Background. Haemoglobinopathies are seen mostly in regions where malaria occurs or has occurred, but population migration has resulted in affected individuals being identified in many countries globally. The first molecular genetics services for diagnostic testing and prenatal diagnosis were established, both worldwide and in South Africa (SA), for haemoglobinopathies.
Objective. To analyse the diagnostic service offered by the Division of Human Genetics, National Health Laboratory Service and University of the Witwatersrand, from 1983 to 2012.
Methods. A retrospective file analysis (N=1 249) was performed for all individuals who had molecular genetic testing for α-thalassaemia, β-thalassaemia and sickle cell anaemia to examine indications for testing, population origins of patients and molecular genetics findings.
Results. The α-thalassaemia testing was requested predominantly to explain microcytic hypochromic haematological indices. Five α-globin deletions were identified, the most common being the -α3.7, in individuals of different ethnicities. For β-thalassaemia and sickle cell anaemia, most testing was performed for prenatal diagnosis purposes. For sickle cell anaemia, most prenatal tests were requested by African families. The β-thalassaemia families were mostly of Indian or Mediterranean origin. The most common mutation identified in all Indian groups was IVS1 nt5 (G>C) (c.92+5G>C) and in individuals from the Mediterranean, IVS1 nt110 (G>A) (c.93-21G>A).
Conclusion. The molecular genetics service for haemoglobinopathies in SA is comprehensive and specific to the needs of local ethnic groups. Clinically significant haemoglobinopathies occur at significant frequencies in specific high-risk ethnic groups. Appropriate screening programmes should be initiated so that genetic counselling and reproductive options can be offered.
Background. Fragile X syndrome (FXS), the most common inherited cause of intellectual disability (ID) worldwide, is caused by the expansion of a CGG repeat in the fragile X mental retardation gene (FMR-1) gene.
Objectives. To review, retrospectively, the genetic services for FXS and other FMR-1-related disorders - including fragile X-associated tremor/ataxia syndrome (FXTAS) and FMR-1-related primary ovarian insufficiency (POI) - at the Division of Human Genetics, Johannesburg, for diagnostic, carrier and prenatal genetic testing.
Methods. The records of 2 690 patients with ID and suspected FXS (ID/?FXS) who had genetic testing for FMR-1 between 1992 and 2012 were reviewed. Of these, 2 239 had diagnostic testing, 430 carrier or cascade testing and 17 prenatal testing for FXS. Four had FXTAS or POI testing. Polymerase chain reaction (PCR) and/or Southern blotting techniques were used to test the patientsâ?? samples for FMR-1 and FMR-2 expansions.
Results. Of the 2 239 patients who had diagnostic testing, 128 (5.7%) had a full mutation, 12 (0.5%) had a premutation and 43 (1.9%) an intermediate allele. In 17 prenatal tests, eight foetuses tested positive for FXS. FMR-1 CGG repeat distribution analysis in 1 532 males negative for the FMR-1 expansion showed that 29 and 30 CGG repeats were the most common (61.1%), but distribution was significantly different in the black and white populations.
Conclusion. The findings support the presence of FXS, as the most common cause of ID, in all local populations. The FMR-1 CGG repeat distribution varied from that found in other studies. The number of family members tested was relatively low suggesting that many at-risk individuals are not being referred.
Background. Genetic testing for Duchenne/Becker muscular dystrophy (DMD/BMD) mutations initially involved multiplex polymerase chain reaction (mPCR), which targeted two mutation hotspots in the gene and detected deletions in affected males. A newer technology, multiplex ligation-dependent probe amplification (MLPA), was introduced for diagnostic testing in 2007.
Objectives. To evaluate MLPA relative to mPCR as a technique for DMD/BMD diagnostic testing and to establish whether the mutation profile in affected individuals differs between different South African ethnic groups.
Methods. From January 2000 - May 2007, genetic diagnostic testing for DMD/BMD was undertaken in 128 male patients using mPCR. From May 2007 onwards, MLPA replaced this technique and 261 males were investigated. MLPA is a kit-based technology available from MRC-Holland.
Results. Of the 128 and 261 probands tested using mPCR and MLPA, respectively, 31% and 34% were found to carry a deletion mutation. Further, MLPA could detect duplication mutations (11.5%), complex rearrangements (1.5%) and small mutations (1.5%). In black patients, deletion mutations were found to cluster in the 3' region of the gene. No population-specific pathogenic mutations were found.
Conclusions. The mutation detection rate for mPCR and MLPA is similar for deletion mutations, but MLPA proved to be a better diagnostic approach as it could detect other types of mutations as well, including duplications, complex rearrangements and small mutations. MLPA could also diagnose mutation status in at-risk female relatives, which is not possible with mPCR.
Background. Null alleles complicate parentage testing because they do not contribute positively to phenotypes.
Objectives. To survey South African populations for null alleles at short tandem repeat (STR) loci used in parentage testing.
Methods. Paternity case data were scanned for apparent contradictions compared with Mendelian inheritance that could be due to null alleles. Estimates of null allele frequencies were obtained from tallies of apparent carriers.
Results. Three of 15 loci appeared to have null alleles at appreciable frequencies and five showed no evidence of null alleles. A null allele at the vWA locus reached a frequency of ~0.3% in the black population and approximately three times this frequency in the coloured population. No apparent vWA null carriers were detected in whites suggesting that the Khoisan were the major contributors of the null alleles to coloureds. The apparent genotypes of a sample of TPOX null carriers changed from homozygous to heterozygous when they were retyped using different polymerase chain reaction primers. The revealed allele was allele 6 in every case. A D13S317 null allele was detected at relatively low frequencies in the black and coloured samples but 2/145 Indian (Asian) parents appear to be carriers, suggesting that it could be common in Indians.
Conclusion. Three of the 15 forensically relevant STR loci investigated had null alleles at significant frequencies in South African populations. Failure to allow for the presence of null alleles can have a large impact on the outcome of parentage tests.
Background. Previous historical, anthropological and genetic data provided overwhelming support for the Semitic origins of the Lemba, a Bantu-speaking people in southern Africa.
Objective. To revisit the question concerning genetic affinities between the Lemba and Jews.
Methods. Y-chromosome variation was examined in two Lemba groups: one from South Africa (SA) and, for the first time, a group from Zimbabwe (Remba), to re-evaluate the previously reported Jewish link.
Results. A sample of 261 males (76 Lemba, 54 Remba, 43 Venda and 88 SA Jews) was initially analysed for 16 bi-allelic and 6 short tandem repeats (STRs) that resulted in the resolution of 102 STR haplotypes distributed across 13 haplogroups. The non-African component in the Lemba and Remba was estimated to be 73.7% and 79.6%, respectively. In addition, a subset of 91 individuals (35 Lemba, 24 Remba, 32 SA Jews) with haplogroup J were resolved further using 6 additional bi-allelic markers and 12 STRs to screen for the extended Cohen modal haplotype (CMH). Although 24 individuals (10 Lemba and 14 SA Jews) were identified as having the original CMH (six STRs), only one SA Jew harboured the extended CMH.
Conclusions. While it was not possible to trace unequivocally the origins of the non-African Y chromosomes in the Lemba and Remba, this study does not support the earlier claims of their Jewish genetic heritage.
People with birth defects have been stigmatised, marginalised and discriminated against for millennia, diminishing their human dignity and abrogating their human rights. Beginning with the United Nations Universal Declaration of Human Rights, promulgated in 1947, the circumstances in which human dignity in healthcare for people with birth defects could be achieved arose, and this was accomplished over the next 65 years through the insight, hard work and dedication of a select group of people and organisations. In 2010 the World Health Organization prioritised services for the care and prevention of birth defects, particularly in middle- and low-income countries. Translating what has been achieved into human rights in healthcare for people with birth defects is the next objective.
Parent support/patient advocacy groups for rare genetic disorders have emerged as an important force. They provide information, encourage research (both by participation in research and by raising money for research), give families and affected family members the opportunity to learn from each other, and open the way for social and intellectual interaction between families, affected individuals, researchers and healthcare providers. New IT technologies increase the opportunities for collaboration and information exchange around the world. These groups have become an important resource for families, genetic counsellors and medical/clinical genetic professionals.
The practice of genetic counselling gives rise to many ethical dilemmas, and counsellors need to be familiar with the principles of biomedical ethics. The primary principles include respect for autonomy, beneficence, non-maleficence and justice. A case of identical twins at 50% risk for Huntington's disease, in which only one twin sought predictive testing for this dominantly inherited disease, created several ethical dilemmas. Another case where predictive testing was carried out on two young children, at high risk, by a laboratory at the request of an adoption agency and a doctor, with a view to giving information to the foster parents, also posed many ethical conundrums for the counsellor. The ethical issues that arose in these cases are discussed in this paper.
Background. At-risk women of advanced maternal age (AMA) can choose to have second-trimester invasive testing for a prenatal genetic diagnosis on the foetus. Being HIV-positive can complicate the decision-making process.
Objective. To document HIV status and prenatal genetic diagnosis choices in women of AMA attending genetic clinics in Johannesburg, South Africa, for counselling on the risks of abnormalities in their foetuses.
Methods. Data on the characteristics of the sample, HIV status and prenatal diagnosis decisions were collected retrospectively from the files of 350 women (>34 years) counselled for AMA in genetic clinics in Johannesburg and Pretoria. The time period was 6 months in 2003 and 6 months in 2004. A sample of the women (n=15) who were HIV-positive were interviewed and completed questionnaires on their understanding of their situation. The data were analysed and submitted to statistical testing.
Results. Of the 350 women, 183 (52.3%) were HIV-negative, 44 (12.6%) HIV-positive, and 123 (35.1%) of unknown status. Significantly more HIV-negative patients (79/183, 43.2%) than those who were HIV-positive (6/44, 13.6%) had amniocentesis performed for foetal diagnosis. Most of the interviewed women (12/15, 80.0%) understood the severity of HIV infection, 5 (33.3%) considered termination of pregnancy based on the transmission risk, and 4 (26.7%) would have requested amniocentesis and prenatal diagnosis if they had been HIV-negative.
Conclusion. Decision-making regarding prenatal genetic diagnosis is influenced by HIV status among older women. Effective access to highly active antiretroviral therapy throughout pregnancy would make decision-making easier for these women.
Cannibalism has been poorly understood and has seldom been studied, since it was often suppressed by missionaries and colonial administrators, and very few societies still practise it. Cannibalistic practices are more complex than was originally thought. They may be supported in societies under stress or in times of famine, to reflect aggression and antisocial behaviour (in cases where the bodies of enemies killed in battle or people who have harmed the family are eaten), or to honour a dead kinsman. It was, for example, noted in Madagascar during the imperial campaigns of Ranavalona I in the period 1829 - 1853. Two types of cannibalism have been described: exocannibalism, where enemies were consumed, and endocannibalism, where dead relatives were eaten to assist their passing to the world of the ancestors, or to prolong contact with beloved and admired family members and absorb their good qualities. This article reviews some of the beliefs and motivations that surrounded the cannibalistic practices of the people of Madagascar in the 19th century.
Spirometry forms an important component in the diagnosis and management of pulmonary diseases in children. In the paediatric setting, there are different challenges in terms of performance and interpretation of good quality and reliable tests. An awareness of the physiological and developmental aspects that exist in children is necessary to improve the quality and reliability of spirometry. We reviewed the recommendations on the technical aspects of performing spirometry in children, from the available guidelines and clinical trials. The focus was on the indications, methods and the interpretation of lung function tests in children <12 years of age. Reliable lung function testing can be performed in children, but an awareness of the limitations, the use of incentives and a dedicated lung function technologist are necessary.