Hapl-o-Mat: open-source software for HLA haplotype frequency estimation from ambiguous and heterogeneous data

BMC Bioinformatics

Software

Jürgen Sauter¹  Alexander H. Schmidt¹  Christian Schäfer¹ 

[1] DKMS gemeinnützige GmbH, Kressbach 1, 72072, Tübingen, Germany;

关键词: HLA;    Immunogenetics;    Population genetics;    Bioinformatics;    Haplotype;    Expectation-maximization algorithm;    Open-source software;   

DOI  :  10.1186/s12859-017-1692-y

 received in 2016-07-21, accepted in 2017-05-18,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundKnowledge of HLA haplotypes is helpful in many settings as disease association studies, population genetics, or hematopoietic stem cell transplantation. Regarding the recruitment of unrelated hematopoietic stem cell donors, HLA haplotype frequencies of specific populations are used to optimize both donor searches for individual patients and strategic donor registry planning. However, the estimation of haplotype frequencies from HLA genotyping data is challenged by the large amount of genotype data, the complex HLA nomenclature, and the heterogeneous and ambiguous nature of typing records.ResultsTo meet these challenges, we have developed the open-source software Hapl-o-Mat. It estimates haplotype frequencies from population data including an arbitrary number of loci using an expectation-maximization algorithm. Its key features are the processing of different HLA typing resolutions within a given population sample and the handling of ambiguities recorded via multiple allele codes or genotype list strings. Implemented in C++, Hapl-o-Mat facilitates efficient haplotype frequency estimation from large amounts of genotype data. We demonstrate its accuracy and performance on the basis of artificial and real genotype data.ConclusionsHapl-o-Mat is a versatile and efficient software for HLA haplotype frequency estimation. Its capability of processing various forms of HLA genotype data allows for a straightforward haplotype frequency estimation from typing records usually found in stem cell donor registries.

【 授权许可】

CC BY   
© The Author(s). 2017

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