Long-read Sequencing Reveals Novel Genetic Polymorphisms in the Major Histocompatibility Complex Region and Their Impacts on the Han Chinese Population

Overview

Journal Sci China Life Sci

Date 2025 Jan 17

PMID 39821835

Authors

Cong Zhou

Tingting Gong

Shuhang Li

Li Jin

Shaohua Fan

Affiliations

Soon will be listed here.

Abstract

Human leukocyte antigen (HLA) genes in the major histocompatibility complex (MHC) region are crucial for immunity and are associated with numerous diseases and phenotypes. The MHC region's complexity and high genetic diversity make it challenging to analyze using short-read sequencing (SRS) technology. We sequence the MHC region of 100 Han Chinese individuals using both long-read sequencing (LRS) and SRS platforms at approximately 30X coverage to study genetic alterations and their potential functional impacts. LRS provides significantly greater coverage of the MHC region and eight classical HLA genes, particularly at the HLA-DRB1 locus, compared with SRS. We detect 78,249 single nucleotide polymorphisms (SNPs) using LRS, with 26.0% undetectable by SRS. Based on SNP and inferred HLA allele types, we construct an LRS-based MHC reference panel for the Han Chinese, containing approximately 2.6 times more genetic variants than the SRS-based Han-MHC reference panel. A phenome-wide association study assessing 26,024 phenotypes across 15 categories identifies significant associations for 7,879 independent variants (including 809 LRS-specific SNPs) with 409 phenotypes in nine categories. This analysis reveals 24 unreported HLA allele associations in the bioelectric and cellular categories. The conditional analysis identifies 530 independent signals across the 409 phenotypes, including 28 previously unreported signals of eight classical HLA genes associated with 33 phenotypes. Of the top-associated SNPs, 191 are detected by LRS only. Fine-mapping identifies 126 independent candidate causal SNPs for three immune-related cellular phenotypes, with 17 detected exclusively by LRS. Our study reveals previously unreported variants and their functional impacts in the MHC region, enhancing our understanding of genetic diversity and its potential biological implications in the Han Chinese population.

References

Bailey J, Gu Z, Clark R, Reinert K, Samonte R, Schwartz S . Recent segmental duplications in the human genome. Science. 2002; 297(5583):1003-7. DOI: 10.1126/science.1072047. View

Bailey J, Yavor A, Massa H, Trask B, Eichler E . Segmental duplications: organization and impact within the current human genome project assembly. Genome Res. 2001; 11(6):1005-17. PMC: 311093. DOI: 10.1101/gr.gr-1871r. View

Benner C, Spencer C, Havulinna A, Salomaa V, Ripatti S, Pirinen M . FINEMAP: efficient variable selection using summary data from genome-wide association studies. Bioinformatics. 2016; 32(10):1493-501. PMC: 4866522. DOI: 10.1093/bioinformatics/btw018. View

Cao H, Wu J, Wang Y, Jiang H, Zhang T, Liu X . An integrated tool to study MHC region: accurate SNV detection and HLA genes typing in human MHC region using targeted high-throughput sequencing. PLoS One. 2013; 8(7):e69388. PMC: 3722289. DOI: 10.1371/journal.pone.0069388. View

Chin C, Wagner J, Zeng Q, Garrison E, Garg S, Fungtammasan A . A diploid assembly-based benchmark for variants in the major histocompatibility complex. Nat Commun. 2020; 11(1):4794. PMC: 7508831. DOI: 10.1038/s41467-020-18564-9. View

Choi W, Luo Y, Raychaudhuri S, Han B . HATK: HLA analysis toolkit. Bioinformatics. 2020; 37(3):416-418. PMC: 8058762. DOI: 10.1093/bioinformatics/btaa684. View

Choo S . The HLA system: genetics, immunology, clinical testing, and clinical implications. Yonsei Med J. 2007; 48(1):11-23. PMC: 2628004. DOI: 10.3349/ymj.2007.48.1.11. View

Cook S, Choi W, Lim H, Luo Y, Kim K, Jia X . Accurate imputation of human leukocyte antigens with CookHLA. Nat Commun. 2021; 12(1):1264. PMC: 7904773. DOI: 10.1038/s41467-021-21541-5. View

Danecek P, Auton A, Abecasis G, Albers C, Banks E, DePristo M . The variant call format and VCFtools. Bioinformatics. 2011; 27(15):2156-8. PMC: 3137218. DOI: 10.1093/bioinformatics/btr330. View

10.

Danecek P, Bonfield J, Liddle J, Marshall J, Ohan V, Pollard M . Twelve years of SAMtools and BCFtools. Gigascience. 2021; 10(2). PMC: 7931819. DOI: 10.1093/gigascience/giab008. View

11.

Das S, Forer L, Schonherr S, Sidore C, Locke A, Kwong A . Next-generation genotype imputation service and methods. Nat Genet. 2016; 48(10):1284-1287. PMC: 5157836. DOI: 10.1038/ng.3656. View

12.

Dilthey A, Mentzer A, Carapito R, Cutland C, Cereb N, Madhi S . HLA*LA-HLA typing from linearly projected graph alignments. Bioinformatics. 2019; 35(21):4394-4396. PMC: 6821427. DOI: 10.1093/bioinformatics/btz235. View

13.

Hirata J, Hosomichi K, Sakaue S, Kanai M, Nakaoka H, Ishigaki K . Genetic and phenotypic landscape of the major histocompatibilty complex region in the Japanese population. Nat Genet. 2019; 51(3):470-480. DOI: 10.1038/s41588-018-0336-0. View

14.

Jain C, Rhie A, Zhang H, Chu C, Walenz B, Koren S . Weighted minimizer sampling improves long read mapping. Bioinformatics. 2020; 36(Suppl_1):i111-i118. PMC: 7355284. DOI: 10.1093/bioinformatics/btaa435. View

15.

Jain M, Koren S, Miga K, Quick J, Rand A, Sasani T . Nanopore sequencing and assembly of a human genome with ultra-long reads. Nat Biotechnol. 2018; 36(4):338-345. PMC: 5889714. DOI: 10.1038/nbt.4060. View

16.

Jia X, Han B, Onengut-Gumuscu S, Chen W, Concannon P, Rich S . Imputing amino acid polymorphisms in human leukocyte antigens. PLoS One. 2013; 8(6):e64683. PMC: 3675122. DOI: 10.1371/journal.pone.0064683. View

17.

Johnson M, Zaretskaya I, Raytselis Y, Merezhuk Y, McGinnis S, Madden T . NCBI BLAST: a better web interface. Nucleic Acids Res. 2008; 36(Web Server issue):W5-9. PMC: 2447716. DOI: 10.1093/nar/gkn201. View

18.

Karnes J, Bastarache L, Shaffer C, Gaudieri S, Xu Y, Glazer A . Phenome-wide scanning identifies multiple diseases and disease severity phenotypes associated with HLA variants. Sci Transl Med. 2017; 9(389). PMC: 5563969. DOI: 10.1126/scitranslmed.aai8708. View

19.

Kim C, Kim Y, Choi W, Jang H, Hwang M, Jung S . Phenome-wide association study of the major histocompatibility complex region in the Korean population identifies novel association signals. Hum Mol Genet. 2022; 31(15):2655-2667. DOI: 10.1093/hmg/ddac016. View

20.

Kronenberg Z, Rhie A, Koren S, Concepcion G, Peluso P, Munson K . Extended haplotype-phasing of long-read de novo genome assemblies using Hi-C. Nat Commun. 2021; 12(1):1935. PMC: 8081726. DOI: 10.1038/s41467-020-20536-y. View