The HLA genes are the most polymorphic loci of the genome, and also the most associated with disease. This places HLA genes among the most studied genes in the genome. However, their extreme polymorphism imposes challenges to methods of expression quantification, and as a consequence the study of HLA expression and regulation is still in its infancy. In our main project, we have developed a computational pipeline to provide reliable expression estimates for HLA genes using standard RNA-seq data, and applied it to a public dataset of 445 individuals to estimate expression and map the genetic variants that regulate it. Now, a natural extension is (1) to integrate our HLA analysis pipeline as a routine in the program QTLtools, and make it publicly available; (2) use this program to extend our analysis of HLA expression to multiple tissues, made available by the GTEx consortium. In order to achieve these goals, we propose a collaboration with the Dermitzakis group at the University of Geneva, which played a main role in the GTEx consortium and has expertise in the development of bioinformatic tools, including an efficient package for QTL mapping.
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