Browsing by Subject "genotyping"

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    Fat mass and obesity associated (FTO) gene influences skeletal muscle phenotypes in non-resistance trained males and elite rugby playing position
    (2017) Heffernan, S M; Stebbings, G K; Kilduff, L P; Erskine, R M; Day, S H; Morse, C I; McPhee, J S; Cook, C J; Vance, B; Ribbans, W J; Raleigh, S M; Roberts, C; Bennett, M A; Wang, G; Collins, M; Pitsiladis, Y P; Williams, A G
    Abstract Background FTO gene variants have been associated with obesity phenotypes in sedentary and obese populations, but rarely with skeletal muscle and elite athlete phenotypes. Methods In 1089 participants, comprising 530 elite rugby athletes and 559 non-athletes, DNA was collected and genotyped for the FTO rs9939609 variant using real-time PCR. In a subgroup of non-resistance trained individuals (NT; n = 120), we also assessed structural and functional skeletal muscle phenotypes using dual energy x-ray absorptiometry, ultrasound and isokinetic dynamometry. In a subgroup of rugby athletes (n = 77), we assessed muscle power during a countermovement jump. Results In NT, TT genotype and T allele carriers had greater total body (4.8% and 4.1%) and total appendicular lean mass (LM; 3.0% and 2.1%) compared to AA genotype, with greater arm LM (0.8%) in T allele carriers and leg LM (2.1%) for TT, compared to AA genotype. Furthermore, the T allele was more common (94%) in selected elite rugby union athletes (back three and centre players) who are most reliant on LM rather than total body mass for success, compared to other rugby athletes (82%; P = 0.01, OR = 3.34) and controls (84%; P = 0.03, OR = 2.88). Accordingly, these athletes had greater peak power relative to body mass than other rugby athletes (14%; P = 2 x 10 -6 ). Conclusion Collectively, these results suggest that the T allele is associated with increased LM and elite athletic success. This has implications for athletic populations, as well as conditions characterised by low LM such as sarcopenia and cachexia.
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    Open Access
    Towards the development of retrospective molecular autopsies in unexplained sudden unexpected death cases
    (2026) Swart, Micaela Louise; Heathfield, Laura Jane; Vandayar, Yuvika
    Sudden unexpected death (SUD) is characterised by the rapid, natural, and unanticipated fatality of a seemingly healthy individual, with up to 10% of SUD cases in South Africa remaining undetermined at autopsy. A molecular autopsy, conducted retrospectively, may be valuable in resolving the cause of death in these cases. However, the samples generally available for retrospective molecular autopsies are those retained at the original autopsy, i.e., formalin-fixed, paraffin-embedded (FFPE) tissue taken for histology and/or blood in white/grey/red top tubes taken for toxicology. Deoxyribonucleic acid (DNA) extraction protocols for these sample types have been developed in-house, however, it was unknown whether the DNA sequencing assays developed for prospective molecular autopsies using high quality DNA samples would be suitable for these alternative sample types. This study aimed to assess and optimise DNA workflows on retrospective unexplained SUD cases, to contribute towards the development of molecular autopsies for medico-legal investigations in South Africa. Unresolved SUD cases (n = 22) were identified for the study, with 17 having only FFPE tissue, and 5 having both sample types. The laboratory's baseline DNA workflow was adequate for blood samples, but the FFPE tissue workflow required further optimisation. Four different DNA extraction methods were applied to FFPE tissue blocks and systematic adjustments were made to optimise the amplification of a target region in a candidate gene, potassium voltage-gated channel subfamily Q member 1 (KCNQ1). Sanger sequencing was successful on all blood-derived DNA samples (5/5; 100.00%), and on 12/22 (54.55%) cases with FFPE tissue-derived DNA, resulting in 13/22 (59.09%) successfully sequenced cases - with no case exhibiting the variant of interest. This study has contributed towards the optimisation of a DNA workflow for archived biological samples enabling retrospective molecular autopsies for the hundreds of unresolved SUD cases in Cape Town and beyond.