Association of prostate cancer risk variants with gene expression in normal and tumor tissue

Cancer Epidemiology Biomarkers and Prevention

Volumn 24, Issue 1, 2015, Pages 255-260

  Penney, Kathryn L ^a,b   Sinnott, Jennifer A ^a,b   Tyekucheva, Svitlana ^a,c   Gerke, Travis ^a   Shui, Irene M ^a   Kraft, Peter ^a   Sesso, Howard D ^a,b   Freedman, Matthew L ^c,d   Loda, Massimo ^b,c,d   Mucci, Lorelei A ^a,b   Stampfer, Meir J ^a,b  

^a HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

^b BRIGHAM AND WOMEN S HOSPITAL   (United States)

^c DANA FARBER CANCER INSTITUTE   (United States)

^d BROAD INSTITUTE OF MIT AND HARVARD   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BONE MORPHOGENETIC PROTEIN RECEPTOR 1B; MESSENGER RNA; STEROID 5ALPHA REDUCTASE 1; TRANSCRIPTOME;

ADULT; AGED; ARTICLE; CANCER RISK; CANCER TISSUE; CONTROLLED STUDY; CORRELATION ANALYSIS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE LOCUS; GENETIC RISK; GENETIC VARIABILITY; GENOME ANALYSIS; GENOTYPE; HUMAN; HUMAN TISSUE; LIPID METABOLISM; MAJOR CLINICAL STUDY; MALE; MICROARRAY ANALYSIS; MRNA EXPRESSION ASSAY; PRIORITY JOURNAL; PROSTATE CANCER; SIGNAL TRANSDUCTION; SINGLE NUCLEOTIDE POLYMORPHISM; GENE EXPRESSION; GENETIC VARIATION; GENETICS; PROCEDURES; PROSPECTIVE STUDY; PROSTATE TUMOR; RISK FACTOR;

GENE EXPRESSION; GENE EXPRESSION PROFILING; GENETIC VARIATION; HUMANS; MALE; POLYMORPHISM, SINGLE NUCLEOTIDE; PROSPECTIVE STUDIES; PROSTATIC NEOPLASMS; RISK FACTORS;

EID: 84921046649     PISSN: 10559965     EISSN: None     Source Type: Journal    
DOI: 10.1158/1055-9965.EPI-14-0694-T     Document Type: Article

References (34)

1. Freedman ML, Haiman CA, Patterson N, McDonald GJ, Tandon A, Waliszewska A, et al. Admixturemapping identifies 8q24 as a prostate cancer risk locus in African-American men. Proc Natl Acad Sci U S A 2006;103: 14068-73.
2. Amundadottir LT, Sulem P, Gudmundsson J, Helgason A, Baker A, Agnarsson BA, et al. A common variant associated with prostate cancer in European and African populations. Nat Genet 2006;38:652-8.
3. Haiman CA, Patterson N, Freedman ML, Myers SR, Pike MC, Waliszewska A, et al. Multiple regions within 8q24 independently affect risk for prostate cancer. Nat Genet 2007;39:638-44.
4. Gudmundsson J, Sulem P, Manolescu A, Amundadottir LT, Gudbjartsson D, Helgason A, et al. Genome-wide association study identifies a second prostate cancer susceptibility variant at 8q24. Nat Genet 2007;39:631-7.
5. Yeager M, Orr N, Hayes RB, Jacobs KB, Kraft P, Wacholder S, et al. Genomewide association study of prostate cancer identifies a second risk locus at 8q24. Nat Genet 2007;39:645-9.
6. Gudmundsson J, Sulem P, Steinthorsdottir V, Bergthorsson JT, Thorleifsson G, Manolescu A, et al. Two variants on chromosome 17 confer prostate cancer risk, and the one in TCF2 protects against type 2 diabetes. Nat Genet 2007;39:977-83.
7. Eeles RA, Kote-Jarai Z, Giles GG, Olama AA, Guy M, Jugurnauth SK, et al. Multiple newly identified loci associated with prostate cancer susceptibility. Nat Genet 2008;40:316-21.
8. Thomas G, Jacobs KB, Yeager M, Kraft P, Wacholder S, Orr N, et al. Multiple loci identified in a genome-wide association study of prostate cancer. Nat Genet 2008;40:310-5.
9. Gudmundsson J, Sulem P, Rafnar T, Bergthorsson JT, Manolescu A, Gudbjartsson D, et al. Common sequence variants on 2p15 and Xp11.22 confer susceptibility to prostate cancer. Nat Genet 2008;40:281-3.
10. Yeager M, Chatterjee N, Ciampa J, Jacobs KB, Gonzalez-Bosquet J, Hayes RB, et al. Identification of a new prostate cancer susceptibility locus on chromosome 8q24. Nat Genet 2009;41:1055-7.
11. Gudmundsson J, Sulem P, Gudbjartsson DF, Blondal T, Gylfason A, Agnarsson BA, et al. Genome-wide association and replication studies identify four variants associated with prostate cancer susceptibility. Nat Genet 2009;41:1122-6.
12. Eeles RA, Kote-Jarai Z, Al Olama AA, Giles GG, Guy M, Severi G, et al. Identification of seven new prostate cancer susceptibility loci through a genome-wide association study. Nat Genet 2009;41:1116-21.
13. Al Olama AA, Kote-Jarai Z, Giles GG, Guy M, Morrison J, Severi G, et al. Multiple loci on 8q24 associated with prostate cancer susceptibility. Nat Genet 2009;41:1058-60.
14. Sun J, Zheng SL, Wiklund F, Isaacs SD, Purcell LD, Gao Z, et al. Evidence for two independent prostate cancer risk-associated loci in the HNF1B gene at 17q12. Nat Genet 2008;40:1153-5.
15. Eeles RA, Olama AA, Benlloch S, Saunders EJ, Leongamornlert DA, Tymrakiewicz M, et al. Identification of 23 new prostate cancer susceptibility loci using the iCOGS custom genotyping array. Nat Genet 2013;45: 385-91.
16. 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;343:78-85.
17. Pomerantz MM, Shrestha Y, Flavin RJ, Regan MM, Penney KL, Mucci LA, et al. Analysis of the 10q11 cancer risk locus implicates MSMB and NCOA4 in human prostate tumorigenesis. PLoS Genet 2010;6: e1001204.
18. Lou H, Yeager M, Li H, Bosquet JG, Hayes RB, Orr N, et al. Fine mapping and functional analysis of a common variant in MSMB on chromosome 10q11.2 associated with prostate cancer susceptibility. Proc Natl Acad SciU S A 2009;106:7933-8.
19. Grisanzio C, Werner L, Takeda D, Awoyemi BC, Pomerantz MM, Yamada H, et al. Genetic and functional analyses implicate the NUDT11, HNF1B, and SLC22A3 genes in prostate cancer pathogenesis. Proc Natl Acad Sci US A 2012;109:11252-7.
20. Harries LW, Perry JR, McCullagh P, Crundwell M. Alterations in LMTK2, MSMB and HNF1B gene expression are associatedwith the development of prostate cancer. BMC Cancer 2010;10:315.
21. Xu X, Hussain WM, Vijai J, Offit K, Rubin MA, Demichelis F, et al. Variants at IRX4 as prostate cancer expression quantitative trait loci. Eur J Hum Genet 2014;22:558-63.
22. Gilad Y, Rifkin SA, Pritchard JK. Revealing the architecture of gene regulation: the promise of eQTL studies. Trends Genet 2008;24:408-15.
23. Final report on the aspirin component of the ongoing Physicians' Health Study. Steering Committee of the Physicians' Health Study Research Group. N Engl J Med 1989;321:129-35.
24. Giovannucci E, Pollak M, Liu Y, Platz EA, Majeed N, Rimm EB, et al. Nutritional predictors of insulin-like growth factor I and their relationships to cancer in men. Cancer Epidemiol Biomarkers Prev 2003;12:84-9.
25. Irizarry RA, Bolstad BM, Collin F, Cope LM, Hobbs B, Speed TP. Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res 2003;31:e15.
26. Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, et al. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 2003;4:249-64.
27. Shui IM, Lindstrom S, Kibel AS, Berndt SI, Campa D, Gerke T, et al. Prostate Cancer (PCa) risk variants and risk of fatal PCa in the National Cancer Institute Breast and Prostate Cancer Cohort Consortium. Eur Urol 2014;65:1069-75.
28. Goeman JJ, van de Geer SA, de Kort F, van Houwelingen HC. A global test for groups of genes: testing association with a clinical outcome. Bioinformatics 2004;20:93-9.
29. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A 2005;102:15545-50.
30. Hazelett DJ, Rhie SK, Gaddis M, Yan C, Lakeland DL, Coetzee SG, et al. Comprehensive functional annotation of 77 prostate cancer risk loci. PLoS Genet 2014;10:e1004102.
31. Innocenti F, Cooper GM, Stanaway IB, Gamazon ER, Smith JD, Mirkov S, et al. Identification, replication, and functional fine-mapping of expression quantitative trait loci in primary human liver tissue. PLoS Genet 2011;7: e1002078.
32. Pelton K, Freeman MR, Solomon KR. Cholesterol and prostate cancer. Curr Opin Pharmacol 2012;12:751-9.
33. Zadra G, Photopoulos C, Loda M. The fat side of prostate cancer. Biochim Biophys Acta 2013;1831:1518-32.
34. Breyer JP, Dorset DC, Clark TA, Bradley KM, Wahlfors TA, McReynolds KM, et al. An expressed retrogene of the master embryonic stem cell gene POU5F1 is associated with prostate cancer susceptibility. AmJ Hum Genet 2014;94:395-404.