Treatment of the X chromosome in mapping multiple quantitative trait loci. Issue 2 (23rd January 2021)

• Record Type: Journal Article
• Authors: Tran, Quoc; Broman, Karl W
• Editors: Threadgill, D
• Is Part Of: G3. Volume 11:Issue 2(2021)
• Publication Date: 2021-01-23
• Subjects: QTL -- model selection -- X chromosome; Genetics -- Research -- Periodicals; Genomics -- Periodicals; Genetics; Genomics; Genes; Genetics -- Research; Genomics; Electronic journals; Periodical; Periodicals; Fulltext; Internet Resources; Periodicals; 572.8
• DOI: 10.1093/g3journal/jkab005
• Languages: English
• ISSNs: 2160-1836

Abstract

Abstract: Statistical methods to map quantitative trait loci (QTL) often neglect the X chromosome and may focus exclusively on autosomal loci. But the X chromosome often requires special treatment: sex and cross-direction covariates may need to be included to avoid spurious evidence of linkage, and the X chromosome may require a separate significance threshold. In multiple-QTL analyses, including the consideration of epistatic interactions, the X chromosome also requires special care and consideration. We extend a penalized likelihood method for multiple-QTL model selection, to appropriately handle the X chromosome. We examine its performance in simulation and by application to a large eQTL data set. The method has been implemented in the package R/qtl.