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. 2019 Aug 16;10:714. doi: 10.3389/fgene.2019.00714

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Copyright © 2019 Mariella, Marotta, Grassi, Gilotto and Provero

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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Schematic representation of the method. Genotypic data paired with RNA-Seq data from a large cohort of individuals are required to perform alternative polyadenylation quantitative trait loci (apaQTL) mapping analysis. RNA-Seq data are exploited, together with an annotation of alternative 3′ untranslated region (UTR) isoforms, to compute for each gene the m/M value that is proportional to the ratio between the expression of its short and long 3′ UTR isoforms. Then, the association between the m/M values of a gene and each nearby genetic variant is evaluated by linear regression. Genotypes are defined in the standard way: 0 means homozygous for the reference allele, 1 means heterozygous, and 2 indicates the presence of two copies of the alternative allele.