Genomic Research in Africa by Africans

Sadly most schools in most parts of Africa are way behind the times. But I hope we will get into the genomes race soon.


Seems like there is some movement in that direction:

The next chapter for African genomics

Nigeria is poised to become a hub for genetics research, but a few stubborn challenges block the way.

After Rotimi joined the US National Institutes of Health (NIH) in Bethesda, Maryland, in 2008, he hatched a plan with director Francis Collins to drive genetics research in Africa. Rotimi wasn’t interested in one-off grants, but rather in building a foundation on which science could thrive. “The major thing to me was to create jobs so that people could do the work locally,” he says. In 2010, the NIH and Wellcome, a biomedical charity in London, announced the H3Africa, or Human Heredity and Health in Africa, project. It’s become a $150-million, 10-year initiative that supports institutes in 12 African countries. The proof of its success will be not in the number of papers published, but rather in the number of African investigators able to charge ahead after the grant ends in 2022.


Africans in Africa should be the ones leading the way in sequencing and studying African genetic data. This is not to exclude others from doing this research too. There is much work to do, but Africans should be sharing in the opportunity to do good science, and they may even have a greater bank of trust to draw upon in doing this critical work.

H3Africa empowers African researchers to be competitive in genomic sciences, establishes and nurtures effective collaborations among African researchers on the African continent, and generates unique data that could be used to improve both African and global health.

There is currently a global effort to apply genomic science and associated technologies to further the understanding of health and disease in diverse populations. These efforts work to identify individuals and populations who are at risk for developing specific diseases, and to better understand underlying genetic and environmental contributions to that risk. Given the large amount of genetic diversity on the African continent, there exists an enormous opportunity to utilize such approaches to benefit African populations and to inform global health.

The Human Heredity and Health in Africa (H3Africa) consortium facilitates fundamental research into diseases on the African continent while also developing infrastructure, resources, training, and ethical guidelines to support a sustainable African research enterprise – led by African scientists, for the African people. The initiative consists of 51 African projects that include population-based genomic studies of common, non-communicable disorders such as heart and renal disease, as well as communicable diseases such as tuberculosis. These studies are led by African scientists and use genetic, clinical, and epidemiologic methods to identify hereditary and environmental contributions to health and disease. To establish a foundation for African scientists to continue this essential work into the future work, the consortium also supports many crucial capacity building elements, such as: ethical, legal, and social implications research; training and capacity building for bioinformatics; capacity for biobanking; and coordination and networking.


I think some progress has been made. For instance, Nigeria was able to sequence the genome of a strain of SARS-CoV-2 independently.

However, such achievements may blind observers to the real nature of events. Many federal universities which carry the bulk of Nigerian students are poorly equipped. Don’t even get me started on the state of laboratories in many Nigerian public universities. Top researchers in my country (at least the ones I know), sometimes send laboratory samples to the US or Europe for things as basic as PCR.

Erratic power supply, unsuitable learning environments (imagine standing for two hours to learn chemistry under poorly ventilated conditions) and a host of other factors deny Nigerian students, especially those in public universities, the chance to have the best education. Thanks to MIT open courseware though, I managed to get solid foundations on some topics.


We sure have the human power for this, but the facilities are insufficient.


That is certainly problematic. I have issues keeping our -70C freezers up and running when ambient temps start to wander towards 32C. I can’t imagine not having climate controlled labs to work in, not to mention lacking basic equipment like thermocyclers.

I’ve been working with Nanopore tech recently, and it is quite impressive relative to its low upfront cost and small physical footprint (I’m not an sales rep, I promise). The reads are much lower quality than Illumina or Sanger sequencing, but the lower cost to entry might be worth it for regions like Africa. The sequencer can fit in your hand:

All you need is a middle of the road laptop to plug it into. However, you will need a computer with a decent GPU for local basecalling. It appears the tech is already being used in the field to detect plant viruses in Africa.


This is valuable info. Per adventure I get into research that involves sequencing, I’d see if this device could be used in the absence of other options.

@Michael_Okoko you are in Nigeria. Are you doing scientific work there? Are you a scientist?


If being a scientist implies active research, then I am not, but if it means having a degree in a field of science, then yes I am.

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Most of that work was done in China by the Beijing Genomics Institute, if that makes you feel any better. No American lab could have handled that volume either.

Whom is this comment for?

It’s for you.

Most of what work?

It’s not a question of opportunity but one of resources, and that includes both material resources and the intellectual resources of trained scientific personnel. A great deal of effort has gone into building genetics and genomics research capacity in Africa, with the result that several places are now getting to the point where Africans can assume genuine leadership of the effort, but substantial outside support is still needed for all of the ones I’m familiar with. I’ve spent many years working with African scientists (including some mentioned in the Nature article), and my overall impression is that enormous progress has been made but that there is still a long way to go – and that a lot, both good and bad, is going on behind the scenes and will never show up in an article like that.


Which work?

We were discussing the new Nature paper with a massive sample of avian genomes. That’s what started this thread.

Apt. Many things are wrong in the Nigerian educational system, and I would daresay most of Africa too.

Oh OK.

Sorry, I hadn’t seen the parent thread yet. I’m rather skeptical that no American lab could have handled the sequencing in the avian paper.


That’s my experience. BGI is incredibly huge. The American rival would be JGI, and it just doesn’t approach the number of sequencers at BGI.