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- ItemThe association between vitamin D, vitamin D Binding proteins and VDR polymorphisms in diabetic and non-diabetic patients(Stellenbosch : Stellenbosch University, 2019-03) Maepa, Setjie Welcome; Matsha, Tandi E.; Erasmus, Rajiv T.; Stellenbosch University. Faculty of Medicine and Health Science. Dept. of Pathology. Chemical Pathology.ENGLISH ABSTRACT: Introduction: Type 2 diabetes mellitus (T2DM) is by far the most prevalent form of diabetes manifesting with insulin resistance (IR), abnormal pancreatic β-cell function and hyperglycaemia. Evidence from epidemiological and observational studies have shown that vitamin D deficiency is associated with increased risk for T2DM although the findings are inconsistent and inconclusive. In the circulation vitamin D is transported bound to vitamin D binding protein (VDBP), evidence showed that vitamin D levels are positively associated with VDBP levels. Several genes such as vitamin D receptor gene (VDR), involved in the metabolic pathway of T2DM have been considered good candidate for susceptibility to T2DM. The present study aimed to investigate the association between vitamin D, vitamin D binding proteins (VDBP) and vitamin D receptor (VDR) polymorphisms in T2DM and non-diabetic patients in the mixed ancestry population. Materials and methods: The current study comprised of 1603 participants (387 males and 1216 females). Vitamin D levels were measured using the paramagnetic particle chemiluminescence test on a Beckman DXI. Vitamin D binding protein (VDBP) in serum samples was measured using the Human Vitamin D BP Quantikine ELISA kit. Fok1 (rs2228570), Apa1 (rs7975232) and Taq1 (rs731236) single nucleotide polymorphisms (SNPs) of the VDR gene were genotyped from a genomic DNA using the TaqMan SNP Genotyping Assays and were confirmed by direct sequencing. Results: Vitamin D deficiency (44%) and insufficiency (42.6%) were highly prevalent and optimal 25(OH)D levels were very low with only 13% having optimal levels. The overall vitamin D status of the whole population group was insufficient (22.0±7.6 ng/mL). 25(OH)D levels and serum VDBP varied according to gender with males having higher 25(OH)D levels (23.6±7 vs 21.5±7.5ng/mL, P=0.0006) and females with significantly higher serum VDBP levels (299.1±71.2 vs 315.9±76.1 µg/mL, P<0.0001). 25(OH)D levels were generally significantly decreased in the hyper-glycemic subgroups. Screen-detected DM males had low 25(OH)D levels compared to normoglycaemic group (17.0±6.1vs 24.2±8.2, P=0.0214). A similar trend was observed in the female groups (21.1±6.0 vs 22.4±7.9, P=0007). Anthropometric measurements including the BMI (kg/m2), Waist C (cm) and Hip C (cm) were significantly higher in hyper-glycaemic group than in normo-glycaemic males and females (All, P<0.0001). In contrast, there were no significant differences in serum VDBP (µg/mL) between the glycaemic sub-groups in either male (P=0.5614) or females (P= 0.4813). The glycaemic parameters, as expected, were significantly increased in the hyperglycaemic sub-groups in both genders, including FBG (mmol/L), 2 hr BG (mmol/L), HbA1c (%), FBI (mIU/L), 2 hr BI (mIU/L) and HOMA-IR (All, both males and females P<0.0001). In general, the lipids, including the triglycerides (mmol/L), LDL-C (mmol/L) and Cholesterol (mmol/L) were also significantly increased in both genders in the hyper-glycaemic sub-groups (All, males P≤0.0300, females P<0.0001), while HDL-C (mmol/L) was significantly decreased in both males and females in the hyperglycaemic sub-groups (All, P≤0.0308). The variant genotype GG of the Fok1, AA of Apa1 and GG of the Taq1 SNPs were not significantly different in hyper-glycaemic patients compared to normo-glycaemic group (58.5% vs 55.1%, P-value, 40.1% vs 38.0%, P-value and 6.9% vs 8.5%, Pvalue,) respectively. Similarly, there was no significant difference in the alleles frequency distribution of these SNPs between the groups. Results also demonstrated no significance difference in the genotype or allele frequency distribution of Fok1 (rs2228570), Apa1 (rs7975232) and Taq1 (rs731236) SNPs between subjects with optimal Vitamin D (25(OH)D ng/mL) levels and those with insufficient/deficient levels (P≥0.2036 and P≥0.6347 respectively). These trends were also observed when serum VDBP levels were evaluated against Fok1, Apa1 and Taq1 genotypes. Multiple linear regression showed that low 25(OH)D was associated with increased LDL-C and PTH in both male and females irrespective of T2DM, but serum VDBP was associated with low 25(OH)D in hyper-glycaemic females only. In normo-glycaemic males 19.5% of the variation in 25(OH)D was attributed to increased LDL-C and in the hyper-glycaemic group 15.5% it was attributed to PTH and CRP. In normo-glycaemic females 12.8% variation in 25(OH)D was attributed to LDL-C, serum creatinine and PTH, whereas in hyper-glycaemic group 16.1% was attributed to increased age, serum VDBP, triglycerides, LDL-C, creatinine and PTH. Conclusion: This study showed prevalence of vitamin D deficiency/insufficiency in the mixed ancestry population group. There was no association between vitamin D (25(OH)D), vitamin D binding proteins (serum VDBP) and VDR polymorphisms in T2DM patients. Serum VDBP levels were associated with low vitamin D levels in hyper-glycaemic females only. Increased LDL-C, PTH and CRP were predictors of low vitamin D levels.
- ItemThe effect of fructosamine 3 kinase (FN3K) genotypes on the glycation gap in type 2 diabetic and non-diabetic mixed ancestry population of South Africa(Stellenbosch : Stellenbosch University, 2018-12) Motshwari, Dipuo Dephney; Erasmus, Rajiv T.; Zemlin, Annalise E.; Matsha, Tandi; Stellenbosch University. Faculty of Medicine and Health Science. Dept. of Pathology. Chemical Pathology.ENGLISH ABSTRACT: Introduction In2017 the International Diabetes Federation (IDF) reported that approximately 425 million adults aged 20-79 years were estimated to have diabetes mellitus (DM) worldwide. The nonenzymatic glycation reactions of proteins such as haemoglobin have been associated with the development of diabetic related complications. These reactions were believed to be irreversible until the discovery of a protein repair enzyme fructosamine 3 kinase (FN3K). This enzyme deglycates glycated haemoglobin (HbA1c) in erythrocytes and other glycated proteins in other tissues. Animal model studies found that the activity of this enzyme varies between individuals leading to differences in HbA1c levels. This results in discrepancies between HbA1c and other glycaemic measures which is termed the glycation gap. The glycation gap is consistent over time within individuals and is associated with diabetic complications. Genetic variants in the FN3K gene have been associated with altered enzyme activity. Therefore, the aim of this study was to examine the role of FN3K genotypes on the glycation gap Methods A total of 1412 subjects (925 normal, 216 pre-diabetic and 271 type 2 diabetics), with 339 males and 1073 females aged ≥ 20 years of mixed ancestry descent, residing in Bellville South, South Africa were included in this study. The diabetics were diagnosed using the oral glucose tolerance test. The glycation gap was determined according to a formula: Glycation gap= HbA1c - FHbA1c, (FHbA1c = {[(fructosamine- mean fructosamine)/SD fructosamine] X SD HbA1c} + mean HbA1c). DNA was extracted from whole blood using the salt extraction method. FN3K single nucleotide polymorphisms (SNPs) were genotyped with the Applied Biosystems™ QuantStudio™ 7 Flex Real-Time PCR System 96 well fast from Thermo Fisher Scientific. HbA1c was measured using HPLC (Biorad Variant Turbo) and fructosamine was measured using a colorimetric test nitro-blue-tetrazolium (NBT). Results SNP c. -232A/T deviated from Hardy Weinberg Equilibrium (HWE) and was left out for the rest of the statistical analysis. The polymorphism G900C followed the Hardy-Weinberg Equilibrium and was therefore studied. The genotype frequencies for SNP G900C in the glycaemic sub-groups were as follows, GG: 45.9 %, GC: 43.7 %, CC: 10.4 % in normal subjects; GG: 48.6 %, GC: 41.7 %, CC: 9.7% in pre-diabetics and GG: 41.7 %, GC: 46.5 %, CC: 11.8 % in diabetics, and they followed the Hardy-Weinberg equilibrium. There were no significant differences in the SNP G900C genotype frequencies between the glycaemic subgroups. The glycation gap significantly decreased across the GG, GC and CC genotype variants in males, mean ± SD were -0.13±0.86, -0.25±0.72 and -0.80±1.04 respectively, (P=0.0239). However the difference was not observed in females. Moreover the glycation gap showed a positive correlation with non glycaemic factors including body mass index (BMI) (r=0.3694, p<0.0001), waist circumference (waistC) (r=0.3749, p<0.0001), hip circumference (hipC) (r0.3151, p<0.0001), triglycerides (r=0.2540, p<0.0001) and a negative correlation with high density lipoprotein cholesterol (HDL-Chol) (r=-0.2031, p<0.0001). Conclusion In conclusion the present study found that the glycation gap might be influenced by genetic In conclusion the present study found that the glycation gap might be influenced by genetic active mechanisms in the intracellular erythrocyte compartment. Identification of the G900C polymorphism in an early stage of diabetes could be useful especially in therapeutic decisions and prediction of improved prognosis. However, there are other confounding factors influencing the glycation gap and future studies are required to confirm these findings.
- ItemFree light chains in patients with HIV: establishing local reference ranges and their association with stage of disease, chronic antigen stimulation and the effect of Haart(Stellenbosch : Stellenbosch University, 2012-03) Germishuys, Jurie J.; Zemlin, Annalise E.; Erasmus, Rajiv T.; Stellenbosch University. Faculty of Health Sciences. Dept. of Pathology. Chemical Pathology.ENGLISH ABSTRACT: Background: Serum free light chains (FLC) are associated with imbalances in heavy and light chain production. Abnormal FLC ratios have been associated with risk of progression in certain diseases. Automated assays are available for their determination and they are used in the followup and management of patients with monoclonal gammopathies. Acceptable imprecision, specificity, accuracy and reproducibility between reagent batches is required to prevent under- or overestimation. Method validation is a standard process in every good laboratory to judge the acceptability of a new method. Reference intervals have been established in an older population, but it was considered important to verify these in our population. HIV is associated with B-cell dysfunction. As B-cell abnormalities are associated with disorders leading to monoclonal gammopathies, we postulated that the FLC levels and FLC ratio would be abnormal in HIV infected individuals. Methods and materials: Controls and pooled patient samples were used for the method validation study which included imprecision studies, linearity, recovery and interference studies, and method comparison studies, the latter compared our method to the same method used in another laboratory. For the reference interval study, blood was obtained from 120 healthy subjects. The following blood tests were performed: total protein, IgG, IgA, IgM, creatinine, protein electrophoresis, kappa FLC and lambda FLC. Using the kappa and lambda FLC results, a FLC ratio was determined. Three hundred and sixty-nine HIV positive subjects were then studied. The same tests were performed, as well as CD4+ counts and viral loads on the majority of them. Results: For the method validation study, precision, linearity and recovery was acceptable. Minimal interference was observed with haemolysis, lipaemia, bilirubin and rheumatoid factor. Our method showed comparable performance with the established method. For the reference interval study, all the creatinine values were normal, as were serum protein values. The serum protein electrophoreses were independently reviewed by 3 pathologists. Most were normal, with a few polyclonal increases seen, but no definite monoclonal bands. The 95% reference intervals for FLC’s as well as the FLC ratio were not statistically significantly different to the manufacturer’s recommendations. When examining the HIV positive study population, we found that FLC and FLC ratio were influenced by markers of HIV disease severity, such as CD4+ count, IgG, viral load, use of antiretroviral treatment and abnormal serum protein electrophoreses. Conclusion: The validation study of FLC showed excellent precision, acceptable bias, good linearity, good recovery and minimal interference, allowing routine introduction of the test. The 95% reference intervals obtained for our population were slightly higher than those recommended by the manufacturer. However, as most of the values fell within the manufacturer’s limits, we could accept the manufacturer’s recommended cut-offs. We found that FLC levels were definitely influenced by markers of HIV disease severity in our population and we postulate that they may be of use for follow-up of patients with HIV.
- ItemHbA1c as a screening tool for diabetes mellitus and its use with traditional and novel biochemical parameters to predict cardiovascular risk in a local urban community(Stellenbosch : Stellenbosh University, 2016-12) Zemlin, Annalise E.; Erasmus, Rajiv T.; Matsha, Tandi E.; Kengne, Andre P.; Stellenbosch University. Faculty of Medicine and Health Sciences. Dept. of Pathology: Chemical Pathology.ENGLISH SUMMARY: Introduction The global obesity pandemic has reached Africa and the diabetes mellitus (DM) prevalence is increasing in parallel. A high prevalence of DM and risk for cardiovascular disease (CVD) has been described in the South African mixed ancestry population. Recent guidelines advocate using HbA1c as a diagnostic tool for DM and prediabetes, which is more convenient. However, various studies have challenged these cut-offs. There is a paucity of studies validating these cut-offs in Africa. As DM is considered a CVD risk equivalent, emerging markers of CVD and adiposity also need evaluation. The adipokine adiponectin has anti-diabetic, anti-atherogenic and anti-inflammatory properties and levels decrease in obesity. E-selectin, a marker of endothelial cell dysfunction, is associated with subclinical atherosclerosis and hyperglycaemia. Carotid intima-media thickness (CIMT) is a noninvasive measure of subclinical atherosclerosis. The aim of this investigation was to verify recommended HbA1c cut-offs to diagnose DM and prediabetes and to examine the usefulness of emerging markers of subclinical CVD in our population. Methods This investigation consists of four substudies and was performed on participants of the Bellville South Africa Study. In the first, we challenged the recommended HbA1c cut-off of 6.5% to diagnose DM in 946 participants using oral glucose tolerance test (OGTT), fasting blood glucose (FBG), and receiver operator characteristic (ROC) curves. In the second, we derived an optimal HbA1c cut-off to detect prediabetes in 667 participants and validated this in two populations, using OGTT and ROC curves. In the third, we determined high molecular weight (hmw)-adiponectin levels in 101 participants, compared these in participants with and without hyperglycaemia and investigated their relationship with two polymorphisms (rs17300539 and rs266729) reported to affect adiponectin values. In the fourth, we determined E-selectin levels in 307 participants, compared these in participants with and without hyperglycaemia and assessed their effect on CIMT. Results The recommended HbA1c cut-off was not sensitive enough to detect DM. Using FBG, 117 (14%) participants were diagnosed with DM and 50% had an HbA1c of 6.5%; using OGTT 147 (18%) had DM and 46% had an HbA1c of 6.5%. Comparing HbA1c to FBG and OGTT, a cut-off of 6.1% gave a better sensitivity and specificity (area under curve (AUC) 0.85 and 0.82 respectively). Also, the recommended HbA1c cut-off to detect prediabetes was not appropriate and we determined that 5.75% was best. However, the low sensitivity and specificity (64.8% and 60.4% respectively for the derivation and first validation sample and 59.6% and 69.8% for the second validation sample), confirmed that HbA1c alone would miss a significant number of prediabetics. Hmw-adiponectin levels were not affected by glycaemia (median 11.6 g/mL in normoglycaemia vs. 10.5 g/mL in hyperglycaemia; p=0.3060) nor by two common polymorphisms. Using robust correlations, a significant correlation was found between hmw-adiponectin and high density lipoprotein cholesterol (HDL-c) (r=0.45; 95%CI: 0.27-0.59), which was similar in both normo-and hyperglycaemia (p>0.99). This association was attenuated in robust linear regressions adjusted for gender and adiposity. Eselectin levels were significantly higher in hyperglycaemia (median 139.8 g/L vs. 118.8 g/L in normoglycaemia; p=0.0007) but not associated with CIMT. Significant correlations were found between E-selectin and age, markers of glycaemia and inflammation, central obesity and lipid variables. Associations remained significant only with age, hyperglycaemia and C-reactive protein (CRP) in multivariable robust linear regression models. In similar regressions models, age and gender were the main predictors of CIMT, which was not associated with E-selectin. Conclusion The international HbA1c cut-offs recommended to detect DM and prediabetes were not appropriate in our population. Though a cut-off of 6.5% to diagnose DM is a good diagnostic tool with high specificity, the low sensitivity limits its screening use. Similarly, recommended HbA1c values to detect prediabetes may underestimate the true numbers. This emphasizes the importance of local evidence-based values being established. Additionally, hmw-adiponectin was not affected by glycaemia or polymorphisms, but correlated significantly with HDL-c which may explain its beneficial cardiovascular effect. Though Eselectin was influenced by glycaemia, possibly reflecting early endothelial damage, it did not correlate with CIMT, which was determined by age and male gender.
- ItemInvestigation of the role of vitamin D metabolism in South African breast cancer patients using a pathology-supported genetic testing platform(Stellenbosch : Stellenbosch University., 2020-03) Okunola, Abisola Oyedele; Kotze, Maritha J.; Erasmus, Rajiv T.; Zemlin, Annalise E.; Torrorey-Sawe, Rispah; Stellenbosch University. Faculty of Medicine and Health Sciences. Dept. of Pathology. Chemical Pathology.ENGLISH ABSTRACT: The high global breast cancer incidence drives the development of novel genomic approaches for disease prevention and targeted treatment. Towards this goal, a pathology-supported genetic testing (PSGT) platform was established to facilitate risk management of non-communicable diseases across the continuum of care, ranging from early-stage to metastatic disease and cancer survivorship. The causes and consequences of low vitamin D levels recently reported in the majority of postmenopausal breast cancer patients treated with aromatase inhibitors at the Tygerberg Academic Hospital, in the Western Cape Province of South Africa, were addressed in this study using PSGT to translate genomic findings into clinical practice. The aim was to determine the relationship between clinical characteristics, tumour histopathology and genetic variation underlying vitamin D metabolism in postmenopausal breast cancer patients at increased risk of osteoporosis, identified as a significant co-morbidity in the study population. Clinical and lifestyle information of 116 postmenopausal women with known vitamin D status diagnosed with breast carcinoma between 2014 and 2017 was extracted from a central genomics database linked to a biobank of DNA samples extracted from blood. Whole exome sequencing (WES) was performed on the Ion Torrent platform, followed by variant calling of vitamin D-related genes, while simultaneously assessing BRCA1/2 mutation status. Allele-specific real-time polymerase chain reaction (PCR), Sanger sequencing and long-range nanopore sequencing using the pocket-size MinION device were used to verify the WES results and to screen for variants in the vitamin D receptor (VDR) and E-cadherin (CDH1) genes beyond the coding regions covered by WES. Seasonal variation (p = 0.009) and high body mass index (BMI) (p = 0.032) contributed significantly to vitamin D levels, with the lowest values recorded during winter. WES initially performed in 10 breast cancer patients selected based on vitamin D levels at extreme upper and lower ranges, identified GC rs4588 (c.1364C>A, T455K) as a potential contributing factor vitamin D deficiency in the five patients with ultra-low vitamin D levels (≤12 ng/mL). However, 2/5 patients with levels in the upper extreme of vitamin D (>30 ng/mL), also tested positive for this variant and no significant association was detected after extended genotyping in 100 South African patients using real-time PCR. Sanger sequencing subsequently performed in 14 breast cancer patients diagnosed with osteoporosis prior to initiation of aromatase inhibitor therapy, highlighted the potential significance of genetic variation in the VDR gene. WES analysis of VDR in an extended sample of 55 breast cancer patients furthermore confirmed the significant effect of genetic variation in this gene on bone health (p < 0.001). The CDH1 gene known to be activated by VDR was furthermore analysed in patients stratified by tumour type. CDH1 c.G671A (p.R224H) detected in a breast cancer patient with invasive carcinoma of no special type (ICNST) was classified as benign, since pathogenic germline CDH1 variants are associated with invasive lobular carcinoma and diffuse gastric cancer, but not ICNST. CDH1 c.A1298G (p.D433G) was detected in a patient with invasive lobular carcinoma together with a pathogenic BRCA1 variant detected by WES. Although this finding supports a likely benign classification for CDH1 p.D433G as reported in the international ClinVar database, a family history of stomach cancer raised the possibility of a CDH1 modifier gene effect on BRCA1 gene expression. New insights gained through integration of pathology and genomic findings were incorporated into a pharmaco-diagnostic algorithm applicable to hormone receptor-positive postmenopausal breast cancer patients. The PSGT platform facilitated interpretation of research results of study participants through use of WES and recommendation of genetic counselling where appropriate.
- ItemLipoprotein X : biochemical predictors and detection by non-denaturing polyacrylamide gradient gel electrophoresis(Stellenbosch : Stellenbosch University, 2007-12) Le Riche, Mia; Marias, David; Erasmus, Rajiv T.; Stellenbosch University. Faculty of Health Sciences. Dept. of Pathology. Chemical Pathology.ENGLISH ABSTRACT: Lipoprotein X (LpX) is an abnormal cholesterol-containing particle that may be present in the serum of subjects with cholestasis, lecithin:cholesterol acyltransferase (LCAT) deficiency and parenteral nutrition. The biochemistry, metabolism, clinical significance and laboratory analysis of LpX is discussed in this study. This laboratory-based project investigated icteric samples received at the Chemical Pathology laboratory, Tygerberg Hospital, for serum predictors of LpX and the use of a modified non-denaturing polyacrylamide gradient gel electrophoresis system in the detection of LpX. The study showed that the non-denaturing polyacrylamide gradient gel electrophoresis system (2-8%) is a useful test in demonstrating LpX in icteric plasma and has potential for a screening test in LCAT deficiency. Serum concentration of conjugated bilirubin, alkaline phosphatase, gamma glutamyltransferase, free cholesterol, phospholipid, free cholesterol: total cholesterol ratio and conjugated bilirubin: total bilirubin ratio are all good predictors of LpX. The ratio of free cholesterol to total cholesterol (FC/TC > 0.6) was the best predictor of LpX. In the setting of obstructive liver disease LpX is seen in 66% of patients if total cholesterol is > 7.5 mmol/L.
- ItemMethodological issues around the validation of models for predicting diabetes risk in developing countries(Stellenbosch : Stellenbosh University, 2016-12) Masconi, Katya Laura; Kengne, Andre Pascal; Erasmus, Rajiv T.; Matsha, Tandi E.; Stellenbosch University. Faculty of Medicine and Health Sciences. Dept. of Pathology: Chemical Pathology.ENGLISH SUMMARY: Background: Multivariable diabetes risk prediction models have the potential to contribute to screening strategies, combining several risk factors to predict undiagnosed diabetes or future risk of developing diabetes. The focus of this study is the prediction of undiagnosed diabetes and diabetes risk prediction in a developing country where no population-specific diabetes risk prediction model currently exists. Existent models have been developed in unrelated populations with different disease prevalence, predictor weightings and methods used for risk factor determination and diabetes diagnosis. For accurate diabetes risk prediction in the mixed ancestry population of Bellville South, Cape Town, methodological issues regarding the validation and performance of these models needs to be addressed. Methodology: Cross-sectional data from the Cape Town Bellville South cohort was used for this study. Missing data in risk prediction research was investigated through a systematic review and a number of imputation methods were explored to deal with missing data in this dataset. Models were identified via recent systematic reviews and validated in the mixed-ancestry population. Discrimination was assessed and compared using the C-statistic and calibration was assessed via calibration plots. Model recalibration in diabetes risk prediction was investigated through a systematic review. In an effort to improve model performance in the new setting, model recalibration and updating strategies were used and performance was compared before and after implementation. Results: The study sample consisted of 1256 individuals, of whom 173 were excluded due to previously diagnosed diabetes. Of the final 1083 individuals, 329 (30.4%) had missing data. Deletion resulted in the lowest model performance and simple imputation, the simplest method, resulted in the highest model performance and was employed for further analysis. A systematic review highlighted the gross underreporting and mishandling of missing data in diabetes risk prediction research. Original model performance during validation was poor-to-average, with both over- and underestimation present: Cambridge [C-statistic: 0.67 (0.62-0.72); E/O: 1.81 (1.09-2.52)], Kuwaiti [C-statistic: 0.68 (0.63-0.73); E/O: 0.72 (0.43-1.12)], Omani [C-statistic: 0.66 (0.61-0.70); E/O: 1.28 (0.63-1.93)], Rotterdam [C-statistic: 0.64 (0.59-0.69); E/O: 0.54 (0.50-1.04)] and Simplified Finnish [C-statistic: 0.67 (0.62-0.71); E/O: 0.26 (0.13-0.39)] diabetes risk prediction models. Recalibration, as shown through a systematic review, was undertaken only in models predicting incident diabetes, and was reported in 22.9% of validation studies, with 77.8% achieving an increase in model performance. Updating results applied to this validation dataset showed an increase in both discrimination and calibration in varying levels across all five models. Overall, the re-estimation of the Cambridge diabetes risk model yielded the best model performance [C-statistic: 0.71 (0.67 – 0.75); E/O: 1.00 (0.86 – 1.17)]. Discussion and conclusion: The frequency of missing data, underreporting and mishandling of missing data, complexity of updating methods and overall model performance of validated models in new settings highlight the challenges in diabetes risk prediction research. This is the first validation study of prevalent diabetes risk prediction models in Sub-Saharan Africa and highlighted important methodological issues. While both simpler imputation and updating methods resulted in similar predictive utility when compared to more complex techniques, model performance was not increased sufficiently to suggest recommendation.
- ItemMolecular investigation of genetic and environmental factors contributing to obesity in adolescent learners residing in the semi-urban/rural areas of the Western Cape Province, South Africa(Stellenbosch : Stellenbosch University, 2012-12) Yako, Yandiswa Yolanda; Erasmus, Rajiv T.; Matsha, Tandi; Janse van Rensburg, Susan; Stellenbosch University. Faculty of Medicine and Health Sciences. Dept. of Pathology. Chemical Pathology.ENGLISH ABSTRACT: Background/Aims: Obesity has increased rapidly in South African children and adolescents with significant variability observed among racial groups. Genes that regulate appetite have been studied in different populations worldwide, but their role in obesity among South African adolescents is unknown. The present study aimed at investigating the role of these genes, and their combined effect with physical activity in the development of obesity among South African adolescents. Methods: A total of 1564 South African school learners of Caucasian (n= 146), Mixed Ancestry (n= 872) and Black African (n= 537) ethnic groups were recruited for a research project that aimed to elucidate diabetes and the metabolic syndrome in children and adolescents attending schools in periurban areas of the Western Cape. The present case-control study included 227 obese-overweight (115 Black Africans and 112 Mixed Ancestry), and 204 normal weight (94 Black Africans and 110 Mixed Ancestry) adolescents learners. The learners were genotyped for nine polymorphisms (LEP: 19G>A, Lys36Arg, Val94Met; LEPR: Lys109Arg; Gln223Arg, Lys656Asn; CART: c.160-33G>A, c.499delA, and c.517A>G; GHRL: Leu72Met; and MC3R: Thr6Lys, Val81Ile) using allele-specific restriction enzyme analysis and automated sequencing. Genotype and haplotype associations with anthropometric variables such as body mass index (BMI), waist, hip, and mid-upper-arm circumferences (WC, HC, MUAC), and metabolic traits (fasting blood glucose, high density lipoproteincholesterol, total cholesterol), and blood pressure were further conducted. Furthermore, the type and frequency of physical activity was assessed by means of structured questionnaires; and its effect on obesity-related variables investigated in learners that were genotyped for the MC3R Thr6Lys and Val81Ile polymorphisms. Results: In a stepwise backward logistic regression analysis (containing age, gender, and LEP, LEPR, CART and GHRL polymorphisms), CART c.517A>G was independently significantly associated with obesity (OR= 5.98; 95%CI= 2.02, 21.27). CART c.517G carriers had higher MUAC (b coefficient= 1.88; 95%CI= 0.31, 3.44) while the LEPR 109Arg allele was significantly associated with decreased BMI (b coefficient = -2.36; 95%CI= -4.24, -0.47), WC (b coefficient = -5.66; 95%CI= -9.89, -1.44) and MUAC (b coefficient = -1.61; 95%CI= -3.00, -0.22); after adjusting for age, gender, and ethnicity. The haplotype containing the three LEP polymorphisms (A-A-A compared to the reference G-A-G haplotype) increased BMI (p= 0.0155), MUAC (p= 0.0146), and HC (p= 0.0128). The minor alleles of the MC3R polymorphisms decreased BMI, HC, WC, MUAC and TC; whilst only the Thr6Lys was associated with systolic and diastolic blood pressure (p= 0.0047 and 0.0027, respectively) in Mixed Ancestry learners. Doing house chores was associated with lower total cholesterol, independently and in the presence of the 81Ile allele (b coefficient = -0.355; 95%CI= 0.148, 0.561). Conclusion: To our knowledge, this is the first study that reports CART c.517A>G polymorphism as a risk factor for obesity in adolescents. Furthermore, the present study demonstrated that the MC3R polymorphisms had a positive effect on total cholesterol, which was further enhanced in physically active individuals. Similar to other studies, LEPR Lys109Arg and LEP polymorphisms were associated with variations in obesity-related variables among Black African and Mixed Ancestry South African learners.
- ItemMolecular investigation of genetic factors associated with insulin resistance and obesity in a South African population(Stellenbosch : Stellenbosh University, 2015-12) Vergotine, Zelda; Erasmus, Rajiv T.; Matsha, Tandi E.; Pillay, Tahir S.; Kotze, Maritha J.; Stellenbosch University. Faculty of Medicine and Health Sciences. Dept. of Pathology: Chemical Pathology.ENGLISH ABSTRACT: Background: The aetiopathogenesis of type 2 diabetes and the associated insulin resistance have been shown to have a strong genetic basis. Several genetic variants of the peroxisome proliferatoractivated receptor gamma (PPARG) and the insulin receptor substrate (IRS) 1 genes have been associated with the metabolic states of obesity, insulin resistance and type 2 diabetes in Caucasian populations. Furthermore, insulin resistance is strongly associated with diabetes and subsequent cardiovascular disease. These are increasingly common in low- to middle -income countries, including South Africa. Limited information is currently available regarding genetic associations with insulin resistance in African populations. Objectives: (1) To identify subjects with insulin resistance and determine the frequencies of the single nucleotide polymorphisms in the PPARG and IRS1 genes and examine the associated risk of insulin resistance and type 2 diabetes mellitus in a mixed-ancestry South African population. (2) To investigate the relationship between indices of insulin resistance and carotid intima media thickness, a marker of subclinical cardiovascular disease/atherosclerosis. Methods: A total of 856 (235 males) mixed-ancestry adults drawn from an urban community of Bellville South, Cape Town were genotyped for PPARG Pro12Ala (rs1801282, G>C), Pro115Gln (rs1800571, G>T), Val290Met (rs72551362, G>A), Pheu388Leu (rs72551363, T>A), Arg397Cys (rs72551364, C>T), His449His (rs3856806, C>T) and IRS1 Gly972Arg (rs 1801278, G>A). The oral glucose tolerance test was performed and cardiometabolic risk factors measured. Insulin resistance was estimated by the homeostasis model assessment of insulin resistance, the homeostasis model assessment of functional beta-cells, the quantitative insulin-sensitivity check index, the fasting insulin resistance index and the glucose/insulin ratio. Carotid intima media thickness was measured in longitudinal section at the far wall of the distal common carotid arteries, 2 cm from the bifurcation, at three consecutive end-points, 5-10 mm apart. Results: The genotype frequencies of PPARG Pro12Ala, IRS1 Gly972Arg and PPARG His449His were 10,4%, 7,7% and 23,8% respectively. No mutations were found for PPARG Pro115Gln, Val290Met, Pheu388Leu and Arg379Cys. In a model containing both PPARG Pro12Ala and IRS1 Gly972Arg alleles and their interaction term, the presence of the PPARG Pro12 resulted in a 64% risk of prevalent type 2 diabetes mellitus and was associated with higher 2 hour post-OGTT insulin levels in subjects with normoglycaemia. The PPARG Pro12 was associated with insulin resistance and interacted with IRS1 Gly972Arg, increasing the risk of type 2 diabetes mellitus. The PPARG His449His allele T frequency was about 14% and in an additive genetic model significantly reduced the risk of diabetes by 44%. After adjustment for age, gender, body mass index and diabetes status, the fasting plasma glucose (β=0,087;p=0,042) and glucose/insulin ratio (β=0,026; p=0,026) were associated with carotid intima media thickness. However, the effect on the overall model performance was marginal, R2<29,7%. Conclusion: The PPARG Pro12 was associated with insulin resistance and showed a gene-gene interaction with the unfavorable polymorphism IRS1 Gly972Arg, leading to an increased risk of type 2 diabetes mellitus. In contrast, the PPARG His449His T allele showed a protective effect against the risk of developing diabetes. Furthermore, indices of insulin resistance such as homeostatis model assessment of insulin resistance, quantitative insulin-sensitivity check index, fasting insulin resistance index and the glucose/insulin ratio were weakly associated with carotid intima media thickness in the risk stratification of cardiovascular disease in this population.
- ItemThe occurance of genetic variations in the MYH9 gene and their association with CKD in a mixed South African population(Stellenbosch : Stellenbosch University, 2012-12) Masconi, Katya; Matsha, Tandi; Erasmus, Rajiv T.; Stellenbosch University. Faculty of Medicine and Health Sciences. Dept. of Pathology.ENGLISH ABSTRACT: The purpose of this study was to investigate the association of the selected MYH9 single nucleotide polymorphisms (SNPs) with chronic kidney disease (CKD) and its related co-morbidities in the South African mixed ancestry population residing in Bellville South, Cape Town. In 2008, two landmark studies identified SNPs in the MYH9 gene which explained most of the increased risk for non-diabetic CKD in African Americans. These polymorphisms were later found to be weakly associated with diabetic nephropathy. Three SNPs that exhibited independent evidence for association with CKD were selected (rs5756152, rs4821480 and rs12107). These were genotyped using a Taqman genotyping assay on a BioRad MiniOpticon and confirmed by sequencing in 724 subjects from Bellville South, Cape Town, South Africa. Prevalent CKD was defined based on the estimated glomerular filtration rate calculated using the modification of diet in renal disease (MDRD) formula. Chronic kidney disease was present in 214 subjects (29.6%), 96.3% were stage 3 and only 8 subjects were stage 4. In additive allelic models, adjusted for age and gender, rs5756152 demonstrated an association with kidney function whereby each G allele of rs5756152 increased eGFR by 3.67 ml/min/1.73, reduced serum creatinine by 4.5% and increased fasting plasma glucose by 0.51 mmol/L. When an interaction model was used, the effect of rs5756152 on serum creatinine, eGFR and blood glucose levels was retained, and enhanced, but only in diabetic subjects. In addition, rs4821480 T allele increased eGFR while rs12107 A allele decreased glucose levels in diabetic subjects. In contrast to reports that MYH9 SNPs are strongly associated with non-diabetic end stage renal disease, our study demonstrated that rs5756152 and rs4821480 are associated with early kidney function derangements in type 2 diabetes whilst rs12107 is associated with glucose metabolism. Our findings, along with previous reports, suggest that the MYH9 gene may have a broader genetic risk effect on different types of kidney diseases than previously thought.
- ItemScreening for Chronic Kidney Disease (CKD) in a high risk population using a Point of Care Instrument for creatinine measurement: A community based study (The Bellville South Africa Study)(Stellenbosch : Stellenbosch University, 2017-12) Krige, Tammy; Erasmus, Rajiv T.; Rensburg, Megan; Stellenbosch University. Faculty of Medicine and Health Science. Dept. of Pathology. Chemical Pathology.ENGLISH ABSTRACT : Chronic kidney disease (CKD) is described as abnormal kidney function in which one third is lost over a period of 3 months and is a global epidemic with a particularly concentrated incidence within developing countries, such as Sub-Sahara Africa (SSA). Health facilities in SSA are limited due to lack of funding and a dearth in disease and medical knowledge. This coupled with the high incidence of both communicable and non-communicable diseases makes for an ideal environment for the implementation of Point-of-Care Testing (POCT), defined as an analytical test that is performed near the patient, delivering results in real time without the need for a conventional laboratory. CKD POCT involves the measurement of creatinine in capillary whole blood samples in order to determine the estimated glomerular filtration rate (eGFR) of patients in order to stage their CKD status from stage 1-6. This study aimed to bridge the gap in knowledge with regard to cut-offs of creatinine levels and eGFR values when screening a mixed ancestry populations. Currently there is only documented and standardized cut-offs for Caucasian and African American populations. This study looked at the African mixed ancestry population and acts as a starting point for standardizing POCT cut-offs for other international mixed ancestry populations. 103 participants were recruited from the Bellville South community, Cape Town, South Africa. The study was a comparative study that was designed to evaluate the Nova Statsensor® point of care instrument for the measurement of creatinine for the detection of CKD in adult mixed ancestry subjects from the Bellville South Community in South Africa. Secondary objectives included (1) the prevalence of CKD based on the results of the instrument, and (2) the correlation between the Nova Statsensor®, and the central laboratory creatinine values (IDMS traceable). Ancillary objectives of the study were to evaluate the technical quality of POC testing for creatinine in a community setting, as well as the evaluation of the cost implications when introducing this form of POCT into a primary care setting. The study found that the Nova Statsensor® in this study had a sensitivity of 66.7% and a specificity of 100%, displaying excellent diagnostic accuracy. It was found that the device displayed negative proportional bias which may lead to future CKD patients being misdiagnosed as healthy within screening programmes. The prevalence was found to be 2.9% within this mixed ancestry population. The device was user friendly and requires a small sample volume, however it is costly to implement. The laboratory evaluation study found that the Nova Statsensor® creatinine meter produced a direct creatinine concentration comparison that was less than expected, possibly due to creatinine levels depending on several factors which include muscle mass, obesity, gender, and age and having a wide reference interval. Thus highlighting the importance of the use of the equations to calculate eGFR in CKD screening in order to obtain the CKD staging results which displayed better correlation to the reference method, compared to creatinine measurement alone. The device was comparable to the reference method when performance was measured based on CKD staging through the calculation of the MDRD equation.