Collaborative Centers

ReMAC – Mark Nicol, Heather Zar, Martin Antonio

Early work by ReMAC has shown that bacteria in the noses of children differ between those who do and do not develop pneumonia, even before pneumonia develops, and that air pollution influences these bacterial communities. This suggests that the types of bacteria in the nose could indicate a child’s susceptibility to developing pneumonia.

AWI-Gen – Michele Ramsay

So far, AWI-Gen has found that hypertension is highly prevalent in eastern and southern Africa and even though many take medication, their hypertension is not always properly controlled. The study has also revealed that obesity is more common in eastern and southern Africa than elsewhere on the continent, and women are at higher risk for these conditions in these regions. In contrast, people in western Africa tend to have lower levels of both hypertension and obesity, regardless of biological sex.

Genomic Characterization and Surveillance of Microbial Threats in West Africa – Christian Happi, Donald Grant, Peter Okokhere, Pardis Sabeti

Viral Research

• Established modern genomics hubs in Nigeria, Senegal, and Sierra Leone that have the ability to identify and analyze unknown circulating viruses.
• Used these hubs to rapidly characterize and track emergent viruses and outbreaks in West Africa including Lassa Virus (Nigeria, Sierra Leone), Yellow Fever (Nigeria), Dengue Virus (Sengal). This brisk action enabled local governments to implement containment strategies and enhanced patient care to effectively reduce the public health impact.
• Helped contain and characterize the Ebola outbreak in Nigeria.

Technology Development

• Developed SHERLOCK, a low-cost genomics test to rapidly identify three types of fever at the bedside, effectively reducing the standard of care diagnostic time and deployed it in the midst of the Lassa outbreak in Nigeria. The goal is to have this technology optimized by 2023.
• Developed additional genomics tests to enable rapid identification of Ebola virus, Zika virus, Chikungunya virus, Yellow fever virus, Dengue virus and West Nile virus, performed trainings, and deployed in Nigeria, Sierra Leone and Senegal.

CAfGEN – Mogomotsi Matshaba

In its first phase, CAfGEN used next-generation sequencing to identify candidate genes influencing pediatric HIV progression and TB disease progression; leverage scientific studies to establish and develop genomics capacity, technology, and expertise in Uganda and Botswana; and effectively engage local communities in addressing ethical, legal and social issues (ELSI) related to genomics research.

CAfGEN also created the Genome Adventures comic book series. The cornerstone of Genome Adventures’ community outreach is the publication of a series of four comic books.  The general plot is that a boy enrolled at a pediatric HIV clinic, named Kitso, receives a letter inviting him to join a study examining the influence of genetic factors on HIV and TB disease progression.  As Kitso grapples with whether or not to join the study, the Genome Adventures superhero team arrives to help him understand what genomics is all about.

CAfGEN has also found that Botswana’s ethnic identities are likely social constructs rather than indication of genetic isolation within the population’s constituent groups.  The study also demonstrated the need for increased survey of the different populations that are currently represented in genomics’ studies.

ACCME – Clement Adebamowo

• Conducted Hands On Training in Whole Genome, Microbiome and Metagenomics Sequencing
• Trained 20 site research associates on colposcopy and are certified as Nurse-Colposcopists. This innovative training which steps down capacity to conduct colposcopic examination to nurses and increases capacity to implement this intervention in Nigeria will be offered to health institutions throughout Nigeria in support of National Scale Up of Cervical Cancer Screening Program.
• Supported the training of 6 pre-doctoral and 3 post-doctoral young scientists from Africa.
• Contributed samples for Whole Genome Analysis used for the manufacture of the H3Africa GWAS chip.

SIREN – Mayowa Owolabi, Bruce Ovbiagele

The study brought many Africans awareness on the knowledge of stroke, its causes, risk factors, effects and methods of prevention. Through SIREN’s community engagement efforts, over 10,000 individuals have received education on cardiovascular risk factors and over 8,000 have been screened for cardiovascular risk factors. The discovery of green leafy vegetable as a protective factor against stroke is also profound.

Kidney Disease Research Network – Dwomoa Adu

• H3AKDRN investigators have recruited over 10,000 subjects with kidney disease and healthy controls from Ghana and Nigeria
  • 23% of healthy subjects from Ghana and Nigeria carry 2 APOL1 renal risk alleles
  • 30.3% of subjects with CKD carry 2 APOL1 renal risk alleles
  • Subjects carrying 2 APOL1 risk alleles have a 45% higher risk of developing CKD compared with subjects with one or no risk alleles
• 2 senior clinicians from the University of Ghana awarded an MSc in Human Genetics from the University of Michigan
• 2 trainees awarded an MPhil in Molecular Biology in the University of Ghana
• Functioning genomics laboratories at the University of Ghana and University of Ibadan
• 7 Investigators trained in Clinical Research Methods and Biostatistics
• Over 100 research coordinators and laboratory Technicians trained

Eyes of Africa – Adeyinke Ashaye

PIs collected more than 4,000 samples for genetic analysis prior to funding. Analysis of these samples identified a new risk factor for glaucoma only found in individuals of African ancestry.  This risk factor is also involved in Alzheimer’s disease, raising the possibility of new treatments that could help patients with both diseases. This finding confirms that African glaucoma differs from glaucoma found in other parts of the world, emphasizing the need for genomics research in Africa.

Research Projects

Immunoglobulin gene diversity in an African population and impact on antibody function in HIV infection – Lynn Morris

Preliminary data using samples from an ethnic Zulu population residing in South Africa revealed that approximately half of the heavy chain variable (IGHV) gene alleles as well as a significant number of single nucleotide polymorphisms (SNPs) in the Fc are not recorded in public databases, despite being used by functional antibodies. Also identified a novel IgG3 allele and demonstrated that IgG3 enhances neutralization potency and Fc effector function of an HIV V2-specific broadly neutralizing antibody.

Clinical and genetic studies of hereditary neurological disorders in Mali – Guida Landoure

• Enrolled 276 families (neurology, rheumatology, and pediatrics), some from neighboring countries.
• Preliminary exome sequencing results have revealed variants in novel genes and novel variants in genes previously linked to a disease.
• Trained over 10 students and three postdoctoral fellows in genetics and molecular biology.
• Developing a Master program in medical genetics and post-university training in genetic topics.

ELSI Projects

Ethical and social issues in informed consent processes in African genomic research – Erisa Sabakaki Mwaka

• Completed content analysis of 243 consent documents and 77 material transfer agreements for studies involving genetics, genomics or the storage of samples for future use. Fourteen consent forms for genetics have been back translated from Luganda (most commonly spoken local language) to English by two independent consultants and the translations are currently being analyzed for accuracy and context.
• Preliminary findings we have realized that principal investigators are not well conversant with the challenges their study teams are facing with regard to consent processes. We therefore submitted a protocol amendment to include study coordinators and nurses who actively participate in the informed consent process to obtain a clear understanding of their experiences and practices.

ELSI Centers

IFGeneRA – Ambroise Wonkam, Jantina De Vries

• Developed mini-documentary on GeneMAP initiative
• Developed short drama production “Drama of DNA” to engage and educate communities on some of the issues that can arise with return of results

Informatics

H3ABioNet – Nicky Mulder

Training and Development

• 40 courses/workshops run (29 of which were face-to-face)
• 2256 individuals trained
• Helped establish 4 bioinformatics degree programs
• 11 accreditations in analysis of genomic data awarded

Enabling Genomic Medicine in Africa

• Designed and developed H3Africa SNP Chip
  • Data from 18 populations used
  • 520 new African genomes utilized in reference panel
  • 27,215,784 core computing hours to design chip
• 225 nurses trained in genomic medicine
• Provide support for clinical data analysis and phenotype harmonization efforts

Computing Infrastructure

• 3432 cores for data processing
• 18 computing facilities developed
• 4 containerized genomic data analysis workflows developed
• 1.2 petabyes available for storage and processing of African genomic data

Data Management, Storage, and Transfer

• 14 African genomics datasets available in archive
• 134.9 terabytes of African genomics data stored
• 8 datasets QC’d and submitted to public repositories
• 77.3 terabytes of African genomic data transferred

Informatics Training

West African Center of Excellence for Global Health Bioinformatics Research Training – Seydou Doumbia

• Designed and organization of the Inaugural Bioinformatics for Global Health Symposium at USTTB
  • March 11-12, 2019 and included: 106 attendees, 19 total oral presentations (4 related to training and 15 scientific), 8 student poster presentations, 4 panel discussions, and a virtual reality demonstration
• Design and delivery of the Second Annual Workshops Series for the West African Center of Excellence for Global Health Bioinformatics training program at USTTB in March 2019.

WASLITBRe – Ezekiel Adebiyi

• Employed 1 Postdoctoral fellow each at CU and KNUST and using the currently existing bioinformatics program at CU and KNUST, there are 6 PhD, 2 MSc and 4 PhD and 2 MSc trainees under the WASLITBRe program at CU and KNUST respectively
• New full pledge Bioinformatics curriculum for the MSc and MPhil/PhD programs at CU and KNUST has been developed and currently undergoing the necessary approvals
• The 2nd WASLITBRe Postgraduate Bioinformatics Workshop & 2nd Annual Consortium/ TAC Meeting at KNUST, 18 Feb. – 29 March, 2019

EANBiT – Daniel Masiga

• Delivered an intensive 5 weeks Bioinformatics Training of Trainers workshop in July-August 2018.
• Established and equipped a bioinformatics lab with a server and a capacity of 12 students at Pwani University.
• Launched the MSc in Bioinformatics course at Pwani University in October 2018, with 10 students
• Supported the approval of MSc in Bioinformatics at Makerere University, due for launching in 2019 and will support MUHAS to establish a program from 2019.

Biorepositories

IBRH3AU – Moses Joloba

• Dedicated H3Africa Biorepository space to store up to 850,000 samples
  • Acquired equipment including Sanger and NGS platforms Sequencing and analysis of shipped samples
  • Received/collected, processed, stored and distributed biospecimen
  • Biorepository science and management course
  • University appointed advisory board and
• business manager, consultant and approved
• creation of a semi-autonomous body as part of sustainability
  • Successful site engagement

CLS – Elizabeth Mayne

• Initiated and completed pilot studies amongst the repositories and between the repository and the submission site
• Published papers looking at key steps in establishing a biorepository in Africa including the ethics of storage and practical guides to selecting a laboratory information system amongst others
• Published guidelines and developed policies for ethical practices in genomic research and biobanking on the continent
• Engaged with institutions to develop ethical oversight including biorepository ethics committees to oversee sample collection, storage and shipping
• Advised the African Union and other organisations on establishing and expanding biorepository services
• Developed novel logistical approaches to address the challenges of transporting samples in Africa
• Developed a core laboratory for nucleic acid extraction

I-HAB – Alash’le Abimiku

• Over 14,750 DNA collections for the consortium
• Introduced re-usable Credo shipping containers to Nigeria CDC as cold chain packaging option used nationwide during the Nigerian HIV/AIDS indicator and impact survey
• Contributed biospecimen data to populate the H3Africa online catalogue
• Trained and mentored over 51 Project Clinical site staff on Sample management, DNA QC, shipment sample packaging and set up the Nigerian National biorepository
• Developed online videos on sample management, DNA QC, shipment sample packaging as training resources for investigators & teams
• Partnered with other H3A biorepositories to harmonize  tools, SOPs  and publish guidelines on  sample deposit and material transfer agreement