US 2011 013.6683A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2011/013.6683 A1 DaVicioni (43) Pub. Date: Jun. 9, 2011 (54) SYSTEMS AND METHODS FOR Publication Classification EXPRESSION-BASED DISCRIMINATION OF DISTINCT CLINICAL DISEASE STATES IN (51) Int. Cl. PROSTATE CANCER C40B 30/04 (2006.01) C40B 40/06 (2006.01) C4DB 60/2 (2006.01) (75) Inventor: Elai Davicioni, Vancouver (CA) (52) U.S. Cl. .................................. 506/7:506/16:506/39 (73) Assignee: GENOMEDX BIOSCIENCES, (57) ABSTRACT INC., Vancouver, BC (CA) A system for expression-based discrimination of distinct (21) Appl. No.: 12/994,408 clinical disease states in prostate cancer is provided that is based on the identification of sets of gene transcripts, which are characterized in that changes in expression of each gene (22) PCT Fled: May 28, 2009 transcript within a set of gene transcripts can be correlated with recurrent or non-recurrent prostate cancer. The Prostate (86) PCT NO.: PCTACA2O09/OOO694 Cancer Prognostic system provides for sets of “prostate can cer prognostic' target sequences and further provides for S371 (c)(1), combinations of polynucleotide probes and primers derived (2), (4) Date: Feb. 17, 2011 there from. These combinations of polynucleotide probes can be provided in solution or as an array. The combination of Related U.S. Application Data probes and the arrays can be used for diagnosis. The invention (60) Provisional application No. 61/056,827, filed on May further provides further methods of classifying prostate can 28, 2008. certissue. P. O Patent Application Publication Jun. 9, 2011 Sheet 1 of 9 US 2011/O136683 A1 P. O Figure 1A Patent Application Publication Jun. 9, 2011 Sheet 2 of 9 US 2011/O136683 A1 SYS PSA NED & 8: & XXX XXX & SSSSSSSXX: Figure 1B Patent Application Publication Jun. 9, 2011 Sheet 3 of 9 US 2011/O136683 A1 Recurrent Non-Recurrent &S Figure 1C Patent Application Publication Jun. 9, 2011 Sheet 4 of 9 US 2011/O136683 A1 526 RNA Metagene Mean it SD - 47 510 + 28 868 - 57 Metagene Value p-0.00001 Figure 2 Patent Application Publication Jun. 9, 2011 Sheet 5 of 9 US 2011/O136683 A1 A 0. -. i. a. a. i {G8 G8 g NED PSA SYS Figure 3 Patent Application Publication Jun. 9, 2011 Sheet 6 of 9 US 2011/O136683 A1 18-RNA POP Scores OO 90 S&S 80 70 60 50 40 30 20 10 NED PSA SYS Clinical Status Figure 4 Patent Application Publication Jun. 9, 2011 Sheet 7 of 9 US 2011/O136683 A1 1O-RNA POP Scores OO 90 - 80 9 60 - c d of 50 40 - 30 2O I 10 -- NED PSA SYS Clinical Status Figure 5 Patent Application Publication Jun. 9, 2011 Sheet 8 of 9 US 2011/O136683 A1 41-RNA POP Scores OO 90 8O 70 60 50 40 3O 2O s to a O NED PSA SYS Clinical Status Figure 6 Patent Application Publication Jun. 9, 2011 Sheet 9 of 9 US 2011/O136683 A1 148-RNA POP Scores OO 90 8O 70 8& 60 50 40 30 2O O NED PSA SYS Clinical Status Figure 7 US 2011/013.6683 A1 Jun. 9, 2011 SYSTEMS AND METHODS FOR ment. The limitations of using the PSA biomarker and the EXPRESSION-BASED DISCRIMINATION OF absence of additional biomarkers for predicting disease DISTINCT CLINICAL DISEASE STATES IN recurrence have led to the development of statistical models PROSTATE CANCER combining several clinical and pathological features includ ing PSA results. Several of these nomograms have been CROSS-REFERENCE TO RELATED shown to improve the predictive powerfor disease recurrence APPLICATIONS in individual patients over any single independent variable. 0001. This application is a continuation of Application These models (see Citation #14) are used routinely in the No. PCT/CA2009/000694 filed May 28, 2009, now pending, clinic and are currently the best available tools for prediction which claims priority benefit of U.S. Provisional Application of outcomes, although they do not provide high levels of No. 61/056,827, filed May 28, 2008, the entire contents both accuracy for groups of patients with highly similar histologi of which are incorporated herein by reference. cal/pathological features or those at intermediate risk of disease recurrence after prostatectomy. FIELD OF THE INVENTION 0007. The use of quantitative molecular analyses has the 0002 This invention relates to the field of diagnostics and potential to increase the sensitivity, specificity and/or overall in particular to systems and methods for classifying prostate accuracy of disease prognosis and provide a more objective cancer into distinct clinical disease states. basis for determination of risk stratification as compared to conventional clinical-pathological risk models (see Citation BACKGROUND #13). The PSA test demonstrates the deficiencies of relying 0003 Prostate cancer is the most common malignancy on the measurement of any single biomarker in clinically affecting U.S. men, with approximately 240,000 new cases heterogeneous and complex prostate cancer genomes. There diagnosed each year. The incidence of prostate cancer is fore, genomic-based approaches measuring combinations of increasing, in part due to increased Surveillance efforts from biomarkers or a signature of disease recurrence are currently the application of routine molecular testing Such as prostate being investigated as better Surrogates for predicting disease specific antigen (PSA). For most men, prostate cancer is a outcome (see Citations # 1-13). For prostate cancer patients slow-growing, organ-confined or localized malignancy that these efforts are aimed at reducing the number of unnecessary poses little risk of death. The most common treatments for Surgeries for patients without progressive disease and avoid prostate cancer in the U.S. are surgical procedures such as inadvertent under-treatment for higher risk patients. To date, radical prostatectomy, where the entire prostate is removed genomic profiling efforts to identify DNA-based (e.g., copy from the patient. This procedure on its own is highly curative number alterations, methylation changes), RNA-based (e.g., for most but not all men. gene or non-coding RNA expression) or protein-based (e.g., 0004. The vast majority of deaths from prostate cancer protein expression or modification) signatures, useful for dis occur in patients with metastasis, believed to be present ease prognosis have not however resulted in widespread clini already at the time of diagnosis in the form of clinically cal use. undetectable micro-metastases. In these patients, it is clear 0008. There are several key reasons explaining why prior that prostatectomy alone is not curative and additional thera genomic profiling methods for prostate cancer have not yet pies such as anti-androgen or radiation therapy are required to been incorporated in the clinic. These include the small control the spread of disease and extend the life of the patient. sample sizes typical of individual studies, coupled with varia 0005 Most prostatectomy patients however face uncer tions due to differences in study protocols, clinical heteroge tainty with respect to their prognosis after Surgery: whether or neity of patients and lack of external validation data, which not the initial surgery will be curative several years from the combined have made identifying a robust and reproducible initial treatment because the current methods for assessment disease signature elusive. Specifically for gene or RNA of the clinical risk Such as the various pathological (e.g., expression based prognostic models; the mitigating techno tumor stage), histological (e.g., Gleason's), clinical (e.g., logical limitations include the quality and quantity of RNA Kattan nomogram) and molecular biomarkers (e.g., PSA) are that can be isolated from routine clinical samples. Routine not reliable predictors of prognosis, specifically disease pro clinical samples of prostate cancer include needle-biopsies gression. Routine PSA testing has certainly increased Surveil and Surgical resections that have been fixed in formalin and lance and early-detection rates of prostate cancer and this has embedded in paraffin wax (FFPE). FFPE-derived RNA is resulted in an increased number of patients being treated but typically degraded and fragmented to between 100-300 bp in not significantly decreased the mortality rate. size and without poly-A tails making it of little use for tradi 0006. Despite the controversies surrounding PSA testing tional 3'-biased gene expression profiling, which requires as a screening tool, most physicians confidently rely on PSA larger microgram quantities of RNA with intact poly-A tails testing to assess pre-treatment prognosis and to monitor dis to prime clNA synthesis. ease progression after initial therapy. Successive increases in 0009 Furthermore, as <2% of the genome encodes for PSA levels above a defined threshold value or variations protein, traditional gene expression profiling in fact captures thereof (i.e. Rising-PSA), also known as biochemical recur only a small fraction of the transcriptome and variation in rence has been shown to be correlated to disease progression expression as most RNA molecules that are transcribed are after first-line therapy (e.g., prostatectomy, radiation and not translated into protein but serve other functional roles and brachytherapy). However, less than a /3 of patients with ris non-coding RNAS are the most abundant transcript species in ing-PSA will eventually be diagnosed with systemic or meta the genome. static disease and several studies have shown that after long 0010. This background information is provided for the term follow up, the majority will never show any symptoms of purpose of making known information believed by the appli disease progression aside from increases in PSA measure cant to be of possible relevance to the present invention. No US 2011/013.6683 A1 Jun. 9, 2011 admission is necessarily intended, nor should be construed, means for correlating the expression level with a classifica that any of the preceding information constitutes prior art tion of prostate cancer status; and means for outputting the against the present invention.