South African Population Groups Research Articles

P08-02. Genetic variation within the gene encoding the HIV-1 CCR5 coreceptor in two South African population groups

P08-02. Genetic variation within the gene encoding the HIV-1 CCR5 coreceptor in two South African population groups

Characterization of the highly discriminatory loci DYS449, DYS481, DYS518, DYS612, DYS626, DYS644 and DYS710

During the study of genetic diversity at non-core Y-STRs in South African population groups, we identified loci with high discrimination capacity. In this study we present a detailed account of the allele diversity, allele sequence data, gene diversity, allele frequency spectrum and informativeness for assignment in the European English, Asian Indian and Xhosa population groups at loci DYS449, DYS481, DYS518, DYS612, DYS626, DYS644 and DYS710. The suitability of these loci for forensic, genealogical and evolutionary studies is discussed, and nomenclature for loci DYS518, DYS612, DYS626 and DYS644 is suggested.

A pharmacogenetic study of CD4 recovery in response to HIV antiretroviral therapy in two South African population groups

South Africa, like many other Southern African countries, has one of the highest HIV infection rates in the world and many individuals consequently receive antiretroviral therapy (ART). However, knowledge regarding (i) the prevalence of functional single nucleotide polymorphisms (SNPs) in pharmacologically relevant genes, and (ii) variance in pharmacotherapy both within and between different populations and ethnic groups is limited. The aim of this study was to determine whether selected polymorphisms in cytochrome P450 (CYP) genes (CYP2B6 and CYP3A4) and the multidrug-resistance 1 (ABCB1) gene underlie altered antiretroviral (ARV) drug response in two South African populations. DNA samples from 182 HIV-positive individuals of Mixed-Ancestry and Xhosa ethnicity on ART were genotyped for the A-392G SNP in CYP3A4, the G516T and A785G SNPs in CYP2B6, and the T-129C, C1236T, G2677T/A and C3435T SNPs in ABCB1. Univariate two-way analysis of variance (ANOVA) testing revealed no apparent effect of ethnicity on immune recovery (in terms of CD4-cell count) in response to ART. Univariate one-way ANOVA testing revealed a discernible effect of genotype on immune recovery in the cases of the T-129C (P=0.03) and G2677A (P<0.01) polymorphisms in the ABCB1 gene. This study serves as a basis for better understanding and possible prediction of pharmacogenetic risk profiles and drug response in individuals and ethnic groups in South Africa.

The influence of age, sex, population group, and dentition on the mandibular angle as measured on a South African sample

The mandibular angle is measured in physical anthropological assessments of human remains to possibly assist with the determination of sex and population affinity. The purpose of this investigation was to establish how the mandibular angle changes with age and loss of teeth among the sexes in South African population groups. The angles of 653 dried adult mandibles from the Pretoria Bone Collection were measured with a mandibulometer. Males and females of both South African whites and blacks were included. To compensate for imbalances in numbers among subgroups, type IV ANOVA testing was applied. No association was found between age and angle within either of the populations, within sexes, or within dentition groups. The angle was the most obtuse in individuals without molars and with an uneven distribution of molars, and most acute in the group with an even distribution of molars on both sides. Statistically significant differences (P < 0.001) were found in the angle between the two population groups and sexes in the overall sample as well as in the subgroup with absent molar teeth (P = 0.003 for sex, males more acute angle, and P = 0.001 for population group, blacks more acute angle), although a very large overlap existed. No significant differences could be demonstrated between the sexes or populations within the subgroups with molars. We concluded that the loss of molars, especially if complete or uneven, has a considerable effect on the mandibular angle. In the assessment of human remains, the mandibular angle is not very usable in determining sex.

Estimation of stature using fragmentary femora in indigenous South Africans

Intact long bones of the upper and lower extremities have been used in the derivation of regression equations for the estimation of stature in different population groups. These bones are sometimes presented to forensic anthropologists in different states of fragmentation thereby making the derived equations unusable. This has necessitated the need to assess the usefulness of measurements of fragments of long bones (e.g., femur) in the estimation of stature. While few studies have reported such equations, which are population and sex specific, it was the aim of this study to derive equations based on measurements of commonly preserved fragments of the femur for the indigenous South African population group. A total of 100 complete skeletons, equally distributed by sex, were obtained from the Raymond A. Dart collection of human skeletons. Stature was estimated for each of the skeleton using the Fully's method (Fully in Ann Med Leg 35:266-273, 1956). Regression equation for the estimation of stature and maximum length of the femur were derived from six measurements of the femur. The standard error of estimate for regression equations for stature estimation (3.72-4.38) was slightly higher than that presented for intact femur. This study confirms the usefulness of fragments of the femur of indigenous South Africans in the estimation of stature.

No relationship observed between human p53 codon‐72 genotype and HPV‐associated cervical cancer in a population group with a low arginine‐72 allele frequency

Infection with high-risk human papillomavirus (HR-HPV) is a necessary but not a sufficient event in the development of cervical cancer, as most infections regress without intervention. Thus, genetic host factors and cellular immune responses could be potential modifiers for the risk of developing cervical cancer. In particular, p53 is considered as the most critical tumour suppressor gene and is involved in regulating cell division. The polymorphism on p53, which encodes either a proline or an arginine amino acid residue at codon 72, has been reported as a possible risk factor for cervical disease. This polymorphism has been shown to differentially affect the efficiency of degradation of p53 protein mediated by HR-HPV E6 oncoprotein. Women with histologically proven cancer of the cervix (n = 111) and hospital-based controls (n = 143) were included in this study. The patients and controls were from the Western Cape Province in South Africa. Genotyping of the p53 polymorphism was conducted using polymerase chain reaction and restriction fragment-length polymorphism method. The distributions of the allelic frequencies were stratified in both patients and controls into two South African ethnic population groups. In this study, we observed no association between the distribution of p53 polymorphism and susceptibility to cervical cancer in the Western Cape Province populations (P = 0.466). However, the frequency of the Pro/Pro residue at codon 72 was increased in the South African population when compared to Caucasians, Indians and Portuguese population groups. Notably, as the distribution of the Pro/Pro at codon 72 of p53 gene was significantly different (P < 0.05) between the control groups of South Africa and other population groups. This result suggests that ethnic disparity may influence the levels of p53 produced.

Inflammation, obesity and cardiovascular function in African and Caucasian women from South Africa: the POWIRS study

The integrated relationship between inflammation, obesity and cardiovascular disease is currently a subject of much research interest. These specific relationships, however, have not been studied in-depth in South African population groups in order to determine the role of ethnicity. It is known that Africans, compared to Caucasians, suffer from a high prevalence of hypertension. It was therefore hypothesized that the levels of inflammatory markers (high-sensitivity C-reactive protein (hsCRP), fibrinogen and leptin) are higher in Africans compared to Caucasians and are notably associated with cardiovascular dysfunction in Africans. Apparently healthy African (N=102) and Caucasian (N=115) women, matched for age and body mass index (BMI), were recruited. Leptin, hsCRP, fibrinogen and lipid levels, waist circumference (WC), BMI, systolic and diastolic blood pressure, cardiac output (CO), total peripheral resistance (TPR) and Windkessel compliance were measured. Results showed that the levels of leptin, hsCRP and fibrinogen were significantly higher (P<0.05) in the African women. The inflammatory markers correlated strongly with cardiovascular parameters, age and obesity (BMI, WC) in both groups, but after adjusting for age and obesity, none of the correlations were significant anymore. Multiple regression analyses (with leptin, hsCRP or fibrinogen as dependent variable) showed that only leptin levels of African women were explained by cardiovascular parameters (BP, TPR and CO). In conclusion, even though African women had significantly higher leptin, hsCRP, fibrinogen and blood pressure levels than Caucasian women, no cardiovascular parameters explained the variation in the inflammatory markers (except for leptin levels of African women).

The allelic distribution of -308 Tumor Necrosis Factor-alpha gene polymorphism in South African women with cervical cancer and control women

BackgroundCervical cancer is due to infection with specific high-risk types of human papillomavirus (HPV). Although the incidence of genital HPV infection in various population groups is high, most of these regress without intervention. Investigating genetic host factors and cellular immune responses, particularly cytokines, could help to understand the association between genital HPV infection and carcinogenesis. The tumor necrosis factor alpha (TNF-α) cytokine plays an important role in all stages of cervical cancer and has the ability to induce the regression of human tumors. Therefore the aim of the study was to investigate the allelic distribution of -308 TNF-α gene polymorphism in South African women with cervical cancer compared to control women.MethodsIncluded in our study were women with histologically proven cancer of the cervix (n = 244) and hospital-based controls (n = 228). All patients and controls were from mixed race and black population groups in South Africa. The detection of a bi-allelic -308 (A/G) polymorphism in the promoter region of TNF-α was investigated using the amplification refractory mutation system-polymerase chain reaction (ARMS-PCR) technique. The distributions of the allelic frequencies were stratified in both patients and controls into two South African ethnic population groups.ResultsIn this study we observed no association between the distribution of -308 TNF-α polymorphism and the risk of developing cervical cancer even after combining the data from the two ethnic populations (X2 = 2.26). In addition, using the chi-squared test we found no significant association between the known risk factors for cervical cancer and the allele distribution of -308 TNF-α. However, the frequency of the rare high-producing allele -308A of TNF-α was significantly lower in the South African population when compared to Caucasians and Chinese population groups.ConclusionWe demonstrated no association between -308 TNF-α polymorphism and the risk of cervical cancer among two South African ethnic population groups. However, as the distribution of the -308A TNF-α was notably different between the control groups of South Africa and other population groups this result suggests that ethnic disparity may influence the levels of TNF-α produced.

Discriminating Sex in South African Blacks Using Patella Dimensions

For many years, sex determination has been carried out on skeletal remains to identify individuals in forensic cases and to assess populations in archaeological cases. Since it has been shown that not all bones are found in a forensic case, discriminant function equations should be derived for all bones of the body to assist in sex determination. Numerous studies have shown the usefulness of bones of the lower extremity (e.g. femur, tibia) in sex determination using discriminant function analysis, but the use of patella measurements has not been extensively investigated for this purpose. It is therefore the aim of this study to derive discriminant function equations for sex determination from measurements of the patella of South African blacks as represented in the Raymond A. Dart Collection of Human Skeletons. A total sample of 120 (60 male, 60 female) patellae were measured using six measurements. The Statistical Product and Service Solutions (SPSS) program was used to derive the equations. Stepwise and direct analyses were performed with the highest rate of classification of 85% thereby making the patella useful for sex determination. Thus, the proposed equations derived from this study should be used with caution and only on the South African black population group.

Metrical and non-metrical assessment of population affinity from the calcaneus

To date, there are no metric standards for differentiating between population groups from measurements of the calcaneus in South Africa. Previously, some of the measurements of the calcaneus have been used for sex determination in Americans, Europeans, Italians and South Africans. However, the variations in the number of articular facet present on the superior surface of the calcaneus have been observed in different population groups. This study aims at investigating the potentials of measurements of the calcaneus in diagnosing population affinity and observes population variations of the number of articular facet present on its superior surface in indigenous South Africans and those of European descent. Nine measurements were taken from 180 non-pathological left calcanei in a sample of known sex and population affinity obtained from the Raymond A. Dart Collection of Human Skeletons. Three articular facet types were observed. A significantly higher incidence of type A was observed in South Africans of European descent (SAED) population group while type B predominated in the indigenous South African (ISA) population group. Type C even though rare was found only in ISA group. The metrical data were subjected to discriminant function analyses. The average accuracy in correct classification (81–89%) obtained for the discriminant function equations derived in this study may assist in the determination of population affinity when the calcaneus is present for analysis in forensic cases.

Screening South African familial adenomatous polyposis families for the five-nucleotide deletion at codon 1309 of the APC gene

We report the occurrence of a common five-nucleotide deletion at codon 1309 of the adenomatous polyposis coli (APC) gene in four different South African population groups. The mutation causes familial adenomatous polyposis (FAP) in 18% (4/22 unrelated patients screened) of affected South Africans, which is similar to the frequency described in several other populations. Knowledge of the gene mutation underlying FAP enabled conclusive genetic testing of at-risk family members of four index patients in which this specific mutation has been characterized. The non-radioactive heteroduplex method described in this study allowed cost-effective molecular diagnosis directly after electrophoresis of enzymatically-amplified DNA in agarose gels. The resulting reduction of uncertainty for at-risk relatives is an important benefit of diagnosis at the DNA level.

Genetic linkage between Huntington disease and the D4S10 locus in South African families: further evidence against non-allelic heterogeneity

A study of genetic linkage between Huntington disease (HD) and the D4S10 locus (G8) has been undertaken in 10 South African (SA) families originating from the black, white and mixed acestry population groups. Allele frequencies at the D4S10 locus have been established in the non-Caucasoid population groups. There are significant differences in the allele frequencies at the D4S10 locus between the various SA populations. Clearly, information about population-specific frequencies for all polymorphisms is essential prior to the implementation of predictive testing in different population groups. Linkage has been demonstrated within this mixed group of HD families in SA using the HindIII, EcoRI and MspI polymorphisms, detected by G8. A maximum lod score of 8.14 at a recombination fraction of 0.00 (confidence limit 0-0.058) has been calculated using a combined haplotype of the HindIII and MspI polymorphisms. Taking into account the diverse ethnic backgrounds of the different SA population groups in this investigation, the data obtained from the study provide further evidence that there is probably only a single HD locus.

Familial hypercholesterolemia in South African Afrikaners

Familial hypercholesterolemia (FH), at a prevalence of more than 1 in 100, is at least five times more common in one South African population group than in populations in North America and Europe. Fourteen homozygotic familial hypercholesterolemic subjects from this South African group were genotyped for two intragenic DNA restriction fragment length polymorphisms (RFLPs) in the LDL-receptor gene. A StuI polymorphism is located in exon 8, and a PvuII polymorphism, in intron 15. Of ten unrelated FH homozygotes genotyped for both RFLPs, nine were homozygous for an S + P- haplotype, and one was heterozygous for an S + P-/S-P + haplotype. The remaining four were genotyped for PvuII only and were homozygous for P-. Compared with a previously determined population frequency for the latter, this represents an association (P less than 0.05) between the frequency for the P- allele and FH in this population, and this finding is consistent with the "founder gene effect" previously postulated to be present on genealogical and biochemical evidence.

A study of the HLA-Dw determinants and their relationship to DR and DQ antigens in three south african population groups: South African caucasoids, South African negroes, and Cape coloureds

The HLA-Dw specificities of a group of 177 unrelated randomly selected healthy individuals consisting of 67 South African Negroes (Xhosa), 57 Cape Coloureds, and 53 South African Caucasoids were determined. HLA-Dw specificities were determined in a mixed lymphocyte culture test using HTCs. Antigen and gene frequencies as well as the associations between HLA-Dr, DQ, and Dw were established in three populations. HLA-Dw gene frequencies in the South African Caucasoids agreed with these frquencies in other Caucasoid groups. The HLA-Dw1 frequency was decreased in the Cape Coloureds and South African Negroes compared to the Caucasoids. The gene frequency of Dw3 was low in the South African Negroes in spite of the fact that DR3 is a common DR antigen in this group. A high frequency of Dw ‘blank’ was observed in the South African Negroes and Cape Coloureds, suggesting the existence of undefined HLA-Dw specificities in these populations. Data concerning the HLA-Dw, DR, and DQ relationships showed that once a certain Dw specificity was associated with a particular DR and DQ antigen, this association remained a fixed entity in the different population groups.

Religie en sosiale geregtigheid in ’n gesegmenteerde samelewing

Religion and social justice in a segmented society. Although almost 80% of the total South African population adheres to one or another Christian denomination, it is not possible to speak of a homogeneous, shared conception regarding the role of religion. Instead one finds factions pursuing their own aims relatively autonomously. Their claims and ideals may differ due to the following: divergent orientations toward reality; own constitution of meaning regarding religion for their unique situation; different modes of expressing religious experience; problematic and controversial religious opinions; divergent approaches to ethical problems; and differing intentions or motivation. To this end the process of bestowing religious meaning on the one hand, and the ensuing social involvement on the other, are analysed in this article. Empirical data were gleaned .. during a multipurpose survey conducted by the HSRC which involved all South African population groups.

Religie en sosiale geregtigheid in 'n gesegmenteerde samelewing / Religion and social justice in a segmented society

Although almost 80% of the total South African population adheres to one or another Christian denomination, it is not possible to speak of a homogeneous, shared conception regarding the role of religion. Instead one finds factions pursuing their own aims relatively autonomously. Their claims and ideals may differ due to the following: divergent orientations toward reality; own constitution of meaning regarding religion for their unique situation; different modes of expressing religious experience; problematic and controversial religious opinions; divergent approaches to ethical problems; and differing intentions or motivation. To this end the process of bestowing religious meaning on the one hand, and the ensuing social involvement on the other, are analysed in this article. Empirical data were gleaned during a multipurpose survey conducted by the HSRC which involved all South African population groups. S. Afr. J. Sociol. 1986, 17(3): 108–113

Nasopalatine duct cyst

The nasopalatine duct cyst appears to be an aggressive and symptomatic condition in the South African black population group. Of a total of 114 cases, 30 patients, all blacks, had cysts in excess of 30 mm in diameter. Two patients with large nasopalatine duct cysts, one of which was infected, underwent computed tomography. Computed tomography is an excellent method of demonstrating the extent, bony destruction and relationship of the lesion to neighbouring structures. A review of the subject with clinical and radiological features is presented.

How successful are motivation theories in practice?

In this study, 503 South African companies are used to ascertain the utilization of various important theories of motivation. Furthermore, utilizing the questionnaire method, the perceived success of the various theories and practices with the main South African population groups was assessed. The findings are of great importance: motivation theories are not applied extensively; but perhaps of greater importance is the finding that companies report less than 50% success rate in the application of these theories.

Market Forecasting for Dual Economies: The Application and Accuracy of Income Elasticities

Forecasts for rapidly growing urban consumer markets of dual economies are badly needed. The marketing forecasting task is complicated by a lack of resources and data. This article explores a possibility to overcome these constraints by using projections based on income elasitcites. Estimation and projection regression models are constructed and applied, using cross-sectional household income and expenditure data for various urban South African population groups. Based on relatively favorable comparisons with some alternative extrapolations and the actual data, replication in other similar markets seems possible. The development of more comprehensive and realistic models should be undertaken as additional data become available.