tag:theconversation.com,2011:/au/topics/genomic-research-28264/articlesGenomic research – The Conversation2024-02-27T12:41:39Ztag:theconversation.com,2011:article/2191402024-02-27T12:41:39Z2024-02-27T12:41:39ZCould a couple of Thai otters have helped the UK’s otter population recover? Our study provides a hint<p>Otter populations crashed in Britain around the 1960s from the lethal effects of chemical pollution in rivers and lakes – or so we thought. <a href="https://academic.oup.com/mbe/article/40/11/msad207/7275014">Our research</a> has looked more closely at what happened to otters in Britain over the last 800 years and has revealed a more complex picture. </p>
<p>Since Eurasian otters (<em>Lutra lutra</em>) are at the top of the aquatic food chain in Britain, any contamination consumed by their prey, and by the prey of their prey, <a href="https://pubs.acs.org/doi/10.1021/acs.est.1c05410">accumulates in otters</a>. So otters are particularly susceptible to any toxic chemicals in their environment. </p>
<p>Following the banning of many chemical pollutants, otter populations began to recover, and we now have otters in <a href="https://onlinelibrary.wiley.com/doi/10.1111/eva.13505">every county in Britain</a>. National otter surveys have been conducted in Wales, Scotland and England since 1977 and have helped to track population recovery. </p>
<p>However, we didn’t have a good grasp on what population sizes were like in the decades before this time. We only had anecdotal evidence that otter hunting was becoming less “successful” over time, and that both sightings and signs of otters were rarer. </p>
<h2>Otter population decline</h2>
<p>Our research shows that roughly between 1950 and 1970, an extreme population decline happened in the east of England, and a strong decline in south-west England. They were probably caused by chemical pollution. </p>
<p>In Scotland, otter populations showed a long-term, but smaller decline, which suggests less chemical pollution. There was a smaller population decline in Wales, which started around 1800, possibly linked to otter hunting and changes in how people shaped and used the landscape. </p>
<p>While both deal with DNA, genetics focuses on individual genes and their roles, while genomics examines the entire set of an organism’s DNA. Although there have been genetic studies of otters in Britain, our research was the first time genomics was used to study Eurasian otters anywhere in the world.</p>
<p>Working with scientists from the Smithsonian Conservation Biology Institute and the Wellcome Sanger’s Darwin Tree of Life project, we looked at the entire otter genome. The upgrade from genetics to genomics threw up a few surprises. </p>
<p>First, there was a mitochondrial DNA sequence found in the east of England, which was very different to the sequences in the rest of Britain. Mitochondrial DNA is a sequence of DNA found in a cell’s mitochondria, which is what generates the energy. Mitochondrial DNA is inherited only from the mother, while the rest of the DNA is a mix of both the mother’s and the father’s DNA.</p>
<p>Another <a href="https://www.tandfonline.com/doi/full/10.1080/19768354.2023.2283763">recent study</a> by our research group, in collaboration with colleagues in South Korea, suggested a divergence between these two lineages at least 80,000 years ago. Finding this mitochondrial lineage (that, based on our data, is otherwise restricted to Asia) in the UK was surprising. </p>
<p>Second, we found high levels of genetic diversity in the east of England. Normally, after an extreme population decline such as the one we identified in this area, genetic diversity decreases. Yet we saw much greater diversity here than in the population in Scotland, where there was no clear evidence for such a decline. </p>
<h2>Thai otters</h2>
<p>With a little detective work, we discovered that a pair of Eurasian otters (the same species that we have in the UK), were brought to Britain from Thailand in the 1960s. Populations of Eurasian otters range right across Europe and Asia. Although they are the same species, there are several genetically distinct subspecies, particularly in Asia. </p>
<p>It seems possible that these genetically different otters from Thailand bred with otters in the east of England. At the time of the population decline, when native UK populations were at their smallest, even a few individuals introduced into the population may have made a big difference. And they left unexpected marks on the genome. </p>
<p>We don’t know for sure if this is what happened, and we need to do more work to find out what effect this may have had on otters in the east of England. High genetic diversity is usually good for a population or species. But on the other hand, conservation often strives to maintain genetic differences between populations, rather than mixing distinct populations.</p>
<p>One way to find out more would be to compare the genome of a Eurasian otter from Thailand to the otters we see in the east of England. Unfortunately, it’s not that easy. Since the 1960s, otters in Thailand and across Asia have become increasingly rare. This is due to habitat loss, pollution and the illegal otter trade. So getting samples for genome sequencing is very difficult. It highlights the importance of conserving the species in Asia, despite population recoveries in Europe.</p>
<p>Our work shows the value of using modern genomic tools to look at the genetic diversity of a threatened species. The application of such tools can uncover surprising facts, even in supposedly well-studied species.</p>
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<img alt="Imagine weekly climate newsletter" src="https://images.theconversation.com/files/434988/original/file-20211201-21-13avx6y.png?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/434988/original/file-20211201-21-13avx6y.png?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=600&fit=crop&dpr=1 600w, https://images.theconversation.com/files/434988/original/file-20211201-21-13avx6y.png?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=600&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/434988/original/file-20211201-21-13avx6y.png?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=600&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/434988/original/file-20211201-21-13avx6y.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=754&fit=crop&dpr=1 754w, https://images.theconversation.com/files/434988/original/file-20211201-21-13avx6y.png?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=754&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/434988/original/file-20211201-21-13avx6y.png?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=754&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
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<p class="fine-print"><em><span>Frank Hailer receives funding from NERC and Dŵr Cymru Welsh Water. </span></em></p><p class="fine-print"><em><span>Elizabeth Chadwick receives funding from the UK Natural Environment Research Council and from the Environment Agency</span></em></p><p class="fine-print"><em><span>Sarah du Plessis receives funding from the UK Natural Environment Research Council and the Global Wales International Mobility Fund.</span></em></p>Research has revealed how British otters may have been able to recover from species loss in the 1950s with the help of otters from Asia.Frank Hailer, Senior Lecturer in Evolutionary Biology, Cardiff UniversityElizabeth Chadwick, Senior Lecturer at the School of Biosciences, Cardiff UniversitySarah du Plessis, PhD Candidate, Cardiff UniversityLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1238142022-02-01T18:47:49Z2022-02-01T18:47:49ZVirtual labs can help students learn, but they can’t replace hands-on experience<p>An ill newborn’s life is hanging by a thread, and only <a href="https://www.nejm.org/doi/full/10.1056/NEJMc2112090?query=featured_home">the right diagnosis</a> will afford her the treatment that may save her life. A cancer patient’s <a href="https://www.cancer.gov/about-cancer/treatment/types/biomarker-testing-cancer-treatment">therapy can be tailored</a> to the specific type of tumour they have, if only the doctors know what the molecular targets are that will make the drugs effective for that patient. Parents may <a href="https://doi.org/10.1038/npjgenmed.2015.12">finally get a name</a> for the syndrome that their child has been living with. </p>
<p>All of this can be achieved by sequencing the genome of a patient. A genome is <a href="https://www.yourgenome.org/facts/what-is-a-genome">a set of genetic instructions</a> that can be deduced through examining blood or saliva. When scientists sequence genomes, they are involved in interpreting the changes between one individual and another and by determining the changes that explain a disease, provide a diagnosis or predict the best treatment.</p>
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<a href="https://theconversation.com/medical-schools-need-to-prepare-doctors-for-revolutionary-advances-in-genetics-158280">Medical schools need to prepare doctors for revolutionary advances in genetics</a>
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<p>At the University of Toronto, I teach students how to <a href="https://moleculargenetics.utoronto.ca/news/learn-more-about-medgen-professor-dr-martina-steiner">run the experiments to analyze a genome</a>. The students learn how to sequence the genome, what the data looks like and how the results can be used to provide a diagnosis or choose the right medication. Virtual labs or “lab simulations” offer a way to experience the experimental steps for a biological experiment on a screen. Even before the pandemic started, I was experimenting with virtual labs in my classroom. </p>
<h2>Some lab work continued in person</h2>
<p>Virtual labs for genome sequencing, like <a href="https://doi.org/10.1152/advan.00241.2020">virtual labs in some other sciences</a>, offer some advantages and opportunities for student learning. However, virtual labs for genome sequencing are not a replacement for hands-on, wet lab experience (<a href="https://www.universitylabpartners.org/blog/wet-lab-vs-dry-lab-for-your-life-science-startup">where biological matter can be analyzed and tested by using various liquids</a>), and are certainly not replacing in-person training for professional purposes. </p>
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<img alt="Graphic illustration of a person in a lab surrounded by equipment." src="https://images.theconversation.com/files/443337/original/file-20220131-21-166uu4p.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/443337/original/file-20220131-21-166uu4p.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=630&fit=crop&dpr=1 600w, https://images.theconversation.com/files/443337/original/file-20220131-21-166uu4p.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=630&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/443337/original/file-20220131-21-166uu4p.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=630&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/443337/original/file-20220131-21-166uu4p.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=792&fit=crop&dpr=1 754w, https://images.theconversation.com/files/443337/original/file-20220131-21-166uu4p.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=792&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/443337/original/file-20220131-21-166uu4p.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=792&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
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<span class="caption">‘Wet lab’ experience where students analyze biological matter is important training for professional work.</span>
<span class="attribution"><span class="source">(Slidesgo)</span></span>
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<p>Even when other instruction was moved online due to COVID-19, some wet <a href="https://www.utoronto.ca/news/u-t-plans-gradual-safe-return-our-campuses-fall-semester-mix-person-and-virtual-learning">lab courses</a> have continued in person since the summer of 2020. I spoke with <a href="http://biochemistry.utoronto.ca/person/ahlia-khan-trottier/">Ahlia Khan-Trottier</a>, director of the division of teaching labs at the Temerty Faculty of Medicine at the University of Toronto, who relayed that in the pandemic, “lab courses took various paths as decided by the course co-ordinators/departments — some remained fully in person with COVID-19 measures in place, some were hybrid and others moved fully online.”</p>
<p>In my case, a lab course in the department of molecular genetics where the students were going to run a sequencing experiment was postponed. It ran five months later with the necessary COVID-19 measures in place.</p>
<h2>Move to online labs</h2>
<p><a href="https://doi.org/10.1186/s12909-016-0620-6">Studies</a> have shown that virtual genetics labs can enhance comprehension and motivation, thus <a href="https://doi.org/10.1007/s11423-019-09690-3">improving the learning experience</a>. Students click on a tube to open the lid of a vessel or turn the wheel of a virtual pipette — a hand-held device to transfer small amounts of liquids — to transfer reagents from one container to another. No lab coat is required, no expensive machines and no dangerous chemicals. </p>
<p>In a virtual lab, there are no restrictions to the cost of an experiment, whether clinical specimens can be used, and no ethical concerns or biohazards to contend with. Virtual labs are very “forgiving.” Students can start over, <a href="https://www.britannica.com/science/reagent">reagents</a> are abundantly available and the game-like feeling is rewarding.</p>
<p>Virtual labs bridge theory and practice by providing a multimedia connection between abstract concepts and practical execution. Students use their laptop or phone to observe, click, drag and type in response to videos, questions and instructions. </p>
<p>Virtual reactions are instantaneous and students do not have to wait to use shared equipment such as <a href="https://www.genome.gov/about-genomics/fact-sheets/Polymerase-Chain-Reaction-Fact-Sheet">PCR machines</a> — a machine used to heat or cool samples to allow chemical reactions and physical processes to occur at a specified temperature. </p>
<h2>Different kinds of virtual labs</h2>
<p>Many virtual labs are now being mostly run through software or online applications developed by developers that are either accessible for free or can be purchased by institutions. </p>
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<figcaption><span class="caption">About Lab Xchange lab simulations (virtual labs).</span></figcaption>
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<p>Resources include free simulations and interactive explorations (like <a href="https://www.labxchange.org/library?">LabXchange</a>), as well as more complex open-ended explorations with immersive animations (like <a href="https://wp.labster.com/introduction-to-labster/">Labster</a>). Such virtual labs combine illustrations, explanations, prompt critical thinking and offer incentives through “gamification.”</p>
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<figcaption><span class="caption">Labster virtual lab about medical genetics simulation.</span></figcaption>
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<p>Some colleagues of mine are also working on building tailored virtual labs for their courses. </p>
<h2>Student experience of virtual labs</h2>
<p>Before the pandemic, the grad students who were using virtual labs in my classroom appreciated the added resource but were very clear that virtual labs could not replace a wet-lab experience. One student described the simulation in the virtual lab like a lab tour, where you get to review the workflow and mentally prepare for the wet-lab but are not directly handing equipment.</p>
<p>It takes years of training to become proficiently skilled in clinical and research laboratory techniques. Dealing with the frustrations of getting equipment to work and developing the <a href="https://bento.bio/protocol/biotechnology-101/introduction-to-pipetting/">muscle memory of performing work hands-on</a> cannot be replicated in the virtual platforms now widely available for genomic sequencing, nor <a href="https://www.taylorfrancis.com/chapters/mono/10.4324/9781315042565-6/introduction-making-move-peer-learning-david-boud-ruth-cohen-jane-university-technology-sampson">can the lessons from learning in a group with peers</a>. </p>
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<img alt="Students are seen in a lab." src="https://images.theconversation.com/files/443336/original/file-20220131-17-12qsupu.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/443336/original/file-20220131-17-12qsupu.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=401&fit=crop&dpr=1 600w, https://images.theconversation.com/files/443336/original/file-20220131-17-12qsupu.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=401&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/443336/original/file-20220131-17-12qsupu.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=401&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/443336/original/file-20220131-17-12qsupu.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=504&fit=crop&dpr=1 754w, https://images.theconversation.com/files/443336/original/file-20220131-17-12qsupu.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=504&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/443336/original/file-20220131-17-12qsupu.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=504&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
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<span class="caption">Learning to troubleshoot challenges with real equipment and learning from a group with peers are both important dimensions of practice in a wet lab.</span>
<span class="attribution"><span class="source">(Shutterstock)</span></span>
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<h2>Labs in the future</h2>
<p>Still, virtual labs were gaining traction even before the pandemic, and their <a href="https://www.universityworldnews.com/post.php?story=2021041813552894">use has been sped up during pandemic-related remote teaching</a>.</p>
<p>Instructors and students will continue to value the enhancements that come from lab simulations. For my students, the simulations are useful to catch up and fill in any gaps that stem from different backgrounds. </p>
<p>Furthermore, running through a lab on a computer is an excellent way to <a href="https://doi.org/10.1371/journal.pone.0155895">prepare for an in-person lab</a>, when there is little room for mistakes. Some topics in genomics lend themselves particularly well to virtual instruction, for example learning how to effectively search databases for research and how to retrieve information about the genome. </p>
<p>And certainly, students will continue to appreciate the animations and lab simulations that illustrate difficult concepts, where a moving image says more than a thousand words.</p><img src="https://counter.theconversation.com/content/123814/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Martina Steiner received funding from ITIF (The University of Toronto Provost’s Instructional Technology Innovation Fund) to study the integration of virtual labs in a graduate course.</span></em></p>A medical genomics professor reflects on how lab simulations offer some advantages for student learning, but developing the muscle memory of performing hands-on lab work is important.Martina Steiner, Assistant Professor, Teaching Stream, Medical Genomics, University of TorontoLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1538732021-01-25T18:56:09Z2021-01-25T18:56:09ZA new 3D koala genome will aid efforts to defend the threatened species<p>Koalas are unique in the animal kingdom, living on a eucalyptus diet that would kill other creatures and <a href="https://www.environment.nsw.gov.au/news/bigger-and-better-blinky-drinkers-to-quench-koalas-thirst-this-summer">drinking so little</a> their name comes from the Dharug word <em>gula</em>, meaning “no water”. Today, many koala populations across Australia are in decline, due to habitat destruction caused by agriculture, urbanisation, droughts and bushfires intensified by climate change, and diseases such as chlamydia and koala retrovirus.</p>
<p>Genetic information can play a key role in the effort to conserve koalas and other species. A detailed map of the koala genome is vital to understanding their susceptibility to disease, their genetic diversity, and how they may respond to new environmental pressures. </p>
<p>We have <a href="https://www.dnazoo.org">created</a> a new “chromosome-length” sequence of the <a href="https://www.uwa.edu.au/news/Home/Article/2021/January/Genetic-analysis-helps-protect-koalas">koala genome</a>, which will allow researchers to study its three-dimensional structure and understand its evolution.</p>
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Read more:
<a href="https://theconversation.com/drones-detection-dogs-poo-spotting-whats-the-best-way-to-conduct-australias-great-koala-count-150634">Drones, detection dogs, poo spotting: what’s the best way to conduct Australia’s Great Koala Count?</a>
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<h2>A unique creature under threat</h2>
<p>The modern koala is the only living representative of the marsupial family <em>Phascolarctidae</em>, a family that once included several genera and species. During the Oligocene and Miocene epochs (from 34 to 5 million years ago), the ancestors of modern koalas lived in rainforests and <a href="https://doi.org/10.1671/039.029.0412">didn’t eat only leaves</a>. </p>
<p>During the Miocene, the Australian continent began drying out, leading to the decline of rainforests and the spread of open eucalyptus woodlands. Koalas evolved <a href="https://www.publish.csiro.au/book/4781">several adaptations</a> that allowed them to live on a specialised eucalyptus diet. This specialisation makes them picky eaters, so they’re very prone to habitat loss. </p>
<p>Koalas are listed as a vulnerable species by the <a href="https://www.iucnredlist.org/species/16892/166496779">International Union for Conservation of Nature</a>. It was hunted heavily in the early 20th century for its fur, and large-scale cullings in Queensland resulted in public outcry, initiating a movement to protect the species. Sanctuaries were established, and koalas whose habitat was disappearing were relocated. </p>
<p>Koalas are particularly vulnerable to bushfires; they are slow moving and eucalypt trees are very flammable. They instinctively seeks refuge in higher branches, exposing them to intense heat and flames. Bushfires also fragment the animal’s habitat, which restricts their movement and leads to population decline and <a href="https://www.publish.csiro.au/book/5722">loss of genetic diversity</a>. </p>
<h2>Piecing together the puzzle</h2>
<p>The koala genome was <a href="https://www.abc.net.au/science/articles/2013/04/09/3733208.htm">first sequenced in 2013</a>. This was only the first step in understanding koala genetics — akin to finding all the pieces of the puzzle, but being unsure how to put them all together into the meaningful patterns of genes and chromosomes.</p>
<p>Our new chromosome-length assembly follows the work of others, especially the <a href="https://australian.museum/get-involved/amri/the-koala-genome/">Koala Genome Consortium</a> and the Koala Genome Project led by Australian geneticist <a href="https://en.wikipedia.org/wiki/Rebecca_Johnson_(geneticist)">Rebecca Johnson</a>. It is based on <a href="https://www.ncbi.nlm.nih.gov/assembly/GCF_002099425.1/">a draft</a> by the Earlham Institute in the UK. </p>
<p>We used big-data sequencing methods such as Hi-C, <a href="https://science.sciencemag.org/content/356/6333/92">3D-DNA</a> and <a href="https://www.biorxiv.org/content/10.1101/254797v1">Juicebox Assembly Tools</a> courtesy of <a href="https://www.dnazoo.org/methods">DNA Zoo</a> labs to create our chromosome-length assembly.</p>
<p>We organised the genome into 8 chromosomes, a great improvement on the <a href="https://www.ncbi.nlm.nih.gov/assembly/GCF_002099425.1/">draft</a> of 1,907 fragments we began with.</p>
<h2>Vital for conservation</h2>
<p>A high-quality genome sequence is <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6895880/">essential</a> if we want to bring genetic insights to conservation management initiatives. Some 200 Australian vertebrate species currently have species recovery plans, and 80% of those plans include genome-based actions. However, only 15% of those species have any genomic data available.</p>
<p>Our chromosome-length koala genome assembly enables a highly detailed 3D view of the genome architecture for koala. It is easier to use than earlier genomes, and means conservation management initiatives will have fast, cost-effective and reliable analysis options available.</p>
<p>This will give us insights into koalas’ genetic susceptibility to diseases like koala retrovirus (KoRV) and chlamydia. It may also form a basis for innovative vaccines. What’s more, it can be used in new conservation management strategies that aim to diversify the koala gene pool.</p>
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Read more:
<a href="https://theconversation.com/to-save-koalas-from-fire-we-need-to-start-putting-their-genetic-material-on-ice-128049">To save koalas from fire, we need to start putting their genetic material on ice</a>
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<img src="https://counter.theconversation.com/content/153873/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Parwinder Kaur's work was enabled by a sample provided by Ranger Red’s Zoo & Conservation Park and supported by resources provided by DNA Zoo Australia, The University of Western Australia, DNA Zoo, Aiden Lab at Baylor College of Medicine, and computational resources and support from the Pawsey Supercomputing Centre and funding from the Australian government and the government of Western Australia.</span></em></p>A detailed map of the koala genome is vital to understanding their susceptibility to disease, their genetic diversity, and how they may respond to new environmental pressures.Parwinder Kaur, Associate Professor | Director, DNA Zoo Australia, The University of Western AustraliaLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1508472020-12-08T19:08:36Z2020-12-08T19:08:36ZIntroducing Edna: the chatbot trained to help patients make a difficult medical decision<figure><img src="https://images.theconversation.com/files/371402/original/file-20201125-23-xswjvt.jpg?ixlib=rb-1.1.0&rect=32%2C57%2C5431%2C3579&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">
</span> <span class="attribution"><span class="source">Shutterstock</span></span></figcaption></figure><p>Allow us to introduce <a href="https://authors.elsevier.com/c/1c6i42dv7nHB2B">Edna</a> — Australia’s first “genomics chatbot”. </p>
<figure class="align-right ">
<img alt="" src="https://images.theconversation.com/files/371415/original/file-20201126-25-aw3voq.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/371415/original/file-20201126-25-aw3voq.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=1300&fit=crop&dpr=1 600w, https://images.theconversation.com/files/371415/original/file-20201126-25-aw3voq.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=1300&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/371415/original/file-20201126-25-aw3voq.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=1300&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/371415/original/file-20201126-25-aw3voq.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=1634&fit=crop&dpr=1 754w, https://images.theconversation.com/files/371415/original/file-20201126-25-aw3voq.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=1634&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/371415/original/file-20201126-25-aw3voq.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=1634&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">The opening dialogue of Edna the chatbot.</span>
</figcaption>
</figure>
<p>Edna (short for “electronic-DNA”) helps patients make <a href="https://www.health.qld.gov.au/__data/assets/pdf_file/0019/143074/ic-guide.pdf">informed decisions</a> about seeking “<a href="https://melbournegenomics.org.au/patients/about-genomics/what-genomic-test">additional findings</a>” testing. </p>
<p>Additional findings testing looks for variants in patients’ genes that aren’t relevant to their current health, but may be later on. For example, it can reveal if someone has an above-average chance of developing a hereditary heart condition. </p>
<p>But these tests can have major implications for patients and their families. Thus, individuals deciding whether they want such a test need support — which Edna can provide. </p>
<p>This chatbot was developed by us and our colleagues at the <a href="https://www.csiro.au/">CSIRO</a> and other members of the <a href="https://www.melbournegenomics.org.au/">Melbourne Genomics Health Alliance</a>.</p>
<h2>Genomic and genetic testing</h2>
<p>A range of medical conditions have underlying <a href="https://medlineplus.gov/genetics/">genetic causes</a>. Historically, this has been tested with <a href="https://www.healthdirect.gov.au/genetic-testing">genetic testing</a>, by looking at either a <a href="https://medlineplus.gov/genetics/gene/">single gene</a> or a panel of genes related to one particular condition.</p>
<p>In <a href="https://www.melbournegenomics.org.au/patients/about-genomics/what-genomic-test">genomic testing</a>, however, almost all the genes in a patient’s DNA are analysed using a biological sample (such as blood).</p>
<p>In Australia, genomic testing is done for patients with certain medical conditions, to provide more information about the condition and medical care required.</p>
<p>But genomic data can be analysed further in an additional findings test, to report on potential gene variants responsible for other preventable and/or treatable conditions.</p>
<p>Although available in the United States, additional findings tests are currently beyond immediate medical need in Australia and are only carried out in research settings. That said, conversations have started about them becoming mainstream here, too.</p>
<p>If additional findings tests were offered in Australia, <a href="https://ahpa.com.au/allied-health-professions/genetic-counselling/">genetic counsellors</a> would have to spend a large proportion of their time helping patients decide whether they want one. This is where chatbots come in.</p>
<h2>Edna the chatbot in training</h2>
<p>For <a href="https://theconversation.com/the-future-of-chatbots-is-more-than-just-small-talk-53293">chatbots</a> to accurately recognise human speech and provide a meaningful response, their “<a href="http://ebooks.iospress.nl/volumearticle">brain</a>” needs to draw on a large body of data.</p>
<p>Many chatbot brains are developed from open source data, but this is inadequate for highly specialised fields. We developed Edna by analysing transcripts of actual counselling sessions that discussed additional findings analysis. </p>
<p><a href="https://www.sciencedirect.com/science/article/abs/pii/S0738399120306315">Edna</a> can emulate the flow of a real patient-counsellor session, explaining various conditions, terms, concepts and the key factors patients should consider when making their decision. </p>
<p>For example, it prompts them to consider the personal and familial implications of undergoing an additional findings analysis. As we all share genes with our family, results from genomic testing can lead to serious conversations. </p>
<figure class="align-center ">
<img alt="" src="https://images.theconversation.com/files/371395/original/file-20201125-23-wvk0zk.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/371395/original/file-20201125-23-wvk0zk.png?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=453&fit=crop&dpr=1 600w, https://images.theconversation.com/files/371395/original/file-20201125-23-wvk0zk.png?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=453&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/371395/original/file-20201125-23-wvk0zk.png?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=453&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/371395/original/file-20201125-23-wvk0zk.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=570&fit=crop&dpr=1 754w, https://images.theconversation.com/files/371395/original/file-20201125-23-wvk0zk.png?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=570&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/371395/original/file-20201125-23-wvk0zk.png?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=570&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">Edna’s database contains myriad details of medical conditions and terminology.</span>
</figcaption>
</figure>
<p>Edna has several other capabilities, such as: </p>
<ul>
<li><p>knowing when to connect a patient with a genetic counsellor, if needed</p></li>
<li><p>providing general information covered in most genetic counselling sessions, allowing counsellors more time to focus on patients with complex needs</p></li>
<li><p>collecting a patient’s family history</p></li>
<li><p>detecting various forms of common language, such as “nan” instead of “grandmother” and “heart attack” instead of “myocardial infarct” (the medical term for heart attack)</p></li>
<li><p>recognising certain temporal markers. For instance, if a patient says “my mother died around Anzac Day two years ago”, Edna will know their mother died around April 25, 2018.</p></li>
</ul>
<figure class="align-center ">
<img alt="" src="https://images.theconversation.com/files/371405/original/file-20201125-21-fnlrxx.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/371405/original/file-20201125-21-fnlrxx.png?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=454&fit=crop&dpr=1 600w, https://images.theconversation.com/files/371405/original/file-20201125-21-fnlrxx.png?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=454&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/371405/original/file-20201125-21-fnlrxx.png?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=454&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/371405/original/file-20201125-21-fnlrxx.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=570&fit=crop&dpr=1 754w, https://images.theconversation.com/files/371405/original/file-20201125-21-fnlrxx.png?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=570&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/371405/original/file-20201125-21-fnlrxx.png?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=570&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">Edna asks about the medical conditions of a patient’s family members.</span>
</figcaption>
</figure>
<p>Edna is currently undergoing a feasibility trial with patients who have already had additional findings analysis done in a research setting, as well as genetic counsellors and students.</p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/aristotle-and-the-chatbot-how-ancient-rules-of-logic-could-make-artificial-intelligence-more-human-142811">Aristotle and the chatbot: how ancient rules of logic could make artificial intelligence more human</a>
</strong>
</em>
</p>
<hr>
<h2>The Eliza Effect and other hurdles</h2>
<p><a href="https://journals.sagepub.com/doi/full/10.1177/2055207619871808">Past research</a> has suggested people prefer chatbots that interact with empathy and sympathy, rather than <a href="https://theconversation.com/emotionless-chatbots-are-taking-over-customer-service-and-its-bad-news-for-consumers-82962">unemotionally</a> giving advice. This is called the “<a href="https://en.wikipedia.org/wiki/ELIZA_effect">Eliza effect</a>” — named after the first ever chatbot. Eliza was able to elicit an emotional response from humans.</p>
<p>Edna is quite advanced on this front. It can detect negative sentiment and even some forms of sarcasm. Still, this isn’t the same as true empathy. </p>
<p>Chatbots can’t yet match genetic counsellors’ ability to detect and respond to emotional cues. And “<a href="https://www.lexalytics.com/technology/sentiment-analysis">sentiment analysis</a>” remains a significant challenge in <a href="https://en.wikipedia.org/wiki/Natural_language_processing">natural language processing</a>. </p>
<figure class="align-left ">
<img alt="" src="https://images.theconversation.com/files/371460/original/file-20201126-15-ml8glu.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/371460/original/file-20201126-15-ml8glu.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=1300&fit=crop&dpr=1 600w, https://images.theconversation.com/files/371460/original/file-20201126-15-ml8glu.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=1300&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/371460/original/file-20201126-15-ml8glu.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=1300&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/371460/original/file-20201126-15-ml8glu.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=1634&fit=crop&dpr=1 754w, https://images.theconversation.com/files/371460/original/file-20201126-15-ml8glu.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=1634&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/371460/original/file-20201126-15-ml8glu.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=1634&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">Edna can identify when a user likely needs to be connected to a real counsellor.</span>
</figcaption>
</figure>
<p>Since Edna provides generic information, it can’t discuss the implications of a future or previous genomic test for a specific patient. It also can’t link the patient with a support group, or provide expert medical advice. </p>
<p>Still, Edna represents a significant move towards a digital health solution that could take some pressure off genetic counsellors.</p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/the-future-of-chatbots-is-more-than-just-small-talk-53293">The future of chatbots is more than just small-talk</a>
</strong>
</em>
</p>
<hr>
<h2>Providing more genomic healthcare</h2>
<p>Edna’s main advantage is accessibility. It can support people living remotely, or who are otherwise unable to attend face-to-face genetic counselling. </p>
<p>It can also be accessed at a patient’s home, where family members may be present. They can then share in the information provided and engage Edna themselves, potentially improving the chances of an accurate history capture. </p>
<p>As a digital interface, Edna is almost endlessly modifiable. It can be updated continuously with data compiled during interactions with patients — whether this be information on new topics, or a new way to respond to a question.</p>
<p>A larger-scale patient trial is planned for the near future.</p><img src="https://counter.theconversation.com/content/150847/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Clara Gaff receives funding from the the State Government of Victoria (Department of Health and Human Services) and the members of the Melbourne Genomics Health Alliance.</span></em></p><p class="fine-print"><em><span>Dana Kai Bradford and David Ireland do not work for, consult, own shares in or receive funding from any company or organisation that would benefit from this article, and have disclosed no relevant affiliations beyond their academic appointment.</span></em></p>It may not be long before Australia’s health sector offers predictive genomic analysis to patients. If this happens, could chatbots help lessen the load on genetic counsellors?David Ireland, Senior Research Scientist at the Australian E-Health Research Centre., CSIROClara Gaff, Executive Director, Melbourne Genomics Health Alliance, Walter and Eliza Hall InstituteDana Kai Bradford, Principal Research Scientist, Australian eHealth Research Centre, CSIROLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1500902020-11-22T09:12:11Z2020-11-22T09:12:11ZMajor new study unveils complexity and vast diversity of Africa’s genetic variation<figure><img src="https://images.theconversation.com/files/369258/original/file-20201113-21-1v5vacu.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">GettyImages</span> </figcaption></figure><p>Africa is the <a href="https://www.wits.ac.za/campus-life/arts-and-culture/cradle-of-humankind/">cradle of humankind</a>. All humans are descendants from this common pool of ancestors. Africa and its multitude of ethnolinguistic groups are therefore fundamental to learning more about humankind and our origins. </p>
<p>A human genome refers to the complete set of genetic information found in a human cell. We inherit our genomes from our parents. Studying the variations in different people’s genomes gives important clues to how genetic information influences people’s appearance and health. It can also tell us about our ancestry. To date, very few African individuals have been included in studies looking at genetic variation. Studying African genomes not only fills a gap in the current understanding of human genetic variation, but also reveals new insights into the history of African populations. </p>
<p>My colleagues and I, who are all members of the <a href="https://h3africa.org/">Human Heredity and Health (H3Africa)</a> consortium, contributed to a <a href="https://www.nature.com/articles/s41586-020-2859-7">landmark genetics study</a>. This study focused on 426 individuals from 13 African countries. More than 50 different ethnolinguistic groups were represented in the study – one of the most diverse groups of Africans ever to be included in such an investigation. We sequenced the whole genome of each of these individuals – this means we could read every part of the genome to look for variation.</p>
<p>This study contributes a major, new source of African genomic data, which showcases the complex and vast diversity of African genetic variation. And it will support research for decades to come. </p>
<p>Our findings have broad relevance, from learning more about African history and migration, to clinical research into the impact of specific variants on health outcomes. </p>
<h2>Gaining new insights</h2>
<p>One of the key outcomes was the discovery of more than three million new genetic variants. This is significant because we are learning more about human genetic diversity in general, and discovering more differences that could be linked to disease or traits in the future.</p>
<p>This study also adds details to what is known about the migration and expansion of groups across the continent. We were able to show that Zambia was most probably an intermediate site on the likely route of migration from west Africa to east and south Africa. Evidence supporting movement from east Africa to central Nigeria between 1,500 and 2,000 years ago was also revealed, through the identification of a substantial amount of east African ancestry in a central Nigerian ethnolinguistic group, the Berom.</p>
<p>The study also enabled us to reclassify certain variants that were previously suspected to cause disease. Variants that cause serious genetic diseases are often rare in the general population, mostly because their effect is so severe that a person with such a variant often does not reach adulthood. But we observed many of these variants at quite common levels in the studied populations. One wouldn’t expect that these types of disease-causing variants would be this common in healthy adults. This finding helps to reclassify these variants for clinical interpretation.</p>
<p>Finally, we found a surprising number of regions with signatures of natural selection that have not been previously reported. Selection means that when individuals are exposed to environmental factors like a viral infection, or a drastic new dietary component, some gene variants may confer an added adaptive advantage to the humans that bear them in their genome. </p>
<p>Our best interpretation of these findings is that as humans across Africa were exposed to different environments – sometimes as a result of migration – these variants were likely important to surviving in those new conditions. This has left an “imprint” on the genome and contributes to genomic diversity across the continent.</p>
<p>Our data has shown that we have not yet found all the variation in the human genome. There is more to learn by adding new, unstudied population groups. We know that <a href="https://doi.org/10.1016/j.cell.2019.02.048">less than a quarter</a> of participants in genomics research are of non-European ancestry. Most available genetic data come from just <a href="https://www.nature.com/articles/s42003-018-0261-x">three countries</a> – the UK (40%), the US (19%) and Iceland (12%). </p>
<p>It is essential to keep adding more genomic data from all global populations – including Africa. This will ensure that everyone can benefit from the advances in health that <a href="https://theconversation.com/antibody-technologies-take-a-step-closer-to-precision-medicine-128183">precision medicine</a> offers. Precision medicine refers to the customisation of healthcare to fit the individual. Including personal genetic information could radically change the nature and scope of healthcare options that would work best for that individual. </p>
<h2>Next steps</h2>
<p>The Human Heredity and Health consortium is now in its eighth year of existence, and supports more than 51 diverse projects. These include studies focusing on diseases like diabetes, HIV and tuberculosis. The reference data generated through our study are already being put to use by many of the consortium’s studies. </p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/what-weve-learnt-from-building-africas-biggest-genome-library-126293">What we've learnt from building Africa's biggest genome library</a>
</strong>
</em>
</p>
<hr>
<p>Next, we are planning to take an even deeper look at the data to better understand what other types of genetic variation exist. We are also hoping to add further unstudied populations to grow and enrich this data set.</p>
<p>Building capacity for genomics research on the African continent is a key goal of Human Heredity and Health. An important aspect of this study is that it was driven and conducted by researchers and scientists from the African continent. Researchers from 24 institutions across Africa participated and led this investigation. This study showcases the availability of both infrastructure and skills for large-scale genomics research on the continent. It also highlights the prospect of future world-class research on this topic from Africa.</p><img src="https://counter.theconversation.com/content/150090/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Zané Lombard receives funding from the National Institute Of Mental Health of the National Institutes of Health. </span></em></p>It is essential to add genomic data from all global populations - including Africa. This will ensure that everyone can benefit from the advances in health.Zané Lombard, Principal Medical Scientist, Associate Professor, University of the WitwatersrandLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1299902020-02-10T13:56:17Z2020-02-10T13:56:17ZDentists in South Africa aren’t being taught genetics. Why they should<figure><img src="https://images.theconversation.com/files/310260/original/file-20200115-134842-1noolzf.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Many genetic abnormalities involve the oral and dental region of the face.</span> <span class="attribution"><span class="source">Shutterstock</span></span></figcaption></figure><p>Genetic and genomic research has improved our understanding of the genetic origin of growth, development and disease and affects all areas of healthcare. There is also mounting <a href="http://www.dmrjournal.org/article.asp?issn=2348-1471;year=2016;volume=4;issue=1;spage=9;epage=17;aulast=Rai">evidence</a> that many complex conditions are the result of interactions between genes. These include diabetes and hypertension.</p>
<p>Genomics has become increasingly important to oral health too. Dentists regularly come across obvious expressions of genetic disorders or genetic-based diseases in the oral and head and neck region. There are <a href="http://www.jdentaled.org/content/72/2_suppl/86">approximately 5,500</a> known inherited conditions. More than 700 of these have abnormalities which involve the oral and dental region of the face. </p>
<p>These insights have been gained through continued and concerted efforts to understand the genetic aspects of diseases. This understanding, in turn, has generated novel approaches to prevent, diagnose and manage them. </p>
<p>In the area of dentistry, teaching has unfortunately not kept up with the science, particularly in Africa. This places dentists at a disadvantage. They can’t – or find it difficult to – contribute to the overall health of patients with genetic disorders because they don’t have the necessary knowledge. This would include the ability to recognise the indicators of genetic disorders and the confidence to manage these patients.</p>
<p>This is why dentists need a sound understanding of genetics. And it’s why genetics and genomics should be included in the undergraduate and postgraduate curriculum. Investing in structured dental genetics programmes in dental schools in Africa would ensure an increase in the dental genetics workforce. This would ultimately improve the management of patients with inherited conditions with oral and dental manifestations. </p>
<p>To evaluate the need for human genetics in the dentistry curriculum my colleagues and I conducted a <a href="https://journals.co.za/content/journal/10520/EJC-100b454c5f">survey</a> at the dental school at a South African university. Academic staff, 4th and 5th-year undergraduate dental students as well as postgraduate dental students participated in the survey.</p>
<p>The results indicated that students and clinicians had limited training and experience pertaining to the diagnosis and management of individuals with genetic disorders. </p>
<h2>The gap, and how to fill it</h2>
<p>Currently, there are no plans in place to train dentists with a sound understanding of genetics. There are also no programmes in place to allow trained African dentists to choose such a career pathway.</p>
<p>As a result, there is an over-dependence of African clinical practice on research findings from technologically advanced Western countries. Secondly, it means that clinical research capacity building isn’t happening. And finally, it means that patients aren’t being offered the best possible diagnosis and treatment.</p>
<p>There are several factors responsible for the lack of dental genetics in Africa. Among a few challenges are poor biomedical research infrastructure, minimal funding and an absence of a structured dentist genetics career pathways. </p>
<p>To address these challenges, African universities and dental schools need to develop and include dental genetics courses in undergraduate and postgraduate programmes. These should be designed to ensure they help members of the dental fraternity to treat patients with hereditary conditions. </p>
<p>The dental genetics workforce would, in turn, increase trained dentists some of whom could have the option of following a research career. This would enhance networking among African dental researchers and lead to better dental research output across the continent.</p>
<p>Several first world universities, such as the universities of Pittsburg, Manchester and Oslo have included dental genetics into their curricula. Their vast research capacity has resulted in evidence-based dentistry being offered to patients in those countries. </p>
<p>Another way to foster an interest and understanding of genetics in the dental community is by developing collaborative relationships. One already exists in South Africa between the division of human genetics at the University of Cape Town and the dental faculty at the University of the Western Cape. This <a href="http://www.scielo.org.za/scielo.php?script=sci_arttext&pid=S0011-85162018000400028&lng=es&nrm=is">partnership</a> runs a dental genetics clinic which serves patients with genetic disorders from across the Western Cape province. Postgraduate students also rotate through the clinic and are mentored in the dental management of children with genetic disorders and congenital abnormalities.</p>
<p>Adding courses on human genetics in the curriculum at dental schools would be a first step to ensuring that more dentists have an understanding of the field.</p><img src="https://counter.theconversation.com/content/129990/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Manogari Chetty does not work for, consult, own shares in or receive funding from any company or organisation that would benefit from this article, and has disclosed no relevant affiliations beyond their academic appointment.</span></em></p>Dentists need to have a sound understanding of genetics to treat and manage patients effectively.Manogari Chetty, HOD Oral Biology and Human Genetics, University of the Western CapeLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1286512019-12-20T07:21:05Z2019-12-20T07:21:05ZAfrica’s genetic material is still being misused<figure><img src="https://images.theconversation.com/files/307390/original/file-20191217-58339-lbsete.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">
</span> <span class="attribution"><span class="source">Shutterstock</span></span></figcaption></figure><p>Biodiversity – the variation in all living organisms – is one of Africa’s richest assets. As a result, its genetic material is coveted by scientists, biotechnology companies and research institutes globally. For decades, there has been a flow of data and biosamples from the African continent to the global north. This has often been in the absence of legitimate participant consent, community engagement or data or material transfer agreements.</p>
<p><a href="https://link.springer.com/referenceworkentry/10.1007%2F978-3-319-05544-2_57-1">Biopiracy</a> – the act of directly or indirectly taking undue advantage of research participants and communities in global health research – has a long and contentious history in Africa. A recent case occurred during the West African Ebola outbreak between 2014 and 2016 when <a href="https://www.who.int/medicines/ebola-treatment/meetings/2nd_who_biobaking-consultation/en/">thousands of biological specimens</a> left the continent without consent. Very often there is <a href="https://bmcmedethics.biomedcentral.com/articles/10.1186/s12910-016-0140-2">minimal benefit sharing</a>.</p>
<p>The issue has been in the news again in South Africa. <a href="https://www.thetimes.co.uk/article/genetics-lab-told-to-hand-back-african-tribes-dna-83xqls5sh">Accusations</a> have been <a href="https://www.sciencemag.org/news/2019/10/major-uk-genetics-lab-accused-misusing-african-dna">levelled</a> against the Wellcome Sanger Institute in the UK for allegedly attempting to commercialise data obtained from various African universities. This has reignited questions around models of consent in research, donor rights, biopiracy and genomic sovereignty.</p>
<p>The latest revelations show that legislation as well as academic research governance bodies have failed to adequately safeguard the rights of vulnerable participants in genomics research. </p>
<p>One missing piece of the puzzle is the limited empirical data on the views of people whose biosamples are taken in the name of research. This would <a href="https://bmcmedethics.biomedcentral.com/articles/10.1186/1472-6939-15-4">include</a> issues of ownership, future use, export, benefit-sharing and commercialisation. </p>
<p>In 2011 and 2012 we <a href="https://bmcmedethics.biomedcentral.com/articles/10.1186/1472-6939-15-4">surveyed</a> participants to better understand their views. We recruited participants who had experience with research, the consent process and use of biological samples. They were engaged in studies at academic research units attached to public hospitals and private research centres. </p>
<p>Our findings remain relevant today as many of the issues raised by the people we spoke to have still not been addressed.</p>
<h2>The issue of consent</h2>
<p>Our study was conducted over a 10 month period from September 2011 to June 2012. We sampled 200 participants in the Western Cape and Gauteng provinces in South Africa. Participants who had already consented to use of their blood for research were asked several questions including the following: how they felt about their samples being stored for future use and about them being sent abroad to foreign countries, as well as the possibility of future commercialisation.</p>
<p>Most participants were supportive of research. But many expressed concerns about export of their blood samples and data out of South Africa. </p>
<p>For their part, researchers viewed the biosamples as donations. But participants believed they had ownership rights and were keen on benefit sharing. Almost half of the participants were not in favour of broad consent delegated to a research ethics committee. Their preference was to be contacted again for consent in the future.</p>
<p>The legitimacy of using broad consent models for genomic research and biobanking occupies a contested space among bioethicists and researchers globally. Broad consent allows researchers to use biosamples and data indefinitely for future research. </p>
<p>Usually, with broad consent, future research must be approved by a Research Ethics Committee (a diverse group of experts from different research, medical, legal and ethics disciplines) and it is then not necessary to contact donors and ask for their permission to conduct research with their samples or data again. </p>
<p>But this type of consent is particularly contentious in resource depleted countries. This is because research participants often don’t understand the complex scientific jargon used in consent documents or processes, especially where use of their samples or data in the future is concerned. This includes commercialisation. </p>
<p>Strong privacy protection <a href="https://ec.europa.eu/commission/sites/beta-political/files/eu_data_protection_rules_-_main_takeways_for_the_future.pdf">legislation</a> and other <a href="https://www.justice.gov.za/inforeg/docs/InfoRegSA-POPIA-act2013-004.pdf">similar laws</a> require specific consent. This means that individual participants need to consent to use of their data in a specific project or disease category. This makes it challenging to understand how broad consent (delegated to a research ethics committee) for unspecified future use can be legally obtained in research. </p>
<p>This is particularly concerning where future commercialisation may be included in broad consent models without being explicitly discussed with participants. The language used to explain commercialisation is often vague and not fully comprehensible by vulnerable populations. </p>
<p>South Africa also has protocols in place. For example, clear, explicit, voluntary informed consent is required for all use of data and samples belonging to research participants. If data or samples are to be transferred to other researchers in South Africa or abroad, participants ought to be aware of this and can then consent or decline. However, this is not always what happens.</p>
<p>In addition, if data is to be shared with another institution, a data transfer agreement or material transfer agreement must be signed prior to the transfer. This too does not always happen.</p>
<h2>Reform is needed</h2>
<p>South Africa needs to up its game and reform governance around research ethics. This is particularly necessary in the context of international collaborative research. Good governance needs to incorporate transparency, fairness and honesty. </p>
<p>Research ethics committees and researchers need to ensure that data transfer agreements or material transfer agreements are in place prior to sharing of samples or data. </p>
<p>More importantly, community representatives on research ethics committees should be empowered to review consent documents to establish if appropriate language is used to explain commercialisation and data or sample sharing. </p>
<p>A <a href="https://www.researchgate.net/publication/336867081_A_framework_for_tiered_informed_consent_for_health_genomic_research_in_Africa">tiered consent model</a> gives participants choice in terms of how their data or samples could be used in the future. This happens when participants choose what they agree to in the consent document. It also allows for specific choices to be voiced on benefit sharing for participants or their respective communities. </p>
<p>In addition, authentic <a href="https://www.liebertpub.com/doi/pdf/10.1089/bio.2018.0136">community engagement</a> with co-creation of knowledge production and benefit sharing is essential to ensure equity in global research.</p><img src="https://counter.theconversation.com/content/128651/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Keymanthri Moodley receives funding from the National Institutes of Health. </span></em></p>Legislation as well as academic research governance bodies have failed to safeguard the rights of participants from Africa in genomics research.Keymanthri Moodley, Director, The Centre for Medical Ethics & Law, Stellenbosch UniversityLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1107552019-02-05T13:41:01Z2019-02-05T13:41:01ZPersonal DNA tests might help research – but they put your data at risk<figure><img src="https://images.theconversation.com/files/256605/original/file-20190131-108338-1q2hixh.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">
</span> <span class="attribution"><a class="source" href="https://www.shutterstock.com/image-photo/close-businessman-holding-glowing-dna-helix-683382997?src=X3fDTVJfgabc-LLmvLaQgQ-1-53">Eetu Mustonen/Shutterstock</a></span></figcaption></figure><p>Your DNA has become a valuable commodity. Companies such as 23andMe may charge you for an analysis of your genetic profile, but they make their real money from <a href="https://www.theguardian.com/commentisfree/2018/aug/10/dna-ancestry-tests-cheap-data-price-companies-23andme">selling that data</a> on to other companies.</p>
<p>Now healthcare providers are following suit by encouraging patients to take genetic tests that will create databases ostensibly for medical research. Britain’s National Health Service (NHS) <a href="https://theconversation.com/nhs-plan-to-sell-genome-sequencing-to-healthy-people-is-premature-110619">recently announced</a> that it was launching such a scheme in an attempt to build a database of anonymised genetic data for researchers.</p>
<p>But <a href="https://www.irishtimes.com/news/health/hospital-investigates-release-of-dna-samples-to-research-firm-1.3773529">recent reports</a> that Our Lady’s Children’s Hospital, Crumlin in Dublin – Ireland’s largest children’s hospital – allegedly shared patient DNA data with a private firm without appropriate consent highlights the potential risk that comes with giving up your genetic records. Your DNA contains sensitive information that can be used to make important personal decisions about you and your family members. When you hand over these details to a large database – whoever is building it – you are ultimately risking it being used in ways you can’t foresee and which aren’t always to your benefit.</p>
<p>The first questions are where your data will end up and who will have access to it. The NHS is attempting to keep control of the genetic data it gathers by sharing it with researchers at its own company, <a href="https://www.genomicsengland.co.uk/">Genomics England</a>. But there has been no indication of what purposes the data can be used for, or what limits will be placed on its use or transfer to other research centres or companies. In the past, Genomics England <a href="https://theconversation.com/google-may-get-access-to-genomic-patient-data-heres-why-we-should-be-concerned-80417">met with Google</a> to discuss how the tech firm might help analyse genetic data gathered under a previous scheme, the <a href="https://www.genomicsengland.co.uk/about-genomics-england/the-100000-genomes-project/">100,000 Genomes Project</a>. </p>
<p>A spokesperson for Genomics England told The Conversation that it had “no formal contractual relationship between Genomics England and Google”. However, it said: “We have a mutual interest in secure data storage and we have meetings from time to time. As part of our mandate to stimulate the UK genomics industry, we are in touch with Google Ventures. They invest in life sciences companies which may be interested in working with us.”</p>
<p>The recent Irish example of data transfer apparently without appropriate consent also reminds us that agreements and rules over who can access data can be broken. In January 2019, <a href="https://www.thetimes.co.uk/edition/ireland/crumlin-hospital-sent-dna-off-without-consent-mm5crwng0">an investigation was launched</a> into the alleged supply of 1,500 DNA samples from the Crumlin children’s hospital to Genomics Medicine Ireland (GMI) without proper authorisation from patients. </p>
<p>If these allegations are true, it would represent a breach of European data protection law, which requires explicit consent for the processing of DNA data. What is perhaps <a href="https://ieeexplore.ieee.org/document/8470173">more of a problem</a> is that even when people are told what will happen with their data, they may not understand those uses or its <a href="https://philpapers.org/rec/SCHTCO-98">potential consequences</a>.</p>
<p>Initiatives such as the NHS project are justified by claims that they offer an efficient way to <a href="https://theconversation.com/why-the-100-000-genomes-project-will-focus-on-rare-diseases-36155">diagnose rare</a> or undiscovered illnesses, speeding up treatment and improving patient outcomes. More broadly, proponents argue, <a href="https://theconversation.com/how-big-data-is-being-mobilised-in-the-fight-against-leukaemia-74281">sharing DNA data</a> can allow researchers to spot patterns that would otherwise go unidentified, increasing scientific understanding and aiding in the development of treatments.</p>
<p>But having your DNA sequenced isn’t just a way of finding out if you are at risk of a disease or making an altruistic contribution to an abstract research project. DNA data exposes our most inherent characteristics, revealing ethnic or racial groupings, as well as outlining current and future health issues. Some people have even tried to link <a href="https://www.technologyreview.com/s/610339/dna-tests-for-iq-are-coming-but-it-might-not-be-smart-to-take-one/">DNA tests to intelligence</a>.</p>
<figure class="align-center ">
<img alt="" src="https://images.theconversation.com/files/256608/original/file-20190131-112314-1ylmkh4.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/256608/original/file-20190131-112314-1ylmkh4.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/256608/original/file-20190131-112314-1ylmkh4.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/256608/original/file-20190131-112314-1ylmkh4.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/256608/original/file-20190131-112314-1ylmkh4.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/256608/original/file-20190131-112314-1ylmkh4.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/256608/original/file-20190131-112314-1ylmkh4.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=503&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">DNA files can easily be transferred.</span>
<span class="attribution"><a class="source" href="https://www.shutterstock.com/image-photo/genetic-engineer-working-analysis-dna-software-509467522?src=FqZaNnPBF2eO5RdpUEstRA-1-28">Angellodeco/Shutterstock</a></span>
</figcaption>
</figure>
<p>Concerns about linking individuals to the characteristics revealed by their DNA are usually countered by claims that the data is anonymised. But both <a href="https://www.telegraph.co.uk/news/health/news/10656893/Hospital-records-of-all-NHS-patients-sold-to-insurers.html">practical experience</a> and <a href="http://science.sciencemag.org/content/347/6221/536.full#ref-26">academic work</a> have shown that anonymised data can often be <a href="https://www.nature.com/articles/srep01376">reassociated with</a> the people it was collected from.</p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/your-nhs-data-is-completely-anonymous-until-it-isnt-22924">Your NHS data is completely anonymous – until it isn't</a>
</strong>
</em>
</p>
<hr>
<p>So sharing your genetic information could expose you to potential discrimination if it ends up with the wrong people or is used for the wrong purposes. Being offered different health insurance coverage and at different prices is the most obvious risk. But depending on who buys the data, pharmaceutical companies, employers and even government authorities could access your DNA and <a href="https://theconversation.com/four-ways-your-google-searches-and-social-media-affect-your-opportunities-in-life-96809">make decisions</a> based on it.</p>
<p>Democratic governments can’t typically gather DNA evidence without the permission of a judge or via another legal procedure. But in the case of the “<a href="http://www.sciencemag.org/news/2018/10/we-will-find-you-dna-search-used-nab-golden-state-killer-can-home-about-60-white">Golden State Killer</a>”, US law enforcement agencies used DNA data from a public genealogy database to obtain evidence they wouldn’t otherwise have been able to collect. This raises concerns about the willingness of governments to use genetic records originally made to explore people’s ancestry for a very different purpose.</p>
<h2>Giving away family secrets</h2>
<p>The Golden State Killer case is all the more important because it highlights the most fundamental issue with DNA-sharing initiatives. When you share your DNA, you’re also sharing data about your entire family, who haven’t necessarily consented. The Golden State Killer didn’t get a DNA test but one of his relatives did. When enough people share their DNA, the genetic profile of entire communities becomes available.</p>
<p>A <a href="http://www.sciencemag.org/news/2018/10/we-will-find-you-dna-search-used-nab-golden-state-killer-can-home-about-60-white">study of the database</a> that was used to catch the killer estimated that it contained the profiles of 0.5% of the US population, yet this represented family members (third cousin or closer) of 60% of white Americans. With 2% of the population, that figure would increase to 90%.</p>
<p>GMI currently <a href="https://www.genengnews.com/insights/using-powered-cohorts-to-speed-drug-discovery-and-development/">plans to build</a> the world’s largest whole-genome database of some 400,000 participants – roughly a tenth of Ireland’s population – from a presence in all the country’s major hospitals. This would likely give the firm information on almost every family group in Ireland and a huge proportion of the Irish diaspora (<a href="https://www.dfa.ie/media/dfa/alldfawebsitemedia/newspress/publications/ministersbrief-june2017/1--Global-Irish-in-Numbers.pdf">estimated at 70m</a>), enabling it to identify the most private characteristics of a global population.</p>
<p>This shows how, when some people allow their DNA data to be shared, it could expose both them and their families to risk and erode the rights of everyone else, meaning we all have a stake in how genetic records are shared. Organisations must be required to be clearer about who will use the DNA data they collect, and for what to prevent risk of misuse.</p><img src="https://counter.theconversation.com/content/110755/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Roisin Costello receives funding from The Irish Research Council. </span></em></p>When you share your genetic data – even with the NHS – you don’t know where it will end up, or how it will be used.Roisin Costello, PhD Candidate, School of Law, Trinity College DublinLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1102122019-01-29T14:05:15Z2019-01-29T14:05:15ZWhy African countries need to give genomic research a major boost<figure><img src="https://images.theconversation.com/files/255162/original/file-20190123-135145-56exbc.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Personalised medicine aims to tailor treatment according to each person’s genetic makeup.</span> <span class="attribution"><span class="source">Shutterstock</span></span></figcaption></figure><p>All organisms are unique. Each having a set of genetic instructions for their build-up and maintenance. This set of genetic instructions is contained in genes that makeup a genome. </p>
<p>The <a href="http://www.who.int/genomics/geneticsVSgenomics/en/">World Health Organisation</a> defines genomics as the study of genes and their complex interplay in influencing the growth and development of an organism. Through genomics, gene sequences can be manipulated to prevent – or manage – certain diseases and hence prolong life and improve public health. </p>
<p>More and more <a href="https://academic.oup.com/bmb/article/112/1/37/2747691">research</a> is showing that a better understanding of the genomics of pathogens can play a crucial role in preventing and treating infectious diseases. Identifying genetic risk factors for diseases can ensure timely interventions. It can also help curtail the spread of emerging infections and drug resistance.</p>
<p>Because of this, genomic research has huge potential in helping African countries address public health issues. The problem is that Africa lags behind other regions. This is true in terms of research, resources as well as policy.</p>
<h2>Burden of disease</h2>
<p>Africa faces a heavy disease burden of both communicable and non-communicable diseases. In the last <a href="http://www.worldbank.org/en/news/feature/2013/09/09/global-burden-of-disease-findings-for-sub-saharan-africa">two decades</a>, the continent has succeeded in decreasing some communicable diseases such as cholera and polio. But others such as <a href="http://www.who.int/bulletin/africanhealth/en/">malaria and HIV</a> remain quite high.</p>
<p>This disease burden has been aggravated with the emergence of drug-resistant strains. </p>
<p>In addition, non-communicable diseases such as cardiovascular diseases, cancer, diabetes and chronic respiratory diseases are also on the rise. The number of deaths from these is <a href="http://www.prb.org/pdf15/ncds-africa-policybrief.pdf">projected</a> to increase over the next decade.</p>
<p>This high disease burden can be significantly reduced. But it needs a proactive approach. This should include a combination of public health strategies as well as the use of genomics to help identify genetic risk factors. </p>
<h2>Why genomics matters</h2>
<p>Some examples of how genomic research has been used to address public health issues include:</p>
<ul>
<li><p>The identification of a new <a href="http://science.sciencemag.org/content/285/5433/1573">antimalarial</a> drug;</p></li>
<li><p>The development of new <a href="https://jamanetwork.com/journals/jama/fullarticle/193523">vaccines</a>; and </p></li>
<li><p>In the <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3706975/">investigation</a> of causes of infectious disease outbreaks, including the Ebola virus.</p></li>
</ul>
<p>Genomic analysis has also provided important prognostic indicators for breast cancer patients. This has helped identify the <a href="http://www.ncbi.nlm.nih.gov/pubmed/15891269">drugs</a> that individuals could best respond to. It opened the door to the new era of <a href="https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/503689/Healthcare_UK_Genomics__Personalised_Medicine__DIGITAL.pdf">personalised medicine</a> that aims to tailor therapy according to each person’s genetic makeup. </p>
<p>A good example was the use of genome sequencing that pointed to a new treatment regimen for <a href="https://cen.acs.org/articles/91/i28/Next-Generation-DNA-Sequencing-Finds.html">Nicholas Volker</a> who had a gastrointestinal disorder that was cured with a bone marrow transplant.</p>
<p>To date, the US Food and Drug Administration has <a href="http://www.fda.gov/MedicalDevices/ProductsandMedicalProcedures/InVitroDiagnostics/ucm330711.htm">approved</a> 45 human genetic tests, and more than 100 nucleic acid-based tests for microbial pathogens. Most of this research is being carried out in the developed world. </p>
<p>But scientists in Africa have also been attempting large-scale genome research studies focused on specific diseases. For example, the international <a href="https://www.genome.gov/10001688/international-hapmap-project/">HapMap</a> project and other previous studies have shown that people who live on the continent have the greatest genetic variation. Therefore understanding the genetic basis of both communicable and non-communicable diseases may provide useful insights into devising <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2953791/">effective strategies</a> to combat diseases that have had a large impact on the continent.</p>
<h2>Challenges</h2>
<p>Africa still lags behind the rest of the world in the field of genomic research. This is largely attributed to the following challenges:</p>
<ul>
<li><p>The cost of research remains prohibitive for African research centres. This is mainly due to lack of enough government funding and support;</p></li>
<li><p>There’s a shortage of African scientists with genomic research and computational expertise who can translate genomic information into clinical medicine;</p></li>
<li><p>A lack of biomedical research infrastructure to undertake genomic research;</p></li>
<li><p>Lack of collaborative research among African scientists;</p></li>
<li><p>A climate of fear about the potential for misuse and misinterpretation of genomic information among the public and health professionals in Africa;</p></li>
<li><p>Poor engagement with national and regional agencies in the uptake of genomic research as novel methodologies to help tackle health problems; and</p></li>
<li><p>No proper policies and clear guidelines to inform medical and public health professionals about the level of confidence and use of genomic information.</p></li>
</ul>
<h2>What to do</h2>
<p>African Union member states have set a target of 1% of GDP to be invested on <a href="http://uis.unesco.org/en/news/rd-data-release">research and development</a>. But most member states don’t meet this target. Only South Africa, Kenya and Senegal are close – at around 0.8%. </p>
<p>It’s crucial that genomic research is given higher priority on the continent. The research should be supported by establishing the infrastructure for genomic studies, capacity building and improving collaborations with credible international partners. </p>
<p>African genomic scientists should also build networks and collaborations that enable the exchange of new ideas and the transfer of knowledge. This could indirectly influence policy makers to support investments in genomic research.</p>
<p>There are programmes that are supporting initiatives like this. These include the <a href="http://aasciences.ac.ke/programmes/easa/alliance-for-accelerating-excellence-in-science-in-africa-aesa/">Alliance for Accelerating Excellence in Africa</a>, created by the <a href="http://aasciences.ac.ke/">African Academy of Sciences</a> and the <a href="http://h3africa.org/">Human Heredity and Health in Africa</a>. These programmes support studies led by African scientists by providing research funds that foster genomics research, <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4138491/">capacity building</a>, as well as specific scientific goals.</p>
<p>But there’s scope for considerable expansion. </p>
<p>Overall, policymakers need to be involved from the beginning in all discussions and debates involving genomics research. They should be engaging with communities, academics and public health professionals to help develop research questions. They should also be involved in preparing to set up legal regulatory frameworks. This would go a long way towards ensuring the translation of genomic research findings into public health benefits.</p><img src="https://counter.theconversation.com/content/110212/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Lamech Mwapagha does not work for, consult, own shares in or receive funding from any company or organisation that would benefit from this article, and has disclosed no relevant affiliations beyond their academic appointment.</span></em></p>Gene sequences can be manipulated to prevent certain diseases and improve public health.Lamech Mwapagha, Lecturer of Biochemistry, Namibia University of Science and TechnologyLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/804172017-07-04T10:43:24Z2017-07-04T10:43:24ZGoogle may get access to genomic patient data – here’s why we should be concerned<figure><img src="https://images.theconversation.com/files/176596/original/file-20170703-32607-qdd3vw.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Would you want Google to know if you have 'criminal genes'?</span> <span class="attribution"><a class="source" href="https://www.shutterstock.com/image-illustration/genome-sequence-medical-breakthrough-science-concept-627118340?src=8ZchIlladpI0r5TyLLCh4w-1-30">kentoh/Shutterstock</a></span></figcaption></figure><p>Artificial intelligence is already being put to use in the NHS, with Google’s AI firm DeepMind providing technology to help monitor patients. Now I have discovered that Google has met with Genomic England – a company set up by the Department of Health to deliver <a href="https://theconversation.com/why-the-100-000-genomes-project-will-focus-on-rare-diseases-36155">the 100,000 Genomes Project</a> – to discuss whether DeepMind could get involved. </p>
<p>If this were to happen, it could help bring down costs and speed up genetic sequencing – potentially helping the science to flourish. But what are the risks of letting a private company have access to sensitive genetic data? </p>
<p>Genomic sequencing has huge potential – it could hold the key to improving our understanding of a range of diseases, including cancer, and eventually help find treatments for them. The 100,000 Genomes Project was set up by the government to sequence genomes of 100,000 people. And it won’t stop there. A new report from the UK’s chief medical officer, Sally Davies, <a href="http://www.bbc.co.uk/news/health-40479533">is calling for an expansion</a> of the project.</p>
<p>However, a statement by the Department of Health in response to a freedom of information (FoI) request I made in February reveals this decision has already been made. The department said in this response that the project will be integrated into a single national genomic database. The purpose of this will be to support “care and research, and the acceleration of industrial usage”. Though it will “inevitably exceed the original 100,000 genomes, we do not anticipate that there will be a set target for how many genomes it should contain”, the statement reads. </p>
<p>The costs of sequencing the genome on a national scale are prohibitive. The first human genome was sequenced at a cost of US$3 billion. However, almost two decades later, Illumina, which is responsible for the sequencing side of the 100,000 Genomes Project, <a href="http://www.nature.com/news/is-the-1-000-genome-for-real-1.14530">produced the first “$1,000 genome”</a> – a staggering reduction in cost. Applying machine learning to genomics – that is, general artificial intelligence – has the potential to significantly reduce the costs further. By building a neural network, these algorithms can interpret huge amounts of genetic, health, and environmental data to predict a persons health status, <a href="https://www.nbcnews.com/mach/science/ai-predicts-heart-attacks-better-doctors-n752011">such as their level of risk of heart attack</a>. </p>
<p>DeepMind is already working with the NHS. As part of a partnership with several NHS trusts, the company has built <a href="https://www.newscientist.com/article/2086454-revealed-google-ai-has-access-to-huge-haul-of-nhs-patient-data/">various platforms</a>, <a href="https://deepmind.com/applied/deepmind-health/streams/">an app</a> and a <a href="https://www.theguardian.com/technology/2016/jul/05/google-deepmind-nhs-machine-learning-blindness">machine learning system</a> to monitor patients in various ways, alerting clinical teams when they are at risk. </p>
<p>But it’s been controversial. The company announced the first of these collaborations in February 2016, saying it was building an app to help hospital staff monitor patients with kidney disease. However, it later emerged that the agreement went far beyond this, giving DeepMind Health access to vast amounts of patient data – including, in one instance, 1.6m patient records. The Information Commissioner’s Office ruled recently that the way patient data was shared by the Royal Free NHS Foundation Trust <a href="http://www.bbc.com/news/technology-40483202">violated UK privacy law</a>. The company asserts that patient data “will never be linked to Google products or services or commercialised”. </p>
<figure class="align-center ">
<img alt="" src="https://images.theconversation.com/files/176595/original/file-20170703-5588-1uvbxvc.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/176595/original/file-20170703-5588-1uvbxvc.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=398&fit=crop&dpr=1 600w, https://images.theconversation.com/files/176595/original/file-20170703-5588-1uvbxvc.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=398&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/176595/original/file-20170703-5588-1uvbxvc.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=398&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/176595/original/file-20170703-5588-1uvbxvc.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=501&fit=crop&dpr=1 754w, https://images.theconversation.com/files/176595/original/file-20170703-5588-1uvbxvc.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=501&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/176595/original/file-20170703-5588-1uvbxvc.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=501&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">DeepMind got access to hospital records with sensitive information such as drug overdoses and abortions.</span>
<span class="attribution"><a class="source" href="https://www.shutterstock.com/image-photo/hard-copy-hospital-records-116827537?src=A1WCtUFa4HKAos0uPFxEZg-1-29">RHIMAGE/shutterstock</a></span>
</figcaption>
</figure>
<p>Google’s ambitions to digitise healthcare continue. I received a response to an FoI request in May which reveals that Google and Genomics England have met to discuss “using Google’s DeepMind among other subjects” to analyse genomic data. </p>
<p>Davies insists that <a href="http://www.bbc.co.uk/news/health-40479533">data could be anonymised</a>. The Department of Health always promise that medical data used in such initiatives will be anonymised, yet one of the reasons that Care.data (an initiative to store all patient data on a single database) <a href="https://theconversation.com/care-data-has-been-scrapped-but-your-health-data-could-still-be-shared-62181">was abandoned</a> is that this was <a href="https://www.theguardian.com/society/2014/jan/19/nhs-patient-data-available-companies-buy">shown to be untrue</a>. I <a href="https://www.theguardian.com/science/political-science/2015/mar/10/privacy-and-the-100000-genome-project">have also shown</a> that the department has misinformed the public about the level of access granted to commercial actors in the 100,000 Genome Project. In particular it said the data would be “pseudonymised” rather than anonymised, meaning there would still be information available such as age or geographical location.</p>
<h2>The danger of personalisation</h2>
<p>But more generally, what could genomic information add to Google’s already far-reaching database of individual information? A hint lies in its self-confessed aspiration to organise our lives for us. The algorithms “will get better, and we will get better at personalisation”, <a href="https://www.ft.com/content/c3e49548-088e-11dc-b11e-000b5df10621">according to Eric Schmidt</a>, executive chairman of Google’s parent company Alphabet. This will “enable Google users to ask the question, ‘what shall I do tomorrow?’, or ‘what job shall I take?’”.</p>
<p>With personalisation as its ultimate “goal”, Google intends to use the machine learning algorithms which track our digital footprint and target users with personalised advertising based on their preferences. It also wants to analyse health and genomic data to make predictions such as when a person <a href="https://www.newscientist.com/article/mg22429921-400-global-agency-needed-for-battling-infectious-diseases/">might develop bipolar disorder</a> or tell us what we should do with our lives. </p>
<p>Let us not forget that data, genomic or otherwise, is the <a href="http://www.economist.com/news/leaders/21721656-data-economy-demands-new-approach-antitrust-rules-worlds-most-valuable-resource">oil of the digital era</a>. What is stopping genomic information from being <a href="http://www.huffingtonpost.com/robert-siciliano/data-brokers-what-are-the_b_5185127.html">captured, bought and sold</a>? We cannot assume that people will make life choices based upon their “genetic profile” without undue pressure – commercial or governmental. </p>
<p>As for how genomic data might be used and what decisions will be taken about us, the <a href="https://www.documentcloud.org/documents/3115985-APPLICANTS-REPLY-to-GOVT-OBSERVATIONS-PDF.html">mass surveillance</a> by government agencies of their own citizens is a chilling reminder of the way information technology can be used. There is something unpalatable about everything being connected and everything being known.</p>
<p>When it comes to genetics, the implications are particularly frightening. For example, there are claims of evidence of a <a href="http://www.bbc.com/news/science-environment-29760212">link between genes and criminality</a>. We know that <a href="https://theconversation.com/sex-offending-may-be-in-the-genes-but-knowing-that-wont-prevent-it-40286">40% of sexual offending risk is down to genetic factors</a>. A “single national knowledge base” as the one the UK government is aiming to create might therefore be used for broad genetic profiling. Although early intervention programmes that buy into genetically deterministic notions of “crime genes” are reductive, serious debate about policies involving genetic information will no doubt happen soon. </p>
<p>We can already see the beginnings of this in the United States. The bill <a href="https://www.congress.gov/bill/115th-congress/house-bill/1313">Preserving Employee Wellness Programs Act</a> – which has received strong backing from <a href="https://www.statnews.com/2017/03/13/genetic-privacy-wellness/">Republicans and business groups</a> – would allow companies to require employees to undergo genetic testing. The results would be seen by employers, and should employees refuse to participate they would face significantly higher insurance costs. </p>
<p>Too much personalisation is likely to be intrusive. The challenge, then, will be to harness the potential of genomics while introducing measures to keep government and big business in check. The UK House of Commons Science and Technology Committee’s <a href="https://www.parliament.uk/business/committees/committees-a-z/commons-select/science-and-technology-committee/inquiries/parliament-2015/inquiry2/">inquiry on genomics and genome editing</a> was cut short (due to the recent snap general election). Its recommendations for further lines of enquiry include creating a quasi-independent body, which could be more attuned to broader, social and ethical concerns. This might introduce more balance at a pivotal time for the future of human genetic technologies.</p>
<p><em>This article was amended to correct that it was Google, the owners of DeepMind, that met with Genomics England.</em></p><img src="https://counter.theconversation.com/content/80417/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Edward Hockings is the Director of EthicsAndGenetics.org He is affiliated with EthicsAndGenetics.org</span></em></p>A freedom of information request reveals that Google wants its AI company DeepMind to get involved in the 100,000 Genomes Project.Edward Hockings, PhD candidate of bioethics, University of the West of ScotlandLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/673262016-11-06T10:37:46Z2016-11-06T10:37:46ZUnderstanding Africa’s diverse gene pool can help fight lifestyle diseases<figure><img src="https://images.theconversation.com/files/144402/original/image-20161103-25339-1r777jp.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">shutterstock</span> </figcaption></figure><p>Africa is home to about 16% of the world’s population. That’s 1.2 billion people. But the continent is disproportionately burdened by a double health challenge: infectious diseases and a <a href="https://theconversation.com/africa-needs-a-fresh-approach-to-lifestyle-diseases-research-66527">recent increase</a> in non-communicable diseases. </p>
<p>Non-communicable diseases such as hypertension, cardiovascular diseases and diabetes are on the march due to an ageing population, a transition to increased urbanisation, dietary changes, a more sedentary lifestyle and an increase in the prevalence of obesity.</p>
<p>Non-communicable diseases result in deaths everywhere in the world. But in Africa they are also a major reason for premature deaths, that is people dying between the ages of 40 and 70. In South Africa there is more than a 25% chance of dying prematurely from non-communicable diseases. On the rest of the continent it ranges between 15% and 24%. This compares to the average of less than 15% for the US and Europe.</p>
<p>The continent’s health systems are struggling to bring these diseases under control. One of the key strategies explored elsewhere is the use of genomics for a precision medicine approach. This opens the door to understanding which genetic drivers are responsible for an increased risk to a particular disease and how genetic variants in a population dictate responses to treatment. </p>
<p>Once scientists understand which treatments have the largest impact they can target therapy accordingly, this known as precision public health.</p>
<p>This approach could help to alleviate the health burden in Africa too but implementing it is more difficult than elsewhere. This is because the continent has added challenges. It has a genomic spectrum that is more diverse than other continents. In addition it has a wide range of different environments, cultures and levels of poverty. </p>
<p>That’s not to say it’s impossible. A precision public health approach would be possible if it was driven by research at a population level with large cohorts. This could help scientists understand how genes respond in the presence of certain environments, and interact with them (known as gene-environment interactions). Cracking this would open a new frontier in the drive against rising non-communicable diseases. </p>
<h2>Genomic research challenges</h2>
<p>There are four main problems with advancing genomic research in Africa. </p>
<p>Firstly, there is sparse data on genomics and gene-environment interactions in African populations. Scientists still do not know how populations with a particular genetic variant spectrum react to changes in the environment, such as an increase in poverty or lifestyle change during urbanisation, and what the likely impact of a particular genetic variants is. </p>
<p>In addition, scientists are prone to using interpretations based on research conducted elsewhere. There’s a particular bias, for example, to apply Eurocentric interpretations. In fact, people’s genetic background could have a profound effect on the way people react to their environment and to treatments. Applying a Eurocentric approach therefore doesn’t make sense. For example, sickle cell disease would not be very relevant in a European setting, but is very common in many regions of Africa and causes an enormous disease burden.</p>
<p>The second challenge is around the regulatory framework and how good practice guidelines are implemented. In many African countries privacy and genetic information is not protected or legislated. There is therefore the potential for harm.</p>
<p>Thirdly, there is a lack of resources to conduct primary research to inform precision public health approaches. These include money, people, infrastructure and electronic public health records. All are critical.</p>
<p>Implementing a precision public health approach is costly and it needs to be reviewed and updated continuously as understanding deepens and the environments that people live in change. </p>
<p>The fourth challenge is around informing people about the approach and what’s involved. Without this there is unlikely to be any buy in.</p>
<h2>First steps</h2>
<p>Genomic research has gained considerable momentum on the continent over the past decade. Two initiatives are boosting the capacity for genomic research on African populations. These are expected to benefit health initiatives elsewhere in the world too. </p>
<p>The International Network for the Demographic Evaluation of Populations and Their Health (INDEPTH) does two things: it collects data on populations. In addition it has launched a new initiative to collect biological specimens from populations. On the basis of this the project, known as <a href="http://www.thelancetnorway.com/pdfs/journals/langlo/PIIS2214-109X(15)00180-1.pdf">CHESS</a>, can provide data on diseases, pathogens and causes of death in specific populations.</p>
<p>The second initiative, the Human Heredity and Health in Africa <a href="http://www.h3africa.org">(H3Africa) Consortium</a>, studies infectious and non-communicable diseases from a genomics point of view. </p>
<p>These initiatives are important because they are studying populations that have been under-represented. </p>
<h2>Longterm goals</h2>
<p>There are several examples for successful use of precision medicine in the developed world (for example in some cancers). </p>
<p>Before Africa can boast its own examples it will first need to generate knowledge and data. This will take time which means that a precision public health approach to tackle disease won’t be yielding immediate results. </p>
<p>Many people on the continent do not get the treatment they need. In the short-term genomic research on drug responses could make a difference by providing governments with guidelines for what effective medication they should be giving their populations. </p>
<p>For longer term impact, researchers need to understand how genetic predisposition works in Africa. Only then will we begin to know how to treat the diseases more effectively.</p><img src="https://counter.theconversation.com/content/67326/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Michèle Ramsay receives funding from the SA Department of Science, the NRF and SAMRC and the National Institute of Health (USA).</span></em></p>Cracking genetic responses to the changing environment in Africa would open a new frontier in the drive against rising non-communicable diseases on the continent.Michèle Ramsay, Director of the Sydney Brenner Institute for Molecular Bioscience, Professor in the Division of Human Genetics , University of the WitwatersrandLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/589622016-06-12T17:42:46Z2016-06-12T17:42:46ZWhy African genomic studies can solve the continent’s health issues<figure><img src="https://images.theconversation.com/files/125892/original/image-20160609-7093-9835mr.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Genomic research in Africa will help explain the genetic risk factors of diseases that affect the world's poorest people.</span> <span class="attribution"><span class="source">Shutterstock</span></span></figcaption></figure><p>Genomic research has proven to be a considerably valuable tool in global attempts to tackle disease. </p>
<p>One crucial part of this research has been identifying diseases and health problems that are more likely to be influenced by genetic factors and assessing the risk of a particular disease in an individual. </p>
<p>Eventually scientists will be in a position to develop new ways to treat, cure or even prevent the thousands of diseases that afflict humankind. And it will also allow them to assess the risk that exposure to toxic agents poses to individuals.</p>
<p>But for the world’s poorest people, the diseases that affect them have remained understudied. This is mainly due to most of these studies focusing on the genetic risk factors for disease in European populations. </p>
<p>For example, recent <a href="http://www.ncbi.nlm.nih.gov/pubmed/27231129">studies</a> from Sweden’s Uppsala University show men with blood cells that don’t carry the Y chromosome – a sex chromosome normally only present in male cells – are at greater risk of being diagnosed with Alzheimer’s disease. They also have an increased risk of death from other causes, including many cancers. </p>
<p>But will African men be affected in the same way? African populations have evolved significantly over time. Their genetic composition is more diverse than that of European and other populations so this may not be the case. Very little is known about the nature and extent of this diversity. </p>
<p>With the high burden of disease in sub-Saharan Africa, medical research needs a significant boost on the continent to identify genetic risk factors for diseases and to tackle the spread of drug resistance and emerging infections. </p>
<p>Genomic research has gained considerable momentum on the continent in the past decade. But challenges, such as a lack of high-quality clinical and epidemiological data across all countries, still hamper efforts. </p>
<h2>A different genetic makeup</h2>
<p>Genetic research taking place in Africa has focused on the genomic and environmental risk factors for cardiometabolic disease in Africans. Cardiometabolic diseases are those associated with the heart and include strokes, heart attacks and diabetes. </p>
<p>According to the statistics, non-communicable diseases such as diabetes, cancer, heart disease and chronic respiratory illness have all <a href="http://www.afro.who.int/en/clusters-a-programmes/dpc/non-communicable-diseases-managementndm/npc-features/1236-non-communicable-diseases-an-overview-of-africas-new-silent-killers.html">skyrocketed</a> in sub-Saharan Africa in the past ten years. </p>
<p>Globally, more than 16 million people die from non-communicable diseases. Of these, 80% are in low- and middle-income countries. </p>
<p>Research teams are trying to understand the interplay between genetic factors, the changes in the way the gene expresses itself, or <a href="http://www.whatisepigenetics.com/fundamentals/">epigenetics</a>, and environmental risk factors for obesity and related heart diseases. They are using existing longitudinal cohorts from four countries: Kenya, South Africa, Ghana and Burkina Faso. And they have six study sites across these countries, which have undergone different population changes as a result of their individual burdens of disease.</p>
<p>The goal of this initiative, the first of its kind in Africa, is to develop the capacity to carry out these kinds of studies in populations around the continent. This would help scientists better understand the genetic and genomic markers for disease. </p>
<p>One of the diseases that the study is attempting to understand is alcoholism. </p>
<p>Global studies have shown that the amount of alcohol one drinks and whether this progresses to alcoholism has a <a href="http://journals.cambridge.org/download.php?file=%2FPSM%2FPSM41_07%2FS003329171000190Xa.pdf&code=fc8c518b7edd5761e6bbfbf916a408e1">genetic influence</a>. Separate <a href="http://www.wales.nhs.uk/sitesplus/documents/888/%2812%29%20Graham%20Burdge.pdf">findings</a> show that processes that are related to factors in the gene, but that do not change the sequence of the DNA, also play a role. These are known as epigenetic processes.</p>
<p>And in European, North American and Asian populations, <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3181942/">research</a> has drawn a correlation between genetic variations for drugs and dependence. </p>
<p>Alcohol consumption and problems related to alcohol vary widely around the world but the burden of disease and death remains significant in most countries. It is the world’s third largest risk factor for disease and disability. </p>
<p>It is also one of the four risk factors that lead to people developing non-communicable diseases such as heart attacks and strokes. In middle-income countries, it is the greatest risk factor. </p>
<p>But very little is known about the risk of alcohol consumption in sub-Saharan African populations. This is despite statistics from the World Health Organisation listing 17 countries on the continent as <a href="http://www.who.int/substance_abuse/publications/global_alcohol_report/msbgsruprofiles.pdf">heavy drinking countries</a>. Nigeria takes the lead. </p>
<p>The high toll of alcohol and drug over-consumption among African populations means that this must become a priority. Understanding the genetic and genomic markers of diseases such as alcoholism would lead to research interrogating whether drug use and abuse are genetically linked. </p>
<p>And this could lead to an evidence-based approach to control drug use and abuse that fits the African context. It would help the continent improve its efforts to eliminate one of the four main risk factors for non-communicable disease.</p>
<h2>Challenges and solutions</h2>
<p>The amount of available genomic information has grown rapidly in the past decade, mainly due to the falling cost and increasing efficiency of DNA sequencing technologies. </p>
<p>But DNA sequencing is still relatively expensive for large-scale studies. Africa lags behind other continents with such studies. This is mainly due to: </p>
<ul>
<li><p>a shortage of African scientists with genomic research expertise; </p></li>
<li><p>lack of biomedical research infrastructure; </p></li>
<li><p>limited computational expertise and resources; </p></li>
<li><p>lack of adequate support for biomedical research by African governments; and</p></li>
<li><p>the participation of many African scientists in collaborative research at no more than the level of <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4138491/">sample collection</a>. </p></li>
</ul>
<p>Although scientists on the continent are unable to match the scale of research produced on other continents, they are continuously attempting large-scale genome-sequencing studies focused on specific diseases. </p>
<p>The <a href="http://h3africa.org/">H3Africa project</a>, funded by the <a href="https://www.nih.gov">National Institutes of Health</a> and the Wellcome Trust, supports several studies involving collaborative centres on the continent.</p>
<p>In addition, ongoing genomic projects in Africa are both establishing infrastructure for genomic research and training local researchers, as well as generating genomic datasets. </p>
<p>Many of these projects have made capacity building one of their core missions. This will in the long run build a critical mass of highly skilled individuals in the field shaping the future of genomic studies in Africa.</p><img src="https://counter.theconversation.com/content/58962/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Nicholas N Ngomi does not work for, consult, own shares in or receive funding from any company or organisation that would benefit from this article, and has disclosed no relevant affiliations beyond their academic appointment.</span></em></p>Genomic research must take place in Africa because African populations have evolved significantly and their genetic composition is more diverse than that of populations elsewhere.Nicholas N Ngomi, Research officer, African Population and Health Research CenterLicensed as Creative Commons – attribution, no derivatives.