Deep sequencing of the MHC region in the Chinese population contributes to studies of complex disease

doi:10.1038/ng.3576

Comparative Study

. 2016 Jul;48(7):740-6.

doi: 10.1038/ng.3576. Epub 2016 May 23.

Deep sequencing of the MHC region in the Chinese population contributes to studies of complex disease

Fusheng Zhou¹, Hongzhi Cao^{2

3

4}, Xianbo Zuo¹, Tao Zhang², Xiaoguang Zhang¹, Xiaomin Liu², Ricong Xu⁵, Gang Chen¹, Yuanwei Zhang^{2

6}, Xiaodong Zheng¹, Xin Jin², Jinping Gao¹, Junpu Mei², Yujun Sheng¹, Qibin Li², Bo Liang¹, Juan Shen², Changbing Shen¹, Hui Jiang^{2

4}, Caihong Zhu¹, Xing Fan¹, Fengping Xu^{2

4}, Min Yue¹, Xianyong Yin¹, Chen Ye², Cuicui Zhang¹, Xiao Liu^{2

4}, Liang Yu¹, Jinghua Wu², Mengyun Chen¹, Xuehan Zhuang², Lili Tang¹, Haojing Shao², Longmao Wu¹, Jian Li^{2

4}, Yu Xu¹, Yijie Zhang², Suli Zhao¹, Yu Wang², Ge Li¹, Hanshi Xu², Lei Zeng¹, Jianan Wang², Mingzhou Bai², Yanling Chen², Wei Chen², Tian Kang², Yanyan Wu¹, Xun Xu², Zhengwei Zhu¹, Yong Cui⁷, Zaixing Wang¹, Chunjun Yang⁸, Peiguang Wang¹, Leihong Xiang¹, Xiang Chen⁹, Anping Zhang¹, Xinghua Gao¹⁰, Furen Zhang¹¹, Jinhua Xu¹², Min Zheng¹³, Jie Zheng¹⁴, Jianzhong Zhang¹⁵, Xueqing Yu⁵, Yingrui Li^{2

3

16}, Sen Yang¹, Huanming Yang², Jian Wang^{2

17}, Jianjun Liu¹, Lennart Hammarström^{2

18}, Liangdan Sun¹, Jun Wang^{2

3

4

19

20

21

22}, Xuejun Zhang^{1

7

8

12}

Affiliations

¹ Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China.
² BGI-Shenzhen, Shenzhen, China.
³ iCarbonX, Shenzhen, China.
⁴ Department of Biology, University of Copenhagen, Copenhagen, Denmark.
⁵ Department of Nephrology, First Affiliated Hospital, Sun Yat-sen University, Key Laboratory of Nephrology, Ministry of Health, Guangzhou, China.
⁶ School of Biological Science and Medical Engineering, Southeast University, Nanjing, China.
⁷ Department of Dermatology, China-Japan Friendship Hospital, Beijing, China.
⁸ Department of Dermatology, No. 2 Hospital, Anhui Medical University, Hefei, China.
⁹ Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China.
¹⁰ Department of Dermatology, No. 1 Hospital of China Medical University, Shenyang, China.
¹¹ Shandong Provincial Institute of Dermatology and Venereology, Shandong Academy of Medical Sciences, Jinan, China.
¹² Department of Dermatology, Huashan Hospital and Collaborative Innovation Center of Complex and Severe Skin Disease, Fudan University, Shanghai, China.
¹³ Department of Dermatology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
¹⁴ Department of Dermatology, Ruijin Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China.
¹⁵ Department of Dermatology, Peking University People's Hospital, Beijing, China.
¹⁶ Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia.
¹⁷ James D. Watson Institute of Genome Sciences, Hangzhou, China.
¹⁸ Department of Laboratory Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, Stockholm, Sweden.
¹⁹ Princess Al-Jawhara Albrahim Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia.
²⁰ Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau, China.
²¹ Department of Medicine, University of Hong Kong, Hong Kong, China.
²² State Key Laboratory of Pharmaceutical Biotechnology, University of Hong Kong, Hong Kong, China.

PMID: 27213287
DOI: 10.1038/ng.3576

Comparative Study

Deep sequencing of the MHC region in the Chinese population contributes to studies of complex disease

Fusheng Zhou et al. Nat Genet. 2016 Jul.

. 2016 Jul;48(7):740-6.

doi: 10.1038/ng.3576. Epub 2016 May 23.

Authors

Affiliations

¹ Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China.
² BGI-Shenzhen, Shenzhen, China.
³ iCarbonX, Shenzhen, China.
⁴ Department of Biology, University of Copenhagen, Copenhagen, Denmark.
⁵ Department of Nephrology, First Affiliated Hospital, Sun Yat-sen University, Key Laboratory of Nephrology, Ministry of Health, Guangzhou, China.
⁶ School of Biological Science and Medical Engineering, Southeast University, Nanjing, China.
⁷ Department of Dermatology, China-Japan Friendship Hospital, Beijing, China.
⁸ Department of Dermatology, No. 2 Hospital, Anhui Medical University, Hefei, China.
⁹ Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China.
¹⁰ Department of Dermatology, No. 1 Hospital of China Medical University, Shenyang, China.
¹¹ Shandong Provincial Institute of Dermatology and Venereology, Shandong Academy of Medical Sciences, Jinan, China.
¹² Department of Dermatology, Huashan Hospital and Collaborative Innovation Center of Complex and Severe Skin Disease, Fudan University, Shanghai, China.
¹³ Department of Dermatology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
¹⁴ Department of Dermatology, Ruijin Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China.
¹⁵ Department of Dermatology, Peking University People's Hospital, Beijing, China.
¹⁶ Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia.
¹⁷ James D. Watson Institute of Genome Sciences, Hangzhou, China.
¹⁸ Department of Laboratory Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, Stockholm, Sweden.
¹⁹ Princess Al-Jawhara Albrahim Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia.
²⁰ Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau, China.
²¹ Department of Medicine, University of Hong Kong, Hong Kong, China.
²² State Key Laboratory of Pharmaceutical Biotechnology, University of Hong Kong, Hong Kong, China.

PMID: 27213287
DOI: 10.1038/ng.3576

Abstract

The human major histocompatibility complex (MHC) region has been shown to be associated with numerous diseases. However, it remains a challenge to pinpoint the causal variants for these associations because of the extreme complexity of the region. We thus sequenced the entire 5-Mb MHC region in 20,635 individuals of Han Chinese ancestry (10,689 controls and 9,946 patients with psoriasis) and constructed a Han-MHC database that includes both variants and HLA gene typing results of high accuracy. We further identified multiple independent new susceptibility loci in HLA-C, HLA-B, HLA-DPB1 and BTNL2 and an intergenic variant, rs118179173, associated with psoriasis and confirmed the well-established risk allele HLA-C*06:02. We anticipate that our Han-MHC reference panel built by deep sequencing of a large number of samples will serve as a useful tool for investigating the role of the MHC region in a variety of diseases and thus advance understanding of the pathogenesis of these disorders.

PubMed Disclaimer

Cited by

Identifying the genetic associations among the psoriasis patients in eastern India.
Das S, Chandra A, Das A, Senapati S, Chatterjee G, Chatterjee R. Das S, et al. J Hum Genet. 2024 Feb 27. doi: 10.1038/s10038-024-01227-8. Online ahead of print. J Hum Genet. 2024. PMID: 38409498
Tumour circular RNAs elicit anti-tumour immunity by encoding cryptic peptides.
Huang D, Zhu X, Ye S, Zhang J, Liao J, Zhang N, Zeng X, Wang J, Yang B, Zhang Y, Lao L, Chen J, Xin M, Nie Y, Saw PE, Su S, Song E. Huang D, et al. Nature. 2024 Jan;625(7995):593-602. doi: 10.1038/s41586-023-06834-7. Epub 2023 Dec 13. Nature. 2024. PMID: 38093017
Fine mapping identifies independent HLA associations in autoimmune hepatitis type 1.
Li Y, Zhou L, Huang Z, Yang Y, Zhang J, Yang L, Xu Y, Shi J, Tang S, Yuan X, Xu J, Li Y, Han X, Li J, Liu Y, Sun Y, Jin X, Xiao X, Wang B, Lin Q, Zhou Y, Song X, Cui Y, Hu L, Song Y, Bao J, Gong L, Gershwin ME, Zuo X, Yan H, Zou Z, Tang R, Ma X; Chinese AIH Consortium. Li Y, et al. JHEP Rep. 2023 Oct 5;6(1):100926. doi: 10.1016/j.jhepr.2023.100926. eCollection 2024 Jan. JHEP Rep. 2023. PMID: 38089552 Free PMC article.
Tutorial: a statistical genetics guide to identifying HLA alleles driving complex disease.
Sakaue S, Gurajala S, Curtis M, Luo Y, Choi W, Ishigaki K, Kang JB, Rumker L, Deutsch AJ, Schönherr S, Forer L, LeFaive J, Fuchsberger C, Han B, Lenz TL, de Bakker PIW, Okada Y, Smith AV, Raychaudhuri S. Sakaue S, et al. Nat Protoc. 2023 Sep;18(9):2625-2641. doi: 10.1038/s41596-023-00853-4. Epub 2023 Jul 26. Nat Protoc. 2023. PMID: 37495751 Free PMC article. Review.
Development of a high-resolution mass-spectrometry-based method and software for human leukocyte antigen typing.
Wang K, Sun Z, Zhu F, Xu Y, Zhou F. Wang K, et al. Front Immunol. 2023 Apr 28;14:1188381. doi: 10.3389/fimmu.2023.1188381. eCollection 2023. Front Immunol. 2023. PMID: 37187759 Free PMC article.

See all "Cited by" articles

References

1. PLoS Genet. 2013 Nov;9(11):e1003926 - PubMed
1. Hum Mol Genet. 2011 Oct 1;20(19):3884-92 - PubMed
1. Hum Mol Genet. 2014 Dec 20;23(25):6916-26 - PubMed
1. Nat Genet. 2012 Jan 29;44(3):291-6 - PubMed
1. Nature. 2012 Nov 1;491(7422):56-65 - PubMed

Publication types

Actions

MeSH terms

Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions

Substances

Actions
Actions
Actions
Actions
Actions
Actions

LinkOut - more resources

Full Text Sources
- Nature Publishing Group
Other Literature Sources
- The Lens - Patent Citations
- scite Smart Citations
Medical
- MedlinePlus Health Information
Research Materials
- NCI CPTC Antibody Characterization Program
Miscellaneous
- NCI CPTAC Assay Portal

[1] PLoS Genet. 2013 Nov;9(11):e1003926 - PubMed

[2] PLoS Genet. 2013 Nov;9(11):e1003926 - PubMed

[3] Hum Mol Genet. 2011 Oct 1;20(19):3884-92 - PubMed

[4] Hum Mol Genet. 2011 Oct 1;20(19):3884-92 - PubMed

[5] Hum Mol Genet. 2014 Dec 20;23(25):6916-26 - PubMed

[6] Hum Mol Genet. 2014 Dec 20;23(25):6916-26 - PubMed

[7] Nat Genet. 2012 Jan 29;44(3):291-6 - PubMed

[8] Nat Genet. 2012 Jan 29;44(3):291-6 - PubMed

[9] Nature. 2012 Nov 1;491(7422):56-65 - PubMed

[10] Nature. 2012 Nov 1;491(7422):56-65 - PubMed

Save citation to file

Email citation

Add to Collections

Add to My Bibliography

Your saved search

Create a file for external citation management software

Your RSS Feed

Deep sequencing of the MHC region in the Chinese population contributes to studies of complex disease

Affiliations

Deep sequencing of the MHC region in the Chinese population contributes to studies of complex disease

Authors

Affiliations

Abstract

Similar articles

Cited by

References

Publication types

MeSH terms

Substances

LinkOut - more resources

Full Text Sources

Other Literature Sources

Medical

Research Materials

Miscellaneous

Abstract

Similar articles

Cited by

References

Publication types

MeSH terms

Substances

Related information

LinkOut - more resources

Full Text Sources

Other Literature Sources

Medical

Research Materials

Miscellaneous