ATHLATES: accurate typing of human leukocyte antigen through exome sequencing - PubMed (original) (raw)
ATHLATES: accurate typing of human leukocyte antigen through exome sequencing
Chang Liu et al. Nucleic Acids Res. 2013 Aug.
Abstract
Human leukocyte antigen (HLA) typing at the allelic level can in theory be achieved using whole exome sequencing (exome-seq) data with no added cost but has been hindered by its computational challenge. We developed ATHLATES, a program that 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. This novel approach should be broadly applicable to research and clinical laboratories.
Figures
Figure 1.
Workflow of allelic HLA typing using exome-seq data. Exome-seq data are first filtered by comparison against all alleles of HLA genes obtained from IMGT/HLA database, and then fed into ATHLATES for in silico allelic HLA typing without human supervision.
Figure 2.
Coverage of target genes by exome-seq data and comparison of HLA typing results among conventional typing, ATHLATES and HLAminer. (A) Fold coverage at exons of each of the five target HLA genes. Paired-end reads are aligned to the typed alleles of individual samples, and the fold coverage data from all 15 samples are presented. Median coverage (gray lines) and range (gray areas) are plotted over alignment positions for individual HLA genes. Dotted lines are exon boundaries, and the exons are numbered below each plot. The disruptions in curves are caused by mapping the reads to an alignment coordinate based on a MSA of all alleles of a target gene. The insertions present in rare alleles make the curves appear to be discontinuous. The one or two exons toward the 3′ end are exceedingly short (e.g. 5 bp for exon 8 of HLA-A) and hence, may not be reliably aligned against. (B) Concordance rates of HLA typing results by ATHLATES and HLAminer as compared with conventional Sanger-based method for the 15 data sets with adequate coverage.
Similar articles
- Using Exome and Amplicon-Based Sequencing Data for High-Resolution HLA Typing with ATHLATES.
Liu C, Yang X. Liu C, et al. Methods Mol Biol. 2018;1802:203-213. doi: 10.1007/978-1-4939-8546-3_14. Methods Mol Biol. 2018. PMID: 29858811 - HLA typing from 1000 genomes whole genome and whole exome illumina data.
Major E, Rigó K, Hague T, Bérces A, Juhos S. Major E, et al. PLoS One. 2013 Nov 6;8(11):e78410. doi: 10.1371/journal.pone.0078410. eCollection 2013. PLoS One. 2013. PMID: 24223151 Free PMC article. - HLAscan: genotyping of the HLA region using next-generation sequencing data.
Ka S, Lee S, Hong J, Cho Y, Sung J, Kim HN, Kim HL, Jung J. Ka S, et al. BMC Bioinformatics. 2017 May 12;18(1):258. doi: 10.1186/s12859-017-1671-3. BMC Bioinformatics. 2017. PMID: 28499414 Free PMC article. - HLA typing by next-generation sequencing - getting closer to reality.
Gabriel C, Fürst D, Faé I, Wenda S, Zollikofer C, Mytilineos J, Fischer GF. Gabriel C, et al. Tissue Antigens. 2014 Feb;83(2):65-75. doi: 10.1111/tan.12298. Tissue Antigens. 2014. PMID: 24447174 Review. - HLA testing in the molecular diagnostic laboratory.
Madden K, Chabot-Richards D. Madden K, et al. Virchows Arch. 2019 Feb;474(2):139-147. doi: 10.1007/s00428-018-2501-3. Epub 2018 Dec 4. Virchows Arch. 2019. PMID: 30515565 Review.
Cited by
- Molecular targets and strategies in the development of nucleic acid cancer vaccines: from shared to personalized antigens.
Chi WY, Hu Y, Huang HC, Kuo HH, Lin SH, Kuo CJ, Tao J, Fan D, Huang YM, Wu AA, Hung CF, Wu TC. Chi WY, et al. J Biomed Sci. 2024 Oct 9;31(1):94. doi: 10.1186/s12929-024-01082-x. J Biomed Sci. 2024. PMID: 39379923 Free PMC article. Review. - A novel framework for human leukocyte antigen (HLA) genotyping using probe capture-based targeted next-generation sequencing and computational analysis.
Lai SK, Luo AC, Chiu IH, Chuang HW, Chou TH, Hung TK, Hsu JS, Chen CY, Yang WS, Yang YC, Chen PL. Lai SK, et al. Comput Struct Biotechnol J. 2024 Apr 2;23:1562-1571. doi: 10.1016/j.csbj.2024.03.030. eCollection 2024 Dec. Comput Struct Biotechnol J. 2024. PMID: 38650588 Free PMC article. - A rigorous benchmarking of alignment-based HLA typing algorithms for RNA-seq data.
Yu D, Ayyala R, Sadek SH, Chittampalli L, Farooq H, Jung J, Nahid AA, Boldirev G, Jung M, Park S, Nguyen A, Zelikovsky A, Mancuso N, Joo JWJ, Thompson RF, Alachkar H, Mangul S. Yu D, et al. bioRxiv [Preprint]. 2024 Jan 16:2023.05.22.541750. doi: 10.1101/2023.05.22.541750. bioRxiv. 2024. PMID: 38293199 Free PMC article. Preprint. - Clinical variables and genetic variants associated with perioperative anaphylaxis in Chinese Han population: A pilot study.
Qi Z, Cheng Y, Su Y, Qiao Y, Zhang J, Yang JJ, Xing Q. Qi Z, et al. World Allergy Organ J. 2023 Dec 27;17(1):100854. doi: 10.1016/j.waojou.2023.100854. eCollection 2024 Jan. World Allergy Organ J. 2023. PMID: 38223133 Free PMC article. - Historical perspective and future directions: computational science in immuno-oncology.
Ricker CA, Meli K, Van Allen EM. Ricker CA, et al. J Immunother Cancer. 2024 Jan 8;12(1):e008306. doi: 10.1136/jitc-2023-008306. J Immunother Cancer. 2024. PMID: 38191244 Free PMC article. Review.
References
- Lind C, Ferriola D, Mackiewicz K, Heron S, Rogers M, Slavich L, Walker R, Hsiao T, McLaughlin L, D'Arcy M, et al. Next-generation sequencing: the solution for high-resolution, unambiguous human leukocyte antigen typing. Hum. Immunol. 2010;71:1033–1042. - PubMed
- Erlich H. HLA DNA typing: past, present, and future. Tissue Antigens. 2012;80:1–11. - PubMed
- Gabriel C, Danzer M, Hackl C, Kopal G, Hufnagl P, Hofer K, Polin H, Stabentheiner S, and Proll J. Rapid high-throughput human leukocyte antigen typing by massively parallel pyrosequencing for high-resolution allele identification. Hum. Immunol. 2009;70:960–964. - PubMed
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
Other Literature Sources
Research Materials