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class="nav-link--research-facilities-genomics-platform is-active" role="menuitem" data-drupal-link-system-path="taxonomy/term/1006" aria-current="page">Genomics platform</a></li></ul></li></ul></div></div></div><div class="where-we-work dropdown" data-parent="3"><div class="row"><div class="col-6 align-self-start"><div class="mt-2"><div class="row"><div class="col-6"> <article class="node node--type-project node--view-mode-teaser clearfix card card-medium text-white border-0" style="background-image: url("/sites/default/files/styles/card/public/global_rangelands_PP.jpg?itok=sRw4UFxv");"> <a href="/index.php/research/projects/international-land-coalition-rangelands-initiative-making-rangelands-secure" class="card-link"></a> <img class="card-img d-none" src='/sites/default/files/styles/card/public/global_rangelands_PP.jpg?itok=sRw4UFxv' alt="International Land Coalition Rangelands Initiative" title="International Land Coalition Rangelands Initiative"/><div class="card-gradient"></div><div class="card-img-overlay"><h3 class="card-title">International Land Coalition Rangelands Initiative: Making rangelands secure</h3></div></article></div><div class="col-6"> <article class="node node--type-project node--view-mode-teaser clearfix card card-medium text-white border-0" style="background-image: url("/sites/default/files/styles/card/public/project/2023/Watering%20camels.jpg?itok=5hfqVJdq");"> <a href="/research/projects/emerging-public-health-threats-africas-drylands" class="card-link"></a> <img class="card-img d-none" src='/sites/default/files/styles/card/public/project/2023/Watering%20camels.jpg?itok=5hfqVJdq' alt="Camels drinking at a water pan in Wajir County, Kenya" title="Camels drinking at a water pan in Wajir County, Kenya"/><div class="card-gradient"></div><div class="card-img-overlay"><h4 class="card-deadline"><em>ACTIVE</em> <i class="fa-solid fa-arrow-right"></i> <time>Feb 2028</time></h4><h3 class="card-title">Emerging public health threats in Africa’s drylands</h3></div></article></div></div></div></div><div class="col-3"><ul class="clearfix nav navbar-nav flex-row justify-content-end" role="menu"><li class="nav-item menu-item--expanded dropdown"> <a href="/where-we-work/eastern-and-southern-africa" data-col="1" class="nav-link nav-link--where-we-work-eastern-and-southern-africa" aria-expanded="false" aria-haspopup="true" role="menuitem" data-drupal-link-system-path="taxonomy/term/916">Eastern and southern africa</a><ul class="dropdown-menu" role="menu"><li class="dropdown-item"> <a href="/where-we-work/eastern-and-southern-africa/kenya" class="nav-link--where-we-work-eastern-and-southern-africa-kenya" role="menuitem" data-drupal-link-system-path="taxonomy/term/917">Kenya</a></li><li class="dropdown-item"> <a href="/where-we-work/eastern-and-southern-africa/ethiopia" class="nav-link--where-we-work-eastern-and-southern-africa-ethiopia" role="menuitem" 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href="/index.php/"><span>Home</span></a></li><li class="breadcrumb-item active"> Research</li><li class="breadcrumb-item active"> Facilities</li></ol> </nav></div></div></div> <section class="container mt-4"><div class="row"><div class="col-12"><h1 class="title">Genomics platform</h1></div></div> <article> <section id="item-5586" class="row single-column-sidebar paragraph"><div class="col-lg-8 col-md-8 col-sm-12"><h2 class="title">ILRI GENOMICS</h2><div class="text-container"><p><span></span></p><p>Whole genome sequencing (WGS) technology is currently revolutionizing genetic research all over the world. However, low-income countries in Africa are still lagging behind even though the current advances suit their unique needs more than ever before. Through Next generation sequencing (NGS), genomic research has been fundamentally transformed and the continually emerging new developments are significantly reducing the cost of sequencing to affordable levels. For clinical microbiology applications, the NGS technology is beginning to show extreme potential for ultra-fast and accurate molecular typing and diagnosis. The combination of low cost and rapid turnaround time offered by the current and the emerging desk-top sequencers, makes pathogen WGS the key to accurate diagnostic tool and the ultimate epidemiological typing method with the digital, portable, and universally applicable capabilities. Compared to the current diagnostic methods, microbial clinical sequencing is by far more informative and capable of distinguishing very closely related strains. Furthermore, microbial genome sequencing is transforming our understanding of the evolution of pathogen virulence factors and the molecular basis that leads to the development and spread of antimicrobial resistance.</p><p><img data-entity-uuid="24b5996a-a285-4bf6-b879-16e6d2af675b" data-entity-type="file" src="/sites/default/files/inline-images/genomic%20and%20data%20analysis.jpg" height="341" width="490"><br></p><div class="cke_widget_wrapper cke_widget_block cke_widget_image align-left cke_widget_selected"> </div><p>Given the complex nature of microbial infection is Sub-Saharan Africa (SSA) where cases of multiple pathogen infection are common, a universal diagnostic approach offered by whole genome sequencing in the context of metagenomics approach, provides the most effective solution to accurate diagnosis and pathogen typing. Setting a genomic pathogen diagnostic and epidemiology platform in SSA will help: 1) develop methods for epidemiological typing to define transmission pathways and support outbreak investigations; 2) develop methods for drug susceptibility testing using known markers for antibiotic resistance especially for slow-growing bacteria such M. tuberculosis complex and also for viral genotyping; 3) develop local resources for capacity building in genomics that will enable Africans to contribute to the global genomics research arena. For the countries in SSA to benefit from the current genomic revolution, there is a need to strengthen research capacity, training, and collaborations that will enable the continent to contribute fully to global health improvement. Although SSA is still poorly resourced in terms of healthcare funding, the universality of pathogen sequencing, means that a single sequencing machine can offer a wider diagnostic repertoire bridging the gap left by the different generic diagnostic methods. Thus, improve efficiency, accuracy and cost reduction. As both research and a clinical tool, WGS platform is valuable in providing genomic information of known and unknown pathogens upon which individual pathogen-specific diagnostic tools can be developed that is sensitive and compatible with the local strains and genotypes.</p><p><span></span></p></div></div> <aside class="col-lg-4 col-md-4 col-sm-12"><div class="card bg-light border-0"><div class="card-body"><div id="item-5582" class="contacts paragraph"><h3>Contacts</h3><div class="style-1"><ul class="list-unstyled"><li> <article class="card card-user border-0 rounded"> <a href="/index.php/people/samuel-o-oyola" class="card-link"></a><div class="row g-0"><div class="col-md-4"> <img src="/index.php/sites/default/files/styles/card/public/Sam-ipad7a.jpg?itok=K5IgpAQe" class="img-fluid rounded" alt="Samuel O. Oyola"></div><div class="col-md-8 d-flex align-self-center"><div class="card-body"><h3 class="card-title mb-1">Samuel O. Oyola</h3><p class="card-text m-0">Senior Scientist: Molecular Biologist and Head of Genomics</p></div></div></div></article></li></ul></div></div><div id="item-5583" class="cta paragraph"> <a class="d-block text-align-center btn btn-primary" href="https://www.ilri.org/genomics-platform-services">Services</a></div><div id="item-5584" class="cta paragraph"> <a class="d-block text-align-center btn btn-primary" href="https://www.ilri.org/sequencing-platforms">sequencing platforms</a></div><div id="item-5585" class="info paragraph"><h3><i class="fa-solid fa-circle-info"></i>Fellowships</h3><div class="text-container"><p>ILRI continues to build genomic capacity in Africa and beyond by offering short- and long-term training to Fellows and Scientists seeking to employ modern genomic technologies in general life science research and also for targeted applications in medicine, diagnostics, public health, One health, climate change, animal health and in agriculture.<br>Currently the ILRI Genomic platform is running short- and long-term fellowships on pathogen genomic surveillance funded by the Rockefeller Foundation and the Africa CDC.<br>Visit this site for new announcements for fellowships and training opportunities on genomics and its applications in life sciences.<br> </p></div></div></div></div> </aside></section> <section id="item-53537" class="banners style-2 paragraph"><div class="row"><div class="col-12"><h2 class="title">Services</h2></div></div><div class="row mb-4"></div><div class="row"><div class="col-lg-3 col-md-3 col-sm-12 mb-lg-m-3"> <article id="item-53533" class="paragraph banner card card-medium text-white border-0 mb-4" style="background-image: url("/index.php/sites/default/files/styles/card/public/banner/2023/Picture10.png?itok=sU5XyPYl");"> <a href="/index.php/genomics-platform-services" class="card-link" target="_blank"></a> <img class="card-img d-none" src='/index.php/sites/default/files/styles/card/public/banner/2023/Picture10.png?itok=sU5XyPYl' alt="Molecular biology " title=""/><div class="card-gradient"></div><div class="card-img-overlay"><h3 class="card-title">Molecular biology</h3></div> </article></div><div class="col-lg-3 col-md-3 col-sm-12 mb-lg-m-3"> <article id="item-53534" class="paragraph banner card card-medium text-white border-0 mb-4" style="background-image: url("/index.php/sites/default/files/styles/card/public/banner/2023/Picture4.png?itok=R1n2YaKO");"> <a href="/index.php/genomics-platform-services" class="card-link" target="_blank"></a> <img class="card-img d-none" src='/index.php/sites/default/files/styles/card/public/banner/2023/Picture4.png?itok=R1n2YaKO' alt="Library preparations" title=""/><div class="card-gradient"></div><div class="card-img-overlay"><h3 class="card-title">Library preparations</h3></div> </article></div><div class="col-lg-3 col-md-3 col-sm-12 mb-lg-m-3"> <article id="item-53535" class="paragraph banner card card-medium text-white border-0 mb-4" style="background-image: url("/index.php/sites/default/files/styles/card/public/banner/2023/Picture9.png?itok=dW03c2mP");"> <a href="/index.php/genomics-platform-services" class="card-link" target="_blank"></a> <img class="card-img d-none" src='/index.php/sites/default/files/styles/card/public/banner/2023/Picture9.png?itok=dW03c2mP' alt="RT-qPCR analysis" title=""/><div class="card-gradient"></div><div class="card-img-overlay"><h3 class="card-title">RT-qPCR analysis</h3></div> </article></div><div class="col-lg-3 col-md-3 col-sm-12 mb-lg-m-3"> <article id="item-53536" class="paragraph banner card card-medium text-white border-0 mb-4" style="background-image: url("/index.php/sites/default/files/styles/card/public/banner/2023/Picture8.png?itok=v_zH7_0O");"> <a href="/index.php/genomics-platform-services" class="card-link" target="_blank"></a> <img class="card-img d-none" src='/index.php/sites/default/files/styles/card/public/banner/2023/Picture8.png?itok=v_zH7_0O' alt="Nucleic acid extractions" title=""/><div class="card-gradient"></div><div class="card-img-overlay"><h3 class="card-title">Nucleic acid extractions</h3></div> </article></div></div> </section> <section id="item-5587" class="full-width-image paragraph"><div class="row"><div class="col-12"><h2 class="title">SEQUENCING PLATFORMS</h2></div></div><div class="row"><div class="col-12 wrapper"> <figure> <img class="img-fluid rounded" src='/sites/default/files/styles/paragraph_full_width_image/public/images/full_width_image/2023/bioinformatics1_0.png?itok=mZM1e6TJ' alt="" title=""/><div class="image-info"></div> </figure><div class="left-wrapper style-1"><div class="text-container"><p>High throughput sequencingtechnologies (HTST) have been build using a combination of expertise from different fields of science including chemistry, molecular biology, software, and engineering. Most of the current HTST (except for the Oxford Nanopore technology) have been built upon the principle of the Sanger’s Nobel prize winning discovery of dideoxynucleotide chain termination reaction. </p></div> <a class="d-inline-block text-align-left btn btn-primary mt-2 read-more" href="https://ilri.org/sequencing-platforms">Read more</a></div></div></div> </section><section id="item-5589" class="in-side-menu row single-column-sidebar paragraph"><div class="col-lg-8 col-md-8 col-sm-12"><h2 class="title add-sidemenu">Bioinformatics</h2><div class="text-container"><p>BIOINFORMATIC INFRASTRUCTURE<br>Success in whole genome sequencing data requires a significant investment in bioinformatics infrastructure. Bioinformatics tools that enable fast and easy quality-controlled data generation and interpretation is our priority. The genomic platform is being developed as a regional bioinformatic hub to offer genomic analysis services and training center for developing bioinformatic capacity in the region.</p><p>We have set up bioinformatic analysis pipelines to analyse the sequence data within the shortest time possible and produce a simplified report on quality, type and distribution of DNA polymorphisms, antibiotic resistance, or virulence markers. Standard data output is generated through analysis software for WGS which has been established and set to extract clinically relevant information in an automated fashion. Interpretation software is integrated with the server system and continuously updated with database containing pathogen genomes and a catalogue of point mutations or drug mutation genes. Mechanisms for remote connection and access to international data centres are being established. </p><p>A metagenomics pipeline has also been set-up with capability of remote connection to the National Centre for Biotechnology Information (NCBI) databases to allow alignment of reads to the reference sequences in order to comprehensively identify bacteria, viruses, fungi and parasites. The connections ensure that useful information of public health benefits are shared nationally, regionally and internationally, as well as with the scientific community to promote progress in basic and translational research.</p><p>Apart from the physical infrastructure, human resource capacity is under continuous development to produce a new generation of African bioinformaticians and genomic scientists. Bioinformatic scientists from various institutions worldwide get invited as technology ambassadors to provide training and support to this initiative.</p></div></div> <aside class="col-lg-4 col-md-4 col-sm-12"><div class="card bg-light border-0"><div class="card-body"><div id="item-5588" class="image card paragraph card-medium border-0" style="background-image: url("/index.php/sites/default/files/styles/card/public/image/2023/side_picture_0.png?itok=4n2ddh9U");"><div class="card-body"> <figure class="d-none"> <img src="/index.php/sites/default/files/styles/card/public/image/2023/side_picture_0.png?itok=4n2ddh9U" alt="" title="" /> </figure></div></div></div></div> </aside></section> <section id="item-5596" class="in-side-menu gallery paragraph"><div class="row"><div class="col-12"><h2 class="title add-sidemenu">Gallery</h2></div></div><div class="row mb-4"></div><div class="row mb-4"><div class="col-lg-4 col-md-4 cold-sm-12"><div id="item-5590" class="gallery-image card paragraph border-0 card-medium" style="background-image: url("/index.php/sites/default/files/styles/card/public/paragraph/gallery/2023/library-title_2.png?itok=4C6w3_Ms");"><div class="card-body"> <figure class="d-none"> <img src="/sites/default/files/styles/slideshow/public/paragraph/gallery/2023/library-title_2.png?itok=oDLfKSyq" alt="" title=""/> </figure></div></div></div><div class="col-lg-4 col-md-4 cold-sm-12"><div id="item-5591" class="gallery-image card paragraph border-0 card-medium" style="background-image: url("/index.php/sites/default/files/styles/card/public/paragraph/gallery/2023/Picture6_2.png?itok=whdRnbUf");"><div class="card-body"> <figure class="d-none"> <img src="/sites/default/files/styles/slideshow/public/paragraph/gallery/2023/Picture6_2.png?itok=d6RbhKJG" alt="" title=""/> </figure></div></div></div><div class="col-lg-4 col-md-4 cold-sm-12"><div id="item-5592" class="gallery-image card paragraph border-0 card-medium" style="background-image: url("/index.php/sites/default/files/styles/card/public/paragraph/gallery/2023/Picture7_1.png?itok=WrP4xSPh");"><div class="card-body"> <figure class="d-none"> <img src="/sites/default/files/styles/slideshow/public/paragraph/gallery/2023/Picture7_1.png?itok=0vbHYY76" alt="" title=""/> </figure></div></div></div></div><div class="row mb-4"><div class="col-lg-4 col-md-4 cold-sm-12"><div id="item-5593" class="gallery-image card paragraph border-0 card-medium" style="background-image: url("/index.php/sites/default/files/styles/card/public/paragraph/gallery/2023/Picture8_1.png?itok=WwKWRKy1");"><div class="card-body"> <figure class="d-none"> <img src="/sites/default/files/styles/slideshow/public/paragraph/gallery/2023/Picture8_1.png?itok=fo3IU326" alt="" title=""/> </figure></div></div></div><div class="col-lg-4 col-md-4 cold-sm-12"><div id="item-5594" class="gallery-image card paragraph border-0 card-medium" style="background-image: url("/index.php/sites/default/files/styles/card/public/paragraph/gallery/2023/Picture13_1.png?itok=Y2qNd40s");"><div class="card-body"> <figure class="d-none"> <img src="/sites/default/files/styles/slideshow/public/paragraph/gallery/2023/Picture13_1.png?itok=Sj4xV5az" alt="" title=""/> </figure></div></div></div><div class="col-lg-4 col-md-4 cold-sm-12"><div id="item-5595" class="gallery-image card paragraph border-0 card-medium" style="background-image: url("/index.php/sites/default/files/styles/card/public/paragraph/gallery/2023/Picture10_0.png?itok=dXjgkEpA");"><div class="card-body"> <figure class="d-none"> <img src="/sites/default/files/styles/slideshow/public/paragraph/gallery/2023/Picture10_0.png?itok=d1pOpxIY" alt="" title=""/> </figure></div></div></div></div> </section> <section id="item-5597" class="full-width-image paragraph full-width"><div class="row"><div class="col-12"><h2 class="title">Genomics Team</h2></div></div><div class="row"><div class="col-12 wrapper"> <figure> <img class="img-fluid rounded" src='/sites/default/files/styles/paragraph_full_width_image/public/images/full_width_image/2023/Genomics-team.png?itok=6FAwBHgk' alt="" title=""/><div class="image-info"></div> </figure></div></div> </section> <section id="item-53538" class="organizations paragraph"><div class="row"><div class="col-12"><h2 class="title">Funders</h2></div></div><div class="row"></div><div class="row"><div class="col-lg-2 col-md-4 col-sm-6"> <article class="taxonomy-term vocabulary-organization card border-0 bg-transparent"> <a href="/about/supporters/german-federal-ministry-economic-cooperation-and-development" class="card-link"></a> <figure class="m-0"> <img class="card-img-top" src="/sites/default/files/styles/logo/public/logo_bmz_en.gif?itok=3Qs4de1U" alt="" title=""/> </figure><div class="card-body border-top border-2 border-primary m-0 p-0"><h3 class="card-title mt-2">The German Federal Ministry of Economic Cooperation and Development</h3></div></article></div><div 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