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Pagkrati I, Duke JL, Mbunwe E, Mosbruger TL, Ferriola D, Wasserman J, Dinou A, Tairis N, Damianos G, Kotsopoulou I, Papaioannou J, Giannopoulos D, Beggs W, Nyambo T, Mpoloka SW, Mokone GG, Njamnshi AK, Fokunang C, Woldemeskel D, Belay G, Maiers M, Tishkoff SA, Monos DS. Genomic characterization of HLA class I and class II genes in ethnically diverse sub-Saharan African populations: A report on novel HLA alleles. HLA 2023; 102:192-205. [PMID: 36999238 PMCID: PMC10524506 DOI: 10.1111/tan.15035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 03/11/2023] [Accepted: 03/11/2023] [Indexed: 04/01/2023]
Abstract
HLA allelic variation has been well studied and documented in many parts of the world. However, African populations have been relatively under-represented in studies of HLA variation. We have characterized HLA variation from 489 individuals belonging to 13 ethnically diverse populations from rural communities from the African countries of Botswana, Cameroon, Ethiopia, and Tanzania, known to practice traditional subsistence lifestyles using next generation sequencing (Illumina) and long-reads from Oxford Nanopore Technologies. We identified 342 distinct alleles among the 11 HLA targeted genes: HLA-A, -B, -C, -DRB1, -DRB3, -DRB4, -DRB5, -DQA1, -DQB1, -DPA1, and -DPB1, with 140 of those alleles containing novel sequences that were submitted to the IPD-IMGT/HLA database. Sixteen of the 140 alleles contained novel content within the exonic regions of the genes, while 110 alleles contained novel intronic variants. Four alleles were found to be recombinants of already described HLA alleles and 10 alleles extended the sequence content of already described alleles. All 140 alleles include complete allelic sequence from the 5' UTR to the 3' UTR that are inclusive of all exons and introns. This report characterizes the HLA allelic variation from these individuals and describes the novel allelic variation present within these specific African populations.
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Affiliation(s)
- Ioanna Pagkrati
- Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia,Pennsylvania, USA
| | - Jamie L. Duke
- Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia,Pennsylvania, USA
| | - Eric Mbunwe
- Department of Genetics and Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Timothy L. Mosbruger
- Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia,Pennsylvania, USA
| | - Deborah Ferriola
- Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia,Pennsylvania, USA
| | - Jenna Wasserman
- Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia,Pennsylvania, USA
| | - Amalia Dinou
- Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia,Pennsylvania, USA
| | - Nikolaos Tairis
- Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia,Pennsylvania, USA
| | - Georgios Damianos
- Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia,Pennsylvania, USA
| | - Ioanna Kotsopoulou
- Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia,Pennsylvania, USA
| | - Joanna Papaioannou
- Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia,Pennsylvania, USA
| | - Diamantoula Giannopoulos
- Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia,Pennsylvania, USA
| | - William Beggs
- Department of Genetics and Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Thomas Nyambo
- Department of Biochemistry, Kampala International University in Tanzania (KIUT), Dar es Salaam, Tanzania
| | - Sununguko W. Mpoloka
- Department of Biological Sciences, Faculty of Science, University of Botswana, Gaborone, Botswana
| | - Gaonyadiwe G. Mokone
- Department of Biomedical Sciences, Faculty of Medicine, University of Botswana, Gaborone, Botswana
| | - Alfred K. Njamnshi
- Department of Neuroscience, Brain Research Africa Initiative (BRAIN), Yaoundé, Cameroon
- Department of Neurology & Neuroscience, Central Hospital Yaoundé, Yaoundé, Cameroon
- Neuroscience Lab, Faculty of Medicine and Biomedical Sciences, The University of Yaoundé I, Yaoundé, Cameroon
| | - Charles Fokunang
- Department of Pharmacotoxicology and Pharmacokinetics, Faculty of Medicine and Biomedical Sciences, The University of Yaoundé I, Yaoundé, Cameroon
| | - Dawit Woldemeskel
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Gurja Belay
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Martin Maiers
- National Marrow Donor Program/Be The Match, Minneapolis, Minnesota, USA
- Center for International Blood and Marrow Transplant Research, Minneapolis, Minnesota, USA
| | - Sarah A. Tishkoff
- Department of Genetics and Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Dimitri S. Monos
- Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia,Pennsylvania, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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