth muscle 46 S.462379 TOM1L2 arget of myb1-like 2 (chicken) 47 S.464813 PSMA8 proteasome (prosome, macropain) subunit, alpha type, 8 48 S.465295 LMAN1 ectin, mannose-binding, 1 49 S.466910 CDA cytidine deaminase 50 S.477009 USP24 ubiquitin specific peptidase 24 51 S.477352 PDIAS protein disulfide isomerase family A, member 5 52 S.4779 GATAD2B GATA zinc finger domain containing 2B 53 S.480364 METAP1 methionyl aminopeptidase 1 S4 S.481836 MTMR12 myotubularin related protein 12 55 S.48.1860 TARS hreonyl-tRNA synthetase 56 S.482873 TMED5 transmembrane emp24 protein transport domain containing 5 57 S.487540 RPA3 replication protein A3, 14 kDa 58 S.49582 PPP1R12A protein phosphatase 1, regulatory (inhibitor) Subunit 12A 59 S.5O12OO RGS10 regulator of G-protein signaling 10 60 SSO2244 EIF3M eukaryotic translation initiation factor 3, Subunit M 61 S.SO382 TP2 ight junction protein 2 (zona occludens 2) 62 S506603 APPL2 adaptor protein, phosphotyrosine interaction, PH domain and leucine Zipper containing 2 63 S.S13 OSS WDR61 WD repeat domain 61 64 S.S13646 VD isovaleryl Coenzyme A dehydrogenase 65 S.514012 MAP2K3 mitogen-activated protein kinase kinase 3 66 S.5141.99 WAT1 vesicle amine transport protein 1 homolog (T. Californica) 67 S.S.14870 ATP5F1 ATP synthase, H+ transporting, mitochondrial FO complex, Subunit B1 68 S.S2OO48 LA-DRA major histocompatibility complex, class II, DRalpha 69 S.524518 TAT6 signal transducer and activator of transcription 6, interleukin-4 induced 70 S.525419 MA1 LIM domain and actin binding 1 71 S.S28952 RIM2S tripartite motif-containing 25 72 S.S29023 NF532 Zinc finger protein 532 73 S.S30096 F3I (includes eukaryotic translation initiation factor 3, Subunit I G: 8668) 74 S.S7349S LC44A1 solute carrier family 44, member 1 75 S.S784SO MESDC2 mesoderm development candidate 2 76 S.S84790 PPP2R1B protein phosphatase 2 (formerly 2A), regulatory Subunit A, beta isoform 77 S.S92771 DGKG diacylglycerol kinase, gamma. 90 kDa 78 S.62O557 ANK2 ankyrin 2, neuronal 79 S.631569 PPP1R14A protein phosphatase 1, regulatory (inhibitor) Subunit 14A 8O S.63348 EMILIN1 elastin microfibrill interfacer 1 8O S.63348 EMILIN1 elastin microfibrill interfacer 1 81 ROS1 protein S (alpha) 82 S.6470.18 CLIP2 CAP-GLY domain containing linker protein 2 83 S.647064 RARRES2 retinoic acid receptor responder (tazaroteine induced) 2 84 S.653.263 CEP110 centrosomal protein 110 kDa 85 S.654.404 HLA-C major histocompatibility complex, class I, C 86 S.654439 APOE apolipoprotein E 87 S.654473 MAOB monoamine oxidase B 88 S.654581 PRPS2 phosphoribosyl pyrophosphate synthetase 2 89 S.654634 CDC42BPB CDC42 binding protein kinase beta (DMPK-like) US 2012/0178642 A1 Jul. 12, 2012 26

TABLE E-continued

international Protein index/UniGene Symbol Entrez Gene Name 90 F2 coagulation factor II (thrombin) 91 HPR (includes haptoglobin-related protein EG: 3250) 92 HS.656274 TNFAIP8 tumor necrosis factor, alpha-induced protein 8 93 HS.656,726 STRN striatin, calmodulin binding protein 94 HS.658434 PSIP1 PC4 and SFRS1 interacting protein 1 95 HS.66O130 CD226 CD226 molecule 96 HS.695926 RASA1 RAS p21 protein activator (GTPase activating protein) 1 97 HS-696O74 DHX15 DEAH (Asp-Glu-Ala-His) box polypeptide 15 98 HS-696326 ANO6 anoctamin 6 99 HS.699.154 LYN v-yes-1 Yamaguchi sarcoma viral related oncogene homolog OO HS-7486 ETHE1 ethylmalonic encephalopathy 1 O1 HS.77S3 CALU calumenin O2 HS.77741 KNG1 (includes kininogen 1 EG: 3827) O3 HS.79322 QARS glutaminyl-tRNA synthetase O4 HS.8004 KALRN kalirin, RhoGEF kinase 05 HS.81934 ACADSB acyl-Coenzyme A dehydrogenase, short branched chain O6 HS.9OO61 PGRMC1 progesterone receptor membrane component 1 O7 HS.904 AGL amylo-1,6-glucosidase, 4-alpha-glucanotransferase O8 PIOOO10951 EPPK1 epiplakin 1 09 PIOOO11891 PRKAA1 protein kinase, AMP-activated, alpha 1 catalytic Subunit 10 PIOO165421 SERPINC1 serpin peptidase inhibitor, clade C (antithrombin), member 1 11 PIOO3O1271 RPN2 ribophorin II 12 PIOO382606 coagulation factor VII (serum prothrombin conversion accelerator) 13 PIOO44892S GHG1 immunoglobulin heavy constant gamma 1 (G1m marker) 14 PIOO783829 POS importin 5 115 IPIOO787190 HLA-B major histocompatibility complex, class I, B 16 PIOO788786 VWF von Willebrand factor 17 PIOO797856 HPSE heparanase

TABLE F

international Protein index/UniGene Symbol Entrez Gene Name PIOOOO1753 MYH4 myosin, heavy chain 4, skeletal muscle HS.110837 UBB4 tubulin, beta 4 : HS132499 RPCSL actin related protein 2/3 complex, subunit 5-like udes : 81873) 33892 PM1 tropomyosin 1 (alpha) 43046 coronin 6 437 glucosidase, alpha; acid 43703 EH-domain containing 4 47433 proliferating cell nuclear antigen 48641 cathepsin H 1 S4O78 ipopolysaccharide binding protein 11 56367 ribosomal protein S29 12 58339 RPINB10 serpin peptidase inhibitor, clade B (ovalbumin), member 10 13 61.357 HB (includes pyruvate dehydrogenase (lipoamide) beta :5162) 14 6355 H10 myosin, heavy chain 10, non-muscle 15 63867 4 CD14 molecule 16 64144 eukaryotic translation initiation factor 5A2 17 69284 phosphoribosyl pyrophosphate synthetase 1-like 1 18 69900 poly(A) binding protein, cytoplasmic 4 (inducible form) 19 70310 cat eye syndrome chromosome region, candidate 1 2O 71626 S-phase kinase-associated protein 1 21 73O43 metastasis associated 1 family, member 2 22 884O1 annexin A10 23 89409 formin binding protein 1 24 HS196437 MOB1, Mps One Binder kinase activator-like 1B (yeast) 25 S.20O333 apolipoprotein B48 receptor 26 S.213470 proteasome (prosome, macropain) subunit, beta type, 7 27 S.22O594 coiled-coil domain containing 58 28 S.2241.71 enolase 3 (beta, muscle) US 2012/0178642 A1 Jul. 12, 2012 27

TABLE F-continued

international Protein index/UniGene Symbol Entrez Gene Name 29 S.236.030 SMARCC2 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, (includes member 2 EG: 6601) 30 S.248746 AGXT2L2 alanine-glyoxylate aminotransferase 2-like 2 31 S.2S2549 CTSZ (includes cathepsin Z EG: 1522) 32 S.258.314 BRE brain and reproductive organ-expressed (TNFRSF1A modulator) 33 S.263,812 NUDC nuclear distribution gene Chomolog (A. nidulians) 34 S.268963 UBAP1 ubiquitin associated protein 1 35 S.279640 TPR translocated promoter region (to activated MET oncogene) 36 S.282901 RBM39 RNA binding motif protein 39 37 S.284491 PDXK pyridoxal (pyridoxine, vitamin B6) kinase 38 S.309090 SFRS7 splicing factor, arginine?serine-rich 7, 35 kDa 39 S.31OO KARS lysyl-tRNA synthetase 40 S.31053 tubulin folding cofactor B 41 S.319334 nuclear autoantigenic sperm protein (histone-binding) 42 S.325978 nuclear mitotic apparatus protein 1 43 S.33S034 dihydropyrimidine dehydrogenase 44 S.337766 ribosomal protein L18a. 45 S.3439 stomatin (EPB72)-like 2 46 S.356604 WNK lysine deficient protein kinase 1 47 S.368.077 serpin peptidase inhibitor, clade B (ovalbumin), member 8 48 S.3682O3 dedicator of cytokinesis 11 49 S.368266 LTC L 1 clathrin, heavy chain-like 1 50 S.36927 heat shock 105 kDa 110 kDa protein 1 51 S.369373 Sec23 homolog B (S. cerevisiae) 52 S.375957 t i. : integrin, beta 2 (complement component 3 receptor 3 and 4 subunit) 53 S.376.933 guanylate kinase 1 S4 S388664 1 ribosomal protein L11 55 S.403436 CI dodecenoyl-Coenzyme A delta isomerase (3.2 trans-enoyl-Coenzyme A isomerase) 56 S.406423 F3B2 splicing factor 3b, subunit 2, 145 kDa 57 S.407190 KC BP5 FK506 binding protein 5 58 S.408061 FA BP5 fatty acid binding protein 5 (psoriasis-associated) 59 S.408236 NDC17 thioredoxin domain containing 17 60 S.4098.34 PT1 phosphohistidine phosphatase 1 61 S.412117 ANXA6 annexin A6 62 S.42918O EIF2S2 eukaryotic translation initiation factor 2, subunit 2 beta, 38 kDa 63 S.432674 LARS leucyl-tRNA synthetase 64 S.433.222 NPC2 Niemann-Pick disease, type C2 65 S.434996 GIT2 G protein-coupled receptor kinase interacting Arf6AP2 66 S.437385 NECAP2 NECAP endocytosis associated 2 67 S.440895 MYH3 myosin, heavy chain 3, skeletal muscle, embryonic 68 S.44O932 9-Sep septin 9 69 S.46OOO2 FLJ11151 hypothetical protein FLJ11151 70 S.461925 RPA1 replication protein A1, 70 kDa 71 S.465224 NARS asparaginyl-tRNA synthetase 72 S.465761 ARHGEF18 rhofrac guanine nucleotide exchange factor (GEF) 18 73 S.465924 SDHB (includes Succinate dehydrogenase complex, Subunit B, iron Sulfur (lp) EG: 6390) 74 S.47O627 LCK lymphocyte-specific protein tyrosine kinase 75 S4712O7 NDUFS1 NADH dehydrogenase (ubiquinone) Fe—S protein 1, 75 kDa (NADH-coenzyme Q reductase) 76 S.477126 ATG3 ATG3 autophagy related 3 homolog (S. cerevisiae) 77 S.484.412 EXOC2 exocyst complex component 2 78 S.491440 PPP2CB protein phosphatase 2 (formerly 2A), catalytic subunit, beta isoform 79 S.494.496 fructose-1,6-bisphosphatase 1 8O S.494-595 TMOD1 tropomodulin 81 S.4975.99 WARS tryptophanyl-tRNA synthetase 82 S.SO2328 CD44 CD44 molecule (Indian blood group) 83 S.SO2756 AHNAK AHNAKnucleoprotein 84 S.SOSO33 KRAS v-Ki-ras2 Kirsten rat Sarcoma viral oncogene homolog 85 S.5086 RBM42 RNA binding motif protein 42 86 S.SO8738 ARHGEF7 Rho guanine nucleotide exchange factor (GEF) 7 87 S.SO9736 HSP90AB1 heat shock protein 90 kDa alpha (cytosolic), class B member 1 88 S.S13726 GBP5 guanylate binding protein 5 89 S.514495 SRP68 signal recognition particle 68 kDa 90 S.514581 ACTG1 actin, gamma 1 91 S.S17307 MX1 myxovirus (influenza virus) resistance 1, interferon-inducible protein p78 (mouse) 92 S.S17949 MAP4 microtubule-associated protein 4 93 S.S18198 CSTA (includes cystatin A (Stefin A) EG: 1475) 94 S.S18662 FAM129A family with sequence similarity 129, member A 95 S.S21924 PUF60 poly-U binding splicing factor 60 KDa US 2012/0178642 A1 Jul. 12, 2012 28

TABLE F-continued

international Protein index/UniGene Symbol Entrez Gene Name 96 HSS29989 RNASET2 ribonuclease T2 97 HSS3.1176 SARS seryl-tRNA synthetase 98 HSS31807 ARHGAP2S Rho GTPase activating protein 25 99 HSS343SO SMARCB1 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1 OO HSS34770 PKM2 pyruvate kinase, muscle O1 HSS35581 TPM3 tropomyosin 3 O2 HSSS682 EIF3D eukaryotic translation initiation factor 3, Subunit D O3 HSS838SS SNX6 Sorting nexin 6 O4 HSS87558 NCF2 neutrophil cytosolic factor 2 OS HS.591176 DYNLL2 dynein, light chain, LC8-type 2 O6 HS.S91768 BTF3 basic transcription factor 3 O7 HS.S91922 SLK STE20-like kinase (yeast) O8 HS.632733 ALDH2 aldehyde dehydrogenase 2 family (mitochondrial) O9 HS.643487 ACAA1 acetyl-Coenzyme A acyltransferase 1 10 HS.64947S RPL24 ribosomal protein L24 11 HS.654.404 HLA-C major histocompatibility complex, class I, C 12 HS.6544.08 NFKB1 nuclear factor of kappa light polypeptide gene enhancer in B-cells 1 13 HS.654.429 SEC24C SEC24 family, member C (S. cerevisiae) (includes EG:9632) 14 HS.654521 WIPF1 WAS WASL interacting protein family, member 1 1S HS.654543 TUBB2A tubulin, beta 2A 16 HS.654597 ACAP2 Arf6AP with coiled-coil, ankyrin repeat and PH domains 2 17 HS.655196 HP haptoglobin 18 HS.656,726 STRN striatin, calmodulin binding protein 19 HS.656870 SLC25A24 Solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 24 20 HS.687OSS PARP14 poly (ADP-ribose) polymerase family, member 14 21 HS.68714 SFRS1 splicing factor, arginine?serine-rich 1 22 HS-690634 HSPA1L, heat shock 70 kDa protein 1-like 23 HS-69293 HEXB hexosaminidase B (beta polypeptide) 24 HS.695973 HNRNPK heterogeneous nuclear ribonucleoprotein K 25 HS-699408 CLINT1 clathrin interactor 1 26 HS-699441 NFATC2 nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2 27 HS.73839 RNASE3 ribonuclease, RNase A family, 3 (eosinophil cationic protein) 28 HS.74368 CKAP4 cytoskeleton-associated protein 4 29 HS.772S4 CBX1 chromobox homolog 1 (HP1 beta homolog Drosophila) 30 HS.77897 SF3A3 splicing factor 3a, Subunit 3, 60 kDa 31 HS7888O LVBL ilvB (bacterial acetolactate synthase)-like 32 HS.791 10 NCL nucleolin 33 HS.836O C11 ORFS4 chromosome 11 open reading frame 54 34 HS.837S3 SNRPB Small nuclear ribonucleoprotein polypeptides B and B1 3S HS.861 MAPK3 mitogen-activated protein kinase 3 36 HS.99936 KRT10 keratin 10 37 IPIOOO74489 NDUFB10 NADH dehydrogenase (ubiquinone) 1 beta Subcomplex, 10, 22 kDa 38 IPIOO384938 IGHG1 immunoglobulin heavy constant gamma 1 (G1m marker) 39 IPIOO396421 KIAAO776 KIAAO776 4.0 IPIOO4O11OS RPS25 ribosomal protein S25 41 IPIOO413108 RPSA (includes ribosomal protein SA EG: 3921) 42 IPIOO456853 FAM21C family with sequence similarity 21, member C 43 IPIOO465022 SMCHD1 structural maintenance of chromosomes flexible hinge domain containing 1

TABLE G Fold Change International (positive numbers Protein are upregulated Index/UniGene Symbol Entrez Gene Name in B1) 1 HS.18OO62 PSMB8 proteasome (prosome, macropain) subunit, beta type, 8 (large 1.74748 multifunctional peptidase 7) 2 IPIOOOO1539 ACAA2 acetyl-Coenzyme A acyltransferase 2 2.53112 3 HS.412117 ANXA6 annexin A6 199146 4 HS.90093 HSPA4 heat shock 70 kDa protein 4 2.72271 S HS.130316 DBN1 drebrin 1 -2.19867 6 IPIOOOO3438 DNAJC8 DnaJ (Hsp40) homolog, subfamily C, member 8 2.74.556 7 HS.1863SO RPL4 ribosomal protein L4 180696 8 HS.175437 EPB41 erythrocyte membrane protein band 4.1 (elliptocytosis 1, RH-linked) 1.37195 US 2012/0178642 A1 Jul. 12, 2012 29

TABLE G-continued Fold Change international (positive numbers Protein are upregulated index/UniGene Symbol Entrez Gene Name in B1) S.21.78 histone cluster 2, H2be .73893 10 S.524630 ubiquitin-conjugating enzyme E2N (UBC13 homolog, yeast) 2.17574. 11 S.411695 hexokinase 3 (white cell) 2.79458 12 S.489284 actin related protein 2/3 complex, subunit 1B, 41 kDa 87474 13 S.S14934 capping protein (actin filament) muscle Z-line, alpha 1 .77014 14 S.431279 N-ethylmaleimide-sensitive factor 4.20439 15 S.155975 TPRCAP protein tyrosine phosphatase, receptor type, C-associated protein -1.77658 16 S.458272 PO myeloperoxidase .71345 17 S.433615 BB2C tubulin, beta 2C -1.76403 18 S.184233 heat shock 70 kDa protein 9 (mortalin) 6.35072 19 S.295917 ATPase, H+ transporting, lysosomal 56/58 kDa, V1 subunit B2 2.24142 2O S.521640 RA RAD23 homolog B (S. cerevisiae) .96378 21 S.69988O S10 ribosomal protein S10 3.17111 22 S.546285 LPO (includes ribosomal protein, large, PO 2.0349S : 6175) 23 S.389649 F4A3 (includes eukaryotic translation initiation factor 4A, isoform 3 89742 :9775) 24 S.S11251 RDL (includes Sulfide quinone reductase-like (yeast) 2.336O2 :58472) 25 S.26O10 phosphofructokinase, platelet -2.73727 26 S.78888 diazepam binding inhibitor (GABA receptor modulator, acyl-Coenzyme 2.47829 A binding protein) 27 S.405144 splicing factor, arginine?serine-rich 3 4.476SS 28 S.413812 ras-related C3 botulinum toxin substrate 1 (rho family, Small GTP 2.76246 binding protein Rac1) 29 S.SS835.1 kinesin heavy chain member 2A 30 S355934 splicing factor proline:glutamine-rich (polypyrimidine tract binding protein associated) 31 S.464,336 prolyl 4-hydroxylase, beta polypeptide 32 S.131151 proteasome (prosome, macropain) 26S subunit, non-ATPase, 9 33 S.247362 dimethylarginine dimethylaminohydrolase 2 34 S.356.654 proteasome (prosome, macropain) 26S subunit, ATPase, 1 35 S.S271 OS heterogeneous nuclear ribonucleoprotein D-like 36 S472838 serine/threonine kinase 4 37 S.373763 heterogeneous nuclear ribonucleoprotein R 38 S.440898 icolin (collagen fibrinogen domain containing) 1 39 S.178551 ribosomal protein L8 40 S.644646 F 5 B kinesin family member 5B 41 S.153837 s myeloid cell nuclear differentiation antigen 42 S.627414 ribosomal protein S18 43 S.546287 PS7 ribosomal protein S7 44 S.497788 PRS glutamyl-prolyl-tRNA synthetase 45 S.S11743 UBB3 tubulin, beta 3 46 S.27O291 CTN4 actinin, alpha 4 47 S.119251 QCRC1 ubiquinol-cytochrome c reductase core protein I 48 S.699298 DV3 CDV3 homolog (mouse) 49 S.111779 SPARC Secreted protein, acidic, cysteine-rich (osteonectin) 50 S.651923 CNN2 calponin 2 51 S.465511 GZMM granzyme M (lymphocyte met-ase 1) 52 S.2853 PCBP1 (includes poly(rC) binding protein 1 EG:5093) 53 S. 6901.98 CDC42 cell division cycle 42 (GTP binding protein, 25 kDa) S4 S.271510 GSR glutathione reductase 55 S.406277 SF3A1 splicing factor 3a, Subunit 1, 120 kDa 56 S.571177 SYNCRIP synaptotagmin binding, cytoplasmic RNA interacting protein 57 S.695941 HK1 hexokinase 1 58 S.2SO758 PSMC3 proteasome (prosome, macropain) 26S subunit, ATPase, 3 59 S.707 KRT2 keratin 2 3.19828 60 S594444 LMNA aminAC 2.425.45 61 S.2490 CASP1 caspase 1, apoptosis-related cysteine peptidase (interleukin 1, beta, 2.18090 convertase) 62 S.75307 H1 histone family, member X 2.6O755 63 SS34639 hydroxyacyl-Coenzyme A dehydrogenase 3-ketoacyl-Coenzyme A 2.04804 hiolase enoyl-Coenzyme A hydratase (trifunctional protein), beta Subunit 64 S.30054 F5 coagulation factor V (proaccelerin, labile factor) -231510 65 S.533040 PDLIM7 PDZ and LIM domain 7 (enigma) -2.15116 66 S. 665429 DDX17 DEAD (Asp-Glu-Ala-Asp) box polypeptide 17 2.97738 67 S.69518S NAP1L1 nucleosome assembly protein 1-like 1 -1561.21 68 S.75841 ERP29 endoplasmic reticulum protein 29 3.53236 69 S.S233O2 PRDX3 peroxiredoxin 3 1.71589 US 2012/0178642 A1 Jul. 12, 2012 30

TABLE G-continued Fold Change international (positive numbers Protein are upregulated index/UniGene Symbol Entrez Gene Name in B1) 70 PIOOO24989 PCMT1 protein-L-isoaspartate (D-aspartate) O-methyltransferase 2.22172 71 S.43O606 CS citrate synthase -2.53628 72 S.S20973 HSPB1 heat shock 27 kDa protein 1 1894O6 73 S.118958 STX11 Syntaxin 11 -1.S7367 74 S. 610830 PRKCSH protein kinase C substrate 80K-H 2.25450 75 S.14601 HCLS1 hematopoietic cell-specific Lyn Substrate 1 2.13579 76 S.632828 HNRNPH2 heterogeneous nuclear ribonucleoprotein H2 (H") 3.09381 77 S.694128 RPS1.4 ribosomal protein S14 2.10304 78 S.356624 NID nidogen 1 -4.10930 79 S.12084 TUFM Tu translation elongation factor, mitochondrial 1.77413 8O S.95990 pyruvate kinase, liver and RBC 2.55932 81 S.654.614 heat shock 70 kDa protein 6 (HSP7OB') 1.28.057 82 S.471441 proteasome (prosome, macropain) subunit, beta type, 2 3.18295 83 HS.7744 NADH dehydrogenase (ubiquinone) flavoprotein 1, 51 kDa 2.82S24 84 S.480073 heterogeneous nuclear ribonucleoprotein D (AU-rich element RNA 2.72172 binding protein 1, 37 kDa) 85 S.98791 ACTR1B (includes ARP1 actin-related protein 1 homolog B, centractin beta (yeast) 3.00772 EG: 10120) 86 PIOOO2962S FLOT2 lotill in 2 3.53456 87 S.11355 TMPO hymopoietin 3.65290 88 S.571841 RPL7 ribosomal protein L7 18109S 89 S.699271 STAT1 signal transducer and activator of transcription 1, 91 kDa 2.36973 90 S.529451 DIAPH1 diaphanous homolog 1 (Drosophila) 1.44181 91 S.S16032 HADHA hydroxyacyl-Coenzyme A dehydrogenase 3-ketoacyl-Coenzyme A 4.431.65 hiolase enoyl-Coenzyme A hydratase (trifunctional protein), alpha Subunit 92 SSO3O43 carnitine palmitoyltransferase 1A (liver) -145S07 93 S.47SO74 parvin, beta -193236 94 S.655396 proteasome (prosome, macropain) 26S subunit, non-ATPase, 11 189081 95 S.122523 staphylococcal nuclease and tudor domain containing 1 2.96927 96 S.444O75 ubiquitin associated and SH3 domain containing, B -1.85814 97 S473144 Cas scaffolding protein family member 4 -2.5823S 98 S.43618.6 calpastatin 148337 99 S.4658O8 heterogeneous nuclear ribonucleoprotein M 2.64995 OO S.S.06759 ATPase, Ca++ transporting, cardiac muscle, slow twitch 2 -1.44671 O1 S.S35581 tropomyosin 3 2.OS422 O2 S. 65472O KIAA1967 3.42772 O3 S.515517 ribosomal protein L18 3.72595 O4 S.438429 ribosomal protein S19 4.78644 05 PIOO216134 tropomyosin 1 (alpha) -1.36995 O6 S.128548 WD repeat domain 1 4.48437 O7 S.S1932O voltage-dependent anion channel 1 1944.43 O8 S.S12675 ribosomal protein S8 3.35144 09 PIOO216633 erythrocyte membrane protein band 4.9 (dematin) -1.84863 10 S.496622 plastin 3 (T isoform) 3.79198 11 S.654438 ankyrin 1, erythrocytic 2.45336 12 S.417303 spectrin, beta, erythrocytic 195917 13 S89497 lamin B1 2.532O6 14 S.172631 TGAM integrin, alpha M (complement component 3 receptor 3 subunit) 6.14877 15 S.6523O8 MTHFD1 methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1, 1.36675 methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthetase 16 S.411312 TGA2B (includes integrin, alpha2b (platelet glycoprotein IIb of IIb.IIIa complex, antigen 3.09010 EG: 3674) CD41) 17 S.76392 ALDH1A1 aldehyde dehydrogenase 1 family, member A1 -1.59383 18 S.SOO756 GOT1 glutamic-Oxaloacetic transaminase 1, Soluble (aspartate 142300 aminotransferase 1) 19 S.5141.96 RPL27 ribosomal protein L27 2.67384 2O S.445351 LGALS1 lectin, galactoside-binding, soluble, 1 214691 21 S.8O828 KRT1 keratin 1 3.95879 22 S.654559 HNRNPL heterogeneous nuclear ribonucleoprotein L. -3.40543 23 S.1198.25 SPTA1 spectrin, alpha, erythrocytic 1 (elliptocytosis 2) 166210 24 S.446588 RPS13 ribosomal protein S13 3.62921 25 S.433427 RPS17 (includes ribosomal protein S17 4.3984O EG: 6218) 26 S-483305 HINT1 histidine triad nucleotide binding protein 1 -2.04.047 27 S476448 FLNB filamin B, beta (actin binding protein 278) -1.82786 28 S.350899 CAPN2 calpain 2, (mII) large subunit 2.86.704 29 S.S2O967 MDH2 malate dehydrogenase 2, NAD (mitochondrial) 2.2O2SO 30 S.371 S63 RAB14 RAB14, member RAS oncogene family 1.66O10 31 S.83722 EPS15 epidermal growth factor receptor pathway substrate 15 2.14994 US 2012/0178642 A1 Jul. 12, 2012 31

TABLE G-continued Fold Change international (positive numbers rotein are upregulated index/UniGene Symbol Entrez Gene Name in B1) 32 S.58O681 SAMHD1 SAM domain and HD domain 1 2.17687 33 S88778 CBR1 carbonyl reductase 1 69.648 34 S.4975.99 WARS tryptophanyl-tRNA synthetase S8361 35 S.S17622 UNC84B unc-84 homolog B (C. elegans) 78160 36 S.S231.45 DDOST dolichyl-diphosphooligosaccharide-protein glycosyltransferase 71412 37 S539684 EIF2S3 eukaryotic translation initiation factor 2, Subunit 3 gamma, 52 kDa 2.0912S 38 S.2O1978 PTGS1 prostaglandin-endoperoxide synthase 1 (prostaglandin GH synthase -1.72382 and cyclooxygenase) 39 S.370770 XPO1 exportin 1 (CRM1 homolog, yeast) 2.13295 40 S.696016 SNX2 Sorting nexin 2 83066 41 S.181301 CTSS cathepsin S 2.66342 42 S.204238 LCN2 ipocalin 2 -2.88567 43 S.212102 PDIA6 protein disulfide isomerase family A, member 6 2.672S6 44 S.465041 HDHD2 haloacid dehalogenase-like hydrolase domain containing 2 S8049 45 S.1251.13 chaperonin containing TCP1, subunit 8 (theta) 2.74.083 46 S.218040 integrin, beta 3 (platelet glycoprotein IIIa, antigen CD61) -2.86872 47 S.126941 amily with sequence similarity 49, member B 2.41970 48 S.140452 mannose-6-phosphate receptor binding protein 1 2.45483 49 S.591940 apolipoprotein A-IV 2.29544 50 S.S19756 serine/threonine kinase 10 2.91394 51 S.2744O2 heat shock 70 kDa protein 1A 3.13788 52 S.S71886 aldo-keto reductase family 7, member A2 (aflatoxin aldehyde 2.51928 reductase) 53 S.599481 eukaryotic translation initiation factor 4A, isoform 2 3.52387 S4 S.352224 EDAR-associated death domain 7.46803 55 S.S34385 THO complex 4 -1.32827 56 S.528668 ribosomal protein L6 3.03691 57 S.368O84 eucine-rich PPR-motif containing -1.71518 58 S.632717 myosin, light chain 6, alkali, Smooth muscle and non-muscle 3.02347 59 S.482O43 nicotinamide nucleotide transhydrogenase 2.26497 60 S.S2S600 HSP90AA1 heat shock protein 90 kDa alpha (cytosolic), class A member 1 2.84.841 61 S.S13530 TGFB11 transforming growth factor beta 1 induced transcript 1 -245685 62 S.36992O RAP1B RAP1B, member of RAS oncogene family -2.37368 63 S.148340 RPL10A (includes ribosomal protein L10a 19962O EG: 4736) 64 S.200716 MECP2 methyl CpG binding protein 2 (Rett syndrome) 2.993.76 65 S.642813 VIM vimentin 1.752O7 66 S.S70791 LAP3 leucine aminopeptidase 3 2.493OO 67 S.S16539 HNRNPA3 heterogeneous nuclear ribonucleoprotein A3 1.70158 68 S.356572 RPS3A ribosomal protein S3A 3.02357 69 S.S18530 PAK2 p21 protein (Cdc42/Rac)-activated kinase 2 2.61046 70 S.37617 MYO1G myosin IG 21 6324 71 S.467408 TRIM28 tripartite motif-containing 28 2.84983 72 S.136905 HUWE1 HECT, UBA and WWE domain containing 1 88641 73 PIOO464990 GP1BB glycoprotein Ib (platelet), beta polypeptide -1.882O6 74 S.617193 CYCS (includes cytochrome c, somatic 64385 EG: 54205) 75 S.S95053 HSPD1 heat shock 60 kDa protein 1 (chaperonin) 76318 76 S.S34770 PKM2 pyruvate kinase, muscle 27869 77 S.166463 HNRNPU heterogeneous nuclear ribonucleoprotein U (scaffold attachment factor A) 78 S.2533 aldehyde dehydrogenase 9 family, member A1 79 S.700575 stathmin 1/oncoprotein 18 8O S.S30687 ribonucleasef angiogenin inhibitor 1 81 S.696.144 thioredoxin reductase 1 82 S.SO2756 AHNAKnucleoprotein 83 S.10842 RAN, member RAS oncogene family 84 S.311609 DEAD (Asp-Glu-Ala-Asp) box polypeptide 39 85 S.S33273 ubiquitin-like modifier activating enzyme 1 86 S.695946 integrin, beta 1 (fibronectin receptor, beta polypeptide, antigen CD29 includes MDF2, MSK12) 87 PIOO646888 -Sep Septin 1 88 S.546292 RPS27A ribosomal protein S27a US 2012/0178642 A1 Jul. 12, 2012 32

TABLE H TABLE H-continued

international international Protein Protein index. index. OniCiene Symbol Entrez Gene Name OniCiene Symbol Entrez Gene Name S.1012 complement component 4 binding 16 HS.S29023 ZNF532 Zinc finger protein 532 protein, alpha 17 HS.594444 LMNA lamin AC S.110675 APOC1 apolipoprotein C-I 18 HS.62OSS7 ANK2 ankyrin 2, neuronal S.116448 GLS Glutaminase 19 HS.653.263 CEP110 centrosomal protein 110 kDa S.191215 CYTH1 cytohesin 1 20 HS.654438 ANK1 ankyrin 1, erythrocytic S.202 TSPO translocator protein (18 kDa) 21 HS.69771 CFB complement factor B S.2O3637 PLS1 plastin 1 (I isoform) 22 HS.77741 KNG1 kininogen 1 S.24889 FMN2 ormin 2 (includes S.3275.27 SMARCA4 SWI/SNF related, matrix associated, EG: 3827) actin dependent regulator of chromatin, 23 HS.83634 HCFC1 host cell factor C1 (VP16-accessory Subfamily a member 4 protein) S.352224 EDARADD S.464813 PSMA8 epiplakin 1 Subunit,ENN, alpha type, 8 2Es25 IPIOO382606 coagulation factor VII (serum 11 S.466910 CDA cytidine deaminase prothrombin conversion accelerator) 12 S.4779 GATAD2B GATA zinc finger domain containing 26 IPIOO641229 IGHA2 immunoglobulin heavy constant alpha 2B 2 (A2m marker) 13 S.482873 TMED5 transmembrane emp24 protein 27 IPIOO6454.52 TUBB tubulin, beta transport domain containing 5 28 IPIOO7871.90 HLA-B major histocompatibility complex, 14 RGS10 regulator of G-protein signaling 10 class I, B 15 OCLAD1 OCIA domain containing 1

TABLE I Unigene IPI Symbol Entrez Gene Name HS.406758 HIBADH 3-hydroxyisobutyrate dehydrogenase HS.65668S HIBCEH 3-hydroxyisobutyryl-Coenzyme A hydrolase HS.643487 ACAA1 acetyl-Coenzyme A acyltransferase 1 HS.SS8296 ACP1 acid phosphatase 1, Soluble HS.S14581 ACTG1 actin, gamma 1 HS.461727 ACSF3 acyl-CoA synthetase family member 3 HS.464137 ACOX1 acyl-Coenzyme A oxidase 1, palmitoyl HS.S1281S AP3D1 adaptor-related protein complex 3, delta 1 subunit HS.47O907 AK2 adenylate kinase 2 1 HS.S2S330 ARF6 ADP-ribosylation factor 6 HS.62578 ARFGEF2 ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited) HS.418167 ALB albumin HS.632733 ALDH2 aldehyde dehydrogenase 2 family (mitochondrial) HS.591631 AGPS alkylglycerone phosphate synthase HS.49972S ANK3 ankyrin 3, node of Ranvier (ankyrin G) HS.696087 ANKFY1 ankyrin repeat and FYVE domain containing 1 HS.4121.17 ANXA6 annexin A6 HS.3346 ANXA9 annexin A9 HS.435771 APIS apoptosis inhibitor 5 HSSO316S ARAP1 Arf6AP with RhoGAP domain, ankyrin repeat and PH domain 1 HS.465224 NARS asparaginyl-tRNA synthetase HS.477126 ATG3 ATG3 autophagy related 3 homolog (S. cerevisiae) Hs.486063 ATG5 (includes ATG5 autophagy related 5 homolog (S. cerevisiae) EG:9474) 24 HS.S849OS ATL1 atlastin GTPase 1 25 HS.85539 ATPSI ATP synthase, H+ transporting, mitochondrial FO complex, subunit E 26 HS.656S 15 ATPS2 ATP synthase, H+ transporting, mitochondrial FO complex, subunit F2 27 HS.444957 ATP8A2 ATPase, aminophospholipid transporter-like, class I, type 8A, member 2 28 HS.S17338 ATP6V1E1 ATPase, H+ transporting, lysosomal 31 kDa, V1 subunit E1 29 HS.491737 ATP6V1B ATPase, H+ transporting, lysosomal 50/57 kDa, V1 subunit H 30 HS.429294 ABCA1 ATP-binding cassette, Sub-family A (ABC1), member 1 31 HS-508423 ABCC4 ATP-binding cassette, Sub-family C (CFTR/MRP), member 4 32 HS.355983 BZW1 basic leucine Zipper and W2 domains 1 33 HS.S91768 BTF3 basic transcription factor 3 34 HS.494.614 BAT2D1 BAT2 domain containing 1 35 HS.631546 BAX BCL2-associated X protein 36 HS.65474O BRWD1 bromodomain and WD repeat domain containing 1 37 HS.418,533 BUB3 budding uninhibited by benzimidazoles 3 homolog (yeast) 38 PIOO797310 CLSTN3 calsyntenin 3 39 HS.S24.809 CLIP1 CAP-GLY domain containing linker protein 1 40 HS.6991.82 CPT2 carnitine palmitoyltransferase 2 41 HSSO4096 CBL Cas-Br-M (murine) ecotropic retroviral transforming sequence US 2012/0178642 A1 Jul. 12, 2012 33

TABLE I-continued

Unigene/IPI Symbol Entrez Gene Name 42 S.654616 CASP6 caspase 6, apoptosis-related cysteine peptidase 43 S.46O232 CNOT1 CCR4-NOT transcription complex, subunit 1 44 S485518 D2AP CD2-associated protein 45 S.SO2328 D44 CD44 molecule (Indian blood group) 46 S.S.S.6638 SD2 CDGSH iron sulfur domain 2 47 S472O27 DS2 CDP-diacylglycerol synthase (phosphatidate cytidylyltransferase) 2 48 S.568242 REG1 cellular repressor of E1A-stimulated genes 1 49 S.31819 ORF128 chromosome 1 open reading frame 128 50 S.368353 ORF71 chromosome 1 open reading frame 71 51 S. 611057 ORF77 chromosome 1 open reading frame 77 52 S.462O33 ORF93 chromosome 1 open reading frame 93 53 S.836O ORFS4 chromosome 11 open reading frame 54 S4 S.5.30753 ORF59 chromosome 11 open reading frame 59 55 PIOO373869 7ORF49 chromosome 17 open reading frame 49 56 S.368266 LTCL1 clathrin, heavy chain-like 1 57 S.S91506 MYCBP c-myc binding protein 58 S.S.O.S.652 PZ1 coatomer protein complex, Subunit Zeta 1 59 S.6S5010 CHD3 coiled-coil-helix-coiled-coil-helix domain containing 3 60 S.3696.14 PS2 COP9 constitutive photomorphogenic homolog subunit 2 (Arabidopsis) 61 S.SO2917 S copper chaperone for Superoxide dismutase 62 S.460923 core-binding factor, beta Subunit 63 S.372.286 L3 cullin 3 64 S.S18198 CSTA (includes cystatin A (Stefin A) EG: 1475) 65 S.481898 CCBL2 cysteine conjugate-beta lyase 2 66 S.S.13803 CYBA cytochrome b-245, alpha polypeptide 67 S.461131 CYB5B cytochrome b5 type B (outer mitochondrial membrane) 68 PIOOO17510 COX2 cytochrome c oxidase II 69 S.696092 CLASP2 cytoplasmic linker associated protein 2 70 S.9912O DDX3Y DEAD (Asp-Glu-Ala-Asp) box polypeptide 3, Y-linked (includes EG: 8653) 71 S.751.89 DAP death-associated protein 72 S.3682O3 DOCK11 dedicator of cytokinesis 11 73 S.654567 ENND4A DENN/MADD domain containing 4A 74 S.407618 SG4 desmoglein 4 75 S.9857 CXR dicarbonyl L-xylulose reductase 76 S.3355S1 LAT dihydrolipoamide S-acetyltransferase 77 S.37916 PP7 dipeptidyl-peptidase 7 78 S.S15210 NAB1 DnaJ (Hsp40) homolog, subfamily B, member 1 79 S.656476 NAJC3 DnaJ (Hsp40) homolog, subfamily C, member 3 8O S.4258O1 USP23 dual specificity phosphatase 23 81 S.522413 NM1 dynamin 1 82 S.S2949S YNC 1 LI 1 dynein, cytoplasmic 1, light intermediate chain 1 83 S.S91176 dynein, light chain, LC8-type 2 84 S.4747 dyskeratosis congenita 1, dyskerin 85 S.412103 FHA1 EF-hand domain family, member A1 86 S.654553 TFB (includes electron-transfer-flavoprotein, beta polypeptide G:2109) 87 S.SO9791 enhancer of rudimentary homolog (Drosophila) 88 S.4298.79 enoyl-Coenzyme A, hydratase 3-hydroxyacyl Coenzyme A dehydrogenase 89 S-419815 epidermal growth factor (beta-urogastrone) 90 S.477498 eukaryotic elongation factor, Selenocysteine-tRNA-specific 91 S.42918O eukaryotic translation initiation factor 2, subunit 2 beta, 38 kDa 92 S.696322 eukaryotic translation initiation factor 2C, 2 93 S.S5682 eukaryotic translation initiation factor 3, Subunit D 94 SSO2244 eukaryotic translation initiation factor 3, Subunit M 95 S.467084 eukaryotic translation initiation factor 4 gamma, 3 96 S.433,702 eukaryotic translation initiation factor 5 97 S.483494 eukaryotic translation termination factor 1 98 S.S17293 1R F11 receptor 99 S.S18662 AM129A family with sequence similarity 129, member A 1OO S.490795 AM62B family with sequence similarity 62 (C2 domain containing) member B 101 S.335918 DPS farnesyl diphosphate synthase (farnesyl pyrophosphate synthetase, dimethylallyltranstransferase, geranyltranstransferase) 102 S86131 FADD (includes Fas (TNFRSF6)-associated via death domain 103 S.408061 fatty acid binding protein 5 (psoriasis-associated) 104 S.4333OO Fc fragment of IgE, high affinity I, receptor for; gamma polypeptide 105 S.SO9343 fermitin family homolog 2 (Drosophila) 106 S.3382O7 FK506 binding protein 12-rapamycin associated protein 1 107 S.407190 FK506 binding protein 5 108 S.409065 flap structure-specific endonuclease 1 109 S.494.496 fructose-1,6-bisphosphatase 1 US 2012/0178642 A1 Jul. 12, 2012 34

TABLE I-continued

Unigene/IPI Symbol Entrez Gene Name 10 HS.654961 FUT8 fucosyltransferase 8 (alpha (1,6) fucosyltransferase) 11 HS.390S67 FYN FYN oncogene related to SRC, FGR, YES 12 HSS30O24 GGCT gamma-glutamyl cyclotransferase 13 HS-27059 GMPPA GDP-mannose pyrophosphorylase A 14 HSS67488 GMPPB GDP-mannose pyrophosphorylase B 15 H.S.S91069 GBAS glioblastoma amplified sequence 16 HS.654.465 GCLC glutamate-cysteine ligase, catalytic Subunit 17 HS.390667 GSTK1 glutathione S-transferase kappa 1 18 HS.S9138 GYPC glycophorin C (Gerbich blood group) 19 HS.344151 GOLGA4 golgi autoantigen, golgin subfamily a 4 20 HS.431.317 GORASP2 golgi reassembly stacking protein 2, 55 kDa 21 HS.290243 GBF1 golgi-specific brefeldin A resistant guanine nucleotide exchange factor 1 22 HS.485449 GTPBP2 GTP binding protein 2 23 HS.495134 GAPVD1 GTPase activating protein and VPS9 domains 1 24 HS.S914.50 GBP 7 guanylate binding protein 7 25 HS.655196 HP haptoglobin 26 HSS3.1785 HS1BP3 HCLS1 binding protein 3 27 HS.36927 HSPH1 heat shock 105 kDa 110 kDa protein 1 28 HS-690634 HSPA1L, heat shock 70 kDa protein 1-like 29 HS.432648 HSPA2 heat shock 70 kDa protein 2 30 HSSO9736. HSP90AB1 heat shock protein 90 kDa alpha (cytosolic), class B member 1 31 HSS2SO84 HECTD3 HECT domain containing 3 32 HS.642618 HEBP1 heme binding protein 1 33 IPIO0784636 HBB (includes hemoglobin, beta EG:3043) 34 HS-699280 HBD hemoglobin, delta 3S HSSO2617 HNRNPCL1 heterogeneous nuclear ribonucleoprotein C-like 1 36 HS-69293 HEXB hexosaminidase B (beta polypeptide) 37 HS.83634 HCFC1 host cell factor C1 (VP16-accessory protein) 38 HS.46OOO2 FLJ11151 hypothetical protein FLJ11151 39 HS7888O LVBL ilvB (bacterial acetolactate synthase)-like 4.0 IPIOO384938 IGHG1 immunoglobulin heavy constant gamma 1 (G1m marker) 41 HS-699240 POS importin 5 42 HS.434102 KBKG inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase gamma 43 HSSOOS46 DE insulin-degrading enzyme 44 H.S.S13225 TFG3 integrin alpha FG-GAP repeat containing 3 45 HS.375957 TGB2 integrin, beta 2 (complement component 3 receptor 3 and 4 subunit) 46 HS.431460 CAM2 intercellular adhesion molecule 2 47 H.S.S91110 DH3A isocitrate dehydrogenase 3 (NAD+) alpha 48 HS.S15247 AK3 Janus kinase 3 (a protein tyrosine kinase, leukocyte) 49 HS.3O1613 TV1 JTV1 gene SO HSS27919 KPNA3 karyopherin alpha 3 (importin alpha 4) S1 HS.27OO43 KIAAO196 KIAAO196 S2 HS.3682SS KIAAO368 KIAAO368 53 HS.368282 KIAAOS64 KIAAOS64 S4 IPIOO396421 KIAAO776 KIAAO776 SS HS.654497 LTBP1 latent transforming growth factor beta binding protein 1 S6 HS.478067 LXN latexin 57 HS.432674 LARS leucyl-tRNA synthetase S8 HS.7OO163 LY6G5B lymphocyte antigen 6 complex, locus G5B 59 HS.3100 KARS lysyl-tRNA synthetase 60 HS.654.404 HLA-C major histocompatibility complex, class I, C 61 HS.75694 MP mannose phosphate isomerase 62 HS.696082 MAPKSP1 MAPK scaffold protein 1 63 HS.444969 MEMO1 mediator of cell motility 1 (includes EG:51072) 64 HS.486.189 MAGI3 membrane associated guanylate kinase, WW and PDZ domain containing 3 6S HSSOO842 MGEAS meningioma expressed antigen 5 (hyaluronidase) 66 HS.3771SS MTDH metadherin 67 H.S.S16157 MAT2A methionine adenosyltransferase II, alpha 68 HS.252457 MVD mevalonate (diphospho) decarboxylase 69 HSS80782 MACF1 microtubule-actin crosslinking factor 1 70 HSS17949 MAP4 microtubule-associated protein 4 71 HSS1586O MAPRE3 microtubule-associated protein, RP/EB family, member 3 72 HS.269944 MTCH2 mitochondrial carrier homolog 2 (C. elegans) 73 HS.861 MAPK3 mitogen-activated protein kinase 3 74 HSSO7681 MAP3K7IP1 mitogen-activated protein kinase kinase kinase 7 interacting protein 1 7S HS.64356S MAPKAPK2 mitogen-activated protein kinase-activated protein kinase 2 76 HS.S91221 MYCBP2 MYC binding protein 2 77 HS.91531 MLLT6 myeloid lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 6 78 HS.655278 MYOF myoferlin 79 HS.286226 MYO1C myosin IC US 2012/0178642 A1 Jul. 12, 2012 35

TABLE I-continued

Unigene/IPI Symbol Entrez Gene Name 80 IPIOO71966.9 MRLC2 myosin regulatory light chain MRLC2 81 IPIOOOO7858 MYEH13 myosin, heavy chain 13, skeletal muscle 82 IPIOOOO17S3 MYEH4 myosin, heavy chain 4, skeletal muscle 83 HS.4633OO MYL4 myosin, light chain 4, alkali; atrial, embryonic 84 HS.926 MX2 myxovirus (influenza virus) resistance 2 (mouse) 85 H.S.S27412 ASAH1 N-acylsphingosine amidohydrolase (acid ceramidase) 1 86 HS.651219 NDUFAS NADH dehydrogenase (ubiquinone) 1 alpha Subcomplex, 5, 13 kDa 87 IPIOOO74489 NDUFB10 NADH dehydrogenase (ubiquinone) 1 beta Subcomplex, 10, 22 kDa 88 HS.S32853 NDUFB7 NADH dehydrogenase (ubiquinone) 1 beta Subcomplex, 7, 18 kDa 89 HS.471207 NDUFS1 NADH dehydrogenase (ubiquinone) Fe—S protein 1, 75 kDa (NADH-coenzyme Q reductase) 90 HS.90443 NDUFS8 NADH dehydrogenase (ubiquinone) Fe—S protein 8, 23 kDa (NADH-coenzyme Q reductase) 91 HS.464572 NDUFV2 NADH dehydrogenase (ubiquinone) flavoprotein 2, 24 kDa 92 HS.473937 NDUFV3 NADH dehydrogenase (ubiquinone) flavoprotein 3, 10 kDa 93 HS.6SS006 NCKIPSD NCK interacting protein with SH3 domain 94 HS.603732 NCKAP1 NCK-associated protein 1 95 HS.4677S9 NBAS neuroblastoma amplified sequence 96 HSS241.16 NRGN neurogranin (protein kinase C Substrate, RC3) 97 HS.587558 NCF2 neutrophil cytosolic factor 2 98 HS.493.164 NAPRT1 nicotinate phosphoribosyltransferase domain containing 1 99 Hs.696.107 NEK9 (includes NIMA (never in mitosis genea)-related kinase 9 EG:91754) 200 HSS24082 NLRX1 NLR family member X1 2O1 HSS32790 NMT1 N-myristoyltransferase 1 202 HS.319334 NASP nuclear autoantigenic sperm protein (histone-binding) 2O3 HS.263,812 NUDC nuclear distribution gene Chomolog (A. nidulians) 204 HS.654408 NFKB1 nuclear factor of kappa light polypeptide gene enhancer in B-cells 1 205 HS.325978 NUMA1 nuclear mitotic apparatus protein 1 206 HS.791 10 NCL nucleolin 207 HS.643487 NUP160 nucleoporin 160 kDa 208 HSSSS956 NUDTS nudix (nucleoside diphosphate linked moiety X)-type motif 5 209 Hs.405410 OGT (includes O-linked N-acetylglucosamine (GlcNAc) transferase (UDP-N- EG: 8473) acetylglucosamine:polypeptide-N-acetylglucosaminyl transferase) 210 HS-6953.79 OPTN optineurin 211 HS.43O849 OSBPL8 oxysterol binding protein-like 8 212 HS.656789 PAK3 p21 protein (Cdc42, Rac)-activated kinase 3 213 HS.98475 PNKD (includes paroxysmal nonkinesigenic dyskinesia EG: 25953) 214 HS.495471 PMPCA peptidase (mitochondrial processing) alpha 215 HS.33455 PADI2 peptidyl arginine deiminase, type II 216 IPIO0745933 PPIA (includes peptidylprolyl isomerase A (cyclophilin A) EG:5478) 217 HS.644938 PCYT2 phosphate cytidylyltransferase 2, ethanolamine 218 HS.372295 PITPNM1 phosphatidylinositol transfer protein, membrane-associated 1 219 Hs. 272759 PITPNM2 phosphatidylinositol transfer protein, membrane-associated 2 220 HS.75812 PCK2 phosphoenolpyruvate carboxykinase 2 (mitochondrial) 221 HS.75160 PFKM phosphofructokinase, muscle 222 HS.26612 PGM2L1 phosphoglucomutase 2-like 1 223 HS.487296 PEHGDH phosphoglycerate dehydrogenase 224 IPIOO786982 PGAMS phosphoglycerate mutase family member 5 225 HS.409834 PHPT1 phosphohistidine phosphatase 1 226 HS.32942 PIK3CG phosphoinositide-3-kinase, catalytic, gamma polypeptide 227 HS.S91953 PLCB3 phospholipase C, beta 3 (phosphatidylinositol-specific) 228 HS.413111 PLCG2 phospholipase C, gamma 2 (phosphatidylinositol-specific) 229 HSS17216 PEA15 phosphoprotein enriched in astrocytes 15 230 HS.675491 PLXNA4 plexin A4 231 HS.6.32833 PLXNB3 blexin B3 232 HS.348609 PARP10 poly (ADP-ribose) polymerase family, member 10 233 HS.482O38 PAIP1 poly(A) binding protein interacting protein 1 234 HSSO7910 PGRMC2 progesterone receptor membrane component 2 23S HSS674.10 PSMD14 proteasome (prosome, macropain) 26S Subunit, non-ATPase, 14 236 IPIOO555590 PSMB2 proteasome (prosome, macropain) subunit, beta type, 2 237 IPIOOO64328 PRMTS protein arginine methyltransferase 5 238 Hs.498.570 PRKCQ protein kinase C, theta 239 HS.631923 PRKAR2A protein kinase, cAMP-dependent, regulatory, type II, alpha 240 HSS14323 PPP1R9B protein phosphatase 1, regulatory (inhibitor) subunit 9B 241 HS.400740 PPP2R4 protein phosphatase 2A activator, regulatory Subunit 4 242 HSS84019 PPP6C protein phosphatase 6, catalytic Subunit 243 HS.S91549 PTPN18 protein tyrosine phosphatase, non-receptor type 18 (brain-derived) 244 HS.4391-52 PCDH12 protocadherin 12 245 HS78524 PRUNE prune homolog (Drosophila) 246 HS.41735 P2RX1 purinergic receptor P2X, ligand-gated ion channel, 1 247 HS.284491 PDXK pyridoxal (pyridoxine, vitamin B6) kinase US 2012/0178642 A1 Jul. 12, 2012 36

TABLE I-continued

Unigene/IPI Symbol Entrez Gene Name 248 S.370781 PDXDC1 pyridoxal-dependent decarboxylase domain containing 1 249 S.47O633 PDK1 pyruvate dehydrogenase kinase, isozyme 1 250 S.S34770 PKM2 pyruvate kinase, muscle 251 S.321541 B11A RAB11A, member RAS oncogene family 252 S.406799 B18 RAB18, member RAS oncogene family 253 S.369.017 RAB2A, member RAS oncogene family 2S4 S.S67328 RAB5B, member RAS oncogene family 255 S.6SO382 BSC RAB5C, member RAS oncogene family 2S6 S.S915S2 RAB6C, member RAS oncogene family 257 S.644420 RAB8A, member RAS oncogene family 258 S.493867 RCSD domain containing 1 259 S.461925 replication protein A1, 70 kDa 260 S.645283 TN4 reticulon 4 261 S.368631 ARHGAP10 Rho GTPase activating protein 10 262 S.S31807 ARHGAP2S Rho GTPase activating protein 25 263 S.SO8738 ARHGEF7 Rho guanine nucleotide exchange factor (GEF) 7 264 S.465761 ARHGEF18 rhofrac guanine nucleotide exchange factor (GEF) 18 26S S.73839 RNASE3 ribonuclease, RNase A family, 3 (eosinophil cationic protein) 266 S388664 RPL11 ribosoma O ein L11 267 S.374588 RPL17 ribosoma O ein L17 268 S.337766 RPL18A ribosoma O ein L183 269 PIOO741405 LOC391282 ribosoma O ein L23a pseudogene 12 270 S. 6494.75 RPL24 ribosoma O ein L24 271 S.652114 RPL28 ribosoma O ein L28 272 S.433701 RPL37A ribosoma O ein L37a (includes EG: 6168) 273 PIOO796861 OC10O13O892 ribosoma O ein L7 pseudogene 32 274 S.546289 PS12 ribosoma O ein S12 (includes EG: 6206) 275 S.370504 PS1SA ribosoma O ein S15a 276 PIOO4O1105 PS25 ribosoma O ein S25 277 PIOO397963 PS27 ribosoma O ein S27 278 S.282376 ribosoma O ein S4, Y-linked 1 279 S.367761 ribosoma O ein S4, Y-linked 2 28O S.408073 PS6 ribosoma O ein S6 281 PIOO413108 PSA (includes ribosoma O ein SA EG: 3921) 282 S.553723 RNF123 ring finger protein 123 (includes EG: 63891) 283 S.306.769 RUFY1 RUN and FYVE domain containing 1 284 S.272822 RUVBL1 RuvB-like 1 (E. coli) 285 S.515846 RUVBL2 RuvB-like 2 (E. coli) 286 S. 632438 EC22B SEC22 vesicle trafficking protein homolog B (S. cerevisiae) 287 S.654.429 EC24C SEC24 family, member C (S. cerevisiae) includes 63 2) 288 PIOO6438.35 selectin P (granule membrane protein 140 kDa, antigen CD62) 289 S. 632460 Selenium binding protein 1 290 S.283743 e p septin 5 291 S.44O932 ep septin 9 292 S.435661 TLC2 serine palmitoyltransferase, long chain base subunit 2 293 S.433343 RM2 serinefarginine repetitive matrix 2 294 S4O9578 K38 serine/threonine kinase 38 295 PIOO1683SO 6-213H19.1 serine/threonine protein kinase MST4 296 S.368.077 RPINB8 serpin peptidase inhibitor, clade B (ovalbumin), member 8 297 S.S31176 RS seryl-tRNA synthetase 298 S.6435.26 SET domain, bifurcated 1 299 S.285666 SH3 and PX domains 2B 3OO S.6O1143 SH3-domain binding protein 1 301 S.514495 P68 signal recognition particle 68 kDa 3O2 S4O9223 SSR4 signal sequence receptor, delta (translocon-associated protein delta) 303 PIOO399.212 LOC389842 similar to RanBP1 3O4 S.591680 SCYE1 Small inducible cytokine Su bfamily E, member 1 (endothelial monocyte-activating) 305 S.356549 SNRPD3 Small nuclear ribonucleoprotein D3 polypeptide 18 kDa 306 S.632166 SNRPN Small nuclear ribonucleoprotein polypeptide N 307 S.837S3 SNRPB Small nuclear ribonucleoprotein polypeptides B and B1 3O8 S.3SO927 SLC25A6 solute carrier family 25 (mi ochondrial carrier; adenine nucleotide translocator), member 6 309 S.656870 solute carrier family 25 (mi ochondrial carrier; phosphate carrier), member 24 310 S.438.723 solute carrier family 27 (fa y acid transporter), member 3 311 S.656699 solute carrier family 27 (fa y acid transporter), member 4 US 2012/0178642 A1 Jul. 12, 2012 37

TABLE I-continued

Unigene/IPI Symbol Entrez Gene Name 312 S.SO2769 Solute carrier family 3 (activators of dibasic and neutral amino acid transport), member 2 313 S.4691.16 LC9A1 Solute carrier family 9 (sodium hydrogen exchanger), member 1 314 S.878 ORD Sorbitol dehydrogenase 315 S.SOS824 AMMSO Sorting and assembly machinery component 50 homolog (S. cerevisiae) 316 S.327O6 PTBN4 spectrin, beta, non-erythrocytic 4 317 S.SS8463 PEN spen homolog, transcriptional regulator (Drosophila) 318 S.436.306 PHKAP SPHK1 interactor, AKAP domain containing 319 S.406423 F3B2 splicing factor 3b, subunit 2, 145 kDa 32O S.679714 FRS1 splicing factor, arginine?serine-rich 1 321 S.309090 FRS7 splicing factor, arginine?serine-rich 7.35 kDa 322 S.591922 LK STE20-like kinase (yeast) 323 S.3439 TOML2 stomatin (EPB72)-like 2 324 S.656,726 S TRN striatin, calmodulin binding protein 325 S44.0475 DHA (includes Succinate dehydrogenase complex, Subunit A, flavoprotein (Fp) G: 6389) 326 S.465924 DHB (includes Succinate dehydrogenase complex, Subunit B, iron Sulfur (Ip) G: 6390) 327 S.494827 USD1 Sushi domain containing 1 328 S.83734 STX4 Syntaxin 4 329 S.53O436 STXBP3 Syntaxin binding protein 3 330 S.643566 TAOK3 TAOkinase 3 331 PIOO642O32 TXNL1 hioredoxin-like 1 332 S.30345 TRAP1 TNF receptor-associated protein 1 333 S.87968 TLR9 oll-like receptor 9 334 S.47S733 TOP2B opoisomerase (DNA) II beta 180 kDa 335 S.496459 TOR1AIP1 orsin A interacting protein 1 336 S.34024 TNIK TRAF2 and NCK interacting kinase 337 S.529618 TFRC transferrin receptor (p90, CD71) 338 S.S17033 TGM2 transglutaminase 2 (C polypeptide, protein-glutamine-gamma-glutamyltransferase) 339 S.96.247 TSNAX translin-associated factor X 340 S. 654824 TM9SF2 transmembrane 9 superfamily member 2 341 SSO2 TAP2 transporter 2, ATP-binding cassette, sub-family B (MDR/TAP) 342 PIOOO18853 TPM1 tropomyosin 1 (alpha) 343 S.S35581 TPM3 tropomyosin 3 344 S.4975.99 WARS tryptophanyl-tRNA synthetase 345 S.31053 TBCB tubulin folding cofactor B 346 S.279669 TUBG1 tubulin, gamma 1 347 S473296 TPD52L2 tumor protein D52-like 2 348 PIOO7942S4 YWHAH tyrosine 3-monooxygenase/trypto phan 5-monooxygenase activation protein, eta polypeptide 349 S.9589 BQLN1 ubiquilin 1 350 S.S3O8 BAS2 ubiquitin A-52 residue ribosomal protein fusion product 1 351 S.474213 FD1 L, ubiquitin fusion degradation 1 like (yeast) 352 S. 632370 BE4B ubiquitination factor E4B (UFD2 homolog, yeast) 353 PIOOO19932 BE2D2 ubiquitin-conjugating enzyme E2 D 2 (UBC4/5 homolog, yeast) 3S4 S.SO3O8 BE2K ubiquitin-conjugating enzyme E2 K (UBC1 homolog, yeast) 355 PIOO216316 ROS uroporphyrinogen III synthase 356 S.292689 SO1 USO1 homolog, vesicle docking protein (yeast) 357 S.499925 PS26A vacuolar protein sorting 26 homo og A (S. pombe) 358 S.418175 PS28 vacuolar protein sorting 28 homo og (S. cerevisiae) 359 S.S92009 PS33A vacuolar protein sorting 33 homo og A (S. cerevisiae) 360 S.631.53S KT2 V-akt murine thymoma viral onco gene homolog 2 361 S.6.32066 CPIP1 valosin containing protein (p97), p.47 complex interacting protein 1 362 S.515469 vasodilator-stimulated phosphoprotein 363 S.66708 A 3 vesicle-associated membrane pro ein 3 (cellubrevin) 364 S.SOSO33 k St. v-Ki-ras2 Kirsten rat Sarcoma viral oncogene homolog 365 S.699.154 LYN v-yes-1 Yamaguchi sarcoma viral related oncogene homolog 366 S.63.5221 WASF3 WAS protein family, member 3 367 S.356604 WNK1 WNK lysine deficient protein kinase 1 368 S3906.23 XPNPEP1 X-prolylaminopeptidase (aminopeptidase P) 1, soluble 369 S.27239 ZDHHCS Zinc finger, DHHC-type containing 5 370 S.37003 Not Annotated Not Annotate 371 S.102696 Not Annotated 372 S.10326 COPE 373 S.10649 C1 orf58 374 S.108049 Not Annotated Not Annotate 375 S.108957 Not Annotated Not Annotate 376 S.111024 Not Annotated Not Annotate 377 S.115242 Not Annotated Not Annotate 378 S.116237 Not Annotated Not Annotate 379 S.11638 ACSLS 380 S.1198.25 Not Annotated Not Annotate 381 S.124027 Not Annotated Not Annotate US 2012/0178642 A1 Jul. 12, 2012 38

TABLE I-continued

Unigene/IPI Symbol Entrez Gene Name 382 24.126 Not Annotated Not Annotated 383 2865 NSFL1C 384 31255 Not Annotated Not Annotated 385 31489 Not Annotated Not Annotated 386 32499 Not Annotated Not Annotated 387 32858 Not Annotated Not Annotated 388 33512 Not Annotated Not Annotated 389 34688 Not Annotated Not Annotated 390 36309 Not Annotated Not Annotated 391 38378 Not Annotated Not Annotated 392 4112S Not Annotated Not Annotated 393 42003 Not Annotated Not Annotated 394 422 R 395 437 GAA 396 43703 397 44O11 398 44447 399 464O6 D 400 466O2 RQ 4O1 4995.7 S6KA1 4O2 SO2O6 ST1H1A 403 50718 AM3 LOC10O1335O2 404 52944 WWASA 40S S4O78 LBP 4O6 55975 PTPRCAP 407 58331 RENBP 4.08 5977 NDUFB9 409 61.357 PDHB 410 621.21 COPA 411 6355 MYH10 412 63867 D14 413 66O11 TNND1 414 66SS1 114A2 415 66924 416 69284 417 69900 418 71626 419 73O43 420 7614 421 793.09 422 8.192 423 82625 424 872 Not Annotated Not Annotated 425 884O1 ANXA10 426 88.882 NUDT3 427 89075 TWF1 428 892S CRBN 429 89409 FNBP1 430 90O86 MRCL3 431 91213 432 94148 YES1 433 95.08O ECE1 434 S. 96437 MOBKL1B 435 S.2O0804 SDCBP 436 S.204041 AHSA1 437 S.2057 Not Annotated Not Annotated 438 S.211463 DNM2 439 S.21160 ME1 440 S.212088 EPHX2 441 S.213389 GOLGB1 442 S.213470 PSMB7 443 S.214142 MTHFR 444 S.22O594 CCDC58 445 S.2241.71 ENO3 446 S.238839 447 S.2398.18 448 S.24956 INF2 449 S.271954 Not Annotated Not Annotated 450 S.296422 Not Annotated Not Annotated 451 S.3O1658 15544.40 at 1554,440 at 452 S.328865 Not Annotated Not Annotated 453 S.351544 Not Annotated Not Annotated 454 S.368359 Not Annotated Not Annotated US 2012/0178642 A1 Jul. 12, 2012 39

TABLE I-continued Unigene/IPI Symbol Entrez Gene Name

4SS HS.370503 Not Annotate Not Annotate 456 HS.37712 AWOO6941 AWOO6941 457 HS.43SOS AFO91453 458 HS.435775 Not Annotate Not Annotate 459 HS.439474 Not Annotate Not Annotate 460 HS.440534 Not Annotate Not Annotate 461 HS.460988 Not Annotate Not Annotate 462 HS.470544 Not Annotate Not Annotate 463 HS.471528 Not Annotate Not Annotate 464 HS.486856 Not Annotate Not Annotate 465 HSSOO674. Not Annotate Not Annotate 466 HS.S90925 Not Annotate Not Annotate 467 H.S.S91005 Not Annotate Not Annotate 468 HS.591366 Not Annotate Not Annotate 469 H.S.S99301 Not Annotate Not Annotate 470 HS.63273S Not Annotate Not Annotate 471 HS.637017 Not Annotate Not Annotate 472 HS.645248 Not Annotate Not Annotate 473 HS.654497 Not Annotate Not Annotate 474 HS.659335 Not Annotate Not Annotate 47S HS-694210 Not Annotate Not Annotate 476 HS-696132 Not Annotate Not Annotate 477 HS.699.333 Not Annotate Not Annotate 478 HS-699367 Not Annotate Not Annotate 479 HS.7OO648 Not Annotate Not Annotate 480 HS.7 OO676 Not Annotate Not Annotate 481 HS.7OO760 Not Annotate Not Annotate 482 IPIOOO11791. Not Annotate Not Annotate 483 IPIOOO26138. Not Annotate Not Annotate 484 IPIOOO27007 Not Annotate Not Annotate 485 IPIOOO61977. Not Annotate Not Annotate 486 IPIOO140827. Not Annotate Not Annotate 487 IPIOO152990 Not Annotate Not Annotate 488 IPIOO165486 Not Annotate 489 IPIOO167258. Not Annotate 490 IPIOO176593 Not Annotate 491 IPIOO176692. Not Annotate 492 IPIOO176854. Not Annotate 493 IPIOO332493 Not Annotate 494 IPIOO38.6403 Not Annotate 495 IPIOO397713 Not Annotate 496 IPIOO397808. Not Annotate 497 IPIOO398.435 Not Annotate 498 IPIOO412216 Not Annotate 499 IPIOO457006 Not Annotate SOO IPIOO478310 Not Annotate SO1 IPIOOSS6589. Not Annotate SO2 IPIOO738O24 Not Annotate SO3 IPIOO745518 Not Annotate 504 IPIOO746177 Not Annotate 505 IPIOO788.196 Not Annotate 506 IPIOO7928SO Not Annotate 507 IPIOO7962O8 Not Annotate SO8 IPIOO797737 Not Annotate 509 IPIOO807559 Not Annotate 510 IPIOO807559 Not Annotate

TABLEJ Fold Change International (positive numbers Protein are upregulated Index/UniGene Symbol Entrez Gene Name in B1) 1 HS.180946 RPL5 (includes ribosomal protein L5 2.991.594141 EG:6125) 2 HSS2OO26 VARS valyl-tRNA synthetase 1788666142 3 HS-664-670 Not Annotated 1863S46477 4 IPIOOOO1539 ACAA2 acetyl-Coenzyme A acyltransferase 2 1.778O126.17 S HS.631827 ANXA7 annexin A7 1.962977658 6 HS.466O44 PKN1 protein kinase N1 2.92621.5231 US 2012/0178642 A1 Jul. 12, 2012 40

TABLE J-continued Fold Change international (positive numbers rotein are upregulated index/UniGene Symbol Entrez Gene Name in B1) S.90093 HSPA4 heat shock 70 kDa protein 4 2.32454O439 S.185172 GNB2 guanine nucleotide binding protein (G protein), beta polypeptide 2 2.321, 199972 PIOOOO3438 DNAJC8 DnaJ (Hsp40) homolog, subfamily C, member 8 3.049698528 10 S.431850 MAPK1 mitogen-activated protein kinase 1 14726766.36 11 S.SO382 TP2 tight junction protein 2 (Zona occludens 2) 2.O14271952 12 S.180414 Not Annotated 16831SS132 13 S.186350 RPL4 ribosomal protein L4 2.71 OS 18039 14 S.6992SO B2M beta-2-microglobulin 2.103571916 15 S.S.91897 Not Annotated 2.715551514 16 S.489284 ARPC1B actin related protein 2/3 complex, subunit 1B, 41 kDa 2.03499.2123 17 S.S14934 CAPZA1 capping protein (actin filament) muscle Z-line, alpha 1 2.337884S11 18 S.431279 NSF N-ethylmaleimide-sensitive factor 2.608040048 19 S.7OOSTO APP amyloid beta (A4) precursor protein -2.3958.93698 2O S.2792.59 EPX eosinophil peroxidase 2.005473585 21 S.644618 SLC25AS Solute carrier family 25 (mitochondrial carrier; adenine nucleotide 2.377793261 translocator), member 5 22 S.477155 ATP6V1A ATPase, H+ transporting, lysosomal 70 kDa, V1 subunit A 1592.166761 23 S.75318 TUBA4A tubulin, alpha 4a 1.410317852 24 S.184233 HSPA9 heat shock 70 kDa protein 9 (mortalin) 3.89OS88764 25 S.521640 RAD23B RAD23 homolog B (S. cerevisiae) 1.945040444 26 S.370581 CAP1 CAP, adenylate cyclase-associated protein 1 (yeast) 2.08626.543 27 S.522969 PADI4 peptidyl arginine deiminase, type IV -2.585597629 28 S.4834.08 Not Annotated 2.427608273 29 S.437594 RPLP2 ribosomal protein, large, P2 1.762376912 30 S.546285 RPLPO (includes ribosomal protein, large, PO 2.4O18091.97 EG: 6175) 31 RAB1B (includes RAB1B, member RAS oncogene family 2.03678.8097 EG: 81876) 32 S.632535 SSB (includes Sjogren syndrome antigen B (autoantigen La) 1848O49688 EG: 6741) 33 S.38449 SERPINE2 Serpin peptidase inhibitor, clade E (nexin, plasminogen activator 1839.116473 inhibitor type 1), member 2 34 S.374,596 TPT1 (includes tumor protein, translationally-controlled 1 1916065103 EG: 7178) 35 S.148559 MMT inner membrane protein, mitochondrial (mitofilin) 2.20881.2239 36 S.405144 SFRS3 splicing factor, arginine?serine-rich 3 1854.287873 37 S.274309 ERAF erythroid associated factor -2.404141665 38 S.413812 RAC1 ras-related C3 botulinum toxin substrate 1 (rho family, Small GTP 3.007255119 binding protein Rac1) 39 S.253.18 RAB27B RAB27B, member RAS oncogene family 1.762O799.78 40 S355934 SFPQ splicing factor proline:glutamine-rich (polypyrimidine tract binding 2.033693659 protein associated) 41 S.464,336 P4HB prolyl 4-hydroxylase, beta polypeptide 2.058272651 42 S.247362 DDAH2 dimethylarginine dimethylaminohydrolase 2 2.191528.732 43 S.S271 OS HNRPDL heterogeneous nuclear ribonucleoprotein D-like 3.3236SOOS4 44 S.502842 CAPN1 calpain 1, (mul) large subunit 844181806 45 S.12970 PSMD3 proteasome (prosome, macropain) 26S subunit, non-ATPase, 3 509756576 46 PIOOO11891 Not Annotated 94939 1219 47 S.373763 HNRNPR heterogeneous nuclear ribonucleoprotein R 3.1832.71632 48 S.440898 FCN1 icolin (collagen fibrinogen domain containing) 1 -1921.894928 49 S.644646 KIFSB kinesin family member 5B -1435375448 50 S.63348 EMILIN1 elastin microfibrill interfacer 1 663O39334 51 S.153837 MINDA myeloid cell nuclear differentiation antigen 68.9289277 52 S.656176 RBM4 RNA binding motif protein 4 899826892 53 S.77793 CSK c-Src tyrosine kinase 724761961 S4 S.627414 RPS18 ribosomal protein S18 3.3482S1322 55 S.497788 EPRS glutamyl-prolyl-tRNA synthetase 466442524 56 S.698.340 92.1786734 57 S.699298 CDV3 homolog (mouse) 486895919 58 S.111779 Secreted protein, acidic, cysteine-rich (osteonectin) -27804451.45 59 PIOOO11891 PRKAA1 protein kinase, AMP-activated, alpha 1 catalytic Subunit 2.7135877 35 60 S.495541 C9CORF167 chromosome 9 open reading frame 167 S99094872 61 S.651923 CNN2 calponin 2 .731782614 62 S.131711 dihydrolipoamide dehydrogenase 948.923988 63 S.644.809 Not Annotated 2.3383.1686S 64 S.643072 RAB10 RAB10, member RAS oncogene family 911 187131 65 S.2853 PCBP1 (includes poly(rC) binding protein 1 878028726 EG:5093) 66 S.19121 AP2A2 adaptor-related protein complex 2, alpha 2 subunit 2.290995374 67 S. 6901.98 CDC42 cell division cycle 42 (GTP binding protein, 25 kDa) 2.382171241 68 S.271510 GSR glutathione reductase 2.161827645 US 2012/0178642 A1 Jul. 12, 2012 41

TABLE J-continued Fold Change international (positive numbers Protein are upregulated index/UniGene Symbol Entrez Gene Name in B1) 69 HS.524161 Ras Suppressor protein 1 1.436279998 70 HS.406277 splicing factor 3a, Subunit 1, 120 kDa 3.356651S2 71 HSSS8314 CP ceruloplasmin (ferroxidase) -4832439476 72 S.7SS14 NP (includes nucleoside phosphorylase 1...SOO961.251 EG:4860) 73 S.5O1684 NAP1L4 nucleosome assembly protein 1-like 4 2.2098.25746 74 S.571177 SYNCRIP synaptotagmin binding, cytoplasmic RNA interacting protein 2.26958.0549 75 S.695941 HK1 hexokinase 1 1.893.698231 76 S.368149 CCTT chaperonin containing TCP1, Subunit 7 (eta) 1.433906814 77 S.695925 DUSP3 dual specificity phosphatase 3 2.286782204 78 S.7SO66 translin -2.048.787544 79 S.4747S1 myosin, heavy chain 9, non-muscle 2.033216171 8O S.644.809 3.01.3475764 81 S.6SS2O7 coagulation factor II (thrombin) -2.86.1439244 82 S.143436 plasminogen -1.893.142835 83 S.42O529 ubiquitin-conjugating enzyme E.2 variant 1 84 S190O28 glutathione S-transferase omega 1 85 S.2O107 kinesin light chain 1 86 S. 6264.04 RAB11B RAB11B, member RAS oncogene family 87 S.46O109 MYH11 myosin, heavy chain 11, Smooth muscle 88 S.490415 ZYX Zyxin 89 S.138860 ARHGAP1 Rho GTPase activating protein 1 90 S.646283 virus-induced signaling adapter 91 HS.8004 kalirin, RhoGEF kinase 92 S.S94673 93 HS.707 keratin 2 94 S.699367 95 S.28O342 protein kinase, cAMP-dependent, regulatory, type I, alpha (tissue specific extinguisher 1) 96 S.73849 APOC3 apolipoprotein C-III 97 S.S.462.SS fibrinogen gamma chain 98 S.75307 H1 histone family, member X 99 S.632729 amily with sequence similarity 62 (C2 domain containing), member A OO S.120759 apolipoprotein B (including Ag(x) antigen) O1 S.72933 platelet factor 4 variant 1 O2 S.S.07866 chromosome 13 open reading frame 15 O3 S.2O3717 fibronectin 1 O4 S.324746 AHSG alpha-2-HS-glycoprotein -4.302298793 05 S.200770 SKAP2 Src kinase associated phosphoprotein 2 .755472125 O6 S.30054 F5 coagulation factor V (proaccelerin, labile factor) -156764.8564 O7 S.372208 HSPC159 galectin-related protein 82.4854.702 O8 S.505735 NACA nascent polypeptide-associated complex alpha Subunit 652441243 09 S.491351 CLTC clathrin, heavy chain (He) 7435O2579 10 S.480042 ANXA3 annexin A3 11 S.509226 FKBP3 FK506 binding protein 3, 25 kDa 12 S.24258 GUCY1A3 guanylate cyclase 1, Soluble, alpha 3 13 S.81934 ACADSB acyl-Coenzyme A dehydrogenase, short branched chain 352.453174 14 S.429608 REEP5 receptor accessory protein 5 -162916S972 15 S.75841 ERP29 endoplasmic reticulum protein 29 2.32777609 16 S.413482 C21 ORF33 chromosome 21 open reading frame 33 -1.33827S818 17 S.SO28.23 PRDX5 peroxiredoxin 5 612O321.87 18 S.S233O2 PRDX3 peroxiredoxin 3 .609936792 19 S.408054 RPL12 (includes ribosomal protein L12 2.804663.OS1 EG: 6136) 2O PIOOO24989 PCMT1 protein-L-isoaspartate (D-aspartate) O-methyltransferase S67802876 21 S.S91095 PDIA3 protein disulfide isomerase family A, member 3 7805995.08 22 S.43O606 CS citrate synthase -2.357926195 23 S.S20973 HSPB1 heat shock 27 kDa protein 1 92.393.1973 24 S.518244 RPN1 ribophorin I 25 S.695918 CAPZA2 capping protein (actin filament) muscle Z-line, alpha 2 26 S.632828 HNRNPH2 heterogeneous nuclear ribonucleoprotein H2 (H") 27 S.43O425 GNB1 guanine nucleotide binding protein (G protein), beta polypeptide 1 .915685862 28 S.469473 RPL31 ribosomal protein L31 971.23746S 29 S.381.072 PPIF peptidylprolyl isomerase F 919712344 30 S.831.90 FASN atty acid synthase S96744982 31 S.356624 NID1 nidogen 1 -156737O157 32 S.12084 TUFM Tu translation elongation factor, mitochondrial 443666367 33 S.95990 PKLR pyruvate kinase, liver and RBC 2.624429792 34 S.489040 SR Sorcin -1.6682S1058 35 S.192374 HSP90B1 heat shock protein 90 kDa beta (Grp94), member 1 227206967 36 CAPG capping protein (actin filament), gelsolin-like .93SO86978 US 2012/0178642 A1 Jul. 12, 2012 42

TABLE J-continued Fold Change international (positive numbers Protein are upregulated index/UniGene Symbol Entrez Gene Name in B1) 37 HS.928 PRTN3 proteinase 3 -2.1913O2631 38 Hs.179986 FLOT1 lotill in 1 2.62551.323 39 S.315137 AARS alanyl-tRNA synthetase 2.13807 1963 40 S.27 S243 S100A6 S100 calcium binding protein A6 -2.091908363 41 S.656274 TNFAIP8 tumor necrosis factor, alpha-induced protein 8 1848.699.684 42 S.654559 HNRNPL heterogeneous nuclear ribonucleoprotein L. 2.064236,514 43 S.471441 proteasome (prosome, macropain) subunit, beta type, 2 3.1894O7689 44 S.S94095 1541410846 45 HS.7744 NADH dehydrogenase (ubiquinone) flavoprotein 1, 51 kDa 1859664494 46 S.S17670 tubulin tyrosine ligase-like family, member 12 1.54.866.9753 47 S.1594.94 Bruton agammaglobulinemia tyrosine kinase 1.744461371 48 S.153961 ACTR1A ARP1 actin-related protein 1 homologA, centractin alpha (yeast) 1.6021746,73 49 S.98791 ACTR1B (includes ARP1 actin-related protein 1 homolog B, centractin beta (yeast) 2.447S61282 EG: 10120) 50 PIOOO2962S FLOT2 lotill in 2 2.7790483.89 51 S.232.375 ACAT1 acetyl-Coenzyme A acetyltransferase 1 1844709235 52 S.529451 DIAPH1 diaphanous homolog 1 (Drosophila) 1472455435 53 S.477352 PDIAS protein disulfide isomerase family A, member 5 2.417726.204 S4 S.S16032 HADHA hydroxyacyl-Coenzyme A dehydrogenase 3-ketoacyl-Coenzyme A 2.91989.3077 hiolase enoyl-Coenzyme A hydratase (trifunctional protein), alpha Subunit 55 S.S28007 U2AF2 (includes U2 small nuclear RNA auxiliary factor 2 2.33690845 EG: 11338) 56 S.6SS340 Not Annotated .9943992OS 57 S.5463O3 Not Annotated 9932S8019 58 S.191346 7-Sep septin 7 42672O758 59 S.SS6296 Not Annotated 91.81571.96 60 S.5464O7 CAND1 cullin-associated and neddylation-dissociated 1 3SS594.109 61 S.122523 SND staphylococcal nuclease and tudor domain containing 1 764952427 62 S.327252 Not Annotated .853845796 63 PIOO154742 IGL(a) immunoglobulin lambda locus -2.322679589 64 S.514,412 PECAM1 platelettendothelial cell adhesion molecule S21872894 65 S.248.267 MPST mercaptopyruvate Sulfurtransferase 80272392S 66 S.43618.6 CAST calpastatin 87.7444004 67 S.390S67 FYN FYN oncogene related to SRC, FGR, YES 721126996 68 PIOO168728 IGHM immunoglobulin heavy constant mu -1.88212SO59 69 S.SS8799 PSMA3 proteasome (prosome, macropain) subunit, alpha type, 3 2.424.171315 70 S.4658O8 HNRNPM heterogeneous nuclear ribonucleoprotein M .745065443 71 S.1491.85 CNDP2 CNDP dipeptidase 2 (metallopeptidase M20 family) 6392943O3 72 PIOO1792.91 XPNPEP1 X-prolylaminopeptidase (aminopeptidase P) 1, soluble 443429746 73 S.555895 TMSL3 thymosin-like 3 -2.98.697.3706 74 S.126SSO VPS4B vacuolar protein sorting 4 homolog B (S. cerevisiae) 5707885 75 S. 65472O KIAA1967 KIAA1967 3.86.1735646 76 S.49582 PPP1R12A protein phosphatase 1, regulatory (inhibitor) Subunit 12A -1985284SOS 77 S.63489 PTPN6 protein tyrosine phosphatase, non-receptor type 6 2.403072934 78 S.S35581 tropomyosin 3 -1.265339887 79 S.496984 membrane protein, palmitoylated 1, 55 kDa 825563177 8O S.515517 ribosomal protein L18 81 S.438429 ribosomal protein S19 82 S.73722 APEX nuclease (multifunctional DNA repair enzyme)1 2.126641285 83 S.461047 glucose-6-phosphate dehydrogenase .33O805366 84 S.128548 WD repeat domain 1 85 S.S1932O voltage-dependent anion channel 1 86 S.S12675 ribosomal protein S8 2.401417871 87 S.494691 profilin 1 824342OO2 88 S.180535 fermitin family homolog 3 (Drosophila) 9331071.42 89 S.417303 spectrin, beta, erythrocytic 2.124657924 90 S.446628 2.08.246.130S 91 HS1869 phosphoglucomutase 1 626.61576 92 S89497 lamin B1 89.2879233 93 S.6523O8 methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1, 96.5807135 methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthetase 94 S.446149 LDHB lactate dehydrogenase B 507117812 95 S.87752 MSN moesin .792.183522 96 S.2S3903 STOM stomatin 66.3466237 97 S.S23836 GSTP1 glutathione S-transferase pi 1 3.12O10713 98 S.S73688 PRDX6 peroxiredoxin 6 768671919 99 S.8O828 KRT1 keratin 1 2.488668295 2OO S.289.123 DCTN2 dynactin 2 (p50) S17636O12 2O1 S.654554 Not Annotated -3.22.12581.93 US 2012/0178642 A1 Jul. 12, 2012 43

TABLE J-continued Fold Change international (positive numbers Protein are upregulated index/UniGene Symbol Entrez Gene Name in B1) 202 HS.9OO61 PGRMC1 progesterone receptor membrane component 1 1.645197721 2O3 HSS14819 AP2B1 adaptor-related protein complex 2, beta 1 subunit 1.9677S2606 204 HS.467284 RPS9 ribosomal protein S9 2.046621121 205 HS.397609 RPS16 ribosomal protein S16 3.41 1967491 206 HS.433427 RPS17 (includes ribosomal protein S17 3.9S408O13 EG: 6218) 207 HS.350899 CAPN2 calpain 2, (mII) large subunit 68O232488 208 HS.363 137 TCP1 t-complex 1 .787923894 209 HSS2O967 MDH2 malate dehydrogenase 2, NAD (mitochondrial) 55961.2551 210 HS 69918O VCL. Vinculin 3.12993.8695 211 HS.371 S63 RAB14 RAB14, member RAS oncogene family 2.101732978 212 HS.83722 EPS15 epidermal growth factor receptor pathway substrate 15 .373102908 213 HS.277035 MGLL monoglyceride lipase 805879512 214 HS.64O16 PROS1 protein S (alpha) -2.623015853 215 H.S.S84790 PPP2R1B protein phosphatase 2 (formerly 2A), regulatory Subunit A, beta -1810743224 isoform 216 HSS80681 SAMHD1 SAM domain and HD domain 1 217 HS.444770 SH3KBP1 SH3-domain kinase binding protein 1 218 HS.88778 CBR1 carbonyl reductase 1 219 HS.339278 COPB1 coatomer protein complex, Subunit beta 1 220 HS.S924.90 FH fumarate hydratase 221 HS.486458 ARHGAP18. Rho GTPase activating protein 18 222 HS.33551.3 F13A1 coagulation factor XIII, A1 polypeptide 2.145284OO2 223 HS.189772 CCT2 chaperonin containing TCP , Subunit 2 (beta) 435.139731 224 HSS39684 EIF2S3 eukaryotic translation initia ion factor 2, Subunit 3 gamma, 52 kDa 225 HS.33642 ARCN1 archain 1 226 HS.370770 XPO1 exportin 1 (CRM1 homolog, yeast) 2.343773987 227 HSS73018 Not Annotated 456482S6S 228 HS.291 O30 QGAP2 IQ motif containing GTPase activating protein 2 .646289191 229 HS.212102 PDIA6 protein disulfide isomerase family A, member 6 2.48O879671 230 HS.499839 RPL7A ribosomal protein L7a 726750017 231 HS.46SO41 HDHD2 haloacid dehalogenase-like hydrolase domain containing 2 2.231.113926 232 HS.654957 PPA2 pyrophosphatase (inorganic) 2 2.076884O27 233 HS.66OO70 Not Annotated 2.04883O3 234 HS.12S113 CCT8 chaperonin containing TCP1, subunit 8 (theta) 2.39782O42 23S HS.2744O2 HSPA1A heat shock 70 kDa protein 1A 2.35821, 1938 236 HS.7528S TIH2 inter-alpha (globulin) inhibitor H2 -2.82S741915 237 HSS71886 AKR7A2 aldo-keto reductase family 7, member A2 (aflatoxin aldehyde 2.1664.98126 reductase) 238 HS.368794 AP1B1 adaptor-related protein complex 1, beta 1 subunit 1872459483 239 H.S.S99481 EIF4A2 eukaryotic translation initiation factor 4A, isoform 2 3.551326775 240 HS.416848 CTSW cathepsin W -1.696934761 241 HSS28668 RPL6 ribosomal protein L6 2.4301.41179 242 HS.368O84 LRPPRC eucine-rich PPR-motif containing -2.37058.1231 243 HSSO9736 HSP90AB1 heat shock protein 90 kDa alpha (cytosolic), class B member 1 2.408626383 244 HS.632717 MYL6 myosin, light chain 6, alkali, Smooth muscle and non-muscle 3.625359469 245 HS.654.614 HSPA6 heat shock 70 kDa protein 6 (HSP7OB') 2.880497988 246 HSS67380 FUBP1 ar upstream element (FUSE) binding protein 1 2.457237888 247 H.S.S2S600 HSP90AA1 heat shock protein 90 kDa alpha (cytosolic), class A member 1 2.305751.68 248 HS-699168 TUBA1B tubulin, alpha1b 343588946 249 IPIOO39813S Not Annotated 706927145 250 HS-12842O VPS4A vacuolar protein sorting 4 homolog A (S. cerevisiae) 2.041.67O779 251 HS.S91054 BID BH3 interacting domain death agonist 977789.146 2S2 HS2OO716 MECP2 methyl CpG binding protein 2 (Rett syndrome) 2S3 HS.155247 ALDOC aldolase C, fructose-bisphosphate 2.390316052 2S4 HSS70791 LAP3 eucine aminopeptidase 3 7773.007 2SS HS.S9811S PPLA (includes peptidylprolyl isomerase A (cyclophilin A) -1.25223.1897 EG:5478) 2S6 HS.356572 RPS3A ribosomal protein S3A 3.36403.3062 2S7 HSS18530 PAK2 p21 protein (Cdc42, Rac)-activated kinase 2 82O573.252 2S8 HS.98510 WDR44 WD repeat domain 44 .71SS15466 259 IPIOO44892S GHG1 immunoglobulin heavy constant gamma 1 (Glm marker) -2.7093983SS 26O HS.41045 UNC13D unc-13 homolog D (C. elegans) 47508.1587 261 HS.380956 Not Annotated 262 HS.404321 GARS glycyl-tRNA synthetase 263 HS.306.769 RUFY1 RUN and FYVE domain containing 1 2.53.1625079 264 HS.292493 XRCC6 X-ray repair complementing defective repair in Chinese hamster cells 6 .7871634.46 26S HS.S95053 HSPD1 heat shock 60 kDa protein 1 (chaperonin) 255650787 266 HS-69928O HBD hemoglobin, delta -2.91.374O187 267 HS.655361 HPR (includes haptoglobin-related protein -4.71 OS60337 EG: 3250) US 2012/0178642 A1 Jul 12, 2012 44

TABLE J-continued Fold Change international (positive numbers Protein are upregulated index/UniGene Symbol Entrez Gene Name in B1) 268 HSS34770 PKM2 pyruvate kinase, muscle 1.537311441 269 HS.2533 ALDH9A1 aldehyde dehydrogenase 9 family, member A1 2.429592O13 270 HSS30687 RNH1 ribonucleasef angiogenin inhibitor 1 1.90523O817 271 HSS17168 TAGLN2 transgelin 2 1822335623 272 HS.14770 BIN2 bridging integrator 2 168853164 273 HS.436439 TWF2 twinfilin, actin-binding protein, homolog 2 (Drosophila) 1884S10405 274 HS.433O68 PRKAR2B protein kinase, cAMP-dependent, regulatory, type II, beta 1.54.914478 275 HSSO2756 AHNAK AHNAKnucleoprotein 2.893577011 276 HSS15876 NRBP1 nuclear receptor binding protein 1 2.746197889 277 HS132858 RAP1GDS1 RAP1, GTP-GDP dissociation stimulator 1 2.1079826OS 279 HS.311609 DDX39 DEAD (Asp-Glu-Ala-Asp) box polypeptide 39 2.84761005 28O HS.438678 TALDO1 transaldolase 1 2.691818999 282 PIOO746976 DNM1L, dynamin 1-like 1.617915807 283 HS270428 SUCLG1 Succinate-CoA ligase, alpha Subunit 2.3722S264 284 HS.471 O14 TLN1 alin 1 2.579118784

TABLE 2 Protein Transcript Matches of 393 mild CAN consensus genes Probe Set ID UniGene ID Gene Title Gene Symbol 212224 at Hs.76392 aldehyde dehydrogenase 1 family, member A1 ALDH1A1 : 209970 x at HS.2490 caspase 1, apoptosis-related cysteine peptidase (interleukin 1, beta, CASP1 convertase) 216799 at HS.24907 Coronin, actin binding protein, 2B CORO2B 202902 s at HS.181301 cathepsin S CTSS 203276 at HS.89497 lamin B1 LMNB1 155905.2 s at HS.S18530 p21 (CDKN1A)-activated kinase 2 PAK2 2028.03 s at HS.375957 integrin, beta 2 (antigen CD18 (p95), lymphocyte function-associated antigen ITGB2 1; macrophage antigen 1 (mac-1) beta Subunit) 224.51.1 s at HS.408236 thioredoxin-like 5 thioredoxin-like 5 TXNLS 216063 at HS2O2OS hemoglobin, beta pseudogene 1 if hemoglobin, beta pseudogene 1 HBBP1 202277 at HS.90458 serine palmitoyltransferase, long chain base subunit 1 SPTLC1

TABLE 3 Protein Transcript Matches of 1066 mild CAN DataSet 1 genes Probe Set ID UniGene ID Gene Title Gene Symbol 212224 a S.76392 aldehyde dehydrogenase 1 family, member A1 201089 a S.295917 ATPase, H+ transporting, lysosomal 56/58 kDa, V1 subunit B, isoform 2 213312 a S.70769 chromosome 6 open reading frame 162 206011 a HS.2490 caspase 1, apoptosis-related cysteine peptidase (interleukin 1, beta, convertase) 202902 s a S.181301 cathepsin S CTSS 204714 s a S.30054 coagulation factor V (proaccelerin, labile factor) F5 202957 a S.14601 Hematopoietic cell-specific Lyn Substrate 1 HCLS1 20593.6 s a S.41 1695 hexokinase 3 (white cell) HK3 204959 a S.153837 myeloid cell nuclear differentiation antigen if myeloid cell nuclear MINDA differentiation antigen 208875 S. a S.S18530 p21 (CDKN1A)-activated kinase 2 PAK2 11 207668 x a S.2121 O2 protein disulfide isomerase family A, member 6 PDIA6 12 227516 a S.406277 splicing factor 3a, Subunit 1, 120 kDa SF3A1 13 217995 a S.S11251 Sulfide quinone reductase-like (yeast) SQRDL 14 220966 x a S. 132499 actin related protein 2/3 complex, subunit 5-like i? actin related protein 2/3 ARPCSL complex, Subunit 5-like 15 219505 a. S.170310 cat eye syndrome chromosome region, candidate 1 CECR1 16 202295 s a S.148641 cathepsin H CTSH 17 20975.9 s a S.403436 dodecenoyl-Coenzyme A delta isomerase (3.2 trans-enoyl-Coenzyme A DCI isomerase) 18 204646 a S.33SO34 dihydropyrimidine dehydrogenase DPYD 19 21861.0 s a S.46OOO2 hypothetical protein FLJ11151 FLJ11151 2O 209876 a S.434996 G protein-coupled receptor kinase interactor 2 GIT2 21 201944 a S. 69293 hexosaminidase B (beta polypeptide) HEXB US 2012/0178642 A1 Jul 12, 2012 45

TABLE 3-continued Protein Transcript Matches of 1066 mild CAN DataSet 1 genes Probe Set ID UniGene ID Gene Title Gene Symbol

22 211023 at HS.161357 pyruvate dehydrogenase (lipoamide) beta PDHB 23 202671 s at HS.284491 pyridoxal (pyridoxine, vitamin B6) kinase PDXK 24 225214 at HS.213470 Proteasome (prosome, macropain) subunit, beta type, 7 PSMB7 25 217983 s at HS.S29989 ribonuclease T2 RNASET2 26 206034 at HS.368.077 serpin peptidase inhibitor, clade B (ovalbumin), member 8 SERPINB8 27 204981 at HSSO868 Solute carrier family 22 (organic cation transporter), member 18 SLC22A18 28 219403 s at HS.44227 heparanase HPSE 29 232359 at HS.226007 Retinol dehydrogenase 11 (all-trans and 9-cis) RDH11 30 203485 at HS.368626 reticulon 1 RTN1 31 221532 s at HS.S13OSS WD repeat domain 61 WDR61 32 208857 s at HS.2792.57 protein-L-isoaspartate (D-aspartate) O-methyltransferase PCMT1

TABLE 4 Protein Transcript Matches of 1429 mild CAN DataSet 2 genes Probe Set ID UniGene ID Gene Title Gene Symbol 201305 X at S.494.604 acidic (leucine-rich) nuclear phosphoprotein 32 family, member B ANP32B 2 216123 x at S.514934 Capping protein (actin filament) muscle Z-line, alpha 1 CAPZA1 209970 X at HS.2490 caspase 1, apoptosis-related cysteine peptidase (interleukin 1, beta, CASP1 convertase) 209789 at S.24907 coronin, actin binding protein, 2B CORO2B 237104 at S.181301 Cathepsin S CTSS 202428 X at S. 78888 diazepam binding inhibitor (GABA receptor modulator, acyl-Coenzyme A DBI binding protein) 235999 at HS.480073 Heterogeneous nuclear ribonucleoprotein D (AU-rich element RNA binding HNRPD protein 1, 37 kDa) 243593 s at S.4658O8 Heterogeneous nuclear ribonucleoprotein M HNRPM 201841 s at S.S20973 heat shock 27 kDa protein 1 HSPB1 10 1566785 X at HS.431279 Ribosomal protein S7 NSF 11 216253 s at S.47SO74 parvin, beta PARVB 12 215628 x at S.4834.08 Protein phosphatase 2 (formerly 2A), catalytic Subunit, alpha isoform PPP2CA 13 200927 s at S.371S63 RAB14, member RAS oncogene family RAB14 14 213941 x at S.546287 ribosomal protein S7 RPS7 15 240855 at HS.417303 Spectrin, beta, erythrocytic (includes spherocytosis, clinical type I) SPTB 16 237875 at HS.S19756 Serine/threonine kinase 10 STK10 17 238749 at HS.258.314 Brain and reproductive organ-expressed (TNFRSF1A modulator) BRE 18 1565868 at S.SO2328 CD44 antigen (homing function and Indian blood group system) 18 1565868 at S.SO2328 CD44 antigen (homing function and Indian blood group system) 19 226875 at HS-3682O3 dedicator of cytokinesis 11 2O 208000 at S.86161 GPI anchored molecule like protein 21 243147 x at S.432674 Leucyl-tRNA synthetase 22 226253 at HS.143774 leucine rich repeat containing 45 23 229851 s at S.836O PTD012 protein 24 208720 s at S.2829O1 RNA-binding region (RNP1, RRM) containing 2 25 201742 X at HS.6871.4 splicing factor, arginine?serine-rich 1 (splicing factor 2, alternate splicing factor) 26 215274 at HS.369271 solute carrier family 12 (sodium chloride transporters), member 3 27 231324 at HSS343SO SWI/SNF related, matrix associated, actin dependent regulator of chromatin, Subfamily b, member 1 28 215416 s at HS.3439 stomatin (EPB72)-like 2 29 206116 s at S.133892 tropomyosin 1 (alpha) 30 224.51.1 s at S.408236 thioredoxin-like 5 thioredoxin-like 5 31 201266 at S.337766 thioredoxin reductase 1 32 243160 at S.363396 Complement factor H C 33 218218 at S.S.O6603 DIP13 beta DIP13B 34 221942 s at S.24258 guanylate cyclase 1, soluble, alpha 3 GUCY1A3 35 232169 X at S.90443 NADH dehydrogenase (ubiquinone) Fe—S protein 8, 23 kDa (NADH-coenzyme Q NDUFS8 reductase) 36 205190 at S.2O3637 plastin 1 (1 isoform) PLS1 37 202429 s at S.435512 protein phosphatase 3 (formerly 2B), catalytic Subunit, alpha isoform PPP3CA (calcineurin A alpha) 38 1555340 x at HS.190334 RAP1A, member of RAS oncogene family RAP1A 39 1569073 x at HS.327S27 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, SMARCA4 Subfamily a member 4 40 212577 at HS.8118 structural maintenance of chromosomes flexible hinge domain containing 1 SMCHD1 US 2012/0178642 A1 Jul. 12, 2012 46

TABLE 5

Protein Transcript Matches of 545 moderatefsevere CAN Data Set 1 genes

Probe Set ID UniGene ID Gene Title Gene Symbol

1 223598 at Hs.521640 RAD23 homolog B (S. cerevisiae) RAD23B 2 208000 at HS.86161 GPI anchored molecule like protein GML 3 1557724 a at Hs.407190 hypothetical protein LOC285847 LOC285847 4 236356 at Hs.471207 NADH dehydrogenase (ubiquinone) Fe—S protein 1, 75 kDa (NADH-coenzyme Q NDUFS1 reductase) 5 238688 at Hs. 133892 Tropomyosin 1 (alpha) TPM1 6 218090 s. at Hs.144447 bromodomain and WD repeat domain containing 2 BRWD2 7 200898 s at Hs.500842 meningioma expressed antigen 5 (hyaluronidase) MGEAS 8 201569 s at Hs.505824 sorting and assembly machinery component 50 homolog (S. cerevisiae) SAMMSO 9 1560854 S at Hs.50216 Zinc finger protein 588 ZNF588

TABLE 6 Protein Transcript Matches of 172 moderate/Severe CAN DataSet 2 genes Probe Set ID UniGene ID Gene Title Gene Symbol 1 216251 s at Hs.517670 KIAAO153 protein KIAAO153 2 204959 at Hs. 153837 myeloid cell nuclear differentiation antigen if myeloid cell nuclear MINDA differentiation antigen 3 2.2777O at Hs. 128420 Vacuolar protein sorting 4A (yeast) VPS4A 4 231324 at HSS343SO SWI/SNF related, matrix associated, actin dependent regulator of chromatin, SMARCB1 Subfamily b, member 1 5, 209029 at Hs.530823 COP9 constitutive photomorphogenic homolog subunit 7A (Arabidopsis) COPS7A 6 218326 s at Hs.502176 leucine-rich repeat-containing G protein-coupled receptor 4 LGR4 7 1568619 s at Hs.53O899 Hypothetical protein LOC162073 LOC162O73 8 204994 at HS.926 myxovirus (influenza virus) resistance 2 (mouse) MX2 9 205325 at Hs.334688 phytanoyl-CoA hydroxylase interacting protein PHYHIP

What is claimed is: 6. The method of claim 3, wherein step (b) further com 1. A method of prognosing, diagnosing or monitoring prises, combining the values or designations for each of the chronic allograft nephropathy and/or interstitial fibrosis and genes to provide a combined value or designation providing tubular atrophy (CAN/IFTA), comprising an indication whether the subject has or is at risk of CAN/ (a) determining expression levels in a Subject of at least 5 IFTA. genes selected from the genes in Table A, B, C, D, E, F, 7. The method of claim 6, wherein the method is repeated G, H, I and/or J.; and at different times on the subject. (b) prognosing, diagnosing or monitoring CAN/IFTA in a 8. The method of claim 6, wherein the subject is receiving subject from the expression levels. a drug, and a change in the combined value or designation 2. The method of claim 1, wherein for each of the at least over time provides an indication of the effectiveness of the five genes, step (b) comprises comparing the expression level drug. of the gene in the Subject to one or more reference expression 9. The method of claim 1, wherein the subject has under levels of the gene associated with CAN/IFTA or lack of gone a kidney transplant within 1-10years of performing step CANAIFTA. (a). 3. The method of claim 2, wherein step (b) further com 10. The method of claim 1, wherein step (a) is performed prises for each of the at least five genes assigning the expres on a blood sample of the subject. sion level of the gene in the Subject a value or other designa 11-25. (canceled) tion providing an indication whether the Subject has or is at 26. An array, comprising a Support or Supports bearing a risk of CANAIFTA. plurality of nucleic acid probes complementary to a plurality 4. The method of claim 3, wherein the expression level of of mRNAs fewer than 5000 in number, wherein the plurality each of the at least five genes is assigned a value on a nor of mRNAs includes mRNAs expressed by at least five genes malized scale of values associated with a range of expression selected from Table A, B, C, D. levels in kidney transplant patients with and without CAN/ 27-28. (canceled) IFTA. 29. The array of claim 26, wherein the plurality of nucleic 5. The method of claim 3, wherein the expression level of acid probes are attached to a planar Support. each of the at least five genes is assigned a value or other 30. The array of claim 26, wherein the plurality of nucleic designation providing an indication that the Subject has is at acid probes are attached to beads. risk of CAN/IFTA, lacks and is not at risk of CAN/IFTA, or 31. The array of claim 26, wherein the at least five genes are that the expression level is uninformative. selected from Table C and D US 2012/0178642 A1 Jul. 12, 2012 47

32. The array of claim 26, wherein the at least five genes are 35-38. (canceled) selected from Table C. 39. The array of claim 34 wherein the at least five proteins 33. The array of claim 26, wherein the at least five genes are are selected from Tables E and F and/or I and J. Selected from Table D. 40. The array of claim 34 wherein the ligands are different 34. An array, comprising a Support or Supports bearing a antibodies, wherein the different antibodies bind to different plurality of ligands that specifically bind to a plurality of proteins of the plurality of proteins. proteins fewer than 5000 in number, wherein the plurality of 41-82. (canceled) proteins includes at least five proteins selected from Table E. F, G, H, I and/or J.