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Cell DOI:10.1016/j.cell.2012.12.034

Integrative eQTL-based analyses reveal the biology of breast cancer risk loci.

Publication TypeJournal Article
Year of Publication2013
AuthorsLi, Q, Seo, J-H, Stranger, B, McKenna, A, Pe'er, I, LaFramboise, T, Brown, M, Tyekucheva, S, Freedman, ML
Date Published2013 Jan 31
KeywordsBreast Neoplasms, Cell Line, Tumor, Gene Expression Profiling, Genetic Predisposition to Disease, Genome-Wide Association Study, Humans, Quantitative Trait Loci

Germline determinants of gene expression in tumors are infrequently studied due to the complexity of transcript regulation caused by somatically acquired alterations. We performed expression quantitative trait locus (eQTL)-based analyses using the multi-level information provided in The Cancer Genome Atlas (TCGA). Of the factors we measured, cis-acting eQTLs accounted for 1.2% of the total variation of tumor gene expression, while somatic copy-number alteration and CpG methylation accounted for 7.3% and 3.3%, respectively. eQTL analyses of 15 previously reported breast cancer risk loci resulted in the discovery of three variants that are significantly associated with transcript levels (false discovery rate [FDR] 


Alternate JournalCell
PubMed ID23374354
PubMed Central IDPMC4165609
Grant ListR01 CA129435 / CA / NCI NIH HHS / United States
R01 CA131341 / CA / NCI NIH HHS / United States
U19 CA148537 / CA / NCI NIH HHS / United States