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

Abstract

Here, we describe how the Collaborative African Genomics Background Network ( of the Human Heredity and Health in Africa (H3Africa) CAfGEN) 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.. :is an H3Africa collaborative centre comprising expertise Methods CAfGEN : The project has focused on utilizing whole-exome sequencing to Results 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.: Our approach offers the prospect of developing a critical mass Conclusions 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.

Role of genomics literacy in reducing the burden of common genetic diseases in Africa

“…For this reason, individuals who have genomic expertise can be asked to deliver expert talks and public engagement to improve the level of knowledge, beliefs, myths, and attitudes about the risk factors for genetic diseases in communities. A variety of platforms can be utilized such as; print media (magazines and new papers), radio/television talk shows, genomics seminars at universities/tertiary institutions as well as secondary and primary school, genomics comic books (Mboowa et al, ), blogs and a range of social media platforms. The media plays a great role in disseminating scientific messages and in propagating or reducing misconceptions to the public (Hurle et al, ).…”

Participants’ Preferences and Reasons for Wanting Feedback of Individual Genetic Research Results From an HIV-TB Genomic Study: A Case Study From Botswana

“…As a result of the HIV/TB burden and other aforementioned characteristics, the Collaborative African Genomics Network (CAfGEN) was initiated to study genes in children with HIV and TB, for the development of new therapies to prevent or suppress these infections ( BBCCCE, 2020b ). The CAfGEN study is a collaborative project which is part of the H3Africa consortium ( Consortium, 2014 ), and uses genomics approaches to identify host genetic factors that are important for the progression of HIV and HIV-TB infection in pediatric and adolescent African populations ( Mboowa et al, 2018 ). The CAfGEN study was conducted at Botswana-Baylor Children's Clinical Center of Excellence (BBCCCE), which is a pediatric and adolescent clinic that provides free of charge state-of-the-art HIV care, treatment, and support to children, adolescents, and their families ( BBCCCE, 2020a ).…”

Unmapped exome reads implicate a role for Anelloviridae in childhood HIV-1 long-term non-progression

“…The study characteristics of the Collaborative African Genomics Network (CAfGEN) cohort have been previously described 81 , but, in brief, it includes children (aged 0–18 years) with laboratory-confirmed evidence of HIV-1 infection who were registered for care at the Baylor College of Medicine Children’s Foundation in Kampala, Uganda, or the Botswana-Baylor Children’s Clinical Centre of Excellence in Gaborone, Botswana, both of which are the major centres for paediatric HIV care in their respective countries. Potential participants meeting clinical criteria were retrospectively identified from electronic health records dating back more than 20 years in the two centres of excellence.…”

“…Potential participants meeting clinical criteria were retrospectively identified from electronic health records dating back more than 20 years in the two centres of excellence. After obtaining informed consent and assent, participants were enrolled as part of a retrospective case–control study investigating the genetics of paediatric HIV disease progression as part of CAfGEN 81 – 83 —a collaborative centre of the Human Heredity and Health in Africa (H3Africa) Consortium 84 . Electronic health records in both centres were retrospectively queried to identify individuals meeting World Health Organization (WHO) clinical and immunologic criteria for RPs, i.e.…”