HLA genotyping software tools | Whole-exome sequencing data analysis
The human leukocyte antigen (HLA) gene cluster plays a crucial role in adaptive immunity and is thus relevant in many biomedical applications. While next-generation sequencing data are often available for a patient, deducing the HLA genotype is difficult because of substantial sequence similarity within the cluster and exceptionally high variability of the loci.
Enables high precision Human Leukocyte Antigen (HLA)-typing even. POLYSOLVER uses relatively low coverage whole exome sequencing (WES) data and a subsequent mutation detection pipeline that is based on the inferred alleles to detect mutations in HLA genes. The tool is able to infer HLA-type information with 97 per cent sensitivity and 98 per cent precision from exome-capture sequencing data. It can extract sequence and mutation information from other polymorphic regions in the genome.
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 tool for HLA typing from NGS data based on read-mapping using a comprehensive reference panel containing all known HLA alleles, followed by de novo assembly of the gene-specific short reads. Accurate HLA typing from NGS data holds much promise for applications in clinical laboratories and biomedical research. Preliminary analysis on both public and local datasets indicates a great potential for broad application of this method.
A tool algorithm named to discover the most probable pair of HLA alleles at four-digit resolution or higher, via a unique integration of a candidate allele selection and a likelihood scoring. PHLAT significantly leverages the accuracy and flexibility of high resolution HLA typing based on genome-wide sequencing data. It may benefit both basic and applied research in immunology and related fields as well as numerous clinical applications.