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Uganda Genome Resource: A rich research database for genomic studies of communicable and non-communicable diseases in Africa.

ABSTRACT: The Uganda Genome Resource (UGR) is a well-characterized genomic database with a range of phenotypic communicable and non-communicable diseases and risk factors generated from the Uganda General Population Cohort (GPC), a population-based open cohort established in 1989. The UGR comprises genotype data on ∼5,000 and whole-genome sequence data on ∼2,000 Ugandan GPC individuals from 10 ethno-linguistic groups. Leveraging other platforms at MRC/UVRI and LSHTM Uganda Research Unit, there is opportunity for additional sample collection to expand the UGR to advance scientific discoveries. Here, we describe UGR and highlight how it is providing opportunities for discovery of novel disease susceptibility genetic loci, refining association signals at new and existing loci, developing and testing polygenic scores to determine disease risk, assessing causal relations in diseases, and developing capacity for genomics research in Africa. The UGR has the potential to develop to a comparable level of European and Asian large-scale genomic initiatives.

SUBMITTER: Fatumo S

PROVIDER: S-EPMC9646479 | biostudies-literature | 2022 Nov

REPOSITORIES: biostudies-literature

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Uganda Genome Resource: A rich research database for genomic studies of communicable and non-communicable diseases in Africa.

Fatumo Segun S Mugisha Joseph J Soremekun Opeyemi S OS Kalungi Allan A Mayanja Richard R Kintu Christopher C Makanga Ronald R Kakande Ayoub A Abaasa Andrew A Asiki Gershim G Kalyesubula Robert R Newton Robert R Nyirenda Moffat M Sandhu Manj S MS Kaleebu Pontiano P

Cell genomics 20221109 11

The Uganda Genome Resource (UGR) is a well-characterized genomic database with a range of phenotypic communicable and non-communicable diseases and risk factors generated from the Uganda General Population Cohort (GPC), a population-based open cohort established in 1989. The UGR comprises genotype data on ∼5,000 and whole-genome sequence data on ∼2,000 Ugandan GPC individuals from 10 ethno-linguistic groups. Leveraging other platforms at MRC/UVRI and LSHTM Uganda Research Unit, there is opportun ...[more]

PMID: 36388767

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Project description:BackgroundNon-communicable diseases (NCDs) cause a large and growing burden of morbidity and mortality in sub-Saharan Africa. Prospective cohort studies are key to study multiple risk factors and chronic diseases and are crucial to our understanding of the burden, aetiology and prognosis of NCDs in SSA. We aimed to identify the level of research output on NCDs and their risk factors collected by cohorts in SSA.MethodsWe conducted a scoping review to map the extent of current NCDs research in SSA by identifying studies published after the year 2000 using prospectively collected cohort data on any of the six NCDs (cardiovascular diseases, diabetes, obesity, chronic kidney disease, chronic respiratory diseases, and cancers), ≥1 major risk factor (other than age and sex), set only within SSA, enrolled ≥500 participants, and ≥12 months of follow-up with ≥2 data collection points (or with plans to). We performed a systematic search of databases, a manual search of references lists from included articles and the INDEPTH network website, and study investigators from SSA were contacted for further articles.ResultsWe identified 30 cohort studies from the 101 included articles. Eighteen countries distributed in West, Central, East and Southern Africa, were represented. The majority (27%) set in South Africa. There were three studies including children, twenty with adults, and seven with both. 53% of cohorts were sampled in general populations, 47% in clinical populations, and 1 occupational cohort study. Hypertension (n = 23) was most commonly reported, followed by obesity (n = 16), diabetes (n = 15), CKD (n = 6), COPD (n = 2), cervical cancer (n = 3), and breast cancer (n = 1). The majority (n = 22) reported data on at least one demographic/environmental, lifestyle, or physiological risk factor but these data varied greatly.ConclusionsMost studies collected data on a combination of hypertension, diabetes, and obesity and few studies collected data on respiratory diseases and cancer. Although most collected data on different risk factors the methodologies varied greatly. Several methodological limitations were found including low recruitment rate, low retention rate, and lack of validated and standardized data collection. Our results could guide potential collaborations and maximize impact to improve our global understanding of NCDs (and their risk factors) in SSA and also to inform future research, as well as policies.

Project description:BackgroundAs Mozambique faces a double burden of diseases, with a rise of Non Communicable Diseases (NCD) superimposed to uncontrolled communicable diseases (CD), routine disease surveillance system does not include NCD. The objectives of our study were to i) upgrade of the current surveillance system by adapting the data collection tools to NCD; ii) describe the occurrence and profile of selected NCD using these data collection tools.MethodsWorkshops were implemented in a first referral urban hospital of Mozambique to train clinical staff, administrative workers and nurses on NCD surveillance, as well as select conditions to be prioritized. Based on the WHO Global Action Plan and Brazaville Declaration for NCD prevention and control, we selected arterial hypertension, diabetes, stroke, chronic respiratory diseases, mental illness and cancers. Data collection tools used for CD were changed to include age, gender, outcome and visit type. Between February/2014 and January/2015 we collected data at an urban hospital in Mozambique's capital.ResultsOver 12 months 92,018 new patients were assisted in this hospital. Data was missing or diagnosis was unreadable in 2637 (2.9%) thus only 89,381 were used for analysis; of these 6423 (median age 27 years; 58.4% female) had at least one selected NCD as their primary diagnosis: arterial hypertension (2397;37.31%), mental illness (1497;23.30%), asthma (1495;23.28%), diabetes (628;9.78%), stroke (299;4.66%), chronic obstructive pulmonary disease 61 (0.95%) and cancers 46 (0.72%). Emergency transfers were needed for 76 patients (1.2%), mainly due to hypertensive emergencies (31; 40.8%) and stroke (18;23.7%). Twenty-four patients died at entry points (0.3%); 10 of them had hypertensive emergencies.ConclusionChanges in existing surveillance tools for communicable diseases provided important data on the burden and outcomes of the selected NCD helping to identify priority areas for training and health care improvement. This information can be used to design the local NCD clinics and to strengthen the health information system in resource-limited settings in a progressive and sustainable way.

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Dataset Information

Uganda Genome Resource: A rich research database for genomic studies of communicable and non-communicable diseases in Africa.

Publications

Uganda Genome Resource: A rich research database for genomic studies of communicable and non-communicable diseases in Africa.

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