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SpecHLA enables full-resolution HLA typing from sequencing data
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 read...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Elsevier
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10545945/ https://www.ncbi.nlm.nih.gov/pubmed/37714157 http://dx.doi.org/10.1016/j.crmeth.2023.100589 |
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author | Wang, Shuai Wang, Mengyao Chen, Lingxi Pan, Guangze Wang, Yanfei Li, Shuai Cheng |
author_facet | Wang, Shuai Wang, Mengyao Chen, Lingxi Pan, Guangze Wang, Yanfei Li, Shuai Cheng |
author_sort | Wang, Shuai |
collection | PubMed |
description | 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 98.6% accuracy for G-group-resolution HLA typing, inferring entire HLA alleles with an average of three mismatches fewer, ten gaps fewer, and 590 bp less edit distance than HISAT-genotype per allele. Additionally, SpecHLA exhibited a 2-field typing accuracy of 98.6% in 875 real samples. Finally, SpecHLA detected HLA loss of heterozygosity with 99.7% specificity and 96.8% sensitivity in simulated samples of cancer cell lines. |
format | Online Article Text |
id | pubmed-10545945 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Elsevier |
record_format | MEDLINE/PubMed |
spelling | pubmed-105459452023-10-04 SpecHLA enables full-resolution HLA typing from sequencing data Wang, Shuai Wang, Mengyao Chen, Lingxi Pan, Guangze Wang, Yanfei Li, Shuai Cheng Cell Rep Methods Report 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 98.6% accuracy for G-group-resolution HLA typing, inferring entire HLA alleles with an average of three mismatches fewer, ten gaps fewer, and 590 bp less edit distance than HISAT-genotype per allele. Additionally, SpecHLA exhibited a 2-field typing accuracy of 98.6% in 875 real samples. Finally, SpecHLA detected HLA loss of heterozygosity with 99.7% specificity and 96.8% sensitivity in simulated samples of cancer cell lines. Elsevier 2023-09-14 /pmc/articles/PMC10545945/ /pubmed/37714157 http://dx.doi.org/10.1016/j.crmeth.2023.100589 Text en © 2023 The Author(s) https://creativecommons.org/licenses/by/4.0/This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Report Wang, Shuai Wang, Mengyao Chen, Lingxi Pan, Guangze Wang, Yanfei Li, Shuai Cheng SpecHLA enables full-resolution HLA typing from sequencing data |
title | SpecHLA enables full-resolution HLA typing from sequencing data |
title_full | SpecHLA enables full-resolution HLA typing from sequencing data |
title_fullStr | SpecHLA enables full-resolution HLA typing from sequencing data |
title_full_unstemmed | SpecHLA enables full-resolution HLA typing from sequencing data |
title_short | SpecHLA enables full-resolution HLA typing from sequencing data |
title_sort | spechla enables full-resolution hla typing from sequencing data |
topic | Report |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10545945/ https://www.ncbi.nlm.nih.gov/pubmed/37714157 http://dx.doi.org/10.1016/j.crmeth.2023.100589 |
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