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

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

doi:10.12688/aasopenres.12832.2

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

AAS Open Res. 2018 Jun 21:1:3. doi: 10.12688/aasopenres.12832.2. eCollection 2018.

Authors

Gerald Mboowa^{1

2}, Savannah Mwesigwa^{1

2}, Eric Katagirya^{1

2}, Gaone Retshabile³, Busisiwe C Mlotshwa³, Lesedi Williams³, Adeodata Kekitiinwa⁴, David Kateete^{1

2}, Eddie Wampande^{1

2

5}, Misaki Wayengera^{1

2}, Betty Nsangi Kintu⁴, Grace P Kisitu⁴, Samuel Kyobe², Chester W Brown^{6

7

8}, Neil A Hanchard^{9

10

11}, Graeme Mardon^{9

12}, Moses Joloba^{1

2}, Gabriel Anabwani^{13

14}, Ed Pettitt¹³, Masego Tsimako-Johnstone³, Ishmael Kasvosve¹⁵, Koketso Maplanka³, Sununguko W Mpoloka³, Makhosazana Hlatshwayo¹⁴, Mogomotsi Matshaba^{13

16}

Affiliations

¹ Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda.
² Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda.
³ Department of Biological Sciences, Faculty of Sciences, University of Botswana, Gaborone, Botswana.
⁴ Baylor College of Medicine Children's Foundation-Uganda, Kampala, Uganda.
⁵ Department of Bio-molecular Resources, College of Veterinary Medicine, Makerere University, Kampala, Uganda.
⁶ Genetics Division, Department of Pediatrics , University of Tennessee Health Science Center, Memphis, Memphis, TN, USA.
⁷ Le Bonheur Children's Hospital, Memphis, Memphis, TN, USA.
⁸ St. Jude Children's Research Hospital, Memphis, TN, USA.
⁹ Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
¹⁰ Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.
¹¹ ARS/USDA/Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine , Houston, TX, USA.
¹² Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA.
¹³ Botswana-Baylor Children's Clinical Centre of Excellence, Gaborone, Botswana.
¹⁴ Baylor College of Medicine Children's Foundation-Swaziland, Mbabane, Swaziland.
¹⁵ Department of Medical Laboratory Sciences, University of Botswana, Gaborone, Botswana.
¹⁶ Pediatric Retrovirology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.

Abstract

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.

Keywords: Bioinformatics; Development; Education; Genetics; Genomics; HIV/AIDS; Pediatrics; Tuberculosis.

Abstract

Grants and funding