SpecHLA enables full-resolution HLA typing from sequencing data.

ABSTRACT: Reconstructing diploid sequences of human leukocyte antigen (HLA) genes, i.e., full-resolution HLA typing, from sequencing data is challenging. The high homogeneity across HLA genes and the high heterogeneity within HLA alleles complicate the identification of genomic source loci for sequencing reads. Here, we present SpecHLA, which utilizes fine-tuned reads binning and local assembly to achieve accurate full-resolution HLA typing. SpecHLA accepts sequencing data from paired-end, 10×-linked-reads, high-throughput chromosome conformation capture (Hi-C), Pacific Biosciences (PacBio), and Oxford Nanopore Technology (ONT). It can also incorporate pedigree data and genotype frequency to refine typing. In 32 Human Genome Structural Variation Consortium, Phase 2 (HGSVC2) samples, SpecHLA achieved

SUBMITTER: Wang S 

PROVIDER: S-EPMC10545945 | biostudies-literature | 2023 Sep

REPOSITORIES: biostudies-literature