Enrichment of colorectal cancer associations in functional regions: Insight for using epigenomics data in the analysis of whole genome sequence-imputed GWAS data

PLoS ONE

Volumn 12, Issue 11, 2017, Pages

  Bien, Stephanie A ^a   Auer, Paul L ^b   Harrison, Tabitha A ^a   Qu, Conghui ^a   Connolly, Charles M ^a   Greenside, Peyton G ^c   Chen, Sai ^d   Berndt, Sonja I ^e   Bézieau, Stéphane ^f   Kang, Hyun M ^d   Huyghe, Jeroen ^a   Brenner, Hermann ^g   Casey, Graham ^h   Chan, Andrew T ⁱ   Hopper, John L ^j   Banbury, Barbara L ^a   Chang Claude, Jenny ^g,k   Chanock, Stephen J ^e   Haile, Robert W ^l   Hoffmeister, Michael ^g   Fuchsberger, Christian ^d   Jenkins, Mark A ^j   Leal, Suzanne M ^m   Lemire, Mathieu ⁿ   Newcomb, Polly A ^a   Gallinger, Steven ^o   Potter, John D ^a   Schoen, Robert E ^p   Slattery, Martha L ^q   Smith, Joshua D ^r   Le Marchand, Loic ^s   White, Emily ^a,r   Zanke, Brent W ^t,u   Abeçasis, Goncalo R ^d   Carlson, Christopher S ^a,r   Peters, Ulrike ^a,r   Nickerson, Deborah A ^r   Kundaje, Anshul ^c   Hsu, Li ^a,r   more..

^a Fred Hutchinson Cancer Research Center   (United States)

^b UNIVERSITY OF WISCONSIN MILWAUKEE   (United States)

^c STANFORD UNIVERSITY   (United States)

^d UNIVERSITY OF MICHIGAN   (United States)

^e NATIONAL CANCER INSTITUTE   (United States)

^f NANTES UNIVERSITY HOSPITAL   (France)

^g GERMAN CANCER RESEARCH CENTER DKFZ   (Germany)

^h UNIVERSITY OF VIRGINIA   (United States)

ⁱ HARVARD MEDICAL SCHOOL   (United States)

^j UNIVERSITY OF MELBOURNE   (Australia)

^k UNIVERSITY MEDICAL CENTER HAMBURG EPPENDORF   (Germany)

^l STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^m BAYLOR COLLEGE OF MEDICINE   (United States)

ⁿ ONTARIO INSTITUTE FOR CANCER RESEARCH   (Canada)

^o CANCER CARE ONTARIO   (Canada)

^p UNIVERSITY OF PITTSBURGH MEDICAL CENTER   (United States)

^q UNIVERSITY OF UTAH HEALTH SCIENCES CENTER   (United States)

^r UNIVERSITY OF WASHINGTON   (United States)

^s UNIVERSITY OF HAWAII CANCER CENTER   (United States)

^t UNIVERSITY OF OTTAWA   (Canada)

^u OTTAWA HOSPITAL RESEARCH INSTITUTE   (Canada)

more..

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTOME;

ACTIVE REGULATORY ELEMENT; ARTICLE; CANCER CLASSIFICATION; CANCER TISSUE; CELLS BY BODY ANATOMY; COLON CARCINOGENESIS; COLON TISSUE; COLORECTAL CANCER; CONTROLLED STUDY; ENHANCER REGION; EPIGENETICS; FEMALE; GENE FREQUENCY; GENE LOCUS; GENETIC ASSOCIATION; GENETIC ENRICHMENT; GENETIC VARIABILITY; GENOME-WIDE ASSOCIATION STUDY; HUMAN; HUMAN CELL; HUMAN TISSUE; IMMUNOCOMPETENT CELL; MAJOR CLINICAL STUDY; NON CODING REGULATORY REGION; PROMOTER REGION; RARE VARIANT ASSOCIATION METHOD; RECTUM; STATISTICAL SIGNIFICANCE; TRANSCRIPTION INITIATION SITE; WHOLE GENOME SEQUENCING; COLORECTAL TUMOR; GENETICS; GENOMICS; PATHOLOGY; QUANTITATIVE TRAIT LOCUS; REGULATORY SEQUENCE; SINGLE NUCLEOTIDE POLYMORPHISM;

COLORECTAL NEOPLASMS; EPIGENOMICS; GENE FREQUENCY; GENOME-WIDE ASSOCIATION STUDY; GENOMICS; HUMANS; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT LOCI; REGULATORY SEQUENCES, NUCLEIC ACID;

EID: 85034777436     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0186518     Document Type: Article

References (28)

1. Jemal A, Bray F, Center MM, Ferlay J, Ward E, Forman D. Global cancer statistics. CA Cancer J Clin. 2011; 61(2):69–90. https://doi.org/10.3322/caac.20107 PMID: 21296855
2. Peters U, Bien S, Zubair N. Genetic architecture of colorectal cancer. Gut. 2015.
3. Czene K, Lichtenstein P, Hemminki K. Environmental and heritable causes of cancer among 9.6 million individuals in the Swedish Family-Cancer Database. Int J Cancer. 2002; 99(2):260–266. https://doi.org/10.1002/ijc.10332 PMID: 11979442
4. Lichtenstein P, Holm NV, Verkasalo PK, Iliadou A, Kaprio J, Koskenvuo M et al. Environmental and heritable factors in the causation of cancer—analyses of cohorts of twins from Sweden, Denmark, and Finland. N Engl J Med. 2000; 343(2):78–85. https://doi.org/10.1056/NEJM200007133430201 PMID: 10891514
5. Jiao S, Peters U, Berndt S, Brenner H, Butterbach K, Caan BJ et al. Estimating the heritability of colorectal cancer. Hum Mol Genet. 2014; 23(14):3898–3905. https://doi.org/10.1093/hmg/ddu087 PMID: 24562164
6. Auer PL, Johnsen JM, Johnson AD, Logsdon BA, Lange LA, Nalls MA et al. Imputation of exome sequence variants into population- based samples and blood-cell-trait-associated loci in African Americans: NHLBI GO Exome Sequencing Project. Am J Hum Genet. 2012; 91(5):794–808. https://doi.org/10.1016/j.ajhg.2012.08.031 PMID: 23103231
7. Abecasis GR, Altshuler D, Auton A, Brooks LD, Durbin RM, Gibbs RA et al. A map of human genome variation from population-scale sequencing. Nature. 2010; 467(7319):1061–1073. https://doi.org/10.1038/nature09534 PMID: 20981092
8. Du M, Auer PL, Jiao S, Haessler J, Altshuler D, Boerwinkle E et al. Whole-exome imputation of sequence variants identified two novel alleles associated with adult body height in African Americans. Hum Mol Genet. 2014; 23(24):6607–6615. https://doi.org/10.1093/hmg/ddu361 PMID: 25027330
9. Johnsen JM, Auer PL, Morrison AC, Jiao S, Wei P, Haessler J et al. Common and rare von Willebrand factor (VWF) coding variants, VWF levels, and factor VIII levels in African Americans: the NHLBI Exome Sequencing Project. Blood. 2013; 122(4):590–597. https://doi.org/10.1182/blood-2013-02-485094 PMID: 23690449
10. Auer PL, Teumer A, Schick U, O’Shaughnessy A, Lo KS, Chami N et al. Rare and low-frequency coding variants in CXCR2 and other genes are associated with hematological traits. Nat Genet. 2014; 46 (6):629–634. https://doi.org/10.1038/ng.2962 PMID: 24777453
11. Crosby J, Peloso GM, Auer PL, Crosslin DR, Stitziel NO, Lange LA et al. Loss-of-function mutations in APOC3, triglycerides, and coronary disease. N Engl J Med. 2014; 371(1):22–31. https://doi.org/10.1056/NEJMoa1307095 PMID: 24941081
12. Pruitt KD, Tatusova T, Klimke W, Maglott DR. NCBI Reference Sequences: current status, policy and new initiatives. Nucleic Acids Res. 2009; 37(Database issue):D32–D36. https://doi.org/10.1093/nar/gkn721 PMID: 18927115
13. Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F et al. GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res. 2012; 22(9):1760–1774. https://doi.org/10.1101/gr.135350.111 PMID: 22955987
14. Pruitt KD, Harrow J, Harte RA, Wallin C, Diekhans M, Maglott DR et al. The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes. Genome Res. 2009; 19(7):1316–1323. https://doi.org/10.1101/gr.080531.108 PMID: 19498102
15. Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A et al. Integrative analysis of 111 reference human epigenomes. Nature. 2015; 518(7539):317–330. https://doi.org/10.1038/nature14248 PMID: 25693563
16. Mifsud B, Tavares-Cadete F, Young AN, Sugar R, Schoenfelder S, Ferreira L et al. Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C. Nat Genet. 2015; 47(6):598–606. https://doi.org/10.1038/ng.3286 PMID: 25938943
17. Maurano MT, Humbert R, Rynes E, Thurman RE, Haugen E, Wang H et al. Systematic localization of common disease-associated variation in regulatory DNA. Science. 2012; 337(6099):1190–1195. https://doi.org/10.1126/science.1222794 PMID: 22955828
18. Sanyal A, Lajoie BR, Jain G, Dekker J. The long-range interaction landscape of gene promoters. Nature. 2012; 489(7414):109–113. https://doi.org/10.1038/nature11279 PMID: 22955621
19. Sun J, Zheng Y, Hsu L. A unified mixed-effects model for rare-variant association in sequencing studies. Genet Epidemiol. 2013; 37(4):334–344. https://doi.org/10.1002/gepi.21717 PMID: 23483651
20. Ionita-Laza I, Lee S, Makarov V, Buxbaum JD, Lin X. Sequence kernel association tests for the combined effect of rare and common variants. Am J Hum Genet. 2013; 92(6):841–853. https://doi.org/10.1016/j.ajhg.2013.04.015 PMID: 23684009
21. Li B, Leal SM. Methods for detecting associations with rare variants for common diseases: application to analysis of sequence data. Am J Hum Genet. 2008; 83(3):311–321. https://doi.org/10.1016/j.ajhg.2008.06.024 PMID: 18691683
22. Vucicevic D, Corradin O, Ntini E, Scacheri PC, Orom UA. Long ncRNA expression associates with tissue-specific enhancers. Cell Cycle. 2015; 14(2):253–260. https://doi.org/10.4161/15384101.2014.977641 PMID: 25607649
23. Gamazon ER, Wheeler HE, Shah KP, Mozaffari SV, Aquino-Michaels K, Carroll RJ et al. A gene-based association method for mapping traits using reference transcriptome data. Nat Genet. 2015; 47 (9):1091–1098. https://doi.org/10.1038/ng.3367 PMID: 26258848
24. Peters U, Jiao S, Schumacher FR, Hutter CM, Aragaki AK, Baron JA et al. Identification of Genetic Susceptibility Loci for Colorectal Tumors in a Genome-Wide Meta-analysis. Gastroenterology. 2013; 144 (4):799–807. https://doi.org/10.1053/j.gastro.2012.12.020 PMID: 23266556
25. Ernst J, Kellis M. ChromHMM: automating chromatin-state discovery and characterization. Nat Methods. 2012; 9(3):215–216. https://doi.org/10.1038/nmeth.1906 PMID: 22373907
26. Ward LD, Kellis M. HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants. Nucleic Acids Res. 2012; 40(Database issue): D930–D934. https://doi.org/10.1093/nar/gkr917 PMID: 22064851
27. Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P et al. A method and server for predicting damaging missense mutations. Nat Methods. 2010; 7(4):248–249. https://doi.org/10.1038/nmeth0410-248 PMID: 20354512
28. R: A language and environment for statistical computing. [computer program]. Vienna, Austria: R Foundation for Statistical Computing; 2015.