Diversity in immunogenomics: the value and the challenge

Kerui Peng; Yana Safonova; Mikhail Shugay; Alice B Popejoy; Oscar L Rodriguez; Felix Breden; Petter Brodin; Amanda M Burkhardt; Carlos Bustamante; Van-Mai Cao-Lormeau; Martin M Corcoran; Darragh Duffy; Macarena Fuentes-Guajardo; Ricardo Fujita; Victor Greiff; Vanessa D Jönsson; Xiao Liu; Lluis Quintana-Murci; Maura Rossetti; Jianming Xie; Gur Yaari; Wei Zhang; Malak S Abedalthagafi; Khalid O Adekoya; Rahaman A Ahmed; Wei-Chiao Chang; Clive Gray; Yusuke Nakamura; William D Lees; Purvesh Khatri; Houda Alachkar; Cathrine Scheepers; Corey T Watson; Gunilla B Karlsson Hedestam; Serghei Mangul

doi:10.1038/s41592-021-01169-5

Diversity in immunogenomics: the value and the challenge

Nat Methods. 2021 Jun;18(6):588-591. doi: 10.1038/s41592-021-01169-5.

Authors

Kerui Peng¹, Yana Safonova^{2

3}, Mikhail Shugay^{4

5}, Alice B Popejoy⁶, Oscar L Rodriguez³, Felix Breden⁷, Petter Brodin^{8

9}, Amanda M Burkhardt¹, Carlos Bustamante⁶, Van-Mai Cao-Lormeau¹⁰, Martin M Corcoran¹¹, Darragh Duffy¹², Macarena Fuentes-Guajardo¹³, Ricardo Fujita¹⁴, Victor Greiff¹⁵, Vanessa D Jönsson¹⁶, Xiao Liu¹⁷, Lluis Quintana-Murci^{18

19}, Maura Rossetti²⁰, Jianming Xie²¹, Gur Yaari²², Wei Zhang²³, Malak S Abedalthagafi²⁴, Khalid O Adekoya²⁵, Rahaman A Ahmed²⁵, Wei-Chiao Chang^{26

27}, Clive Gray^{28

29}, Yusuke Nakamura³⁰, William D Lees³¹, Purvesh Khatri^{32

33}, Houda Alachkar^#¹, Cathrine Scheepers^#^{34

35}, Corey T Watson^#³, Gunilla B Karlsson Hedestam^#¹¹, Serghei Mangul^#³⁶

Affiliations

¹ Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, CA, USA.
² Computer Science and Engineering Department, University of California San Diego, San Diego, CA, USA.
³ Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA.
⁴ Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.
⁵ Pirogov Russian National Research Medical University, Moscow, Russia.
⁶ Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.
⁷ Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada.
⁸ Science for Life Laboratory, Department of Women's and Children Health, Karolinska Institutet, Stockholm, Sweden.
⁹ Pediatric Rheumatology, Karolinska University Hospital, Stockholm, Sweden.
¹⁰ Laboratory of Research on Infectious Vector-borne Diseases, Institut Louis Malardé, Papeete, French Polynesia.
¹¹ Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
¹² Translational Immunology Laboratory, Institut Pasteur, Paris, France.
¹³ Departamento de Tecnología Médica, Facultad de Ciencias de la Salud, Universidad de Tarapacá, Arica, Chile.
¹⁴ Centro de Genética y Biología Molecular, Universidad de San Martín de Porres, La Molina, Lima, Perú.
¹⁵ Department of Immunology, University of Oslo, Oslo, Norway.
¹⁶ Departments of Computational and Quantitative Medicine and Hematology, Beckman Research Institute, City of Hope, Duarte, CA, USA.
¹⁷ Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China.
¹⁸ Human Evolutionary Genetics Unit, Institut Pasteur, UMR 2000, CNRS, Paris, France.
¹⁹ Department of Human Genomics and Evolution, Collège de France, Paris, France.
²⁰ UCLA Immunogenetics Center, Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
²¹ Department of Pharmacology & Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, USA.
²² Faculty of Engineering, Bar Ilan Institute of Nanotechnologies and Advanced Materials, Bar Ilan University, Ramat Gan, Israel.
²³ Department of Computer Science, City University of Hong Kong, Hong Kong, China.
²⁴ Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia.
²⁵ Department of Cell Biology and Genetics, University of Lagos, Lagos, Nigeria.
²⁶ Department of Clinical Pharmacy, School of Pharmacy, Taipei Medical University, New Taipei City, Taiwan.
²⁷ Division of Nephrology, Department of Internal Medicine, Taipei Medical University-Shuang Ho Hospital, New Taipei City, Taiwan.
²⁸ Division of Immunology, Institute of Infectious Disease and Molecular Medicine and Department of Pathology, University of Cape Town, Cape Town, South Africa.
²⁹ Laboratory of Tissue Immunology, National Health Laboratory Services and Groote Schuur Hospital, Cape Town, South Africa.
³⁰ Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan.
³¹ Institute of Structural and Molecular Biology, Birkbeck College, London, UK.
³² Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, CA, USA.
³³ Center for Biomedical Research, Department of Medicine, School of Medicine, Stanford University, Stanford, CA, USA.
³⁴ Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.
³⁵ South African Medical Research Council Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa.
³⁶ Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, CA, USA. serghei.mangul@gmail.com.

^# Contributed equally.

Abstract

Immunogenomics studies have been largely limited to individuals of European ancestry, restricting the ability to identify variation in human adaptive immune responses across populations. Inclusion of a greater diversity of individuals in immunogenomics studies will substantially enhance our understanding of human immunology.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

B-Lymphocytes / immunology
Databases, Genetic
Genomics*
Germ Cells
Humans
Immunogenetics*
Receptors, Antigen, B-Cell / genetics
Receptors, Antigen, B-Cell / immunology
Receptors, Antigen, T-Cell / genetics
Receptors, Antigen, T-Cell / immunology
T-Lymphocytes / immunology
Whole Genome Sequencing

Substances

Receptors, Antigen, B-Cell
Receptors, Antigen, T-Cell

Abstract

Publication types

MeSH terms

Substances

Grants and funding