Deconstructing Jaco: genetic heritage of an Afrikaner

Tendon and Ligament Genetics: How Do They Contribute to Disease and Injury? A Narrative Review

A significant proportion of patients requiring musculoskeletal management present with tendon and ligament pathology. Our understanding of the intrinsic and extrinsic mechanisms that lead to such disabilities is increasing. However, the complexity underpinning these interactive multifactorial elements is still not fully characterised. Evidence highlighting the genetic components, either reducing or increasing susceptibility to injury, is increasing. This review examines the present understanding of the role genetic variations contribute to tendon and ligament injury risk. It examines the different elements of tendon and ligament structure and considers our knowledge of genetic influence on form, function, ability to withstand load, and undertake repair or regeneration. The role of epigenetic factors in modifying gene expression in these structures is also explored. It considers the challenges to interpreting present knowledge, the requirements, and likely pathways for future research, and whether such information has reached the point of clinical utility.

Prioritization of candidate genes for a South African family with Parkinson's disease using in-silico tools

Parkinson's disease (PD) is a neurodegenerative disorder exhibiting Mendelian inheritance in some families. Next-generation sequencing approaches, including whole exome sequencing (WES), have revolutionized the field of Mendelian disorders and have identified a number of PD genes. We recruited a South African family with autosomal dominant PD and used WES to identify a possible pathogenic mutation. After filtration and prioritization, we found five potential causative variants in CFAP65, RTF1, NRXN2, TEP1 and CCNF. The variant in NRXN2 was selected for further analysis based on consistent prediction of deleteriousness across computational tools, not being present in unaffected family members, ethnic-matched controls or public databases, and its expression in the substantia nigra. A protein model for NRNX2 was created which provided a three-dimensional (3D) structure that satisfied qualitative mean and global model quality assessment scores. Trajectory analysis showed destabilizing effects of the variant on protein structure, indicated by high flexibility of the LNS-6 domain adopting an extended conformation. We also found that the known substrate N-acetyl-D-glucosamine (NAG) contributed to restoration of the structural stability of mutant NRXN2. If NRXN2 is indeed found to be the causal gene, this could reveal a new mechanism for the pathobiology of PD.

Patterns of African and Asian admixture in the Afrikaner population of South Africa

BACKGROUND

The Afrikaner population of South Africa is the descendants of European colonists who started to colonize the Cape of Good Hope in the 1600s. In the early days of the colony, mixed unions between European males and non-European females gave rise to admixed children who later became incorporated into either the Afrikaner or the Coloured populations of South Africa. Differences in ancestry, social class, culture, sex ratio and geographic structure led to distinct and characteristic admixture patterns in the Afrikaner and Coloured populations. The Afrikaner population has a predominant European composition, whereas the Coloured population has more diverse ancestries. Genealogical records previously estimated the contribution of non-Europeans into the Afrikaners to be between 5.5 and 7.2%.

RESULTS

To investigate the genetic ancestry of the Afrikaner population today (11-13 generations after initial colonization), we genotyped approximately five million genome-wide markers in 77 Afrikaner individuals and compared their genotypes to populations across the world to determine parental source populations and admixture proportions. We found that the majority of Afrikaner ancestry (average 95.3%) came from European populations (specifically northwestern European populations), but that almost all Afrikaners had admixture from non-Europeans. The non-European admixture originated mostly from people who were brought to South Africa as slaves and, to a lesser extent, from local Khoe-San groups. Furthermore, despite a potentially small founding population, there is no sign of a recent bottleneck in the Afrikaner compared to other European populations. Admixture amongst diverse groups from Europe and elsewhere during early colonial times might have counterbalanced the effects of a small founding population.

CONCLUSIONS

While Afrikaners have an ancestry predominantly from northwestern Europe, non-European admixture signals are ubiquitous in the Afrikaner population. Interesting patterns and similarities could be observed between genealogical predictions and our genetic inferences. Afrikaners today have comparable inbreeding levels to current-day European populations.

A molecular analysis of the GBA gene in Caucasian South Africans with Parkinson's disease

Background

The molecular basis of Parkinson's disease in South African population groups remains elusive. To date, substitutions in the GBA gene are the most common large‐effect genetic risk factor for Parkinson's disease. The primary objective of this study was to determine the prevalence of GBA substitutions in South Africans with idiopathic Parkinson's disease.

Methods

Participants were recruited from tertiary hospitals in the Gauteng Province in South Africa. All participants were screened for substitutions in GBA exon 8‐11 and the full coding region was analysed in 20 participants. Peripheral β‐glucocerebrosidase enzymatic activity of GBA‐carriers was measured in mixed leukocytes.

Results

Of 105 Caucasian Parkinson's disease participants (82.7% Afrikaner) with an average age of disease onset of 61.9 ± 12.2 years and 40 controls (age 73.4 ± 12.4 years) were included. Heterozygous GBA substitutions were identified in 12.38% of affected participants (p.G35A, p.E326K, p.I368T, p.T369M, p.N370S, p.P387L and p.K441N) and 5.00% of controls (p.E326K and p.T369M). The substitutions ranged from predicted benign to moderately damaging; with p.E326K and p.T369M most prevalent, followed by the Afrikaner Gaucher disease substitution p.P387L. Severe Gaucher disease mutations, like p.L444P, were absent in this cohort. Enzyme activity analysis revealed a nonsignificant reduction in the GBA‐Parkinson's disease individuals (14.49 ± 2.30 nmol/h/mg protein vs. 15.98 ± 3.06 nmol/h/mg in control samples). GBA substitutions occur in both young‐onset and late‐onset Parkinson's cases in the cohort.

Conclusion

Mild GBA substitutions that may not cause Gaucher disease were a common risk factor for Parkinson's disease in the participant group.

Population differences in the postcrania of modern South Africans and the implications for ancestry estimation

The cranium is widely recognized as the most important skeletal element to use when evaluating population differences and estimating ancestry. However, the cranium is not always intact or available for analysis, which emphasizes the need for postcranial alternatives. The purpose of this study was to quantify postcraniometric differences among South Africans that can be used to estimate ancestry. Thirty-nine standard measurements from 11 postcranial bones were collected from 360 modern black, white and coloured South Africans; the sex and ancestry distribution were equal. Group differences were explored with analysis of variance (ANOVA) and Tukey's honestly significant difference (HSD) test. Linear and flexible discriminant analysis (LDA and FDA, respectively) were conducted with bone models as well as numerous multivariate subsets to identify the model and method that yielded the highest correct classifications. Leave-one-out (LDA) and k-fold (k=10; FDA) cross-validation with equal priors were used for all models. ANOVA and Tukey's HSD results reveal statistically significant differences between at least two of the three groups for the majority of the variables, with varying degrees of group overlap. Bone models, which consisted of all measurements per bone, resulted in low accuracies that ranged from 46% to 63% (LDA) and 41% to 66% (FDA). In contrast, the multivariate subsets, which consisted of different variable combinations from all elements, achieved accuracies as high as 85% (LDA) and 87% (FDA). Thus, when using a multivariate approach, the postcranial skeleton can distinguish among three modern South African groups with high accuracy.

Three hundred years of low non-paternity in a human population

When cuckoldry is frequent we can expect fathers to withhold investment in offspring that may not be theirs. Human paternal investment can be substantial and is in line with observations from tens of thousands of conceptions that suggest that cuckoldry is rare in humans. The generality of this claim seems to be in question as the rate of cuckoldry varies across populations and studies have mostly been on Western populations. Two additional factors complicate our conclusions, (1) current estimates of the rate of cuckoldry in humans may not reflect our past behaviour as adultery can be concealed by the use of contraceptives; and (2) it is difficult to obtain samples that are random with respect to their paternity certainty. Studies that combine genealogies with Y-chromosome haplotyping are able to circumvent some of these problems by probing into humans' historical behaviour. Here we use this approach to investigate 1273 conceptions over a period of 330 years in 23 families of the Afrikaner population in South Africa. We use haplotype frequency and diversity and coalescent simulations to show that the male population did not undergo a severe bottleneck and that paternity exclusion rates are high for this population. The rate of cuckoldry in this Western population was 0.9% (95% confidence interval 0.4-1.5%), and we argue that given the current data on historical populations we have to conclude that, at least for Western human populations, cuckoldry rate is probably in the range of 1%.

Clinical and genetic characterization of a founder PKHD1 mutation in Afrikaners with ARPKD

BACKGROUND

Autosomal recessive polycystic kidney disease (ARPKD; MIM 263200) occurs in 1:20,000 live births. Disease expression is widely variable, with approximately 30 % of affected neonates dying perinatally, while others survive to adulthood. Mutations at the PKHD1 locus are responsible for all typical presentations. The objectives of this study were to define the clinical and genetic characteristics in a cohort of South African patients of Afrikaner origin, a population with a high prevalence of ARPKD.

METHODS

DNA from the cohort was analyzed for background haplotypes and the p.M627K mutation previously identified in two unrelated Afrikaner patients. The clinical phenotype of the homozygous group was characterized.

RESULTS

Analysis of 36 Afrikaner families revealed that 27 patients, from 24 (67 %) families, were homozygous for the p.M627K substitution, occurring on a common haplotype. The clinical phenotype of the homozygous individuals was variable.

CONCLUSIONS

Our data provide strong evidence that the p.M627K substitution is a founder mutation in the Afrikaner population and can be used for streamlined diagnostic testing for at-risk pregnancies. The observed clinical variability suggests that disease expression is modulated by other genetic loci or by gene-environment interactions.

Genetic diversity in black South Africans from Soweto

Background

Due to the unparalleled genetic diversity of its peoples, Africa is attracting growing research attention. Several African populations have been assessed in global initiatives such as the International HapMap and 1000 Genomes Projects. Notably excluded, however, is the southern Africa region, which is inhabited predominantly by southeastern Bantu-speakers, currently suffering under the dual burden of infectious and non-communicable diseases. Limited reference data for these individuals hampers medical research and prevents thorough understanding of the underlying population substructure. Here, we present the most detailed exploration, to date, of genetic diversity in 94 unrelated southeastern Bantu-speaking South Africans, resident in urban Soweto (Johannesburg).

Results

Participants were typed for ~4.3 million SNPs using the Illumina Omni5 beadchip. PCA and ADMIXTURE plots were used to compare the observed variation with that seen in selected populations worldwide. Results indicated that Sowetans, and other southeastern Bantu-speakers, are a clearly distinct group from other African populations previously investigated, reflecting a unique genetic history with small, but significant contributions from diverse sources. To assess the suitability of our sample as representative of Sowetans, we compared our results to participants in a larger rheumatoid arthritis case–control study. The control group showed good clustering with our sample, but among the cases were individuals who demonstrated notable admixture.

Conclusions

Sowetan population structure appears unique compared to other black Africans, and may have clinical implications. Our data represent a suitable reference set for southeastern Bantu-speakers, on par with a HapMap type reference population, and constitute a prelude to the Southern African Human Genome Programme.

Appel Botha: The abc of a three hundred year old divorce case

In 1683 Maria Kickers and Jan Cornelitz got married in Cape Town. Today, 330 years later, the living patrilineal descendants of Maria's four sons, number in excess of 76,000 people. Curiously, none of them carry the surname Cornelitz - in fact, they are all called Botha and include former President P.W. Botha, general Louis Botha and Minister Pik Botha. The reason for this anomaly is also the reason why Jan got divorced from Maria in 1700. According to Maria's testimonies she did indeed have a long term relationship with Frederik Botha, but in her defence she claimed that her husband was impotent and that he actually encouraged her. Other witnesses, presumably prompted by Jan, gave testimonies that implied that Maria was in fact licentious. We combined haplotyping with the AmpFℓSTR(®) Yfiler™ kit with deep-rooting genealogies to show that Maria's first son was actually fathered by Ferdinandus Appel and that roughly half the living Bothas (38,000 people) actually descend from Ferdinandus Appel while the remaining three sons all stem from the same father, presumably Frederik Botha, and this implies that Maria's husband did not father any of her sons.

Pharmacogenomic Research in South Africa: Lessons Learned and Future Opportunities in the Rainbow Nation

South Africa, like many other developing countries, stands to benefit from novel diagnostics and drugs developed by pharmacogenomics guidance due to high prevalence of disease burden in the region. This includes both communicable (e.g., HIV/AIDS and tuberculosis) and non-communicable (e.g., diabetes and cardiovascular) diseases. For example, although only 0.7% of the world's population lives in South Africa, the country carries 17% of the global HIV/AIDS burden and 5% of the global tuberculosis burden. Nobel Peace Prize Laureate Archbishop Emeritus Desmond Tutu has coined the term Rainbow Nation, referring to a land of wealth in its many diverse peoples and cultures. It is now timely and necessary to reflect on how best to approach new genomics biotechnologies in a manner that carefully considers the public health needs and extant disease burden in the region. The aim of this paper is to document and review the advances in pharmacogenomics in South Africa and importantly, to evaluate the direction that future research should take. Previous research has shown that the populations in South Africa exhibit unique allele frequencies and novel genetic variation in pharmacogenetically relevant genes, often differing from other African and global populations. The high level of genetic diversity, low linkage disequilibrium and the presence of rare variants in these populations question the feasibility of the use of current commercially available genotyping platforms, and may partially account for genotype-phenotype discordance observed in past studies. However, the employment of high throughput technologies for genomic research, within the context of large clinical trials, combined with interdisciplinary studies and appropriate regulatory guidelines, should aid in acceleration of pharmacogenomic discoveries in high priority therapeutic areas in South Africa. Finally, we suggest that projects such as the H3Africa Initiative, the SAHGP and PGENI should play an integral role in the coordination of genomic research in South Africa, but also other African countries, by providing infrastructure and capital to local researchers, as well as providing aid in addressing the computational and statistical bottlenecks encountered at present.

SNaPshot minisequencing to resolve mitochondrial macro-haplogroups found in Africa

African mitochondrial DNA (mtDNA) haplogroups are divided into seven macro-haplogroups (L0'1'2'3'4'5'6), while the rest of the world's lineages are classified as subgroups of macro-haplogroups M, N and R. The most common approach to characterizing mtDNA variation is the sequencing of hypervariable segments I and II of the non-coding control region of the molecule. Given the higher mutation rate within the control region compared with the coding regions of the molecule, recurrent mutations in the former can sometimes hide possible phylogenetic structure. The incorporation of haplogroup-defining coding region mutations has helped in overcoming this limitation. By judiciously selecting 14 coding region SNPs and incorporating them into a multiplex minisequencing assay we were able to resolve mtDNA sequences from some sub-Saharan African populations into ten macro-haplogroups (L0-L6, M, N and R). We tested the efficacy of the panel by screening 699 individuals, consisting mostly of Khoe-San, Bantu speakers and individuals with mixed ancestries (Coloreds) and found no inconsistencies compared with hypervariable segment sequencing results. The panel provided a fast and efficient means of classifying mtDNA into the ten mitochondrial macro-haplogroups and provided a reliable screening to distinguish African from non-African-derived mtDNA lineages.

Of founder populations, long QT syndrome, and destiny

Founder populations, characterized by a single ancestor affected by long QT syndrome (LQTS) and by a large number of individuals and families who all are related to the ancestor and thereby carry the same disease-causing mutation, represent the ideal human model for studying the role of "modifier genes" in LQTS. This article reviews some of the fundamental concepts related to founder populations and provides the necessary historical background to understand why so many can be found in South Africa. The focus then moves to a specific LQT1 founder population, carrier of the A341V mutation, that has been studied extensively during the last 10 years and has provided a significant amount of previously unforeseen information. These novel findings range from an unusually high clinical severity not explained by the electrophysiologic characteristics of the mutation, to the importance of tonic and reflex control of heart rate for risk stratification, to the identification of the first modifier genes for clinical severity of LQTS.