Chemical Pathology

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Browsing Chemical Pathology by browse.metadata.advisor "Janse van Rensburg, Susan"

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    Development of a high-throughput genotyping assay for detection of functional polymorphisms involved in homocysteine metabolism and the methylation process implicated in multiple sclerosis
    (Stellenbosch : Stellenbosch University, 2013-12) Davis, William Henry; Janse van Rensburg, Susan; Kotze, Maritha J.; Stellenbosch University. Faculty of Medicine and Health Sciences. Dept. of Pathology. Chemical Pathology.
    ENGLISH ABSTRACT: The aetiology of multiple sclerosis (MS) remains largely unknown due to the multifactorial nature of disease susceptibility determined by both environmental and genetic factors. Progress has been made in identifying the genetic component of MS , as well as the possible interactions with the environment. In this study single nucleotide polymorphisms (SNPs) in the FTO (rs9939609, Intron 1 T>A), MTR (rs1805087, 2756 A>G), MTRR (rs1801394, 66 A>G), MTHFR (rs1801133, 677 C>T and rs1801131, 1298 A>C) and COMT (rs4680, 472 G>A) genes involved in the methylation metabolic pathway were studied in the context of MS. The overall objective of this study was to elucidate the mechanism underlying raised homocysteine levels in MS patients. The specific aims were 1) to analytically validate high throughput real-time polymerase chain reaction (RT-PCR) genotyping assays for the 6 selected SNPs against direct sequencing as the gold standard for 2) possible integration into a pathology-supported genetic testing strategy aimed at improved clinical management of MS. The study population included a total of 114 unrelated Caucasian MS patients (98 females and 16 males) and 195 unrelated Caucasian control individuals without a diagnosis of neurological disease (128 females and 67 males). A novel finding of this study was that the risk-associated FTO rs9939609 A-allele was associated with raised homocysteine levels (p=0.003) in patients diagnosed with MS, but not in controls. Furthermore, homocysteine levels correlated significantly with bo dy mass index (BMI) (p=0.046) and total cholesterol levels (p=0.048). Both homocysteine (p=0.011) and BMI (p=0.017) were significantly reduced with increasing intake of folate in the diet, while high saturated/trans fat intake correlated significantly with increased BMI (p<0.001). High physical activity correlated with reduced BMI (p<0.006) in the study population, adjusted for age, gender and disease status. Daily intake of at least five fruit and vegetable portions and the COMT rs4680 (472 G>A) AA genotype had a favourable lowering effect on MS disability as assessed by the expanded disability status scale (EDSS) (p=0.035), while smoking increased MS disability significantly (p<0.001). All SNPs studied were found to be in Hardy-Weinberg equilibrium (HWE), with no significant differences detected between patients and control individuals in genotype distribution or allele frequencies. This study has shown for the first time that the underlying disease process of MS moderates the effect of the FTO rs9939609 polymorphism on homocysteine levels , which is consistent with the role of FTO in demethylation and epigenetic changes. Identification of FTO rs9939609 reinforces the importance of adequate folate intake in the diet that can be assessed accurately with use of the Medical History and Lifestyle Questionnaire applied in this study. Finally, the finding that raised homocysteine levels and BMI are significantly influenced by lifestyle factors such as diet and physical activity in our study cohort , offers a solution to counteract the detrimental effects of genetic risk factors contributing to the development of these established vascular risk factors for MS. Combining this information with FTO rs9939609 and COMT rs4680 genotyping may in future translate into a comprehensive pathology supported genetic testing strategy aimed at improved risk management and quality of life in MS patients.
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    Development of a pathology-supported genetic test for improved clinical management of patients diagnosed with multiple sclerosis
    (Stellenbosch : University of Stellenbosch, 2010-12) Jalali Sefid Dashti, Mahjoubeh; Janse van Rensburg, Susan; Kotze, Maritha J.; University of Stellenbosch. Faculty of Health Sciences. Dept. of Pathology. Chemical Pathology.
    ENGLISH ABSTRACT: The aetiology of multiple sclerosis (MS) remains largely unknown, due to its multifactorial nature with environmental and genetic factors contributing to the risk. Several investigations highlighted the important role of the genetic component influencing disease susceptibility and progression. In the present study genetic variations in the MTHFR (1298 A>C and 677 C>T) and HFE (845 G>A) genes previously, shown to affect folate and iron metabolism respectively, were studied in the context of MS. The aim of the study was to contribute the laboratory component of a pathology supported genetic testing approach used to identify a subgroup of MS patients with altered nutritional requirements due to genetic susceptibilities. The study population included 90 patients with a clinical diagnosis of MS and 49 control individuals, without any signs or symptoms of the disease, drawn from the same age- and population group. Three mutation detection systems were compared in terms of accuracy, sensitivity, cost effectiveness and ease of operation in relation to the MTHFR and HFE gene mutations analysed. Analytical validity of the genetic assays was an important consideration; therefore the respective real-time polymerase chain reaction (RT-PCR) methods were compared with direct DNA sequencing as the gold standard. The methodology included use of the ABI™ 7900HT, the Roche LightCycler® 480 II system and the Corbett Rotor-Gene™ 6000 5-plex HRM. The same genotype results were obtained for the DNA samples tested with the three RT-PCR methods. In terms of cost effectiveness, ease of operation and optimization, the Corbett Rotor-Gene™ 6000 5-plex HRM thermal cycler, with use of the ABI™ TaqMan Genotyping assays was found to be the most efficient for mutation detection using relatively small sample batches. Following successful standardization of the RT-PCR assays, genotype-phenotype correlation studies was performed in a subset of 43 MS patients with available data. Biochemical tests were previously done on blood samples at the National Health Laboratory Service (NHLS) chemical pathology laboratory at Tygerberg Academic Hospital. A novel finding of this study was that heterozygotes and homozygotes for mutation 1298 A>C in the MTHFR gene presented with lower serum iron levels (12.37 ± 5.91 μmol/l) in comparison to subjects without the C-allele (18.64 ± 7.15 μmol/l; P = 0.02). Furthermore, C-reactive protein (CRP) levels were found to be marginally significantly higher (P = 0.07) in the MTHFR 1298 A>C mutation-positive heterozygotes compared to subjects without the C-allele (6.65 ± 4.96 mg/l vs 2.93 ± 2.31 mg/l), linking inflammation to the presence of the MTHFR 1298 A>C mutation. In comparison, the MTHFR 677 C>T as well as the HFE 845 G>A mutation showed no correlation with transferrin saturation, ferritin, haemoglobin or CRP levels. The absence of increased iron status in HFE mutation carriers was in accordance previous findings suggesting altered iron metabolism in MS patients with this mutation. For the first time, high-throughput assays for functional polymorphisms in the MTHFR and HFE genes can now be offered as a routine service at the Tygerberg Academic Hospital. This application is used in combination with blood biochemistry tests as part of a comprehensive gene-based, pathology supported screening and intervention program aimed at improved quality of life in patients diagnosed with MS.
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    Molecular 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.