Whole-exome sequencing of over 4100 men of African ancestry and prostate cancer risk

• Published in: Human molecular genetics 2016-01, Vol.25 (2), p.371-381
• Main Authors: Rand, Kristin A, Rohland, Nadin, Tandon, Arti, Stram, Alex, Sheng, Xin, Do, Ron, Pasaniuc, Bogdan, Allen, Alex, Quinque, Dominique, Mallick, Swapan, Le Marchand, Loic, Kaggwa, Sam, Lubwama, Alex, Stram, Daniel O, Watya, Stephen, Henderson, Brian E, Conti, David V, Reich, David, Haiman, Christopher A
• Format: Article
• Language: English
• Subjects: Adult; Aged; Association Studies; Black or African American; Black People - genetics; Exome; Genetic Association Studies; Genetic Predisposition to Disease; Humans; Male; Middle Aged; Polymorphism, Single Nucleotide; Prostatic Neoplasms - epidemiology; Prostatic Neoplasms - genetics; Risk; Sequence Analysis, DNA
• ISSN: 0964-6906; 1460-2083; 1460-2083
• DOI: 10.1093/hmg/ddv462

Prostate cancer is the most common non-skin cancer in males, with a ∼1.5-2-fold higher incidence in African American men when compared with whites. Epidemiologic evidence supports a large heritable contribution to prostate cancer, with over 100 susceptibility loci identified to date that can explain ∼33% of the familial risk. To explore the contribution of both rare and common variation in coding regions to prostate cancer risk, we sequenced the exomes of 2165 prostate cancer cases and 2034 controls of African ancestry at a mean coverage of 10.1×. We identified 395 220 coding variants down to 0.05% frequency [57% non-synonymous (NS), 42% synonymous and 1% gain or loss of stop codon or splice site variant] in 16 751 genes with the strongest associations observed in SPARCL1 on 4q22.1 (rs13051, Ala49Asp, OR = 0.78, P = 1.8 × 10(-6)) and PTPRR on 12q15 (rs73341069, Val239Ile, OR = 1.62, P = 2.5 × 10(-5)). In gene-level testing, the two most significant genes were C1orf100 (P = 2.2 × 10(-4)) and GORAB (P = 2.3 × 10(-4)). We did not observe exome-wide significant associations (after correcting for multiple hypothesis testing) in single variant or gene-level testing in the overall case-control or case-case analyses of disease aggressiveness. In this first whole-exome sequencing study of prostate cancer, our findings do not provide strong support for the hypothesis that NS coding variants down to 0.5-1.0% frequency have large effects on prostate cancer risk in men of African ancestry. Higher-coverage sequencing efforts in larger samples will be needed to study rarer variants with smaller effect sizes associated with prostate cancer risk.