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

Area of Science:

• Immunogenetics
• Computational Biology

Background:

• Human leukocyte antigen (HLA) haplotype knowledge is crucial for disease association studies, population genetics, and hematopoietic stem cell transplantation.
• Accurate HLA haplotype frequencies are essential for optimizing donor searches and registry planning in hematopoietic stem cell transplantation.
• Estimating HLA haplotype frequencies is challenging due to large datasets, complex nomenclature, and ambiguous typing records.

Purpose of the Study:

• To develop an efficient open-source software solution for estimating HLA haplotype frequencies.
• To address the challenges of large datasets, complex nomenclature, and ambiguous typing records in HLA frequency estimation.

Main Methods:

• Developed Hapl-o-Mat, an open-source software utilizing an expectation-maximization algorithm.
• Implemented Hapl-o-Mat in C++ for efficient processing of large genotype datasets.
• Designed to handle varying HLA typing resolutions and ambiguous data formats.

Main Results:

• Hapl-o-Mat successfully estimates HLA haplotype frequencies from population data with multiple loci.
• The software efficiently processes diverse HLA typing resolutions and ambiguous genotype records.
• Demonstrated accuracy and performance using both artificial and real-world genotype data.

Conclusions:

• Hapl-o-Mat is a versatile and efficient software for HLA haplotype frequency estimation.
• The software simplifies haplotype frequency estimation from typical stem cell donor registry typing records.
• Facilitates improved donor selection and registry management through accurate HLA frequency data.