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


RESULTS
To 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.


CONCLUSIONS
Hapl-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.
['Schäfer|Christian|C|', 'Schmidt|Alexander H|AH|', 'Sauter|Jürgen|J|http://orcid.org/0000-0001-8485-2945']
D000465:Algorithms D000483:Alleles D005787:Gene Frequency D005838:Genotype D006680:HLA Antigens D006239:Haplotypes D006650:Histocompatibility Testing D006801:Humans D012984:Software
Open-source software HLA Haplotype Population genetics Expectation-maximization algorithm Bioinformatics Immunogenetics