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The contribution of rare variation to prostate cancer heritability.

ABSTRACT: We report targeted sequencing of 63 known prostate cancer risk regions in a multi-ancestry study of 9,237 men and use the data to explore the contribution of low-frequency variation to disease risk. We show that SNPs with minor allele frequencies (MAFs) of 0.1-1% explain a substantial fraction of prostate cancer risk in men of African ancestry. We estimate that these SNPs account for 0.12 (standard error (s.e.) = 0.05) of variance in risk (?42% of the variance contributed by SNPs with MAF of 0.1-50%). This contribution is much larger than the fraction of neutral variation due to SNPs in this class, implying that natural selection has driven down the frequency of many prostate cancer risk alleles; we estimate the coupling between selection and allelic effects at 0.48 (95% confidence interval [0.19, 0.78]) under the Eyre-Walker model. Our results indicate that rare variants make a disproportionate contribution to genetic risk for prostate cancer and suggest the possibility that rare variants may also have an outsize effect on other common traits.

SUBMITTER: Mancuso N

PROVIDER: S-EPMC7534691 | biostudies-literature | 2016 Jan

REPOSITORIES: biostudies-literature

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The contribution of rare variation to prostate cancer heritability.

Mancuso Nicholas N Rohland Nadin N Rand Kristin A KA Tandon Arti A Allen Alexander A Quinque Dominique D Mallick Swapan S Li Heng H Stram Alex A Sheng Xin X Kote-Jarai Zsofia Z Easton Douglas F DF Eeles Rosalind A RA Le Marchand Loic L Lubwama Alex A Stram Daniel D Watya Stephen S Conti David V DV Henderson Brian B Haiman Christopher A CA Pasaniuc Bogdan B Reich David D

Nature genetics 20151116 1

We report targeted sequencing of 63 known prostate cancer risk regions in a multi-ancestry study of 9,237 men and use the data to explore the contribution of low-frequency variation to disease risk. We show that SNPs with minor allele frequencies (MAFs) of 0.1-1% explain a substantial fraction of prostate cancer risk in men of African ancestry. We estimate that these SNPs account for 0.12 (standard error (s.e.) = 0.05) of variance in risk (∼42% of the variance contributed by SNPs with MAF of 0.1 ...[more]

PMID: 26569126

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Project description:ObjectiveAssess radiologists' contribution to variation in clinically significant prostate cancer (csPCa) detection in patients with elevated prostate-specific antigen (PSA) and multiparametric MRI (mpMRI).MethodsThis institutional review board-approved, retrospective cohort study was performed at a tertiary, academic, National Cancer Institute-designated Comprehensive Cancer Center with a multidisciplinary prostate cancer program. Men undergoing mpMRI examinations from January 1, 2015, to December 31, 2019, with elevated PSA (≥4 ng/mL) and biopsy within 6 months pre- or post-MRI or prostatectomy within 6 months post-mpMRI were included. Univariate and multivariable hierarchical logistic regression assessed impact of patient, provider, mpMRI examination, mpMRI report, and pathology factors on the diagnosis of Grade Group ≥ 2 csPCa.ResultsStudy cohort included 960 MRIs in 928 men, mean age 64.0 years (SD ± 7.4), and 59.8% (555 of 928) had csPCa. Interpreting radiologist was not significant individually (P > .999) or combined with mpMRI ordering physician and physician performing biopsy or prostatectomy (P = .41). Prostate Imaging Reporting and Data System (PI-RADS) category 2 (odds ratio [OR] 0.18, P = .04), PI-RADS category 4 (OR 2.52, P < .001), and PI-RADS category 5 (OR 4.99, P < .001) assessment compared with no focal lesion; PSA density of 0.1 to 0.15 ng/mL/cc (OR 2.46, P < .001), 0.15 to 0.2 ng/mL/cc (OR 2.77, P < .001), or ≥0.2 ng/mL/cc (OR 4.52, P < .001); private insurance (reference = Medicare, OR 0.52, P = .001), and unambiguous extraprostatic extension on mpMRI (OR 2.94, P = .01) were independently associated with csPCa. PI-RADS 3 assessment (OR 1.18, P = .56), age (OR 0.99, P = .39), and African American race (OR 0.90, P = .75) were not.DiscussionAlthough there is known in-practice variation in radiologists' interpretation of mpMRI, in our multidisciplinary prostate cancer program we found no significant radiologist-attributable variation in csPCa detection.

Project description:ContextSkeletal muscle mass (SMM) is one of the major components of human body composition, with deviations from normal values often leading to sarcopenia.ObjectiveOur major aim was to conduct a genome-wide DNA methylation study in an attempt to identify potential genomic regions associated with SMM.DesignThis was a mixed cross-sectional and longitudinal study.SettingCommunity-based study.ParticipantsA total of 1550 middle-aged United Kingdom twins (monozygotic [MZ] and dizygotic [DZ]), 297 of which were repeatedly measured participated in the study.Main outcome measureAppendicular lean mass assessed using dual-energy X-ray absorptiometry technology, and methylated DNA immunoprecipitation sequencing DNA methylation profiling genome-wide were obtained from each individual.ResultsHeritability estimate of SMM, with simultaneous adjustment for covariates obtained using variance decomposition analysis, was h(2) = 0.809 ± 0.050. After quality control and analysis of longitudinal stability, the DNA methylation data comprised of 723 029 genomic sites, with positive correlations between repeated measurements (Rrepeated = 0.114-0.905). Correlations between MZ and DZ twins were 0.51 and 0.38 at a genome-wide average, respectively, and clearly increased with Rrepeated. Testing for DNA methylation association with SMM in 50 discordant MZ twins revealed 36 081 nominally significant results, of which the top-ranked 134 signals (P < .01 and Rrepeated > 0.40) were subjected to replication in the sample of 1196 individuals. Seven SMM methylation association signals replicated at a false discovery rate less than 0.1, and these were located in or near genes DNAH12, CAND1, CYP4F29P, and ZFP64, which have previously been highlighted in muscle-related studies. Adjusting for age, smoking, and blood cell heterogeneity did not alter significance of these associations.ConclusionThis epigenome-wide study, testing longitudinally stable methylation sites, discovered and replicated a number of associations between DNA methylation at CpG loci and SMM. Four replicated signals were related to genes with potential muscle functions, suggesting that the methylome of whole blood may be informative of SMM variation.

Project description:BackgroundThe view of prostate cancer (PCa) progression as a result of the interaction of epithelial cancer cells with the host's immune system is supported by the presence of tumor infiltrating lymphocytes (TILs). TILs fate and interaction with the tumor microenvironment is mediated by accessory molecules such as CD5 and CD6, two signal-transducing coreceptors involved in fine-tuning of T cell responses. While the nature of the CD5 ligand is still controversial, CD6 binds CD166/ALCAM, a cell adhesion molecule involved in progression and dissemination of epithelial cancers, including PCa. The purpose of the present study was to determine the role of CD5, CD6, and CD166/ALCAM gene variants in PCa.MethodsFunctionally relevant CD5 (rs2241002 and rs2229177), CD6 (rs17824933, rs11230563, and rs12360861) and CD166/ALCAM (rs6437585, rs579565, rs1044243, and rs35271455) single nucleotide polymorphisms (SNPs) were genotyped in germline DNA samples from 376 PCa patients. Their association with PCa prognostic factors, namely biochemical recurrence (BCR) and International Society of Urological Pathology (ISUP) grade was analyzed by generalized linear models and survival analyses.ResultProportional hazards regression showed that the minor CD6 rs12360861AA and CD166/ALCAM rs579565AA genotypes were associated with earlier BCR, with hazard ratios of 2.65 (95% CI: 1.39-5.05, p = 0.003) and 1.86, (95% CI: 1.02-3.39, p = 0.043), respectively. Individually, none of the analyzed SNPs was significantly associated with ISUP grade, but haplotype analyses revealed association of the CD5 rs2241002C -rs2229177T haplotype with ISUP grade ≥2, with odds ratio of 1.52 (95% CI: 1.05-2.21, p = 0.026).ConclusionThe results show the impact on PCa aggressiveness and recurrence brought about by gene variants involved in modulation of lymphocyte activation (CD5, CD6) and immune-epithelial cell adhesion (CD166/ALCAM) in PCa aggressiveness and recurrence, thus supporting a role for host immune response in PCa pathophysiology.

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The contribution of rare variation to prostate cancer heritability.

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The contribution of rare variation to prostate cancer heritability.

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