DOCSLIB.ORG

The Association of Single Nucleotide Polymorphisms in Intronic Regions of Islet Cell Autoantigen 1 and Type 1 Diabetes Mellitus

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
The Association of Single Nucleotide Polymorphisms in Intronic Regions of Islet Cell Autoantigen 1 and Type 1 Diabetes Mellitus THE ASSOCIATION OF SINGLE NUCLEOTIDE POLYMORPHISMS IN INTRONIC REGIONS OF ISLET CELL AUTOANTIGEN 1 AND TYPE 1 DIABETES MELLITUS by Carrie Lynn Blout B.S., Dickinson College, 2004 Submitted to the Graduate Faculty of Department of Human Genetics – Genetic Counseling the University of Pittsburgh in partial fulfillment of the requirements for the degree of Masters of Science University of Pittsburgh 2006 UNIVERSITY OF PITTSBURGH THE GRADUATE SCHOOL OF PUBLIC HEALTH This thesis was presented by Carrie Lynn Blout It was defended on March 30, 2006 and approved by Committee Member: Elizabeth Gettig, MS, CGC Associate Professor of Human Genetics Director, Genetic Counseling Program Graduate School of Public Health University of Pittsburgh Committee Member: John W. Wilson, PhD Assistant Professor Department of Biostatistics Graduate School of Public Health University of Pittsburgh Committee Member: Michael M. Barmada, Ph.D. Associate Professor of Human Genetics Director, Human Genetics Department Computational Resources Division Graduate School of Public Health University of Pittsburgh Thesis Advisor: Massimo Pietropaolo, M.D. University of Pittsburgh Physicians Faculty UPMC Department of Pediatrics Rangos Research Center Genetic Immunology University of Pittsburgh ii THE ASSOCIATION OF SINGLE NUCLEOTIDE POLYMORPHISMS, LOCATED WITHIN INTRONIC REGIONS OF ISLET CELL AUTOANTIGEN 1 AND TYPE 1 DIABETES MELLITUS Carrie L. Blout, M.S. University of Pittsburgh, 2006 Type 1 diabetes mellitus is a multifactorial autoimmune disease caused by a combination of genetic and environmental factors. Further knowledge and understanding about the genes which play a role in type 1 diabetes has a clear public health significance in that it will aid in the prediction, treatment and a possible cure. Type 1 diabetes is a chronic disease with a lengthy preclinical course, which eventually results in pancreatic beta cell destruction and inability of the body to produce insulin hormone. Type 1 diabetic patients generally require exogenous insulin to survive. Several genetic loci have been proposed to be linked to type 1 diabetes; however, the HLA and VNTR regions are currently believed to account for the majority of genetic risk, contributing to about 42% and 10% of an individual’s risk to develop type 1 diabetes, respectively. This study focuses on the candidate gene Islet Cell Autoantigen 1 (ICA1), which codes for the protein ICA69. This protein product is expressed in the islets of Langerhans, the neuroendocrine system and in the thymic medulla; this last location is an area of the body known to play a major role in immunologic tolerance. Preliminary studies in the NOD and B6 mouse models suggest that a SNP within the promoter region of Ica1 affects transcription and may account for altered expression in the thymus. Our current study aimed to determine whether single nucleotide polymorphisms within intronic regions of the human ICA1 gene differed between a diabetic case population and non-diabetic controls. It was hypothesized that SNPs within the ICA1 gene differ between cases and controls and play a role in the onset of type 1 diabetes. Polymerase Chain Reaction (PCR) was applied for DNA amplification and the pyrosequencing technique was used to genotype all samples. At SNP location rs2058519 there was a clear genotypic difference between the cases and controls (p= .0003). These results suggest that genetic variation at this specific SNP location in the ICA1 may be associated with type 1 diabetes susceptibility. The ultimate goal of this study is to determine whether our candidate gene ICA1 appears to play a role in the pathogenesis of type 1 diabetes. iii TABLE OF CONTENTS ACKNOWLEDGEMENTS .......................................................................................................IX 1.0 INTRODUCTION........................................................................................................ 1 1.1 PURPOSE OF THE STUDY .............................................................................. 1 2.0 BACKGROUND AND SIGNIFICANCE .................................................................. 2 2.1 DIABETES OVERVIEW ................................................................................... 2 2.2 ENVIRONMENTAL FACTORS....................................................................... 3 2.3 PHYSIOLOGY .................................................................................................... 4 2.4 GENETIC SUSCEPTIBILITY .......................................................................... 5 2.5 ROLE OF THE HLA COMPLEX..................................................................... 8 2.6 ROLE OF THE INSULIN GENE.................................................................... 11 2.7 IMMUNE SYSTEM .......................................................................................... 12 2.8 AUTOANTIBODIES......................................................................................... 15 2.9 CANDIDATE GENE APPROACH ................................................................. 16 2.10 ISLET CELL AUTOANTIGEN 69KDA (ICA69).......................................... 18 2.11 THE PYROSEQUENCING METHOD .......................................................... 20 2.12 SPECIFIC AIMS ............................................................................................... 22 3.0 MATERIALS AND METHODS .............................................................................. 23 3.1 STUDY POPULATION .................................................................................... 23 3.2 SNP IDENTIFICATION................................................................................... 24 3.3 PRIMER DESIGN AND TESTING ................................................................ 25 3.4 SNP LOCATIONS............................................................................................. 27 3.5 PCR AMPLIFICATION FOR SEQUENCING PRODUCTS ...................... 28 3.6 DNA SEQUENCING AND GENOTYPE DETERMINATION.................... 30 3.7 STATISTICAL METHODS............................................................................. 34 iv 4.0 RESULTS ................................................................................................................... 36 4.1 GENOTYPE COMPARISON AT THREE SNP LOCI................................. 36 T4.2 HWE ANALYSIS OF GENOTYPING DATA ............................................... 41 5.0 DISCUSSION ............................................................................................................. 42 5.1 SNP SIGNIFICANCE ....................................................................................... 42 5.2 POSSIBLE FUNCTIONAL RELATIONSHIP OF AN INTRONIC POLYMORPHISM ............................................................................................................ 42 5.3 IDEAL SAMPLE SIZE..................................................................................... 43 5.4 FUTURE STUDIES/APPROACH................................................................... 44 5.5 GENOTYPING TROUBLE SHOOTING....................................................... 45 5.6 OTHER POSSIBLE TECHNIQUES............................................................... 46 5.7 SUMMARY........................................................................................................ 46 BIBLIOGRAPHY....................................................................................................................... 48 v LIST OF TABLES Table 1. Empiric risks of type 1 diabetes. These estimates are for North American Caucasian* and Scandinavian populations** , ‡ 1-15% range depending on the populations (10-15)............. 6 Table 2. ICA1 SNPs considered to be ‘true’ which were previously validated or found in multiple databases......................................................................................................................... 24 Table 3. ICA1 SNPs which were not used in this study because they were not previously validated and were identified in only a single database................................................................ 24 Table 4. SNP locations within the ICA1 gene. ............................................................................. 25 Table 5. PCR and Sequencing Primers for each SNP.................................................................. 30 Table 6. Pyrosequencing Assay Information…………………………………………………….32 Table 7. Genotype data for rs3807830 in diabetics and controls.................................................. 36 Table 8. Genotype data for rs2348895 in diabetics and controls.................................................. 36 Table 9. Genotype data for rs2058519 in diabetics and controls.................................................. 37 Table 10. Comparison of original diabetic samples versus additional diabetic samples for SNP rs3807830...................................................................................................................................... 37 Table 11. Comparison of original diabetic samples versus additional diabetic samples for SNP rs2348895...................................................................................................................................... 37 Table 12. Comparison of original diabetic samples versus additional diabetic samples for SNP rs2058519...................................................................................................................................... 38 Table 13. 3x2 Table
Load more

Recommended publications
  • Comparative Genome Mapping in the Sequence-Based Era: Early Experience with Human Chromosome 7
    Downloaded from genome.cshlp.org on May 28, 2019 - Published by Cold Spring Harbor Laboratory Press First Glimpses/Report Comparative Genome Mapping in the Sequence-based Era: Early Experience with Human Chromosome 7 James W. Thomas,1 Tyrone J. Summers,1 Shih-Queen Lee-Lin,1 Valerie V. Braden Maduro,1 Jacquelyn R. Idol,1 Stephen D. Mastrian,1 Joseph F. Ryan,1 D. Curtis Jamison,1 and Eric D. Green1,2 1Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892 USA The success of the ongoing Human Genome Project has resulted in accelerated plans for completing the human genome sequence and the earlier-than-anticipated initiation of efforts to sequence the mouse genome. As a complement to these efforts, we are utilizing the available human sequence to refine human-mouse comparative maps and to assemble sequence-ready mouse physical maps. Here we describe how the first glimpses of genomic sequence from human chromosome 7 are directly facilitating these activities. Specifically, we are actively enhancing the available human-mouse comparative map by analyzing human chromosome 7 sequence for the presence of orthologs of mapped mouse genes. Such orthologs can then be precisely positioned relative to mapped human STSs and other genes. The chromosome 7 sequence generated to date has allowed us to more than double the number of genes that can be placed on the comparative map. The latter effort reveals that human chromosome 7 is represented by at least 20 orthologous segments of DNA in the mouse genome. A second component of our program involves systematically analyzing the evolving human chromosome 7 sequence for the presence of matching mouse genes and expressed-sequence tags (ESTs).
    [Show full text]
  • Meta-Analysis of Gene Signatures and Key Pathways Indicates
    www.nature.com/scientificreports OPEN Meta‑analysis of gene signatures and key pathways indicates suppression of JNK pathway as a regulator of chemo‑resistance in AML Parastoo Modarres1, Farzaneh Mohamadi Farsani1,3, Amir Abas Nekouie2 & Sadeq Vallian1* The pathways and robust deregulated gene signatures involved in AML chemo‑resistance are not fully understood. Multiple subgroups of AMLs which are under treatment of various regimens seem to have similar regulatory gene(s) or pathway(s) related to their chemo‑resistance phenotype. In this study using gene set enrichment approach, deregulated genes and pathways associated with relapse after chemotherapy were investigated in AML samples. Five AML libraries compiled from GEO and ArrayExpress repositories were used to identify signifcantly diferentially expressed genes between chemo‑resistance and chemo‑sensitive groups. Functional and pathway enrichment analysis of diferentially expressed genes was performed to assess molecular mechanisms related to AML chemotherapeutic resistance. A total of 34 genes selected to be diferentially expressed in the chemo‑ resistance compared to the chemo‑sensitive group. Among the genes selected, c-Jun, AKT3, ARAP3, GABBR1, PELI2 and SORT1 are involved in neurotrophin, estrogen, cAMP and Toll‑like receptor signaling pathways. All these pathways are located upstream and regulate JNK signaling pathway which functions as a key regulator of cellular apoptosis. Our expression data are in favor of suppression of JNK pathway, which could induce pro‑apoptotic gene expression as well as down regulation of survival factors, introducing this pathway as a key regulator of drug‑resistance development in AML. Acute myeloid leukemia (AML) is one of the most aggressive, life-threatening hematological malignancies char- acterized by uncontrolled proliferation of abnormal diferentiated and nonfunctional myeloid precursor cells1.
    [Show full text]
  • 393LN V 393P 344SQ V 393P Probe Set Entrez Gene
    393LN v 393P 344SQ v 393P Entrez fold fold probe set Gene Gene Symbol Gene cluster Gene Title p-value change p-value change chemokine (C-C motif) ligand 21b /// chemokine (C-C motif) ligand 21a /// chemokine (C-C motif) ligand 21c 1419426_s_at 18829 /// Ccl21b /// Ccl2 1 - up 393 LN only (leucine) 0.0047 9.199837 0.45212 6.847887 nuclear factor of activated T-cells, cytoplasmic, calcineurin- 1447085_s_at 18018 Nfatc1 1 - up 393 LN only dependent 1 0.009048 12.065 0.13718 4.81 RIKEN cDNA 1453647_at 78668 9530059J11Rik1 - up 393 LN only 9530059J11 gene 0.002208 5.482897 0.27642 3.45171 transient receptor potential cation channel, subfamily 1457164_at 277328 Trpa1 1 - up 393 LN only A, member 1 0.000111 9.180344 0.01771 3.048114 regulating synaptic membrane 1422809_at 116838 Rims2 1 - up 393 LN only exocytosis 2 0.001891 8.560424 0.13159 2.980501 glial cell line derived neurotrophic factor family receptor alpha 1433716_x_at 14586 Gfra2 1 - up 393 LN only 2 0.006868 30.88736 0.01066 2.811211 1446936_at --- --- 1 - up 393 LN only --- 0.007695 6.373955 0.11733 2.480287 zinc finger protein 1438742_at 320683 Zfp629 1 - up 393 LN only 629 0.002644 5.231855 0.38124 2.377016 phospholipase A2, 1426019_at 18786 Plaa 1 - up 393 LN only activating protein 0.008657 6.2364 0.12336 2.262117 1445314_at 14009 Etv1 1 - up 393 LN only ets variant gene 1 0.007224 3.643646 0.36434 2.01989 ciliary rootlet coiled- 1427338_at 230872 Crocc 1 - up 393 LN only coil, rootletin 0.002482 7.783242 0.49977 1.794171 expressed sequence 1436585_at 99463 BB182297 1 - up 393
    [Show full text]
  • Dissecting the Genetic Etiology of Lupus at ETS1 Locus
    Dissecting the Genetic Etiology of Lupus at ETS1 Locus A dissertation submitted to the Graduate School of the University of Cincinnati in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Immunobiology of the College of Medicine 2017 by Xiaoming Lu B.S. Sun Yat-sen University, P.R. China June 2011 Dissertation Committee: John B. Harley, MD, PhD Harinder Singh, PhD Leah C. Kottyan, PhD Matthew T. Weirauch, PhD Kasper Hoebe, PhD Lili Ding, PhD i Abstract Systemic lupus erythematosus (SLE) is a complex autoimmune disease with strong evidence for genetics factor involvement. Genome-wide association studies have identified 84 risk loci associated with SLE. However, the specific genotype-dependent (allelic) molecular mechanisms connecting these lupus-genetic risk loci to immunological dysregulation are mostly still unidentified. ~ 90% of these loci contain variants that are non-coding, and are thus likely to act by impacting subtle, comparatively hard to predict mechanisms controlling gene expression. Here, we developed a strategic approach to prioritize non-coding variants, and screen them for their function. This approach involves computational prioritization using functional genomic databases followed by experimental analysis of differential binding of transcription factors (TFs) to risk and non-risk alleles. For both electrophoretic mobility shift assay (EMSA) and DNA affinity precipitation assay (DAPA) analysis of genetic variants, a synthetic DNA oligonucleotide (oligo) is used to identify factors in the nuclear lysate of disease or phenotype-relevant cells. This strategic approach was then used for investigating SLE association at ETS1 locus. Genetic variants at chromosomal region 11q23.3, near the gene ETS1, have been associated with systemic lupus erythematosus (SLE), or lupus, in independent cohorts of Asian ancestry.
    [Show full text]
  • Aire-Deficient C57BL/6 Mice Mimicking the Common Human 13-Base Pair Deletion Mutation Present with Only a Mild Autoimmune Phenotype
    Aire-Deficient C57BL/6 Mice Mimicking the Common Human 13-Base Pair Deletion Mutation Present with Only a Mild Autoimmune Phenotype This information is current as of September 30, 2021. François-Xavier Hubert, Sarah A. Kinkel, Pauline E. Crewther, Ping Z. F. Cannon, Kylie E. Webster, Maire Link, Raivo Uibo, Moira K. O'Bryan, Anthony Meager, Simon P. Forehan, Gordon K. Smyth, Lauréane Mittaz, Stylianos E. Antonarakis, Pärt Peterson, William R. Heath and Hamish S. Scott Downloaded from J Immunol 2009; 182:3902-3918; ; doi: 10.4049/jimmunol.0802124 http://www.jimmunol.org/content/182/6/3902 http://www.jimmunol.org/ References This article cites 67 articles, 27 of which you can access for free at: http://www.jimmunol.org/content/182/6/3902.full#ref-list-1 Why The JI? Submit online. by guest on September 30, 2021 • Rapid Reviews! 30 days* from submission to initial decision • No Triage! Every submission reviewed by practicing scientists • Fast Publication! 4 weeks from acceptance to publication *average Subscription Information about subscribing to The Journal of Immunology is online at: http://jimmunol.org/subscription Permissions Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Email Alerts Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts The Journal of Immunology is published twice each month by The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2009 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. The Journal of Immunology Aire-Deficient C57BL/6 Mice Mimicking the Common Human 13-Base Pair Deletion Mutation Present with Only a Mild Autoimmune Phenotype1 Franc¸ois-Xavier Hubert,2* Sarah A.
    [Show full text]
  • Mouse Ica1 Conditional Knockout Project (CRISPR/Cas9)
    https://www.alphaknockout.com Mouse Ica1 Conditional Knockout Project (CRISPR/Cas9) Objective: To create a Ica1 conditional knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Ica1 gene (NCBI Reference Sequence: NM_010492 ; Ensembl: ENSMUSG00000062995 ) is located on Mouse chromosome 6. 14 exons are identified, with the ATG start codon in exon 2 and the TGA stop codon in exon 14 (Transcript: ENSMUST00000038403). Exon 3 will be selected as conditional knockout region (cKO region). Deletion of this region should result in the loss of function of the Mouse Ica1 gene. To engineer the targeting vector, homologous arms and cKO region will be generated by PCR using BAC clone RP23-82N21 as template. Cas9, gRNA and targeting vector will be co-injected into fertilized eggs for cKO Mouse production. The pups will be genotyped by PCR followed by sequencing analysis. Note: Homozygous mutation of this gene results in diabetes and spontaneous lethality at 4-5 months of age on a NOD background, however mice on a 129/Sv background are normal. Onset of diabetes starts 4 weeks later than wild-typeNOD mice and mutants are resistant to cyclophospamide-accelerated diabetes. Exon 3 starts from about 1.26% of the coding region. The knockout of Exon 3 will result in frameshift of the gene. The size of intron 2 for 5'-loxP site insertion: 3614 bp, and the size of intron 3 for 3'-loxP site insertion: 4821 bp. The size of effective cKO region: ~663 bp. The cKO region does not have any other known gene. Page 1 of 8 https://www.alphaknockout.com Overview of the Targeting Strategy Wildtype allele gRNA region 5' gRNA region 3' 1 3 14 Targeting vector Targeted allele Constitutive KO allele (After Cre recombination) Legends Exon of mouse Ica1 Homology arm cKO region loxP site Page 2 of 8 https://www.alphaknockout.com Overview of the Dot Plot Window size: 10 bp Forward Reverse Complement Sequence 12 Note: The sequence of homologous arms and cKO region is aligned with itself to determine if there are tandem repeats.
    [Show full text]
  • Milger Et Al. Pulmonary CCR2+CD4+ T Cells Are Immune Regulatory And
    Milger et al. Pulmonary CCR2+CD4+ T cells are immune regulatory and attenuate lung fibrosis development Supplemental Table S1 List of significantly regulated mRNAs between CCR2+ and CCR2- CD4+ Tcells on Affymetrix Mouse Gene ST 1.0 array. Genewise testing for differential expression by limma t-test and Benjamini-Hochberg multiple testing correction (FDR < 10%). Ratio, significant FDR<10% Probeset Gene symbol or ID Gene Title Entrez rawp BH (1680) 10590631 Ccr2 chemokine (C-C motif) receptor 2 12772 3.27E-09 1.33E-05 9.72 10547590 Klrg1 killer cell lectin-like receptor subfamily G, member 1 50928 1.17E-07 1.23E-04 6.57 10450154 H2-Aa histocompatibility 2, class II antigen A, alpha 14960 2.83E-07 1.71E-04 6.31 10590628 Ccr3 chemokine (C-C motif) receptor 3 12771 1.46E-07 1.30E-04 5.93 10519983 Fgl2 fibrinogen-like protein 2 14190 9.18E-08 1.09E-04 5.49 10349603 Il10 interleukin 10 16153 7.67E-06 1.29E-03 5.28 10590635 Ccr5 chemokine (C-C motif) receptor 5 /// chemokine (C-C motif) receptor 2 12774 5.64E-08 7.64E-05 5.02 10598013 Ccr5 chemokine (C-C motif) receptor 5 /// chemokine (C-C motif) receptor 2 12774 5.64E-08 7.64E-05 5.02 10475517 AA467197 expressed sequence AA467197 /// microRNA 147 433470 7.32E-04 2.68E-02 4.96 10503098 Lyn Yamaguchi sarcoma viral (v-yes-1) oncogene homolog 17096 3.98E-08 6.65E-05 4.89 10345791 Il1rl1 interleukin 1 receptor-like 1 17082 6.25E-08 8.08E-05 4.78 10580077 Rln3 relaxin 3 212108 7.77E-04 2.81E-02 4.77 10523156 Cxcl2 chemokine (C-X-C motif) ligand 2 20310 6.00E-04 2.35E-02 4.55 10456005 Cd74 CD74 antigen
    [Show full text]
  • Answer Key Genomic Medicine and Sequencing Tools
    Genomics Exam 1 Key Fall, 2003 Fall 2003 Genomics Exam #1 Answer Key Genomic Medicine and Sequencing Tools There is no time limit on this test, though I have tried to design one that you should be able to complete within 4 hours, except for typing and web searches. There are three pages for this test, including this cover sheet. You are not allowed discuss the test with anyone until all exams are turned in at 11:30 am on Wednesday October 1. EXAMS ARE DUE AT CLASS TIME ON WEDNESDAY OCTOBER 1. You may use a calculator, a ruler, your notes, the book and the internet. I have to say, this is a challenging test, so do NOT put it off too long. You may take it in as many blocks of time as you need to. The answers to the questions must be typed on a separate sheet of paper unless the question specifically says to write the answer in the space provided. If you do not write your answers in the appropriate location, I may not find them. You will need to capture screen images as a part of your answers which you may do without seeking permission since your test answers will not be in the public domain. If you are asked to print out any pages, you do not have to print in color, though it is permitted. -3 pts if you do not follow this direction. Please do not write or type your name on any page other than this cover page. Staple all your pages (INCLUDING THE TEST PAGES) together when finished with the exam.
    [Show full text]
  • Research Article in Silico Xpressed E Uence Tag
    Hindawi Publishing Corporation BioMed Research International Volume 2013, Article ID 704818, 9 pages http://dx.doi.org/10.1155/2013/704818 Research Article In Silico �xpressed �e�uence Tag Analysis in Identi�cation o� Probable Diabetic Genes as Virtual Therapeutic Targets Pabitra Mohan Behera,1 Deepak Kumar Behera,2 Aparajeya Panda,2 Anshuman Dixit,3 and Payodhar Padhi2 1 Centre of Biotechnology, Siksha O Anusandhan University, Bhubaneswar, Odisha 751030, India 2 Hi-TechResearchandDevelopmentCentre,KonarkInstituteofScienceandTechnology,TechnoPark,Jatni, Bhubaneswar, Odisha 752050, India 3 DepartmentofTranslationalResearchandTechnologyDevelopment,InstituteofLifeSciences,NalcoSquare, Bhubaneswar, Odisha 751023, India Correspondence should be addressed to Payodhar Padhi; [email protected] Received 25 September 2012; Revised 12 December 2012; Accepted 17 December 2012 Academic Editor: Ying Xu Copyright © 2013 Pabitra Mohan Behera et al. is is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. e expressed sequence tags (ESTs) are major entities for gene discovery, molecular transcripts, and single nucleotide polymorphism (SNPs) analysis as well as functional annotation of putative gene products. In our quest for identi�cation of novel diabetic genes as virtual targets for type II diabetes, we searched various publicly available databases and found 7 reported genes. e in silico EST analysis of these reported genes produced 6 consensus contigs which illustrated some good matches to a number of chromosomes of the human genome. Again the conceptual translation of these contigs produced 3 protein sequences. e functional and structural annotations of these proteins revealed some important features which may lead to the discovery of novel therapeutic targets for the treatment of diabetes.
    [Show full text]
  • Active Module Discovery: Integrated Approaches of Gene Co-Expression and PPI Networks and Microrna Data
    Active Module Discovery: Integrated Approaches of Gene Co-Expression and PPI Networks and MicroRNA Data Dissertation Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Ayat Hatem, M.Sc. Graduate Program in Electrical and Computer Engineering The Ohio State University 2014 Dissertation Committee: Umit¨ V. C¸ataly¨urek,Advisor Yuejie Chi Kun Huang F¨usun Ozg¨uner¨ c Copyright by Ayat Hatem 2014 Abstract Integrating protein-protein interaction (PPI) networks with gene expression data to extract active modules is shown to be promising in detecting meaningful biomark- ers for cancer and other diseases. However, current algorithms suffer from many drawbacks such as focusing only on the highly differentially expressed genes, ana- lyzing dependencies between genes in the PPI network only; totally neglecting the genes whose interactions are not known yet, and finally using mRNA gene expression data; ignoring other types of data such as gene mutation information and microRNAs expressions. In addition, lately, using the next generation sequencing technology to sequence the mRNA (RNA-Seq) has become the new standard for gene expression. However, existing algorithms either cannot handle the RNA-Seq data, or they return large modules which are hard to analyze. Therefore, we need new approaches to ad- dress the current drawbacks while utilizing and integrating the RNA-Seq data to the module discovery process. This work explores some of the drawbacks of current active module discovery algorithms. We first discuss the differences between RNA-Seq data and microarray data. With experimental evidence, we show that RNA-Seq is more powerful than microarray in providing better active modules at the expense of generating larger ones.
    [Show full text]
  • Melanoma Genome Sequencing Reveals Frequent PREX2 Mutations
    LETTER doi:10.1038/nature11071 Melanoma genome sequencing reveals frequent PREX2 mutations Michael F. Berger1{*, Eran Hodis1*, Timothy P. Heffernan2{*, Yonathan Lissanu Deribe2{*, Michael S. Lawrence1, Alexei Protopopov2{, Elena Ivanova2, Ian R. Watson2{, Elizabeth Nickerson1, Papia Ghosh2, Hailei Zhang2, Rhamy Zeid2, Xiaojia Ren2, Kristian Cibulskis1, Andrey Y. Sivachenko1, Nikhil Wagle2,3, Antje Sucker4, Carrie Sougnez1, Robert Onofrio1, Lauren Ambrogio1, Daniel Auclair1, Timothy Fennell1, Scott L. Carter1, Yotam Drier5, Petar Stojanov1, Meredith A. Singer2{, Douglas Voet1, Rui Jing1, Gordon Saksena1, Jordi Barretina1, Alex H. Ramos1,3, Trevor J. Pugh1,2,3, Nicolas Stransky1, Melissa Parkin1, Wendy Winckler1, Scott Mahan1, Kristin Ardlie1, Jennifer Baldwin1, Jennifer Wargo6, Dirk Schadendorf4, Matthew Meyerson1,2,3,7, Stacey B. Gabriel1, Todd R. Golub1,7,8,9, Stephan N. Wagner10, Eric S. Lander1,11*, Gad Getz1*, Lynda Chin1,2,3{* & Levi A. Garraway1,2,3,7* Melanoma is notable for its metastatic propensity, lethality in the comparable to other solid tumour types (3 and 14 mutations per advanced setting and association with ultraviolet exposure early in Mb)5,6, whereas melanomas from the trunk harboured substantially life1. To obtain a comprehensive genomic view of melanoma in more mutations, in agreement with previous studies3,7,8. In particular, humans, we sequenced the genomes of 25 metastatic melanomas sample ME009 exhibited a striking rate of 111 somatic mutations per and matched germline DNA. A wide range of point mutation rates Mb, consistent with a history of chronic sun exposure. was observed: lowest in melanomas whose primaries arose on non- In tumours with elevated mutation rates, most nucleotide substitu- ultraviolet-exposed hairless skin of the extremities (3 and 14 per tions were C R TorGR A transitions consistent with ultraviolet megabase (Mb) of genome), intermediate in those originating from irradiation9.
    [Show full text]
  • Analyses of Copy Number Variation of GK Rat Reveal New Putative Type 2 Diabetes Susceptibility Loci
    Analyses of Copy Number Variation of GK Rat Reveal New Putative Type 2 Diabetes Susceptibility Loci Zhi-Qiang Ye1,2, Shen Niu1, Yang Yu1, Hui Yu1,2, Bao-Hong Liu2, Rong-Xia Li1, Hua-Sheng Xiao1, Rong Zeng1, Yi-Xue Li1,2, Jia-Rui Wu1*, Yuan-Yuan Li1,2* 1 Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China, 2 Shanghai Center for Bioinformation Technology, Shanghai, China Abstract Large efforts have been taken to search for genes responsible for type 2 diabetes (T2D), but have resulted in only about 20 in humans due to its complexity and heterogeneity. The GK rat, a spontanous T2D model, offers us a superior opportunity to search for more diabetic genes. Utilizing array comparative genome hybridization (aCGH) technology, we identifed 137 non- redundant copy number variation (CNV) regions from the GK rats when using normal Wistar rats as control. These CNV regions (CNVRs) covered approximately 36 Mb nucleotides, accounting for about 1% of the whole genome. By integrating information from gene annotations and disease knowledge, we investigated the CNVRs comprehensively for mining new T2D genes. As a result, we prioritized 16 putative protein-coding genes and two microRNA genes (rno-mir-30b and rno-mir- 30d) as good candidates. The catalogue of CNVRs between GK and Wistar rats identified in this work served as a repository for mining genes that might play roles in the pathogenesis of T2D. Moreover, our efforts in utilizing bioinformatics methods to prioritize good candidate genes provided a more specific set of putative candidates.
    [Show full text]