BaseQTL: a Bayesian method to detect eQTLs from RNA-seq data with or without genotypes
BaseQTL: a Bayesian method to detect eQTLs from RNA-seq data with or without genotypes
Abstract Available methods to detect molecular quantitative trait loci (QTL) require study individuals to be genotyped. Here, we describe BaseQTL, a Bayesian method that exploits allele-specific expression to map molecular QTL from sequencing reads even when no genotypes are available. When used with genotypes, BaseQTL has lower error rates and increased power compared with existing QTL mapping methods. Running without genotypes limits how many tests can be performed, but due to the proximity of QTL variants to gene bodies, the 2.8% of variants within a 100kB-window that could be tested, contained 26% of QTL variants detectable with genotypes. eQTL effect estimates were invariably consistent between analyses performed with and without genotypes. Often, sequencing data may be generated in absence of genotypes on patients and controls in differential expression studies, and we identified an apparent psoriasis-specific effect for GSTP1 in one such dataset, providing new insights into disease-dependent gene regulation.
Wallace Chris、Starr Colin、Lin Wei-Yu、Kirk Paul DW、White Simon R、Vigorito Elena
MRC Biostatistics Unit, University of Cambridge||Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of CambridgeMRC Biostatistics Unit, University of CambridgeMRC Biostatistics Unit, University of CambridgeMRC Biostatistics Unit, University of Cambridge||Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of CambridgeMRC Biostatistics Unit, University of Cambridge||Department of Psychiatry, University of CambridgeMRC Biostatistics Unit, University of Cambridge
基础医学生物科学研究方法、生物科学研究技术分子生物学
Wallace Chris,Starr Colin,Lin Wei-Yu,Kirk Paul DW,White Simon R,Vigorito Elena.BaseQTL: a Bayesian method to detect eQTLs from RNA-seq data with or without genotypes[EB/OL].(2025-03-28)[2025-05-28].https://www.biorxiv.org/content/10.1101/2020.07.16.203851.点此复制
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