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Gene expression imputation identifies candidate genes and susceptibility loci associated with cutaneous squamous cell carcinoma.

ABSTRACT: Cutaneous squamous cell carcinoma (cSCC) is a common skin cancer with genetic susceptibility loci identified in recent genome-wide association studies (GWAS). Transcriptome-wide association studies (TWAS) using imputed gene expression levels can identify additional gene-level associations. Here we impute gene expression levels in 6891 cSCC cases and 54,566 controls in the Kaiser Permanente Genetic Epidemiology Research in Adult Health and Aging (GERA) cohort and 25,558 self-reported cSCC cases and 673,788 controls from 23andMe. In a discovery-validation study, we identify 19 loci containing 33 genes whose imputed expression levels are associated with cSCC at false discovery rate?

SUBMITTER: Ioannidis NM

PROVIDER: S-EPMC6189170 | biostudies-literature | 2018 Oct

REPOSITORIES: biostudies-literature

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Gene expression imputation identifies candidate genes and susceptibility loci associated with cutaneous squamous cell carcinoma.

Ioannidis Nilah M NM Wang Wei W Furlotte Nicholas A NA Hinds David A DA Bustamante Carlos D CD Jorgenson Eric E Asgari Maryam M MM Whittemore Alice S AS

Nature communications 20181015 1

Cutaneous squamous cell carcinoma (cSCC) is a common skin cancer with genetic susceptibility loci identified in recent genome-wide association studies (GWAS). Transcriptome-wide association studies (TWAS) using imputed gene expression levels can identify additional gene-level associations. Here we impute gene expression levels in 6891 cSCC cases and 54,566 controls in the Kaiser Permanente Genetic Epidemiology Research in Adult Health and Aging (GERA) cohort and 25,558 self-reported cSCC cases a ...[more]

PMID: 30323283

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