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bioRxiv · 10.1101/2020.09.11.294017

Treatment of the X chromosome in mapping multiple quantitative trait loci

Tran, Q.·Broman, K. W.
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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.

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Tran, Q., Broman, K. W.. 2020-09-11. Treatment of the X chromosome in mapping multiple quantitative trait loci. https://doi.org/10.1101/2020.09.11.294017

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