ArticleBMC bioinformatics2017
Hapl-o-Mat: open-source software for HLA haplotype frequency estimation from ambiguous and heterogeneous data.
Article in BMC bioinformatics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- HLA Alleles and Haplotype Distribution Across Russian Population Groups.International journal of molecular sciences · 2026Article
- Development and validation of a pipeline for the systematic search for new HLA alleles in WGS data.Frontiers in bioinformatics · 2026Article
- Article
- HLA allele and haplotype frequencies of eight Indian populations based on 130,518 registered stem cell donors.Frontiers in immunology · 2025Article
- Association of human leucocyte antigen loci with vaccine-induced immune thrombotic thrombocytopenia: Potential role of the interaction between platelet factor 4-derived peptides and MHC-II.British journal of haematology · 2025Article
- Optimisation of global stem cell donor recruitment based on analysis of unsuccessful donor searches.HLA · 2024Article
- PGG.MHC: toward understanding the diversity of major histocompatibility complexes in human populations.Nucleic acids research · 2023Article
- 5 years DKMS Chile: approach, results and impact of the first unrelated stem cell donor center in Chile.Frontiers in medicine · 2023Article
- HLA allele and haplotype frequencies of registered stem cell donors in Chile.Frontiers in immunology · 2023Article
- Distributions of the HLA-A, HLA-B, HLA-C, HLA-DRB1, and HLA-DQB1 alleles and haplotype frequencies of 1763 stem cell donors in the Colombian Bone Marrow Registry typed by next-generation sequencing.Frontiers in immunology · 2022Article
- Distribution ofFrontiers in pharmacology · 2022Article
- Article
- Estimating HLA haplotype frequencies from homozygous individuals - A Technical Report.International journal of immunogenetics · 2021Article
- Should results of HLA haplotype frequency estimations be normalized?International journal of immunogenetics · 2021Article
- A high-resolution HLA reference panel capturing global population diversity enables multi-ancestry fine-mapping in HIV host response.Nature genetics · 2021Article
- Next-generation sequencing of 11 HLA loci in a large dengue vaccine cohort from the Philippines.Human immunology · 2020Article
- Hepatitis B infection outcome is associated with novel human leukocyte antigen variants in Ghanaian cohort.Experimental biology and medicine (Maywood, N.J.) · 2020Article
- Diversity of HLA Class I and Class II blocks and conserved extended haplotypes in Lacandon Mayans.Scientific reports · 2020Article
- Immunogenetics in stem cell donor registry work: The DKMS example (Part 1).International journal of immunogenetics · 2020Review
- HLA Haplotype Frequencies and Genetic Profiles of the Kuwaiti Population.Medical principles and practice : international journal of the Kuwait University, Health Science Centre · 2020Article
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3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
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.
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