HLA-MA: Simple yet powerful matching of samples using HLA typing results

Abstract

SummaryWe propose the simple method HLA-MA for consistency checking in pipelines operating on human HTS data. The method is based on the HLA typing result of the state-of-the-art method Opti-Type. Provided that there is sufficient coverage of the HLA loci, comparing HLA types allows for simple, fast, and robust matching of samples from whole genome, exome, and RNA-seq data. This approach is reliable for sample re-identification even for samples with high mutational loads, e.g., caused by microsatellite instability or POLE1 defects.\n\nAvailability and ImplementationThe software is implemented In Python 3 and freely available under the MIT license at https://github.com/bihealth/hlama and via Bioconda.\n\nContactdieter.beule@bihealth.de