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

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 XieGur 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

Bar-Ilan University - The Alexander Kofkin Faculty of Engineering

Research output: Contribution to journal › Comment/debate

37 Scopus citations

Original language	English
Pages (from-to)	588-591
Number of pages	4
Journal	Nature Methods
Volume	18
Issue number	6
DOIs	https://doi.org/10.1038/s41592-021-01169-5
State	Published - Jun 2021

Bibliographical note

Funding Information:
We thank Nicky Mulder for comments that greatly improved the manuscript. Y.S. was supported by the National Science Foundation EAGER award (no. 2032783). M.S. is supported by Ministry of Science and Higher Education of the Russian Federation grant no. 075-15-2020-807. A.B.P. and C.D.B. are supported by an award from the National Human Genome Research Institute of the National Institutes of Health (U41HG009649). C.T.W. and O.L.R. are supported in part by the National Institute of Allergy and Infectious Diseases of the National Institutes of Health under award numbers R24AI138963 and R21AI142590. V.G. is supported by a UiO World-Leading Research Community grant, the UiO:LifeScience Convergence Environment Immunolingo, EU Horizon 2020 iReceptorplus (no. 825821) and a Research Council of Norway FRIPRO project (#300740). V.D.J. was supported by an award from the National Cancer Institute of the National Institutes of Health (K12CA001727). The laboratory of L.Q.-M. is supported by the Institut Pasteur, the Collège de France, the CNRS, the Fondation Allianz-Institut de France and the French Government’s Investissement d’Avenir program, Laboratoires d’Excellence ‘Integrative Biology of Emerging Infectious Diseases’ (ANR-10-LABX-62-IBEID) and ‘Milieu Intérieur’ (ANR-10-LABX-69-01). R.A.A. is supported by the Fogarty International Center of the National Institute of Health under award number D43TW010934. P.K. is supported by the Bill and Melinda Gates Foundation (OPP1113682), National Institute of Allergy and Infectious Diseases (NIAID) (1U19AI109662, U19AI057229, 5R01AI125197), Department of Defense (W81XWH1910235) and Catalyst and Transformational Awards from the Dr. Ralph & Marian Falk Medical Research Trust. C.S. is supported by NIAID of the National Institutes of Health under award number U01AI136677. G.K.H is supported by a grant from the Swedish Research Council (award number 532 2017-00968). S.M. is partially supported by National Science Foundation grants 2041984.

Funding

We thank Nicky Mulder for comments that greatly improved the manuscript. Y.S. was supported by the National Science Foundation EAGER award (no. 2032783). M.S. is supported by Ministry of Science and Higher Education of the Russian Federation grant no. 075-15-2020-807. A.B.P. and C.D.B. are supported by an award from the National Human Genome Research Institute of the National Institutes of Health (U41HG009649). C.T.W. and O.L.R. are supported in part by the National Institute of Allergy and Infectious Diseases of the National Institutes of Health under award numbers R24AI138963 and R21AI142590. V.G. is supported by a UiO World-Leading Research Community grant, the UiO:LifeScience Convergence Environment Immunolingo, EU Horizon 2020 iReceptorplus (no. 825821) and a Research Council of Norway FRIPRO project (#300740). V.D.J. was supported by an award from the National Cancer Institute of the National Institutes of Health (K12CA001727). The laboratory of L.Q.-M. is supported by the Institut Pasteur, the Collège de France, the CNRS, the Fondation Allianz-Institut de France and the French Government’s Investissement d’Avenir program, Laboratoires d’Excellence ‘Integrative Biology of Emerging Infectious Diseases’ (ANR-10-LABX-62-IBEID) and ‘Milieu Intérieur’ (ANR-10-LABX-69-01). R.A.A. is supported by the Fogarty International Center of the National Institute of Health under award number D43TW010934. P.K. is supported by the Bill and Melinda Gates Foundation (OPP1113682), National Institute of Allergy and Infectious Diseases (NIAID) (1U19AI109662, U19AI057229, 5R01AI125197), Department of Defense (W81XWH1910235) and Catalyst and Transformational Awards from the Dr. Ralph & Marian Falk Medical Research Trust. C.S. is supported by NIAID of the National Institutes of Health under award number U01AI136677. G.K.H is supported by a grant from the Swedish Research Council (award number 532 2017-00968). S.M. is partially supported by National Science Foundation grants 2041984.

Funders	Funder number
Collège de France
EU Horizon 2020 iReceptorplus	825821
Fondation Allianz-Institut de France	ANR-10-LABX-69-01, ANR-10-LABX-62-IBEID
UiO World-Leading Research Community
National Science Foundation	2032783
National Institutes of Health
U.S. Department of Defense	W81XWH1910235
National Human Genome Research Institute	U41HG009649
National Cancer Institute	K12CA001727
National Institute of Allergy and Infectious Diseases	5R01AI125197, R21AI142590, R24AI138963, U01AI136677, U19AI057229, U19AI109662
Fogarty International Center	D43TW010934
Bill and Melinda Gates Foundation	OPP1113682
Dr. Ralph and Marian Falk Medical Research Trust
Ministry of Education and Science of the Russian Federation	075-15-2020-807
Institut Pasteur
Vetenskapsrådet	2041984, 532 2017-00968
Centre National de la Recherche Scientifique
Norges Forskningsråd	300740

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Peng, K., Safonova, Y., Shugay, M., Popejoy, A. B., Rodriguez, O. L., Breden, F., Brodin, P., Burkhardt, A. M., Bustamante, C., Cao-Lormeau, V. M., Corcoran, M. M., Duffy, D., Fuentes-Guajardo, M., Fujita, R., Greiff, V., Jönsson, V. D., Liu, X., Quintana-Murci, L., Rossetti, M., ... Mangul, S. (2021). Diversity in immunogenomics: the value and the challenge. Nature Methods, 18(6), 588-591. https://doi.org/10.1038/s41592-021-01169-5

@article{bac37ffe10434c8cbc739f1c1a1d9059,

title = "Diversity in immunogenomics: the value and the challenge",

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

note = "Funding Information: We thank Nicky Mulder for comments that greatly improved the manuscript. Y.S. was supported by the National Science Foundation EAGER award (no. 2032783). M.S. is supported by Ministry of Science and Higher Education of the Russian Federation grant no. 075-15-2020-807. A.B.P. and C.D.B. are supported by an award from the National Human Genome Research Institute of the National Institutes of Health (U41HG009649). C.T.W. and O.L.R. are supported in part by the National Institute of Allergy and Infectious Diseases of the National Institutes of Health under award numbers R24AI138963 and R21AI142590. V.G. is supported by a UiO World-Leading Research Community grant, the UiO:LifeScience Convergence Environment Immunolingo, EU Horizon 2020 iReceptorplus (no. 825821) and a Research Council of Norway FRIPRO project (#300740). V.D.J. was supported by an award from the National Cancer Institute of the National Institutes of Health (K12CA001727). The laboratory of L.Q.-M. is supported by the Institut Pasteur, the Coll{\`e}ge de France, the CNRS, the Fondation Allianz-Institut de France and the French Government{\textquoteright}s Investissement d{\textquoteright}Avenir program, Laboratoires d{\textquoteright}Excellence {\textquoteleft}Integrative Biology of Emerging Infectious Diseases{\textquoteright} (ANR-10-LABX-62-IBEID) and {\textquoteleft}Milieu Int{\'e}rieur{\textquoteright} (ANR-10-LABX-69-01). R.A.A. is supported by the Fogarty International Center of the National Institute of Health under award number D43TW010934. P.K. is supported by the Bill and Melinda Gates Foundation (OPP1113682), National Institute of Allergy and Infectious Diseases (NIAID) (1U19AI109662, U19AI057229, 5R01AI125197), Department of Defense (W81XWH1910235) and Catalyst and Transformational Awards from the Dr. Ralph & Marian Falk Medical Research Trust. C.S. is supported by NIAID of the National Institutes of Health under award number U01AI136677. G.K.H is supported by a grant from the Swedish Research Council (award number 532 2017-00968). S.M. is partially supported by National Science Foundation grants 2041984.",

year = "2021",

month = jun,

doi = "10.1038/s41592-021-01169-5",

language = "אנגלית",

volume = "18",

pages = "588--591",

journal = "Nature Methods",

issn = "1548-7091",

publisher = "Nature Research",

number = "6",

}

Peng, K, Safonova, Y, Shugay, M, Popejoy, AB, Rodriguez, OL, Breden, F, Brodin, P, Burkhardt, AM, Bustamante, C, Cao-Lormeau, VM, Corcoran, MM, Duffy, D, Fuentes-Guajardo, M, Fujita, R, Greiff, V, Jönsson, VD, Liu, X, Quintana-Murci, L, Rossetti, M, Xie, J, Yaari, G, Zhang, W, Abedalthagafi, MS, Adekoya, KO, Ahmed, RA, Chang, WC, Gray, C, Nakamura, Y, Lees, WD, Khatri, P, Alachkar, H, Scheepers, C, Watson, CT, Karlsson Hedestam, GB & Mangul, S 2021, 'Diversity in immunogenomics: the value and the challenge', Nature Methods, vol. 18, no. 6, pp. 588-591. https://doi.org/10.1038/s41592-021-01169-5

TY - JOUR

T1 - Diversity in immunogenomics

T2 - the value and the challenge

AU - Peng, Kerui

AU - Safonova, Yana

AU - Shugay, Mikhail

AU - Popejoy, Alice B.

AU - Rodriguez, Oscar L.

AU - Breden, Felix

AU - Brodin, Petter

AU - Burkhardt, Amanda M.

AU - Bustamante, Carlos

AU - Cao-Lormeau, Van Mai

AU - Corcoran, Martin M.

AU - Duffy, Darragh

AU - Fuentes-Guajardo, Macarena

AU - Fujita, Ricardo

AU - Greiff, Victor

AU - Jönsson, Vanessa D.

AU - Liu, Xiao

AU - Quintana-Murci, Lluis

AU - Rossetti, Maura

AU - Xie, Jianming

AU - Yaari, Gur

AU - Zhang, Wei

AU - Abedalthagafi, Malak S.

AU - Adekoya, Khalid O.

AU - Ahmed, Rahaman A.

AU - Chang, Wei Chiao

AU - Gray, Clive

AU - Nakamura, Yusuke

AU - Lees, William D.

AU - Khatri, Purvesh

AU - Alachkar, Houda

AU - Scheepers, Cathrine

AU - Watson, Corey T.

AU - Karlsson Hedestam, Gunilla B.

AU - Mangul, Serghei

N1 - Funding Information: We thank Nicky Mulder for comments that greatly improved the manuscript. Y.S. was supported by the National Science Foundation EAGER award (no. 2032783). M.S. is supported by Ministry of Science and Higher Education of the Russian Federation grant no. 075-15-2020-807. A.B.P. and C.D.B. are supported by an award from the National Human Genome Research Institute of the National Institutes of Health (U41HG009649). C.T.W. and O.L.R. are supported in part by the National Institute of Allergy and Infectious Diseases of the National Institutes of Health under award numbers R24AI138963 and R21AI142590. V.G. is supported by a UiO World-Leading Research Community grant, the UiO:LifeScience Convergence Environment Immunolingo, EU Horizon 2020 iReceptorplus (no. 825821) and a Research Council of Norway FRIPRO project (#300740). V.D.J. was supported by an award from the National Cancer Institute of the National Institutes of Health (K12CA001727). The laboratory of L.Q.-M. is supported by the Institut Pasteur, the Collège de France, the CNRS, the Fondation Allianz-Institut de France and the French Government’s Investissement d’Avenir program, Laboratoires d’Excellence ‘Integrative Biology of Emerging Infectious Diseases’ (ANR-10-LABX-62-IBEID) and ‘Milieu Intérieur’ (ANR-10-LABX-69-01). R.A.A. is supported by the Fogarty International Center of the National Institute of Health under award number D43TW010934. P.K. is supported by the Bill and Melinda Gates Foundation (OPP1113682), National Institute of Allergy and Infectious Diseases (NIAID) (1U19AI109662, U19AI057229, 5R01AI125197), Department of Defense (W81XWH1910235) and Catalyst and Transformational Awards from the Dr. Ralph & Marian Falk Medical Research Trust. C.S. is supported by NIAID of the National Institutes of Health under award number U01AI136677. G.K.H is supported by a grant from the Swedish Research Council (award number 532 2017-00968). S.M. is partially supported by National Science Foundation grants 2041984.

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Diversity in immunogenomics: the value and the challenge

Bibliographical note

Funding

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