Diversity in immunogenomics: the value and the challenge

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.

PMID: 34002093
PMCID: PMC8842483
DOI: 10.1038/s41592-021-01169-5

Diversity in immunogenomics: the value and the challenge

Kerui Peng et al. Nat Methods. 2021 Jun.

. 2021 Jun;18(6):588-591.

doi: 10.1038/s41592-021-01169-5.

Authors

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.

PMID: 34002093
PMCID: PMC8842483
DOI: 10.1038/s41592-021-01169-5

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.

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Conflict of interest statement

Competing interests

V.G. declares advisory board positions in aiNET GmbH and Enpicom B.V. P.K. is a co-founder of Inflammatix, Inc. He is also a consultant to Inflammatix, Inc., Vir Biotechnology, Cepheid, and Genentech. G.K.H and M.C. are founders of ImmuneDiscover Sweden AB.

References

1. Sirugo G, Williams SM & Tishkoff SA Cell 177, 1080 (2019). - PubMed
1. Ben-Eghan C et al. Nature 585, 184–186 (2020). - PubMed
1. Choudhury A et al. Nature 586, 741–748 (2020). - PMC - PubMed
1. Retshabile G et al. Am. J. Hum. Genet 102, 731–743 (2018). - PMC - PubMed
1. Freeman JD, Warren RL, Webb JR, Nelson BH & Holt RA Genome Res. 19, 1817–1824 (2009). - PMC - PubMed

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Diversity in immunogenomics: the value and the challenge

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Diversity in immunogenomics: the value and the challenge

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Abstract

Conflict of interest statement

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