Effects of different missing data imputation techniques on the performance of undiagnosed diabetes risk prediction models in a mixed-ancestry population of South Africa

BACKGROUND: Imputation techniques used to handle missing data are based on the principle of replacement. It is widely advocated that multiple imputation is superior to other imputation methods, however studies have suggested that simple methods for filling missing data can be just as accurate as complex methods. The objective of this study was to implement a number of simple and more complex imputation methods, and assess the effect of these techniques on the performance of undiagnosed diabetes risk prediction models during external validation. METHODS: Data from the Cape Town Bellville-South cohort served as the basis for this study. Imputation methods and models were identified via recent systematic reviews. Models’ discrimination was assessed and compared using C-statistic and non-parametric methods, before and after recalibration through simple intercept adjustment. 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. Family history had the highest proportion of missing data (25%). Imputation of the outcome, undiagnosed diabetes, was highest in stochastic regression imputation (163 individuals). Overall, deletion resulted in the lowest model performances while simple imputation yielded the highest C-statistic for the Cambridge Diabetes Risk model, Kuwaiti Risk model, Omani Diabetes Risk model and Rotterdam Predictive model. Multiple imputation only yielded the highest C-statistic for the Rotterdam Predictive model, which were matched by simpler imputation methods. CONCLUSIONS: Deletion was confirmed as a poor technique for handling missing data. However, despite the emphasized disadvantages of simpler imputation methods, this study showed that implementing these methods results in similar predictive utility for undiagnosed diabetes when compared to multiple imputation

Paraoxonase1 Genetic Polymorphisms in a Mixed Ancestry African Population

Paraoxonase 1 (PON1) activity is markedly influenced by coding polymorphisms, Q/R at position 192 and M/L at position 55 of the PON1 gene. We investigated the frequencies of these polymorphisms and their effects on PON1 and antioxidant activities in 844 South African mixed ancestry individuals. Genotyping was done using allele-specific TaqMan technology, PON1 activities were measured using paraoxon and phenylacetate, oxidative status was determined by measuring the antioxidant activities of ferric reducing antioxidant power and trolox equivalent antioxidant capacity, and lipid peroxidation markers included malondialdehyde and oxidized LDL. The frequencies of Q192R and L55M were 47.6% and 28.8%, respectively, and the most common corresponding alleles were 192R (60.4%) and 55M (82.6%). The Q192 was significantly associated with 5.8 units’ increase in PON1 concentration and 15.4 units’ decrease in PONase activity after adjustment for age, sex, BMI, and diabetes, with suggestion of differential effects by diabetes status. The PON1 L55 variant was associated with none of the measured indices. In conclusion, we have shown that the Q192R polymorphism is a determinant of both PON1 concentration and activity and this association appeared to be enhanced in subjects with diabetes

Rare Mutations of Peroxisome Proliferator-Activated Receptor Gamma: Frequencies and Relationship with Insulin Resistance and Diabetes Risk in the Mixed Ancestry Population from South Africa

Background. Genetic variants in the nuclear transcription receptor, PPARG, are associated with cardiometabolic traits, but reports remain conflicting. We determined the frequency and the clinical relevance of PPARG SNPs in an African mixed ancestry population. Methods. In a cross-sectional study, 820 participants were genotyped for rs1800571, rs72551362, rs72551363, rs72551364, and rs3856806, using allele-specific TaqMan technology. The homeostatic model assessment of insulin (HOMA-IR), β-cells function (HOMA-B%), fasting insulin resistance index (FIRI), and the quantitative insulin-sensitivity check index (QUICKI) were calculated. Results. No sequence variants were found except for the rs3856806. The frequency of the PPARG-His447His variant was 23.8% in the overall population group, with no difference by diabetes status (). The His447His allele T was associated with none of the markers of insulin resistance overall and by diabetes status. In models adjusted for 2-hour insulin, the T allele was associated with lower prevalent diabetes risk (odds ratio 0.56 (95% CI 0.31–0.95)). Conclusion. Our study confirms the almost zero occurrences of known rare PPARG SNPs and has shown for the first time in an African population that one of the common SNPs, His447His, may be protective against type 2 diabetes

Genome-wide DNA methylation in mixed ancestry individuals with diabetes and prediabetes from South Africa

Aims. To conduct a genome-wide DNA methylation in individuals with type 2 diabetes, individuals with prediabetes, and control mixed ancestry individuals from South Africa. Methods. We used peripheral blood to perform genome-wide DNA methylation analysis in 3 individuals with screen detected diabetes, 3 individuals with prediabetes, and 3 individuals with normoglycaemia from the Bellville South Community, Cape Town, South Africa, who were age-, gender-, body mass index-, and duration of residency-matched. Methylated DNA immunoprecipitation (MeDIP) was performed by Arraystar Inc. (Rockville, MD, USA). Results. Hypermethylated DMRs were 1160 (81.97%) and 124 (43.20%), respectively, in individuals with diabetes and prediabetes when both were compared to subjects with normoglycaemia. Our data shows that genes related to the immune system, signal transduction, glucose transport, and pancreas development have altered DNA methylation in subjects with prediabetes and diabetes. Pathway analysis based on the functional analysis mapping of genes to KEGG pathways suggested that the linoleic acid metabolism and arachidonic acid metabolism pathways are hypomethylated in prediabetes and diabetes. Conclusions. Our study suggests that epigenetic changes are likely to be an early process that occurs before the onset of overt diabetes. Detailed analysis of DMRs that shows gradual methylation differences from control versus prediabetes to prediabetes versus diabetes in a larger sample size is required to confirm these findings

APOL1 genetic variants, chronic kidney diseases and hypertension in mixed ancestry South Africans

BackgroundThe frequencies of apolipoprotein L1 (APOL1) variants and their associations with chronic kidney disease (CKD) vary substantially in populations from Africa. Moreover, available studies have used very small sample sizes to provide reliable estimates of the frequencies of these variants in the general population. We determined the frequency of the two APOL1 risk alleles (G1 and G2) and investigated their association with renal traits in a relatively large sample of mixed-ancestry South Africans. APOL1 risk variants (G1: rs60910145 and rs73885319; G2: rs71785313) were genotyped in 859 African mixed ancestry individuals using allele-specific TaqMan technology. Glomerular filtration rate (eGFR) was estimated using the Modification of Diet in Renal Disease (MDRD) and Chronic Kidney Disease Epidemiology Collaboration (CKD-EPI) equations.ResultsThe frequencies of rs73885319, rs60910145 and rs71785313 risk alleles were respectively, 3.6%, 3.4%, and 5.8%, resulting in a 1.01% frequency of the APOL1 two-risk allele (G1:G1 or G1:G2 or G2:G2). The presence of the two-risk allele increased serum creatinine with a corresponding reduction in eGFR (either MDRD or CKD-EPI based). In dominant and log-additive genetic models, significant associations were found between rs71785313 and systolic blood pressure (both p ≤ 0.025), with a significant statistical interaction by diabetes status, p = 0.022, reflecting a negative non-significant effect in nondiabetics and a positive effect in diabetics.ConclusionsAlthough the APOL1 variants are not common in the mixed ancestry population of South Africa, the study does provide an indication that APOL1 variants may play a role in conferring an increased risk for renal and cardiovascular risk in this population

The agreement between fasting glucose and markers of chronic glycaemic exposure in individuals with and without chronic kidney disease: a cross-sectional study

Abstract Background To assess whether the agreement between fasting glucose and glycated proteins is affected by chronic kidney disease (CKD) in a community-based sample of 1621 mixed-ancestry South Africans. Methods CKD was defined as an estimated glomerular filtration rate < 60 ml/min/1.73 m2. Fasting plasma glucose and haemoglobin A1c (HbA1c) concentrations were measured by enzymatic hexokinase method and high-performance liquid chromatography, respectively, with fructosamine and glycated albumin measured by immunoturbidimetry and enzymatic method, respectively. Results Of those with CKD (n = 96), 79, 16 and 5% where in stages 3, 4 and 5, respectively. Those with CKD had higher levels of HbA1c (6.2 vs. 5.7%; p < 0.0001), glycated albumin (15.0 vs. 13.0%; p < 0.0001) and fructosamine levels (269.7 vs. 236.4 μmol/l; p < 0.0001), compared to those without CKD. Higher fasting glucose levels were associated with higher HbA1c, glycated albumin and fructosamine, independent of age, gender, and CKD. However, the association with HbA1c and glycated albumin differed by CKD status, at the upper concentrations of the respective markers (interaction term for both: p ≤ 0.095). Conclusion Our results suggest that although HbA1c and glycated albumin perform acceptably under conditions of normoglycaemia, these markers correlate less well with blood glucose levels in people with CKD who are not on dialysis

Tooth loss in relation to serum cotinine levels - A cross-sectional study from the Belville South area in South Africa

Tooth loss constitutes a major public health challenge, sharing common risk factors with non-communicable diseases. To report the relationship between tooth loss and serum cotinine levels in a population sample of mixed ethnic heritage from the Belville South area in South Africa. Cross-sectional epidemiological study.Subjects were invited from 2014 to 2016 according to a consecutive sampling technique and all those who met the inclusion criteria were included. In all, 1876 individuals were included, being 1416 females (75.5%), with a combined average age of 49.5 ± 15.3 years. In total 46.7% of the sample was edentulous, with females presenting a higher proportion than males (50.7% vs. 34.1%, p &lt; 0.001). The relative risk (RR) of being edentulous was higher for females (RR=1.8, 95% CI=1.35-2.41, p&lt;0.001) and for participants with cotinine levels 15-299 ng/ml (RR = 1.37, 95% CI=1.02=1.83, p=0.04) and ≥300 ng/ml (RR=1.51, 95% CI=1.09-2.08, p=0.01). Maxillary incisors and mandibular molars were the most prevalent missing teeth. The burden of tooth loss is high in the studied population sample, as well their unmet needs for dental care. Female gender, tobacco exposure, and aging were associated with partial and total edentulism

Association between dental and periodontal conditions with chronic kidney disease: A cross-sectional analysis of urban South Africans

Oral diseases are preventable causes of poor health outcomes in people with chronic kidney disease (CKD). Investigate the association between dental and periodontal conditions with kidney function and determine whether inflammation mediate the association between periodontitis and CKD. Cross-sectional analysis of 1551 South African adults of mixed ancestry. CKD was classified as estimated glomerular filtration rate (eGFR) &lt;60mL/min/1.73m2. Oral profile was captured by decayed, missing, filled teeth index (DMFTi), bleeding on probing (BOP), pocket depth (PD), clinical attachment loss (CAL), and periodontitis classified as PD ≥4 mm.Overall, 6% had CKD, with 93% and 66% of participants with and without CKD, respectively having a high DMFTi (p&lt;0.0001). Further, 84% (CKD) and 43% (without CKD) were edentulous (p&lt;0.0001). A great proportion of the dentate sub-sample (n=846) had periodontitis, however, BOP, PD ≥4mm and CAL ≥4mm were similar between the groups. DMFTi was associated with eGFR and prevalent CKD (p&lt;0.023), with this association driven by the Missing component. Periodontitis was not associated with eGFR nor CKD (p&gt;0.282). In routine care of people with CKD, attention should be given to oral health

Optimal waist-to-height ratio values for cardiometabolic risk screening in an ethnically diverse sample of South African urban and rural school boys and girls

BACKGROUND: The proposed waist-to-height ratio (WHtR) cut-off of 0.5 is less optimal for cardiometabolic risk screening in children in many settings. The purpose of this study was to determine the optimal WHtR for children from South Africa, and investigate variations by gender, ethnicity and residence in the achieved value. METHODS: Metabolic syndrome (MetS) components were measured in 1272 randomly selected learners, aged 10-16 years, comprising of 446 black Africans, 696 mixed-ancestry and 130 Caucasians. The Youden's index and the closest-top-left (CTL) point approaches were used to derive WHtR cut-offs for diagnosing any two MetS components, excluding the waist circumference. RESULTS: The two approaches yielded similar cut-off in girls, 0.465 (sensitivity 50.0, specificity 69.5), but two different values in boys, 0.455 (42.9, 88.4) and 0.425 (60.3, 67.7) based on the Youden's index and the CTL point, respectively. Furthermore, WHtR cut-off values derived differed substantially amongst the regions and ethnic groups investigated, whereby the highest cut-off was observed in semi-rural and white children, respectively, Youden's index0.505 (31.6, 87.1) and CTL point 0.475 (44.4, 75.9). CONCLUSION: The WHtR cut-off of 0.5 is less accurate for screening cardiovascular risk in South African children. The optimal value in this setting is likely gender and ethnicity-specific and sensitive to urbanization

Increase in blood pressure over a 7-year period in a mixed-ancestry South African population

Background. An increase in the prevalence of high blood pressure (BP) has been reported globally and in the South African (SA) population.Objectives. To investigate temporal changes in absolute BP levels and hypertension prevalence in the mixed-ancestry South Africans.Methods. Participants were from two independent cross-sectional surveys conducted during 2008/09 (N=928) and 2014/16 (N=1 969) in Bellville South, Cape Town, SA. Participants’ eligibility was based on several criteria, including age &gt;20 years and neither bedridden nor pregnant. Data were obtained by administered questionnaires, clinical measurements (BP and anthropometry) and biochemical assessments (oral glucose tolerance tests and cotinine levels). Known hypertension was based on a self-reported history of doctor-diagnosed hypertension and ongoing treatment. Comparison across years was based on the crude prevalence of hypertension as well as direct age-standardised prevalence, based on the SA 2011 mixed-ancestry population distribution, in 10-year age increments.Results. In all, 708 participants (76.3%) in 2008/09 and 1 488 (75.6%) in 2014/16 were female. Between 2008/09 and 2014/16, mean systolic BP increased from 124 to 136 mmHg (absolute mean difference 15 mmHg) and mean diastolic BP from 75 to 85 mmHg (absolute mean difference 9 mmHg) in the overall sample. The prevalence of screen-detected hypertension increased from 11.6% to 24.8%, with a similar increase in males and females, while the prevalence of known cases remained stable. These changes remained significant after adjustment for age and gender.Conclusions. A rightward shift in absolute BP translated into a significant increase in the prevalence of hypertension over time in this population. The predominant increases in screen-detected hypertension suggest that the deteriorating profile was not matched by efforts to detect and manage individuals with higher-than-optimal BP levels.