The Collaborative African Genomics Network (CAfGEN): Applying Genomic technologies to probe host factors important to the progression of HIV and HIV-tuberculosis infection in sub-Saharan Africa [version 2; peer review: 2 approved]
Background: Here, we describe how the Collaborative African Genomics Network (CAfGEN) of the Human Heredity and Health in Africa (H3Africa) consortium is using genomics to probe host genetic factors important to the progression of HIV and HIV-tuberculosis (TB) coinfection in sub-Saharan Africa. Th...
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| Format: | Article |
| Language: | English |
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F1000 Research Ltd
2018-06-01
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| Series: | AAS Open Research |
| Online Access: | https://aasopenresearch.org/articles/1-3/v2 |
| _version_ | 1797726219701059584 |
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| author | Gerald Mboowa Savannah Mwesigwa Eric Katagirya Gaone Retshabile Busisiwe C. Mlotshwa Lesedi Williams Adeodata Kekitiinwa David Kateete Eddie Wampande Misaki Wayengera Betty Nsangi Kintu Grace P. Kisitu Samuel Kyobe Chester W. Brown Neil A. Hanchard Graeme Mardon Moses Joloba Gabriel Anabwani Ed Pettitt Masego Tsimako-Johnstone Ishmael Kasvosve Koketso Maplanka Sununguko W. Mpoloka Makhosazana Hlatshwayo Mogomotsi Matshaba |
| author_facet | Gerald Mboowa Savannah Mwesigwa Eric Katagirya Gaone Retshabile Busisiwe C. Mlotshwa Lesedi Williams Adeodata Kekitiinwa David Kateete Eddie Wampande Misaki Wayengera Betty Nsangi Kintu Grace P. Kisitu Samuel Kyobe Chester W. Brown Neil A. Hanchard Graeme Mardon Moses Joloba Gabriel Anabwani Ed Pettitt Masego Tsimako-Johnstone Ishmael Kasvosve Koketso Maplanka Sununguko W. Mpoloka Makhosazana Hlatshwayo Mogomotsi Matshaba |
| author_sort | Gerald Mboowa |
| collection | DOAJ |
| description | Background: Here, we describe how the Collaborative African Genomics Network (CAfGEN) of the Human Heredity and Health in Africa (H3Africa) consortium is using genomics to probe host genetic factors important to the progression of HIV and HIV-tuberculosis (TB) coinfection in sub-Saharan Africa. The H3Africa was conceived to facilitate the application of genomics technologies to improve health across Africa.. Methods: CAfGEN is an H3Africa collaborative centre comprising expertise from the University of Botswana; Makerere University; Baylor College of Medicine Children’s Clinical Centers of Excellence (COEs) in Botswana, Uganda, and Swaziland; as well as Baylor College of Medicine, Texas. The COEs provide clinical expertise for community engagement, participant recruitment and sample collection while the three University settings facilitate processing and management of genomic samples and provide infrastructure and training opportunities to sustain genomics research. Results: The project has focused on utilizing whole-exome sequencing to identify genetic variants contributing to extreme HIV disease progression phenotypes in children, as well as RNA sequencing and integrated genomics to identify host genetic factors associated with TB disease progression among HIV-positive children. These cohorts, developed using the COEs’ electronic medical records, are exceptionally well-phenotyped and present an unprecedented opportunity to assess genetic factors in individuals whose HIV was acquired by a different route than their adult counterparts in the context of a unique clinical course and disease pathophysiology. Conclusions: Our approach offers the prospect of developing a critical mass of well-trained, highly-skilled, continent-based African genomic scientists. To ensure long term genomics research sustainability in Africa, CAfGEN contributes to a wide range of genomics capacity and infrastructure development on the continent, has laid a foundation for genomics graduate programs at its institutions, and continues to actively promote genomics research through innovative forms of community engagement brokered by partnerships with governments and academia to support genomics policy formulation. |
| first_indexed | 2024-03-12T10:42:36Z |
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| institution | Directory Open Access Journal |
| issn | 2515-9321 |
| language | English |
| last_indexed | 2024-03-12T10:42:36Z |
| publishDate | 2018-06-01 |
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| spelling | doaj.art-5abf5c8052074cd398adeb6d10ee244f2023-09-02T07:57:45ZengF1000 Research LtdAAS Open Research2515-93212018-06-01110.12688/aasopenres.12832.213951The Collaborative African Genomics Network (CAfGEN): Applying Genomic technologies to probe host factors important to the progression of HIV and HIV-tuberculosis infection in sub-Saharan Africa [version 2; peer review: 2 approved]Gerald Mboowa0Savannah Mwesigwa1Eric Katagirya2Gaone Retshabile3Busisiwe C. Mlotshwa4Lesedi Williams5Adeodata Kekitiinwa6David Kateete7Eddie Wampande8Misaki Wayengera9Betty Nsangi Kintu10Grace P. Kisitu11Samuel Kyobe12Chester W. Brown13Neil A. Hanchard14Graeme Mardon15Moses Joloba16Gabriel Anabwani17Ed Pettitt18Masego Tsimako-Johnstone19Ishmael Kasvosve20Koketso Maplanka21Sununguko W. Mpoloka22Makhosazana Hlatshwayo23Mogomotsi Matshaba24Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, UgandaDepartment of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, UgandaDepartment of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, UgandaDepartment of Biological Sciences, Faculty of Sciences, University of Botswana, Gaborone, BotswanaDepartment of Biological Sciences, Faculty of Sciences, University of Botswana, Gaborone, BotswanaDepartment of Biological Sciences, Faculty of Sciences, University of Botswana, Gaborone, BotswanaBaylor College of Medicine Children's Foundation-Uganda, Kampala, UgandaDepartment of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, UgandaDepartment of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, UgandaDepartment of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, UgandaBaylor College of Medicine Children's Foundation-Uganda, Kampala, UgandaBaylor College of Medicine Children's Foundation-Uganda, Kampala, UgandaDepartment of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, UgandaGenetics Division, Department of Pediatrics , University of Tennessee Health Science Center, Memphis, Memphis, TN, USADepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USADepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USADepartment of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, UgandaBotswana-Baylor Children's Clinical Centre of Excellence, Gaborone, BotswanaBotswana-Baylor Children's Clinical Centre of Excellence, Gaborone, BotswanaDepartment of Biological Sciences, Faculty of Sciences, University of Botswana, Gaborone, BotswanaDepartment of Medical Laboratory Sciences, University of Botswana, Gaborone, BotswanaDepartment of Biological Sciences, Faculty of Sciences, University of Botswana, Gaborone, BotswanaDepartment of Biological Sciences, Faculty of Sciences, University of Botswana, Gaborone, BotswanaBaylor College of Medicine Children's Foundation-Swaziland, Mbabane, SwazilandBotswana-Baylor Children's Clinical Centre of Excellence, Gaborone, BotswanaBackground: Here, we describe how the Collaborative African Genomics Network (CAfGEN) of the Human Heredity and Health in Africa (H3Africa) consortium is using genomics to probe host genetic factors important to the progression of HIV and HIV-tuberculosis (TB) coinfection in sub-Saharan Africa. The H3Africa was conceived to facilitate the application of genomics technologies to improve health across Africa.. Methods: CAfGEN is an H3Africa collaborative centre comprising expertise from the University of Botswana; Makerere University; Baylor College of Medicine Children’s Clinical Centers of Excellence (COEs) in Botswana, Uganda, and Swaziland; as well as Baylor College of Medicine, Texas. The COEs provide clinical expertise for community engagement, participant recruitment and sample collection while the three University settings facilitate processing and management of genomic samples and provide infrastructure and training opportunities to sustain genomics research. Results: The project has focused on utilizing whole-exome sequencing to identify genetic variants contributing to extreme HIV disease progression phenotypes in children, as well as RNA sequencing and integrated genomics to identify host genetic factors associated with TB disease progression among HIV-positive children. These cohorts, developed using the COEs’ electronic medical records, are exceptionally well-phenotyped and present an unprecedented opportunity to assess genetic factors in individuals whose HIV was acquired by a different route than their adult counterparts in the context of a unique clinical course and disease pathophysiology. Conclusions: Our approach offers the prospect of developing a critical mass of well-trained, highly-skilled, continent-based African genomic scientists. To ensure long term genomics research sustainability in Africa, CAfGEN contributes to a wide range of genomics capacity and infrastructure development on the continent, has laid a foundation for genomics graduate programs at its institutions, and continues to actively promote genomics research through innovative forms of community engagement brokered by partnerships with governments and academia to support genomics policy formulation.https://aasopenresearch.org/articles/1-3/v2 |
| spellingShingle | Gerald Mboowa Savannah Mwesigwa Eric Katagirya Gaone Retshabile Busisiwe C. Mlotshwa Lesedi Williams Adeodata Kekitiinwa David Kateete Eddie Wampande Misaki Wayengera Betty Nsangi Kintu Grace P. Kisitu Samuel Kyobe Chester W. Brown Neil A. Hanchard Graeme Mardon Moses Joloba Gabriel Anabwani Ed Pettitt Masego Tsimako-Johnstone Ishmael Kasvosve Koketso Maplanka Sununguko W. Mpoloka Makhosazana Hlatshwayo Mogomotsi Matshaba The Collaborative African Genomics Network (CAfGEN): Applying Genomic technologies to probe host factors important to the progression of HIV and HIV-tuberculosis infection in sub-Saharan Africa [version 2; peer review: 2 approved] AAS Open Research |
| title | The Collaborative African Genomics Network (CAfGEN): Applying Genomic technologies to probe host factors important to the progression of HIV and HIV-tuberculosis infection in sub-Saharan Africa [version 2; peer review: 2 approved] |
| title_full | The Collaborative African Genomics Network (CAfGEN): Applying Genomic technologies to probe host factors important to the progression of HIV and HIV-tuberculosis infection in sub-Saharan Africa [version 2; peer review: 2 approved] |
| title_fullStr | The Collaborative African Genomics Network (CAfGEN): Applying Genomic technologies to probe host factors important to the progression of HIV and HIV-tuberculosis infection in sub-Saharan Africa [version 2; peer review: 2 approved] |
| title_full_unstemmed | The Collaborative African Genomics Network (CAfGEN): Applying Genomic technologies to probe host factors important to the progression of HIV and HIV-tuberculosis infection in sub-Saharan Africa [version 2; peer review: 2 approved] |
| title_short | The Collaborative African Genomics Network (CAfGEN): Applying Genomic technologies to probe host factors important to the progression of HIV and HIV-tuberculosis infection in sub-Saharan Africa [version 2; peer review: 2 approved] |
| title_sort | collaborative african genomics network cafgen applying genomic technologies to probe host factors important to the progression of hiv and hiv tuberculosis infection in sub saharan africa version 2 peer review 2 approved |
| url | https://aasopenresearch.org/articles/1-3/v2 |
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