H3ABioNet, a sustainable pan-African bioinformatics network for human heredity and health in Africa

doi:10.1101/gr.196295.115

. 2016 Feb;26(2):271-7.

doi: 10.1101/gr.196295.115. Epub 2015 Dec 1.

H3ABioNet, a sustainable pan-African bioinformatics network for human heredity and health in Africa

Nicola J Mulder¹, Ezekiel Adebiyi², Raouf Alami³, Alia Benkahla⁴, James Brandful⁵, Seydou Doumbia⁶, Dean Everett⁷, Faisal M Fadlelmola⁸, Fatima Gaboun⁹, Simani Gaseitsiwe¹⁰, Hassan Ghazal¹¹, Scott Hazelhurst¹², Winston Hide¹³, Azeddine Ibrahimi¹⁴, Yasmina Jaufeerally Fakim¹⁵, C Victor Jongeneel¹⁶, Fourie Joubert¹⁷, Samar Kassim¹⁸, Jonathan Kayondo¹⁹, Judit Kumuthini²⁰, Sylvester Lyantagaye²¹, Julie Makani²², Ahmed Mansour Alzohairy²³, Daniel Masiga²⁴, Ahmed Moussa²⁵, Oyekanmi Nash²⁶, Odile Ouwe Missi Oukem-Boyer²⁷, Ellis Owusu-Dabo²⁸, Sumir Panji¹, Hugh Patterton²⁹, Fouzia Radouani³⁰, Khalid Sadki³¹, Fouad Seghrouchni³², Özlem Tastan Bishop³³, Nicki Tiffin³⁴, Nzovu Ulenga³⁵; H3ABioNet Consortium

Collaborators, Affiliations

Collaborators

H3ABioNet Consortium:
Marion Adebiyi, Azza E Ahmed, Rehab I Ahmed, Maaike Alearts, Mohamed Alibi, Shaun Aron, Shakuntala Baichoo, Hocine Bendou, Gerrit Botha, David Brown, Emile Chimusa, Alan Christoffels, Jennifer Cornick, Jean-Baka Domelevo Entfellner, Chris Fields, Anne Fischer, Junaid Gamieldien, Kais Ghedira, Amel Ghouila, Shannan Ho Sui, Itunuoluwa Isewon, Raphael Isokpehi, Mahjoubeh Jalali, Sefid Dashti, Arox Kamng'ona, Radhika S Khetani, Anmol Kiran, Benard Kulohoma, Benjamin Kumwenda, Dan Lapine, Liudmila Sergeevna Mainzer, Suresh Maslamoney, Mamana Mbiyavanga, Ayton Meintjes, Flora Elias Mlyango, Bruno Mmbando, Somia A Mohammed, Phelelani Mpangase, Chisomo Msefula, Siana Nkya Mtatiro, Dunfunk Mugutso, Zahra Mungloo-Dilmohammud, Patrick Musicha, Victoria Nembaware, Victor Chukwudi Osamor, Jelili Oyelade, Gloria Rendon, Gustavo A Salazar, Samson Pandam Salifu, Raphael Sangeda, Oussema Souiai, Peter Van Heusden, Mamadou Wele

Affiliations

¹ Computational Biology Group, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa 7925;
² Covenant University Bioinformatics Research (CUBRe) and Department of Computer and Information Sciences, Covenant University, Ota, Ogun State, Nigeria, P.M.B. 1023;
³ Centre National de Transfusion Sanguine, Rabat, Morocco 10100;
⁴ Institute Pasteur of Tunis, Tunis, Tunisia 1002;
⁵ Noguchi Memorial Institute for Medical Research, University of Ghana, Ghana, LG;
⁶ University of Sciences, Techniques and Technology of Bamako, Bamako, Mali BPE 3206;
⁷ Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi, 3/Institute of Infection and Global Health, University of Liverpool, Liverpool L69 3BX, United Kingdom;
⁸ Centre for Bioinformatics and Systems Biology, Faculty of Science, University of Khartoum/Future University of Sudan, Khartoum, Sudan 11115;
⁹ Institut National de Recherche Agronomique, Rabat, Morocco 10000;
¹⁰ Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana;
¹¹ University Mohammed First, Oujda, Morocco 60000;
¹² Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa 2193;
¹³ Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA/Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, Sheffield S10 2HQ, United Kingdom;
¹⁴ Faculté de Médecine et de Pharmacie de Rabat, Université Mohammed V Souissi, Rabat, Morocco 10100;
¹⁵ University of Mauritius, Reduit, Mauritius 80837;
¹⁶ National Center for Supercomputing Applications and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA;
¹⁷ Department of Biochemistry, University of Pretoria, Pretoria, South Africa 0083;
¹⁸ Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt 11566;
¹⁹ Uganda Virus Research Institute, Entebbe, Uganda 31301;
²⁰ Centre for Proteomic and Genomic Research, Cape Town, South Africa 7925;
²¹ University of Dar es Salaam, Dar es Salaam, Tanzania, 73;
²² Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania 00255;
²³ Genetics Department, Faculty of Agriculture, Zagazig University, Sharkia, Egypt 44519;
²⁴ International Centre of Insect Physiology and Ecology, Nairobi, Kenya 00100;
²⁵ Abdelmalek Essaadi University, ENSA, Tangier, Morocco 90000;
²⁶ National Biotechnology Development Agency, Abuja, Nigeria 10099;
²⁷ Centre de Recherche Medicale et Sanitaire, Niamey, Niger, BP 10887;
²⁸ Kumasi Centre for Collaborative Research in Tropical Medicine/Kwame Nkrumah University of Science and Technology, Kumasi, Ghana, PMB;
²⁹ University of the Free State, Bloemfontein, South Africa 9300;
³⁰ Institut Pasteur du Maroc, Casablanca, Maroc, Morocco 20360;
³¹ Faculty of Sciences of Rabat, University Mohammed V of Rabat, Rabat, Morocco 10000;
³² Institut National d'Hygiène, Rabat, Morocco 10090;
³³ Research Unit in Bioinformatics, Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa 6140;
³⁴ South African National Bioinformatics Institute/Medical Research Council of South Africa Bioinformatics Unit, University of the Western Cape, Cape Town, South Africa 7530;
³⁵ Management and Development for Health, Dar es Salaam, Tanzania, 61.

PMID: 26627985
PMCID: PMC4728379
DOI: 10.1101/gr.196295.115

H3ABioNet, a sustainable pan-African bioinformatics network for human heredity and health in Africa

Nicola J Mulder et al. Genome Res. 2016 Feb.

. 2016 Feb;26(2):271-7.

doi: 10.1101/gr.196295.115. Epub 2015 Dec 1.

Authors

Collaborators

H3ABioNet Consortium:
Marion Adebiyi, Azza E Ahmed, Rehab I Ahmed, Maaike Alearts, Mohamed Alibi, Shaun Aron, Shakuntala Baichoo, Hocine Bendou, Gerrit Botha, David Brown, Emile Chimusa, Alan Christoffels, Jennifer Cornick, Jean-Baka Domelevo Entfellner, Chris Fields, Anne Fischer, Junaid Gamieldien, Kais Ghedira, Amel Ghouila, Shannan Ho Sui, Itunuoluwa Isewon, Raphael Isokpehi, Mahjoubeh Jalali, Sefid Dashti, Arox Kamng'ona, Radhika S Khetani, Anmol Kiran, Benard Kulohoma, Benjamin Kumwenda, Dan Lapine, Liudmila Sergeevna Mainzer, Suresh Maslamoney, Mamana Mbiyavanga, Ayton Meintjes, Flora Elias Mlyango, Bruno Mmbando, Somia A Mohammed, Phelelani Mpangase, Chisomo Msefula, Siana Nkya Mtatiro, Dunfunk Mugutso, Zahra Mungloo-Dilmohammud, Patrick Musicha, Victoria Nembaware, Victor Chukwudi Osamor, Jelili Oyelade, Gloria Rendon, Gustavo A Salazar, Samson Pandam Salifu, Raphael Sangeda, Oussema Souiai, Peter Van Heusden, Mamadou Wele

Affiliations

¹ Computational Biology Group, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa 7925;
² Covenant University Bioinformatics Research (CUBRe) and Department of Computer and Information Sciences, Covenant University, Ota, Ogun State, Nigeria, P.M.B. 1023;
³ Centre National de Transfusion Sanguine, Rabat, Morocco 10100;
⁴ Institute Pasteur of Tunis, Tunis, Tunisia 1002;
⁵ Noguchi Memorial Institute for Medical Research, University of Ghana, Ghana, LG;
⁶ University of Sciences, Techniques and Technology of Bamako, Bamako, Mali BPE 3206;
⁷ Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi, 3/Institute of Infection and Global Health, University of Liverpool, Liverpool L69 3BX, United Kingdom;
⁸ Centre for Bioinformatics and Systems Biology, Faculty of Science, University of Khartoum/Future University of Sudan, Khartoum, Sudan 11115;
⁹ Institut National de Recherche Agronomique, Rabat, Morocco 10000;
¹⁰ Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana;
¹¹ University Mohammed First, Oujda, Morocco 60000;
¹² Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa 2193;
¹³ Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA/Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, Sheffield S10 2HQ, United Kingdom;
¹⁴ Faculté de Médecine et de Pharmacie de Rabat, Université Mohammed V Souissi, Rabat, Morocco 10100;
¹⁵ University of Mauritius, Reduit, Mauritius 80837;
¹⁶ National Center for Supercomputing Applications and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA;
¹⁷ Department of Biochemistry, University of Pretoria, Pretoria, South Africa 0083;
¹⁸ Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt 11566;
¹⁹ Uganda Virus Research Institute, Entebbe, Uganda 31301;
²⁰ Centre for Proteomic and Genomic Research, Cape Town, South Africa 7925;
²¹ University of Dar es Salaam, Dar es Salaam, Tanzania, 73;
²² Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania 00255;
²³ Genetics Department, Faculty of Agriculture, Zagazig University, Sharkia, Egypt 44519;
²⁴ International Centre of Insect Physiology and Ecology, Nairobi, Kenya 00100;
²⁵ Abdelmalek Essaadi University, ENSA, Tangier, Morocco 90000;
²⁶ National Biotechnology Development Agency, Abuja, Nigeria 10099;
²⁷ Centre de Recherche Medicale et Sanitaire, Niamey, Niger, BP 10887;
²⁸ Kumasi Centre for Collaborative Research in Tropical Medicine/Kwame Nkrumah University of Science and Technology, Kumasi, Ghana, PMB;
²⁹ University of the Free State, Bloemfontein, South Africa 9300;
³⁰ Institut Pasteur du Maroc, Casablanca, Maroc, Morocco 20360;
³¹ Faculty of Sciences of Rabat, University Mohammed V of Rabat, Rabat, Morocco 10000;
³² Institut National d'Hygiène, Rabat, Morocco 10090;
³³ Research Unit in Bioinformatics, Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa 6140;
³⁴ South African National Bioinformatics Institute/Medical Research Council of South Africa Bioinformatics Unit, University of the Western Cape, Cape Town, South Africa 7530;
³⁵ Management and Development for Health, Dar es Salaam, Tanzania, 61.

PMID: 26627985
PMCID: PMC4728379
DOI: 10.1101/gr.196295.115

Abstract

The application of genomics technologies to medicine and biomedical research is increasing in popularity, made possible by new high-throughput genotyping and sequencing technologies and improved data analysis capabilities. Some of the greatest genetic diversity among humans, animals, plants, and microbiota occurs in Africa, yet genomic research outputs from the continent are limited. The Human Heredity and Health in Africa (H3Africa) initiative was established to drive the development of genomic research for human health in Africa, and through recognition of the critical role of bioinformatics in this process, spurred the establishment of H3ABioNet, a pan-African bioinformatics network for H3Africa. The limitations in bioinformatics capacity on the continent have been a major contributory factor to the lack of notable outputs in high-throughput biology research. Although pockets of high-quality bioinformatics teams have existed previously, the majority of research institutions lack experienced faculty who can train and supervise bioinformatics students. H3ABioNet aims to address this dire need, specifically in the area of human genetics and genomics, but knock-on effects are ensuring this extends to other areas of bioinformatics. Here, we describe the emergence of genomics research and the development of bioinformatics in Africa through H3ABioNet.

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Figures

**Figure 1.**
Map of Africa showing the distribution of nodes in the H3ABioNet network. The dot on the *right* is for Mauritius, and two additional sites not shown include one in the USA and one in the UK.

**Figure 2.**
Summary of H3ABioNet courses run and number of people trained.

See this image and copyright information in PMC

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References

1. The 1000 Genomes Project Consortium. 2010. A map of human genome variation from population-scale sequencing. Nature 467: 1061–1073. - PMC - PubMed
1. Attwood TK, Bongcam-Rudloff E, Brazas MD, Corpas M, Gaudet P, Lewitter F, Mulder N, Palagi PM, Schneider MV, van Gelder CWG, et al. 2015. GOBLET: the Global Organisation for Bioinformatics Learning, Education and Training. PLOS Comput Biol 11: e1004143. - PMC - PubMed
1. Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, Hall KP, Evers DJ, Barnes CL, Bignell HR, et al. 2008. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456: 53–59. - PMC - PubMed
1. Brown D, Penkler DL, Musyoka TM, Bishop ÖT. 2015. JMS: an open source workflow management system and web-based cluster front-end for high performance computing. PLoS One 10: e0134273. - PMC - PubMed
1. Bustamante CD, Burchard EG, De la Vega FM. 2011. Genomics for the world. Nature 475: 163–165. - PMC - PubMed

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[1] The 1000 Genomes Project Consortium. 2010. A map of human genome variation from population-scale sequencing. Nature 467: 1061–1073. - PMC - PubMed

[2] The 1000 Genomes Project Consortium. 2010. A map of human genome variation from population-scale sequencing. Nature 467: 1061–1073. - PMC - PubMed

[3] Attwood TK, Bongcam-Rudloff E, Brazas MD, Corpas M, Gaudet P, Lewitter F, Mulder N, Palagi PM, Schneider MV, van Gelder CWG, et al. 2015. GOBLET: the Global Organisation for Bioinformatics Learning, Education and Training. PLOS Comput Biol 11: e1004143. - PMC - PubMed

[4] Attwood TK, Bongcam-Rudloff E, Brazas MD, Corpas M, Gaudet P, Lewitter F, Mulder N, Palagi PM, Schneider MV, van Gelder CWG, et al. 2015. GOBLET: the Global Organisation for Bioinformatics Learning, Education and Training. PLOS Comput Biol 11: e1004143. - PMC - PubMed

[5] Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, Hall KP, Evers DJ, Barnes CL, Bignell HR, et al. 2008. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456: 53–59. - PMC - PubMed

[6] Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, Hall KP, Evers DJ, Barnes CL, Bignell HR, et al. 2008. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456: 53–59. - PMC - PubMed

[7] Brown D, Penkler DL, Musyoka TM, Bishop ÖT. 2015. JMS: an open source workflow management system and web-based cluster front-end for high performance computing. PLoS One 10: e0134273. - PMC - PubMed

[8] Brown D, Penkler DL, Musyoka TM, Bishop ÖT. 2015. JMS: an open source workflow management system and web-based cluster front-end for high performance computing. PLoS One 10: e0134273. - PMC - PubMed

[9] Bustamante CD, Burchard EG, De la Vega FM. 2011. Genomics for the world. Nature 475: 163–165. - PMC - PubMed

[10] Bustamante CD, Burchard EG, De la Vega FM. 2011. Genomics for the world. Nature 475: 163–165. - PMC - PubMed

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H3ABioNet, a sustainable pan-African bioinformatics network for human heredity and health in Africa

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Affiliations

H3ABioNet, a sustainable pan-African bioinformatics network for human heredity and health in Africa

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