Cohort Profile: South African Population Research Infrastructure Network (SAPRIN).
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ABSTRACT:
SUBMITTER: Collinson MA
PROVIDER: S-EPMC9365637 | biostudies-literature | 2022 Aug
REPOSITORIES: biostudies-literature
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Cohort Profile: South African Population Research Infrastructure Network (SAPRIN).
Collinson Mark A MA Mudzana Taurayi T Mutevedzi Tinofa T Kahn Kathleen K Maimela Eric E Gómez-Olivé F Xavier FX Mngomezulu Thobeka T Gareta Dickman D Kabudula Chodziwadziwa W CW Nemuramba Rathani R Tlouyamma Joseph J Tollman Stephen S Herbst Kobus K
International journal of epidemiology 20220801 4
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Project description:PurposeThe South African HIV Cancer Match (SAM) Study is a national cohort of people living with HIV (PLWH). It was created using probabilistic record linkages of routine laboratory records of PLWH retrieved by National Health Laboratory Services (NHLS) and cancer data from the National Cancer Registry. The SAM Study aims to assess the spectrum and risk of cancer in PLWH in the context of the evolving South African HIV epidemic. The SAM Study's overarching goal is to inform cancer prevention and control programmes in PLWH in the era of antiretroviral treatment in South Africa.ParticipantsPLWH (both adults and children) who accessed HIV care in public sector facilities and had HIV diagnostic or monitoring laboratory tests from NHLS.Findings to dateThe SAM cohort currently includes 5 248 648 PLWH for the period 2004 to 2014; 69% of these are women. The median age at cohort entry was 33.0 years (IQR: 26.2-40.9). The overall cancer incidence in males and females was 235.9 (95% CI: 231.5 to 240.5) and 183.7 (181.2-186.2) per 100 000 person-years, respectively.Using data from the SAM Study, we examined national cancer incidence in PLWH and the association of different cancers with immunodeficiency. Cancers with the highest incidence rates were Kaposi sarcoma, cervix, breast, non-Hodgkin's lymphoma and eye cancer.Future plansThe SAM Study is a unique, evolving resource for research and surveillance of malignancies in PLWH. The SAM Study will be regularly updated. We plan to enrich the SAM Study through record linkages with other laboratory data within the NHLS (eg, tuberculosis, diabetes and lipid profile data), mortality data and socioeconomic data to facilitate comprehensive epidemiological research of comorbidities among PLWH.
| S-EPMC9003610 | biostudies-literature
Project description:PurposeSouth Africa's National Health Laboratory Service (NHLS) National HIV Cohort was established in 2015 to facilitate monitoring, evaluation and research on South Africa's National HIV Treatment Programme. In South Africa, 84.8% of people living with HIV know their HIV status; 70.7% who know their status are on ART; and 87.4% on ART are virologically suppressed.ParticipantsThe NHLS National HIV Cohort includes the laboratory data of nearly all patients receiving HIV care in the public sector since April 2004. Patients are included in the cohort if they have received a CD4 count or HIV RNA viral load (VL) test. Using an anonymised unique patient identifier that we have developed and validated to linked test results, we observe patients prospectively through their laboratory results as they receive HIV care and treatment. Patients in HIV care are seen for laboratory monitoring every 6-12 months. Data collected include age, sex, facility location and test results for CD4 counts, VLs and laboratory tests used to screen for potential treatment complications.Findings to dateFrom April 2004 to April 2018, 63 million CD4 count and VL tests were conducted at 5483 facilities. 12.6 million unique patients had at least one CD4 count or VL, indicating they had accessed HIV care, and 7.1 million patients had a VL test indicating they had started antiretroviral therapy. The creation of NHLS National HIV Cohort has enabled longitudinal research on all lab-monitored patients in South Africa's national HIV programme, including analyses of (1) patient health at presentation; (2) care outcomes such as 'CD4 recovery', 'retention in care' and 'viral resuppression'; (3) patterns of transfer and re-entry into care; (4) facility-level variation in care outcomes; and (5) impacts of policies and guideline changes.Future plansContinuous updating of the cohort, integration with available clinical data, and expansion to include tuberculosis and other lab-monitored comorbidities.
| S-EPMC9582381 | biostudies-literature
Project description:PurposeObservational population-based research is a very suitable non-invasive method for studies in the vulnerable populations of pregnant women and children. Therefore, the PHARMO Perinatal Research Network (PPRN) was set up as a resource for life course perinatal and paediatric research by linking population-based data from existing registrations.ParticipantsFrom 1999 to 2017, the PPRN captures approximately 542 900 pregnancies of 387 100 mothers ('Pregnancy Cohort'). Additionally, mother-child linkage is currently available for a quarter of these pregnancies ('Child Cohort'). The PPRN contains preconceptional information on maternal healthcare, as well as detailed pregnancy and neonatal data, extending into long-term follow-up and outcomes after birth for both mother and child up to nearly 20 years. It includes linked data from different primary and secondary healthcare settings.Findings to dateThrough record linkage of the Netherlands Perinatal Registry and the PHARMO Database Network, we have established a large population-based research network including data on demographics, medication use, medical conditions and details concerning labour, birth and neonatal outcomes. Here, we provide an overview of record types available from the PPRN, available database follow-up and pregnancy characteristics of the PPRN cohorts. The PPRN has been used for a number of different pharmacoepidemiological studies, for example, to confirm that preterm-born infants were more likely than full-term infants to be hospitalised or use medication. Similar long-term comparisons showed that children born following spontaneous preterm labour were at increased risk of neurodevelopmental and respiratory conditions. Most recently, the PPRN provided important evidence on the trends in use of potentially harmful medication during pregnancy.Future plansThe PPRN provides a unique and rich data set facilitating large-scale observational pharmacoepidemiological perinatal research. The patient-level linkage of many different healthcare data sources allows for long-term follow-up of mother and child, with ongoing annual updates.
| S-EPMC7520848 | biostudies-literature
Project description:PurposeThe Scottish Diabetes Research Network (SDRN)-diabetes research platform was established to combine disparate electronic health record data into research-ready linked datasets for diabetes research in Scotland. The resultant cohort, 'The SDRN-National Diabetes Dataset (SDRN-NDS)', has many uses, for example, understanding healthcare burden and socioeconomic trends in disease incidence and prevalence, observational pharmacoepidemiology studies and building prediction tools to support clinical decision making.ParticipantsWe estimate that >99% of those diagnosed with diabetes nationwide are captured into the research platform. Between 2006 and mid-2020, the cohort comprised 472 648 people alive with diabetes at any point in whom there were 4 million person-years of follow-up. Of the cohort, 88.1% had type 2 diabetes, 8.8% type 1 diabetes and 3.1% had other types (eg, secondary diabetes). Data are captured from all key clinical encounters for diabetes-related care, including diabetes clinic, primary care and podiatry and comprise clinical history and measurements with linkage to blood results, microbiology, prescribed and dispensed drug and devices, retinopathy screening, outpatient, day case and inpatient episodes, birth outcomes, cancer registry, renal registry and causes of death.Findings to dateThere have been >50 publications using the SDRN-NDS. Examples of recent key findings include analysis of the incidence and relative risks for COVID-19 infection, drug safety of insulin glargine and SGLT2 inhibitors, life expectancy estimates, evaluation of the impact of flash monitors on glycaemic control and diabetic ketoacidosis and time trend analysis showing that diabetic ketoacidosis (DKA) remains a major cause of death under age 50 years. The findings have been used to guide national diabetes strategy and influence national and international guidelines.Future plansThe comprehensive SDRN-NDS will continue to be used in future studies of diabetes epidemiology in the Scottish population. It will continue to be updated at least annually, with new data sources linked as they become available.
| S-EPMC9562713 | biostudies-literature
Project description:Several studies have reported a possible association between leucocyte telomere length (LTL) and cardio-metabolic diseases (CMDs). However, studies investigating such association are lacking in South Africa despite having a very high prevalence of CMDs. We investigated the association between LTL and CMD risk profile in a black South African population. This was a cross-sectional study with participants > 21 years of age and residing in five townships in Cape Town. CMD markers were compared between men and women and across quartiles of LTL. Linear and logistic regressions relate increasing quartile and Log10LTL with CMD risk profile, with appropriate adjustment. Among 676-participants, diabetes, obesity and hypertension prevalence were 11.5%, 23.1% and 47.5%. Waist-circumference, hip-circumference and highly sensitive c-reactive protein values were significantly higher in women (all p < 0.001), while HDL-C (p = 0.023), creatinine (p = 0.005) and gamma glutamyl transferase (p < 0.001) values were higher in men. In age, sex and BMI adjusted linear regression model, Log10 of LTL was associated with low HDL-C (beta = 0.221; p = 0.041) while logistic regression showed a significant association between Log10LTL and prevalent dyslipidaemia characterised by high LDL-C. In this population, the relationship between LTL and CMD is weak given its association with only HDL-C and LDL-C.
| S-EPMC8885820 | biostudies-literature
Project description:IntroductionLimited diagnostics are available for inherited neuromuscular diseases (NMD) in South Africa and (excluding muscle disease) are mainly aimed at the most frequent genes underlying genetic neuropathy (GN) and spastic ataxias in Europeans. In this study, we used next-generation sequencing to screen 61 probands with GN, hereditary spastic paraplegia (HSP), and spastic ataxias for a genetic diagnosis.MethodsAfter identifying four GN probands with PMP22 duplication and one spastic ataxia proband with SCA1, the remaining probands underwent whole exome (n = 26) or genome sequencing (n = 30). The curation of coding/splice region variants using gene panels was guided by allele frequencies from internal African-ancestry control genomes (n = 537) and the Clinical Genome Resource's Sequence Variant Interpretation guidelines.ResultsOf 32 GN probands, 50% had African-genetic ancestry, and 44% were solved: PMP22 (n = 4); MFN2 (n = 3); one each of MORC2, ATP1A1, ADPRHL2, GJB1, GAN, MPZ, and ATM. Of 29 HSP probands (six with predominant ataxia), 66% had African-genetic ancestry, and 48% were solved: SPG11 (n = 3); KIF1A (n = 2); and one each of SPAST, ATL1, SPG7, PCYT2, PSEN1, ATXN1, ALDH18A1, CYP7B1, and RFT1. Structural variants in SPAST, SPG11, SPG7, MFN2, MPZ, KIF5A, and GJB1 were excluded by computational prediction and manual visualisation.DiscussionIn this preliminary cohort screening panel of disease genes using WES/WGS data, we solved ~50% of cases, which is similar to diagnostic yields reported for global cohorts. However, the mutational profile among South Africans with GN and HSP differs substantially from that in the Global North.
| S-EPMC10497947 | biostudies-literature
Project description:Rationale: Older African Americans undergoing surgery are a vulnerable and growing population at high risk for poor surgical outcomes and disparities. Few programs have focused on this population due to a fragmented understanding of the needs of this population.
Objectives: While socioecological determinants of health (SEDOH) such as health literacy and socioeconomic status are known drivers of surgical disparities, an estimated 36-47% of surgical disparities remains unexplained. This gap results from limitations of current clinical datasets in capturing SEDOHs. This pilot study aims to fill this gap by (i) collecting granular SEDOH data, (ii) identifying barriers to surgical care for older African Americans, and (iii) establishing a multi-institutional clinical database through a socioecological context. These findings will help understand how SEDOHs drive surgical disparities and inform development of interventions to eliminate them in elderly African Americans.
Design and Methods: Guided by the socioecological model of health, the investigators will use mixed-methods to achieve the objectives. First, the investigators will assess the acceptability and feasibility of a 58-item SEDOH survey based on the NIH PhenX toolkit. After distributing this survey to 36 elderly (≥65 years) African American patients undergoing surgery at 3 rural, UAB-affiliated hospitals (Alex-City, Greenville, Demopolis) the investigators will conduct detailed theory guided assessments of acceptability and feasibility (SA1). Second, the investigators will conduct key informant interviews of individuals from all 5 socioecological levels at each rural hospital (n=10) to identify additional barriers and facilitators to surgical care. The investigators will purposively sample 100% of participants at the patient and caregiver level (n=12) to be elderly African Americans (SA2). Finally, the investigators will link measured SEDOH data with standardized clinical data at each hospital to establish a novel database (SA3). These findings will establish a process to measure SEDOHs across the Deep South and set the foundation for a unique database to study surgical disparities.
Significance: Development of effective multilevel interventions to eliminate surgical disparities in older African Americans is dependent on a clearer understanding of the contextual drivers of these disparities. This pilot study will accelerate understanding of these mechanism(s) through SEDOHs. It will establish a process to measure SEDOHs, identify additional barriers to surgical care not captured by NIH instruments, and build the database to study these relationships. Such findings will have the potential to impact vulnerable surgical populations in the Deep South and support the Deep South RCMAR mission to promote health and optimize health outcomes for older and rural African Americans.
| 2720055 | ecrin-mdr-crc
Project description:PurposeThe Research on Obesity and Diabetes among African Migrants (RODAM) prospective (RODAM-Pros) cohort study was established to identify key changes in environmental exposures and epigenetic modifications driving the high burden of cardiovascular disease (CVD) risk among sub-Saharan African migrants.ParticipantsAll the participants in the RODAM cross-sectional study that completed the baseline assessment (n=5114) were eligible for the follow-up of which 2165 participants (n=638 from rural-Ghana, n=608 from urban-Ghana, and n=919 Ghanaian migrants in Amsterdam, the Netherlands) were included in the RODAM-Pros cohort study. Additionally, we included a subsample of European-Dutch (n=2098) to enable a comparison to be made between Ghanaian migrants living in the Netherlands and the European-Dutch host population.Findings to dateFollow-up data have been collected on demographics, socioeconomic status, medical history, psychosocial environment, lifestyle factors, nutrition, anthropometrics, blood pressure, fasting blood, urine and stool samples. Biochemical analyses included glucose metabolism, lipid profile, electrolytes and renal function, liver metabolism and inflammation. In a subsample, we assessed DNA methylation patterns using Infinium 850K DNA Methylation BeadChip. Baseline results indicated that migrants have higher prevalence of CVD risk factors than non-migrants. Epigenome-wide association studies suggest important differences in DNA methylation between migrants and non-migrants. The follow-up study will shed further light on key-specific environmental exposures and epigenetic modifications contributing to the high burden of CVD risk among sub-Saharan African migrants.Future plansFollow-up is planned at 5-year intervals, baseline completed in 2015 and first follow-up completed in 2021.
| S-EPMC9756160 | biostudies-literature
Project description:BACKGROUND AND METHODS: Little is known about antiretroviral therapy (ART) outcomes in prisoners in Africa. We conducted a retrospective review of outcomes of a large cohort of prisoners referred to a public sector, urban HIV clinic. The review included baseline characteristics, sequential CD4 cell counts and viral load results, complications and co-morbidities, mortality and loss to follow-up up to 96 weeks on ART. FINDINGS: 148 inmates (133 male) initiated on ART were included in the study. By week 96 on ART, 73% of all inmates enrolled in the study and 92% of those still accessing care had an undetectable viral load (<400 copies/ml). The median CD4 cell count increased from 122 cells/mm(3) at baseline to 356 cells/mm(3) by 96 weeks. By study end, 96 (65%) inmates had ever received tuberculosis (TB) therapy with 63 (43%) receiving therapy during the study: 28% had a history of TB prior to ART initiation, 33% were on TB therapy at ART initiation and 22% developed TB whilst on ART. Nine (6%) inmates died, 7 in the second year on ART. Loss to follow-up (LTF) was common: 14 (9%) patients were LTF whilst still incarcerated, 11 (7%) were LTF post-release and 9 (6%) whose movements could not be traced. 16 (11%) inmates had inter-correctional facility transfers and 34 (23%) were released of whom only 23 (68%) returned to the ART clinic for ongoing follow-up. CONCLUSIONS: Inmates responded well to ART, despite a high frequency of TB/HIV co-infection. Attention should be directed towards ensuring eligible prisoners access ART programs promptly and that inter-facility transfers and release procedures facilitate continuity of care. Institutional TB control measures should remain a priority.
| S-EPMC3310000 | biostudies-other
Project description:ObjectivesThe objectives were to characterise the haematological profile of screen-detected chronic kidney disease (CKD) participants and to correlate the complete blood count measures with the commonly advocated kidney function estimators.MethodsThe current cross-sectional study used data, collected between February 2015 and November 2016, of 1564 adults of mixed-ancestry, who participated in the Cape Town Vascular and Metabolic Health study. Kidney function was estimated using the Modification of Diet in Renal Disease (MDRD) and Chronic Kidney Disease Epidemiology Collaboration (CKD-EPI) equations. CKD was defined as estimated glomerular filtration rate (eGFR) <60 mL/min/1.73 m2, and anaemia as haemoglobin level <13.5 g/dL (men) and <12 g/dL (women).ResultsBased on the MDRD and CKD-EPI equations, the crude prevalence of CKD was 6% and 3%. Irrespective of the equation used, median red blood cell (RBC) indices were consistently lower in those with CKD compared with those without CKD (all p<0.0001). Despite not showing any significant difference in total white blood cell (WBC) count between the two groups, the number of lymphocytes were lower (p=0.0001 and p<0.0001 for MDRD and CKD-EPI, respectively) and neutrophil count (both p<0.0297) and the ratio of lymphocytes to neutrophil (both p<0.0001) higher in the CKD group compared with those without CKD; with the remaining WBC indices similar in the two groups. The platelet count was similar in both groups. Of the screen-detected CKD participants, 45.5% (MDRD) and 57.8% (CKD-EPI) were anaemic, with the prevalence increasing with increasing severity of CKD, from 37.2% (stage 3) to 82.4% (stages 4-5). Furthermore, CKD-EPI-estimated kidney function, but not MDRD, was positively associated with RBC indices.ConclusionThough it remains unclear whether common kidney function estimators provide accurate estimates of CKD in Africans, the correlation of their estimates with deteriorating RBC profile, suggests that advocated estimators, to some extent approximate kidney function in African populations.
| S-EPMC6231601 | biostudies-literature