ArticlePhilosophical transactions of the Royal Society of London. Series B, Biological sciences2013
Deconvoluting complex tissues for expression quantitative trait locus-based analyses.
Article in Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed, 8 citations in OpenAlex.
- Cancer-associated adipocytes: metabolic reprogramming, crosstalk and therapeutic implications in tumor progression.Signal transduction and targeted therapy · 2026Review
- Functional annotation of breast cancer risk loci: current progress and future directions.British journal of cancer · 2022Review
- Expression Quantitative Trait loci (QTL) in tumor adjacent normal breast tissue and breast tumor tissue.PloS one · 2017Article
- FGFR2 risk SNPs confer breast cancer risk by augmenting oestrogen responsiveness.Carcinogenesis · 2016Article
- An assessment of computational methods for estimating purity and clonality using genomic data derived from heterogeneous tumor tissue samples.Briefings in bioinformatics · 2015Review
- Single nucleotide polymorphisms of caudal type homeobox 1 and 2 are associated with Barrett's esophagus.Digestive diseases and sciences · 2014Article
- Regulation from a distance: long-range control of gene expression in development and disease.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2013Article
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Authors and funding
8 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Breast cancer genome-wide association studies have pinpointed dozens of variants associated with breast cancer pathogenesis. The majority of risk variants, however, are located outside of known protein-coding regions. Therefore, identifying which genes the risk variants are acting through presents an important challenge. Variants that are associated with mRNA transcript levels are referred to as expression quantitative trait loci (eQTLs). Many studies have demonstrated that eQTL-based strategies provide a direct way to connect a trait-associated locus with its candidate target gene. Performing eQTL-based analyses in human samples is complicated because of the heterogeneous nature of human tissue. We addressed this issue by devising a method to computationally infer the fraction of cell types in normal human breast tissues. We then applied this method to 13 known breast cancer risk loci, which we hypothesized were eQTLs. For each risk locus, we took all known transcripts within a 2 Mb interval and performed an eQTL analysis in 100 reduction mammoplasty cases. A total of 18 significant associations were discovered (eight in the epithelial compartment and 10 in the stromal compartment). This study highlights the ability to perform large-scale eQTL studies in heterogeneous tissues.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.