April 25th marks National DNA Day, a chance to celebrate the initial discovery of the DNA double helix structure in 1953 and the completion of the Human Genome Project in 2003. This year, editors at Nature Communications and Communications Biology wanted to celebrate National DNA Day by highlighting researchers that have emphasized genomic analyses in historically underrepresented populations. Here, we asked researchers about their own achievements, the importance of diversity when pursuing genomic studies, and how to achieve better inclusivity in STEM.
Dr. Palwende Romuald Boua is a Research Associate at the Clinical Research Unit of Nanoro (CRUN)/IRSS-DRCO in Burkina Faso. His work is part of the AWI-Gen study founded by the NIH through The Human Heredity and Health in Africa initiative (H3Africa). His research focuses on understanding the genetic susceptibility of African populations to cardiometabolic risk factors using a GWAS approach.
The topic of my research has led me to primarily studying atherosclerosis in a cohort of middle-aged adults living in different settings and regions on the African continent. My research on atherosclerosis is trying to unravel how genetic risk can be triggered by environment through gene-environment interactions and also influenced by specific effects in particular populations. I also investigate genetic drivers of behavioural risk factors for cardiovascular diseases, such as smoking and alcohol consumption. It is important to consider both genomic and environmental risk factors for diseases in Africa in order to ensure the continent benefits from the era of precision medicine and public health.
The high genetic diversity on the African continent has yet to be unravelled and this is a challenge young African scientists should take in order to write the chapters of Africa’s genetic research ourselves. From my early exposure with health research as a research assistant, I noticed that the demographic transition or traditional risk factors alone could not explain the increase in prevalence of cardiometabolic diseases in Africa. Genetics research in Africa is still at the very early stages and Africa is a continent with multiple diseases burdens ranging from infectious to chronic disease. Since the completion of the Human Genome Project in 2003, genetic research has been at the edge of advances in biology and medicine; the best example being the contribution of genomics in the management of the current COVID-19 pandemic. Therefore, I see tremendous potential for genomic research in Africa to shed some light on complex biological phenomena and to contribute to disease management. This motivated me to become a geneticist in Africa.
From the outmigration of humans from Africa 300,000 years ago, a large amount of genetic diversity has stayed on the continent compared to the rest of the world. Nonetheless, there has been an overrepresentation of European ancestry in genetic association studies, including only about 2% of participants from African ancestry (mostly African Americans). There is therefore a gap that needs to be filled with regards to the high genetic diversity of the African population and the particular evolutionary history that shaped human beings. Recent publication on 426 whole genome sequences (from 50 ethnolinguistic groups in Africa) uncovered more than 3 million previously undescribed variants, as well as 62 previously unreported loci that are under strong selection. There is now evidence that variants which have been categorized as pathogenic using limited populations were found to be common in African populations and without phenotypic consequences. This illustrates how newly sampled ethnolinguistic groups can improve our understanding of traits and diseases. The more diverse our genetic resources are, the more inferable genetic information there will be for the whole world.
I acknowledge that an academic career and research in particular is still a domain of a privileged few in Africa, even though the system is not specifically favouring a group of the society. The resource-limited environment that African children and young adults are struggling in does not allow the vast majority to access postgraduate studies. That’s why part of the strategic policy of my research group is to support the next generation of researchers through international collaborations and by promoting new paths or research areas. We have a strong commitment in promoting early career scientists regardless of gender of any other social origin. Qualification and motivation to undertake a career in research are the criteria of selection for PhD and post-doctoral candidates. Over the last ten years, our research centre has grown and expanded our research topics, adding nutrition, infectious diseases, chronic diseases and neglected tropical diseases like malaria, though the latter remains the main topic. Our research participants come from all parts of the community; we work with children, adolescents, women, pregnant women and older adults. A plan for the future is to encourage female researchers, for instance those who are facing more challenges in pursuing an academic career due to cultural beliefs. Our flagship success is our former scientific director of our research unit who has just been appointed to the position of Ministry of Research and Innovation, she represents a role model for young female scientists in the country.
Dr. Lucia Hindorff is a Program Director in the Division of Genomic Medicine at NHGRI, where she scientifically manages research efforts related to genetic epidemiology or genomic medicine.
The need to increase the quality and quantity of data in diverse and underrepresented populations is important in the way that we generate genomic data and use it in the clinical setting. Many of the programs and consortia that I manage have evolved over time in the direction of increasing and characterizing diversity. For example, the Clinical Sequencing Evidence-Generating Research (CSER) program is assessing the clinical utility of genome sequencing in diverse settings and populations; the PRS Diversity Consortium is refining and improving prediction of polygenic risk scores across diverse populations, and the Population Architecture using Genomics and Epidemiology (PAGE) project is expanding understanding of ancestral differences in genomic disease associations in large, diverse, well-characterized cohorts. I am also Project Scientist for the NHGRI-EBI Genome-wide Association Studies (GWAS) Catalog, an enduring resource with an iconic visual representation that is often used to help identify causal genetic variants and understand disease mechanisms.
Resources play an important role in translational research, where the findings from basic scientific research are applied to improving human health. We know that biases in the availability or quality of data at one stage of research, specifically in diverse and underrepresented populations, propagate to subsequent stages. The result of these accumulated biases is that the evidence base for applying research to human health may not reflect populations in whom disease burden may be greatest. A good example of this is how relatively sparse data for non-European populations in GWAS leads to incomplete information about allele frequencies across populations. These allele frequencies are used to evaluate whether genetic variants may or may not be pathogenic, so incomplete information could result in misinterpretation of variant pathogenicity as well as potential misdiagnoses. Some colleagues and I wrote about this type of health information disparity in more detail (PubMed ID: 30209973).
The simple answer to why I chose a career in genetics research is that I came for the intellectual challenge and stayed for the community. In my academic training I became interested in research that spanned multiple disciplines, and there was (and still is) so much happening at the intersection of genomics, medicine, public health, and ethics. When I left academics, I was a genetic epidemiologist by training, but as the NHGRI’s mission has evolved, my interests and expertise have, as well. My portfolio now includes genomic medicine in addition to epidemiology, and I have worked with trainees, researchers and advisors across multiple disciplines and career stages. To me, the most exciting thing about my job is the opportunity to bring together smart people to solve important problems in genomics and there is no shortage of those (either smart people or important problems) in genomics!
The nature of my job requires strategic communication and consensus building. In this vein, I enjoy working with trainees and experienced investigators alike and building diverse teams, whether in consortia or among our extramural staff. A team with good chemistry is really something to behold: everyone has something valuable to contribute, whether it’s as an expert, a colleague, an advisor or another stakeholder role. Acknowledging the interdisciplinarity and multidisciplinarity that is needed to develop and achieve common research goals is also important, because people from different disciplines have different ways of approaching and solving problems. When confronted with a group challenge, I try to isolate expectations for the group from the perspectives of individual people. You can learn a lot from one-on-one conversations with people to understand where they’re coming from. I am also interested in coaching as a way to help people learn what drives them and deepen engagement with their work (though this is mostly an extracurricular activity for now).
Dr. Yoichiro Kamatani is a professor at the University of Tokyo. His group obtains deeper and comprehensive phenotypes from the subjects of hospital-based cohort in Japan, including multi-omics data and time-series EHR data, for the integrative interpretation of genetic susceptibility variants and polygenic scores.
When I started my career in 2006, I was excited about the completion of the human genome project and the progress of the HapMap project, and wanted to join this field. I was interested in searching for the disease susceptibility genetic variants that could explain the difference in disease susceptibility between individuals. I was also fascinated with the idea to construct equal medical service to everyone by taking these genetic differences into account.
To construct genetics-aware medicine, we first need to know the medical value of the genetic information content that each patient has. Since genomic sequence patterns are somehow different between populations, we need to investigate each genetic population.
The diversity of the genomic sequence between populations may also lead to finding unique genetic insights into both rare and common diseases. A population-specific susceptibility variant may give a new clue to the biological elucidation of the diseases as well as improve genetic prediction, and a difference of association signals given by different linkage disequilibrium structure or allele frequency spectrum will hint at narrowing the candidates of causal variants. Another important aspect might be that it could give a chance to young researchers in diverse regions on earth! Although the data protection of genetic information and EHR data are essential, we are trying to set up a secure computational environment to accept diverse students to the laboratory.
Professor Collen Masimirembwa is the founding President and Chief Scientific Officer of the African Institute of Biomedical Science and Technology, AiBST, (www.aibst.com). Professor Masimirembwa is also a Distinguished Professors of Health Sciences at the University of Witwatersrand. His research focuses on drug metabolism, pharmacokinetics, and pharmacogenomics in support of medical drug discovery, development, and clinical deployment. His work also includes population genetic polymorphism studies in search of biomarkers of drug response, molecular modelling to understand effects of genetic variants on structure and function of drug metabolising enzymes, He is also a Fellow the Zimbabwe Academy of Sciences and the African Academy of Sciences.
My research is on the implementation of preemptive pharmacogenomic testing for effective treatment outcomes in African populations. This is because most drugs in use were discovered, developed and optimised for safety and efficacy for white populations, and clinical evidence shows that some of the drugs are not either associated with more adverse drug reactions or reduced efficacy when used in African populations. Towards this, I have developed an open array chip, GenoPharm that tests for 120 variants in 38 pharmacogenes, results which can assist doctors individualise pharmacotherapy with respect to choice of the appropriate drug and dose for safe and effective outcomes. The GenoPharm Chip is unique in that I integrated genetic variants unique to African populations and also drug-gene interactions unique to drugs commonly used in the treatment of neglected tropical diseases.
Whilst conducting research on drug metabolism to understand drug safety and efficacy I was introduced to then-emerging research on genetic variation in genes coding for the drug metabolising enzymes I was using in my studies. This genetic polymorphism was fascinatingly able to predict interindividual variation in response to some drugs. Besides inter-individual variation, the genetic variability also seemed to explain some inter-population differences in response. That triggered my now over 25-year career of exploring the genomic diversity of African populations and its implications for drug discovery, development and clinical deployment.
Whole genome sequencing programs of world populations have shown that African populations are the most diverse, but of the total genomes sequenced, Africa is poorly represented. This is glaringly visible in the number of genome wide association studies that aim to discover biomarkers for disease risk and treatment response: only 2% have been done in African populations. This is again demonstrated in pharmacogenomic studies, where studies in Africa are less than 1%. This will result in poor access to the emerging medical solutions from genomic research. There is therefore a need to enhance Africa’s capacity to generate genomic information and apply it to drugs, diagnostics, and vaccine innovations that can impact human health. My work and that of other scientists in Africa and the international community has realised the need to generate diverse genetic data, especially for Africa and that this will not only be important for the continent but for global public health.
Since 2003, I recognised the continental need of skilled geneticists and started training master and PhD students from across Africa. I have therefore hosted students from Ghana, Nigeria, Kenya, Tanzania, South Africa, Malawi, Benin and Zambia, who, together have created a continuously diverse community with a shared vision for harnessing the power of genomics in addressing human health issues. My long-term idea being that when they go back to their countries, they will become the seeds of local capacity and build a sustainable ecosystem of international collaborations. I have also realised that few countries in Africa have a critical mass of highly skilled senior scientists to properly train the students in genomics and bioinformatics. To address this, I have created a Global Virtual Faculty of over 30 world-leading scientists in industry and academia who contribute to the training of students I bring to my research group. This way, young scientists have access to some of the best scientists in genomics, thus further promoting a diverse and inclusive environment in the group.