African Genomic Medicine Portal: A Web Portal for Biomedical Applications

Houcemeddine Othman (1) , Lyndon Zass (2) , Jorge E. B. da Rocha (1) , Fouzia Radouani (3) , Chaimae Samtal (4) , Ichrak Benamri (3, 5) , Judit Kumuthini (6) , Yasmina J. Fakim (7) , Yosr Hamdi (8, 9) , Nessrine Mezzi (8, 9, 10) , Maroua Boujemaa (8, 9) , Chiamaka Jessica Okeke (11) , Maureen B. Tendwa (11) , Kholoud Sanak (3) , Melek Chaouch (8, 9) , Sumir Panji (2) , Rym Kefi (8, 9) , Reem M. Sallam (12, 13) , Anisah W. Ghoorah (7) , Lilia Romdhane (8, 9, 10) , Anmol Kiran (14, 15) , Ayton P. Meintjes (2) , Perceval Maturure (2) , Haifa Jmel (8, 9) , Ayoub Ksouri (8, 9) , Maryame Azzouzi (3) , Mohammed A. Farahat (16) , Samah Ahmed (17) , Rania Sibira (17) , Michael E. E. Turkson (18) , Alfred Ssekagiri (19) , Ziyaad Parker (2) , Faisal M. Fadlelmola (17) , Kais Ghedira (8, 9) , Nicola Mulder (2) , Samar Kamal Kassim (13)

1 WITS - University of the Witwatersrand [Johannesburg]
2 University of Cape Town
3 Institut Pasteur du Maroc
4 USMBA - Université Sidi Mohamed Ben Abdellah
5 UAE - Université Abdelmalek Essaâdi
6 UWC - University of the Western Cape
7 University of Mauritius
8 Institut Pasteur de Tunis
9 UTM - Université de Tunis El Manar
10 Faculté des Sciences de Bizerte [Université de Carthage]
11 Rhodes University, Grahamstown
12 Galala University [Suez, Egypt]
13 ASU - Ain Shams University
14 MLW - Malawi Liverpool Wellcome Trust Clinical Research Programme
15 University of Liverpool
16 Future Academy - Higher Future Institute for Specialized Technological Studies [Cairo]
17 University of Khartoum
18 KNUST - Kwame Nkrumah University of Science and Technology
19 UVRI - Uganda Virus Research Institute

Genomics data are currently being produced at unprecedented rates, resulting in increased knowledge discovery and submission to public data repositories. Despite these advances, genomic information on African-ancestry populations remains significantly low compared with European- and Asian-ancestry populations. This information is typically segmented across several different biomedical data repositories, which often lack sufficient fine-grained structure and annotation to account for the diversity of African populations, leading to many challenges related to the retrieval, representation and findability of such information. To overcome these challenges, we developed the African Genomic Medicine Portal (AGMP), a database that contains metadata on genomic medicine studies conducted on African-ancestry populations. The metadata is curated from two public databases related to genomic medicine, PharmGKB and DisGeNET. The metadata retrieved from these source databases were limited to genomic variants that were associated with disease aetiology or treatment in the context of African-ancestry populations. Over 2000 variants relevant to populations of African ancestry were retrieved. Subsequently, domain experts curated and annotated additional information associated with the studies that reported the variants, including geographical origin, ethnolinguistic group, level of association significance and other relevant study information, such as study design and sample size, where available. The AGMP functions as a dedicated resource through which to access African-specific information on genomics as applied to health research, through querying variants, genes, diseases and drugs. The portal and its corresponding technical documentation, implementation code and content are publicly available.

Keywords: clinical genetics; database; genomic medicine; portal; Africa

Domains: Life Sciences [q-bio]

Houcemeddine Othman, Lyndon Zass, Jorge E. B. da Rocha, Fouzia Radouani, Chaimae Samtal, et al.. African Genomic Medicine Portal: A Web Portal for Biomedical Applications. Journal of Personalized Medicine, 2022, 12 (2), pp.265. ⟨10.3390/jpm12020265⟩. ⟨pasteur-03597541⟩