Alan ChristoffelsCredit: Morgan Morris
Alan Christoffels was part of the first doctoral intake of the South African National Bioinformatics Institute (SANBI). He joined the Institute in 1997, shortly after its founding at South Africa’s University of the Western Cape.
Its mission was simple: develop bioinformatics capacity in South Africa. Over the past three decades, the Institute has become the trailblazer for the discipline across Africa. Over the past few years, it has worked closely with the World Health Organization (WHO) and the Africa Centres for Disease Control and Prevention (Africa CDC), as well as major funders, to develop bioinformatics capacity and expertise across the continent.
He was appointed head of the Institute in 2009, and today, it is playing its part in addressing the low numbers of Black, Indigenous, People of Colour (BIPOC) researchers in its global fold.
We spoke to Christoffels about efforts to address the shortage of skills and capacity in Africa as a way of getting more BIPOC researchers into the field.
What was the state of bioinformatics at in the late 90s?
At that time, globally, the Human Genome Project was the big activity. It was the race to complete the sequencing of the human genome. We had DNA sequencing, but high-throughput sequencing and portable technology, wasn’t there. The machines were enormous, and in South Africa, the experimental work was still mostly done using Sanger sequencing — reading small, targeted regions of the genome mostly to test for known familial variants.
When did the field really take off in Africa?
Around 2007/8, when researchers in the field launched the African Society for Bioinformatics and Computational Biology (ASBCB) and that became the vehicle through which a lot of activities happened. At the time, the emphasis was on agriculture and veterinary science. But at the same time, the human-genetics fraternity recognised the value of sequencing African genomes and in 2011 the Southern African Human Genome Programme was formally launched. I recall analysing the first next generation sequencing data in 2012 for a partial apple genome together with Jasper Rees, then professor of biochemistry at UWC.
Is South Africa the leader in this field in Africa, or have other countries caught up?
Other countries have caught up in terms of skill sets. The difficulty lies in maintaining that critical mass. We’ve been fortunate in South Africa to have an environment where you can nurture that. But in a lot of countries, people would move on and look for opportunities elsewhere, particularly Canada, the US, Europe. There are just not enough opportunities in their own countries, at the moment.
The expansion of the number of working groups in ASBCB is a reflection of the expansion of the field. We have working groups for: pathogens, agriculture, molecular modelling, population genomics and system administration. The fact that the working groups got started shows how the field has grown. As the membership grew, and people’s involvement grew, you saw the need for people working in different sectors.
Do we have enough people and capacity in the computational sciences in place in Africa?
The short answer is no. Not enough to keep up with the demand in addressing key health issues.
Is anything being done to address that?
As a continent we’ve enjoyed funding from a range of organisations for development, including from the Africa CDC, WHO, the US National Institutes of Health and Wellcome Trust. And of course, the Trump administration’s decision to cut off critical funding has been devastating, compromising the continuity of life-saving health programmes. It has been particularly painful because of how abrupt its impacts were. However, capacity-building programmes have largely relied on donations from philanthropic organisations, whose support continue. That is a double-edged sword, however, as those grants and funding often have short-term goals and objectives, while these programmes do often need longer timelines. So, the onus is on academics to see how to incorporate longer-term sustainable programmes at universities, for example.
As a whole, we see the field of bioinformatics taking off and being entrenched in public health systems on the continent, thanks to international networks like the Public Health Alliance for Genomic Epidemiology (PHA4GE), which looks to turn bioinformatics from an academic subject into an applied science. Another example would be the role of the H3Africa Bioinformatics Network (H3Abionet), which over the past 10 years has strengthened human genomics applications of bioinformatics in Africa. And the more that happens, the more opportunities we create here in Africa, the more students we can attract, and the more likely we are to retain some of them after they graduate.
