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Novel pleiotropic risk loci for melanoma and nevus density implicate multiple biological pathways.

ABSTRACT: The total number of acquired melanocytic nevi on the skin is strongly correlated with melanoma risk. Here we report a meta-analysis of 11 nevus GWAS from Australia, Netherlands, UK, and USA comprising 52,506 individuals. We confirm known loci including MTAP, PLA2G6, and IRF4, and detect novel SNPs in KITLG and a region of 9q32. In a bivariate analysis combining the nevus results with a recent melanoma GWAS meta-analysis (12,874 cases, 23,203 controls), SNPs near GPRC5A, CYP1B1, PPARGC1B, HDAC4, FAM208B, DOCK8, and SYNE2 reached global significance, and other loci, including MIR146A and OBFC1, reached a suggestive level. Overall, we conclude that most nevus genes affect melanoma risk (KITLG an exception), while many melanoma risk loci do not alter nevus count. For example, variants in TERC and OBFC1 affect both traits, but other telomere length maintenance genes seem to affect melanoma risk only. Our findings implicate multiple pathways in nevogenesis.

SUBMITTER: Duffy DL

PROVIDER: S-EPMC6235897 | biostudies-literature | 2018 Nov

REPOSITORIES: biostudies-literature

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Novel pleiotropic risk loci for melanoma and nevus density implicate multiple biological pathways.

Duffy David L DL Zhu Gu G Li Xin X Sanna Marianna M Iles Mark M MM Jacobs Leonie C LC Evans David M DM Yazar Seyhan S Beesley Jonathan J Law Matthew H MH Kraft Peter P Visconti Alessia A Taylor John C JC Liu Fan F Wright Margaret J MJ Henders Anjali K AK Bowdler Lisa L Glass Dan D Ikram M Arfan MA Uitterlinden André G AG Madden Pamela A PA Heath Andrew C AC Nelson Elliot C EC Green Adele C AC Chanock Stephen S Barrett Jennifer H JH Brown Matthew A MA Hayward Nicholas K NK MacGregor Stuart S Sturm Richard A RA Hewitt Alex W AW Kayser Manfred M Hunter David J DJ Newton Bishop Julia A JA Spector Timothy D TD Montgomery Grant W GW Mackey David A DA Smith George Davey GD Nijsten Tamar E TE Bishop D Timothy DT Bataille Veronique V Falchi Mario M Han Jiali J Martin Nicholas G NG

Nature communications 20181114 1

The total number of acquired melanocytic nevi on the skin is strongly correlated with melanoma risk. Here we report a meta-analysis of 11 nevus GWAS from Australia, Netherlands, UK, and USA comprising 52,506 individuals. We confirm known loci including MTAP, PLA2G6, and IRF4, and detect novel SNPs in KITLG and a region of 9q32. In a bivariate analysis combining the nevus results with a recent melanoma GWAS meta-analysis (12,874 cases, 23,203 controls), SNPs near GPRC5A, CYP1B1, PPARGC1B, HDAC4, ...[more]

PMID: 30429480

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Project description:Alzheimer's disease is a highly heritable, common neurodegenerative disease characterized neuropathologically by the accumulation of ?-amyloid plaques and tau-containing neurofibrillary tangles. In addition to the well-established risk associated with the APOE locus, there has been considerable success in identifying additional genetic variants associated with Alzheimer's disease. Major challenges in understanding how genetic risk influences the development of Alzheimer's disease are clinical and neuropathological heterogeneity, and the high level of accompanying comorbidities. We report a multimodal analysis integrating longitudinal clinical and cognitive assessment with neuropathological data collected as part of the Brains for Dementia Research study to understand how genetic risk factors for Alzheimer's disease influence the development of neuropathology and clinical performance. Six hundred and ninety-three donors in the Brains for Dementia Research cohort with genetic data, semi-quantitative neuropathology measurements, cognitive assessments and established diagnostic criteria were included in this study. We tested the association of APOE genotype and Alzheimer's disease polygenic risk score-a quantitative measure of genetic burden-with survival, four common neuropathological features in Alzheimer's disease brains (neurofibrillary tangles, ?-amyloid plaques, Lewy bodies and transactive response DNA-binding protein 43 proteinopathy), clinical status (clinical dementia rating) and cognitive performance (Mini-Mental State Exam, Montreal Cognitive Assessment). The APOE ?4 allele was significantly associated with younger age of death in the Brains for Dementia Research cohort. Our analyses of neuropathology highlighted two independent pathways from APOE ?4, one where ?-amyloid accumulation co-occurs with the development of tauopathy, and a second characterized by direct effects on tauopathy independent of ?-amyloidosis. Although we also detected association between APOE ?4 and dementia status and cognitive performance, these were all mediated by tauopathy, highlighting that they are a consequence of the neuropathological changes. Analyses of polygenic risk score identified associations with tauopathy and ?-amyloidosis, which appeared to have both shared and unique contributions, suggesting that different genetic variants associated with Alzheimer's disease affect different features of neuropathology to different degrees. Taken together, our results provide insight into how genetic risk for Alzheimer's disease influences both the clinical and pathological features of dementia, increasing our understanding about the interplay between APOE genotype and other genetic risk factors.

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Novel pleiotropic risk loci for melanoma and nevus density implicate multiple biological pathways.

Publications

Novel pleiotropic risk loci for melanoma and nevus density implicate multiple biological pathways.

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