HLA genotyping software tools | Whole-exome sequencing data analysis

A HLA genotyping algorithm based on integer linear programming, capable of producing accurate predictions from NGS data not specifically enriched for the HLA cluster. OptiType significantly outperformed previously published in silico approaches with an overall accuracy of 97% enabling its use in a broad range of applications.

Determines human leukocyte antigen (HLA) matching at epitope level in alloantibody responses. HLAMatchmaker utilizes an algorithm where each HLA antigen is considered as a string of amino acid configurations in antibody-accessible positions. This program can be used as a quantitative tool to define the degree of a mismatch such as mismatched eplets of triplets.

A software for HLA class I and II predictions from next-generation shotgun (NGS) sequence read data that supports direct read alignment and targeted assembly of sequence reads. This approach circumvents the additional time and cost of generating HLA-specific data and capitalizes on the increasing accessibility and affordability of massively parallel sequencing.

Applies assembly, allele identification and allelic pair inference to short read sequences, and applied it to data from Illumina platforms. In 15 data sets with adequate coverage for HLA-A, -B, -C, -DRB1 and -DQB1 genes, ATHLATES correctly reported 74 out of 75 allelic pairs with an overall concordance rate of 99% compared with conventional typing.

A NGS data analysis pipeline allowing user to make HLA alleles genotyping quickly and efficiently. HLATyphon supports all cDNA template of HLA locus A, B, C, DPA1, DPB1, DQA1, DQB1 and DRB1 in IMGT/HLA database. Currently the internal HLA allele reference sequences of HLATyphon were from IMGT/HLA database release 3.17.0 including 12,010 alleles.