Browsing by Author "Tiffin, Nicki"
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- ItemThe development of computational biology in South Africa : successes achieved and lessons learnt(PLoS, 2016) Mulder, Nicola J.; Christoffels, Alan; De Oliveira, Tulio; Gamieldien, Junaid; Hazelhurst, Scott; Joubert, Fourie; Kumuthini, Judit; Pillay, Che S.; Snoep, Jacky L.; Bishop, Ozlem Tastan; Tiffin, NickiBioinformatics is now a critical skill in many research and commercial environments as biological data are increasing in both size and complexity. South African researchers recognized this need in the mid-1990s and responded by working with the government as well as international bodies to develop initiatives to build bioinformatics capacity in the country. Significant injections of support from these bodies provided a springboard for the establishment of computational biology units at multiple universities throughout the country, which took on teaching, basic research and support roles. Several challenges were encountered, for example with unreliability of funding, lack of skills, and lack of infrastructure. However, the bioinformatics community worked together to overcome these, and South Africa is now arguably the leading country in bioinformatics on the African continent. Here we discuss how the discipline developed in the country, highlighting the challenges, successes, and lessons learnt.
- ItemIncident tuberculosis disease in patients receiving biologic therapies in the Western Cape, South Africa from 2007 to 2018(BMC (part of Springer Nature), 2019) Du Toit, Tessa; Esterhuizen, Tonya M.; Tiffin, Nicki; Abulfathi, Ahmed A.; Reuter, Helmuth; Decloedt, Eric H.Background: South Africa has one of the highest tuberculosis incidence rates. Biologic disease-modifying antirheumatic drugs are associated with an increased risk of tuberculosis. The objective of this study was to describe the tuberculosis disease incidence rate among public sector patients receiving biologic therapies in the Western Cape Province. Methods: A retrospective, descriptive analysis was undertaken using routine health data collated by the Provincial Health Data Centre from January 2007 (first use of biologic therapy in the Western Cape) to September 2018. Results: We identified 609 patients treated with tumour necrosis factor-alpha (TNF-α) or non-TNF-α biologic therapies. Thirty-seven (37) patients developed tuberculosis after biologic therapy exposure, of whom the majority (78%) had an immune mediated inflammatory disease and the remainder (22%) a haematologic malignancy. The incidence rate of tuberculosis per 100,000 person-years was 2227 overall [95% confidence interval (CI): 1591, 3037]. Patients treated with TNF-α inhibitors and non-TNF-α inhibitors had estimated incidence rates of 2819 [95% CI: 1669, 4480] and 1825 [95% CI: 1131, 2797], respectively (p = 0.10). Conclusion: Patients exposed to both TNF-α and non-TNF-α biologic therapies may have a higher incidence of tuberculosis disease compared to the background risk of 681 cases per 100,000 per year in the Western Cape.
- ItemWhere do HIV-infected adolescents go after transfer? – Tracking transition/transfer of HIV-infected adolescents using linkage of cohort data to a health information system platform(Wiley Open Access, 2017) Davies, Mary-Ann; Tsondai, Priscilla; Tiffin, Nicki; Eley, Brian; Rabie, Helena; Euvrard, Jonathan; Orrell, Catherine; Prozesky, Hans; Wood, Robin; Cogill, Dolphina; Haas, Andreas D.; Sohn, Annette H.; Boulle, AndrewIntroduction: To evaluate long-term outcomes in HIV-infected adolescents, it is important to identify ways of tracking outcomes after transfer to a different health facility. The Department of Health (DoH) in the Western Cape Province (WCP) of South Africa uses a single unique identifier for all patients across the health service platform. We examined adolescent outcomes after transfer by linking data from four International epidemiology Databases to Evaluate AIDS Southern Africa (IeDEA-SA) cohorts in the WCP with DoH data. Methods: We included adolescents on antiretroviral therapy who transferred out of their original cohort from 10 to 19 years of age between 2004 and 2014. The DoH conducted the linkage separately for each cohort and linked anonymized data were then combined. The primary outcome was successful transfer defined as having a patient record at a facility other than the original facility after the transfer date. Secondary outcomes included the proportion of patients retained, with HIV-RNA <400 copies/ml and CD4 > 500 cells/μl at 1, 2 and 3 years post-transfer. Results: Of 460 adolescents transferred out (53% female), 72% transferred at 10–14 years old, and 79% transferred out of tertiary facilities. Overall, 81% of patients transferred successfully at a median (interquartile range) of 56 (27–134) days following transfer date; 95% reached the transfer site <18 months after transfer out. Among those transferring successfully, the proportion retained decreased from 1 to 3 years post-transfer (90–84%). There was no significant difference between transfer and 1–3 years post-transfer in the proportion of retained adolescents with HIV-RNA <400 copies/ml and CD4 > 500 cells/μl except for HIV-RNA <400 copies/ml at 3 years (86% vs. 75%; p = 0.007). The proportion virologically suppressed and with CD4 > 500 cells/μl was significantly lower at 1 and 2 years post-transfer in those transferring at 15–19 vs. 10–14 years of age. Using laboratory data alone over-estimated time to successful transfer. Conclusions: Linking cohort data to health information system data allowed efficient assessment of post-transfer outcomes. Although >80% of adolescents transferred successfully with nearly 85% of them retained for 3 years post-transfer, the decline in the proportion virologically suppressed and poorer outcomes in older adolescents are concerns.