Elizabeth J. van Rensburg

Elucidating the genetic architecture of familial schizophrenia using rare copy number variant and linkage scans

To elucidate the genetic architecture of familial schizophrenia we combine linkage analysis with studies of fine-level chromosomal variation in families recruited from the Afrikaner population in South Africa. We demonstrate that individually rare inherited copy number variants (CNVs) are more frequent in cases with familial schizophrenia as compared to unaffected controls and affect almost exclusively genic regions. Interestingly, we find that while the prevalence of rare structural variants is similar in familial and sporadic cases, the type of variants is markedly different. In addition, using a high-density linkage scan with a panel of nearly 2,000 markers, we identify a region on chromosome 13q34 that shows genome-wide significant linkage to schizophrenia and show that in the families not linked to this locus, there is evidence for linkage to chromosome 1p36. No causative CNVs were identified in either locus. Overall, our results from approaches designed to detect risk variants with relatively low frequency and high penetrance in a well-defined and relatively homogeneous population, provide strong empirical evidence supporting the notion that multiple genetic variants, including individually rare ones, that affect many different genes contribute to the genetic risk of familial schizophrenia. They also highlight differences in the genetic architecture of the familial and sporadic forms of the disease.

Large genomic rearrangements of the BRCA1 and BRCA2 genes: review of the literature and report of a novel BRCA1 mutation.

Germline mutations in BRCA1 and BRCA2 increase the risk for developing breast and ovarian cancer. Previously, the techniques available allowed only for the identification of small genomic alterations, but the dawn of new technology now allows for the rapid detection of large genomic rearrangements (LGRs). LGRs in BRCA1 are responsible for between 0 and 27% of all BRCA1 disease-causing mutations identified in numerous populations. Such alterations are far less common in the BRCA2 gene. To determine the impact of BRCA1 and BRCA2 LGRs in South Africa, 52 hereditary breast and/or ovarian South African families (36 were Afrikaners) were screened for BRCA1 and BRCA2 LGRs using multiplex ligation-dependent probe amplification. These patients were previously shown to be BRCA1 and BRCA2 small mutation negative. One LGR was detected in BRCA1 in a South African family with Greek ancestry. This is a novel deletion of both exons 23 and 24 (NG_005905.2:g.169527_180579del). This first study of BRCA rearrangements in South Africa reveals that LGRs comprise ~3% of identified BRCA1 mutations, a low rate in comparison to other populations. In addition, we have reviewed all 98 previously characterized BRCA1/2 LGRs and re-named them according to the recommended HGVS nomenclature, using the recently released RefSeqGene records, NG_005905.2 and NG_012772.1 for BRCA1 and BRCA2. A standardized resource is now provided which will assist researchers in determining whether their LGRs are novel. Furthermore, we have clarified some of the previously misunderstood rules of nomenclature, which will make uniform reporting of BRCA1/2 easier in the future.

BRCA1 R1699Q variant displaying ambiguous functional abrogation confers intermediate breast and ovarian cancer risk

Background Clinical classification of rare sequence changes identified in the breast cancer susceptibility genes BRCA1 and BRCA2 is essential for appropriate genetic counselling of individuals carrying these variants. We previously showed that variant BRCA1 c.5096G>A p.Arg1699Gln in the BRCA1 transcriptional transactivation domain demonstrated equivocal results from a series of functional assays, and proposed that this variant may confer low to moderate risk of cancer. Methods Measures of genetic risk (report of family history, segregation) were assessed for 68 BRCA1 c.5096G>A p.Arg1699Gln (R1699Q) families recruited through family cancer clinics, comparing results with 34 families carrying the previously classified pathogenic BRCA1 c.5095C>T p.Arg1699Trp (R1699W) mutation at the same residue, and to 243 breast cancer families with no BRCA1 pathogenic mutation (BRCA-X). Results Comparison of BRCA1 carrier prediction scores of probands using the BOADICEA risk prediction tool revealed that BRCA1 c.5096G>A p.Arg1699Gln variant carriers had family histories that were less ‘BRCA1-like’ than BRCA1 c.5095C>T p.Arg1699Trp mutation carriers (p<0.00001), but more ‘BRCA1-like’ than BRCA-X families (p=0.0004). Further, modified segregation analysis of the subset of 30 families with additional genotyping showed that BRCA1 c.5096G >A p.Arg1699Gln had reduced penetrance compared with the average truncating BRCA1 mutation penetrance (p=0.0002), with estimated cumulative risks to age 70 of breast or ovarian cancer of 24%. Conclusions Our results provide substantial evidence that the BRCA1 c.5096G>A p.Arg1699Gln (R1699Q) variant, demonstrating ambiguous functional deficiency across multiple assays, is associated with intermediate risk of breast and ovarian cancer, highlighting challenges for risk modelling and clinical management of patients of this and other potential moderate-risk variants.

BRCA1 mutations in South African breast and/or ovarian cancer families: Evidence of a novel founder mutation in Afrikaner families

Germ‐line mutations within BRCA1 are responsible for different proportions of inherited susceptibility to breast/ovarian cancer, and the spectrum of mutations within this gene is often unique to certain populations. At this time, there have been no reports regarding the role of BRCA1 in South African breast and/or ovarian cancer families. We therefore screened 90 South African breast/ovarian cancer families for BRCA1 mutations by means of PCR‐based mutation detection assays. Eighteen families (20%) were identified with BRCA1 disease‐causing mutations. Four Ashkenazi Jewish families were identified with the 185delAG mutation, whereas 2 Afrikaner and 1 Ashkenazi Jewish family were found to harbor the 5382insC mutation. Five of the families (5.56%), all of whom are Afrikaners, were found to carry the novel E881X mutation. Genotype analyses show that these patients share a common ancestor. Genealogic studies have identified 3 possible founding couples for this mutation, all of whom arrived in the Cape from France in the late 1600s. Of the remaining mutations detected, 3 have not been reported previously and include the S451X, 1493delC (detected twice) and 4957insC mutations.

A possible role of the cytochrome P450c17α gene (CYP17) polymorphism in the pathobiology of uterine leiomyomas from black South African women: a pilot study

Background.  To investigate the role of the CYP17 gene promoter polymorphism in the pathobiology of uterine leiomyomas in African and Caucasian women.

DNA supercoiled domains and radiosensitivity of subpopulations of human peripheral blood lymphocytes

Enriched human B- and T-lymphocyte subpopulations were isolated by means of a Percoll step gradient centrifugation procedure. 60Co gamma-irradiation dose-response curves for these subpopulations were obtained by applying a modified nucleoid sedimentation technique, which was also employed for the determination of the superhelical content by means of ethidium bromide intercalation. Although a similarity in the average superhelical density of B- and T1-lymphocytes was shown, B-lymphocytes exhibited a more pronounced reduction in sedimentation ratio, suggesting a higher radiosusceptibility than the T1-lymphocytes. By applying the single hit kinetics of the target theory to the dose-response curves, an estimation of the supercoil domain sizes was made: B- cells, 5.5 X 10(9), 1.78 X 10(9) and 7.78 X 10(8) D; T-cells, 4.55 X 10(9), 1.75 X 10(9) and 7.67 X 10(8) D. The differences in radiosensitivity of lymphocyte subpopulations can not, therefore, be entirely ascribed to differences in DNA superstructure.

Changes in DNA Supercoiling during Repair of Gamma-radiation-induced Damage

Enriched human B-lymphocyte and T-lymphocyte subpopulations were isolated by means of two Percoll density gradient centrifugation steps. Strand-break repair kinetics of 60Co gamma-irradiation-damaged DNA were obtained by applying a modified nucleoid sedimentation technique. Although no variations in the strand-break repair patterns of B-cells and T-cells within an individual could be detected, variations between individuals were evident. Changes in DNA supercoiling during the repair process were studied by means of ethidium bromide intercalation. The supercoiled conformation of DNA in peripheral lymphocyte subpopulations displayed similar undulating patterns within an individual, variations occurring between individuals. The results of this study indicate that alterations to the higher-order structure (supercoiling) of DNA are integral to the repair process.

Report of a Black South African Child With Oculodentodigital Dysplasia and a Novel GJA1 Gene Mutation

Liviu Feller,* Neil H. Wood, Michelle D. Sluiter, Claudia Noffke, Erich J. Raubenheimer, Johan Lemmer, and Elizabeth J. van Rensburg Department of Periodontology and Oral Medicine, School of Dentistry, University of Limpopo (Medunsa Campus), Pretoria, South Africa Department of Genetics, University of Pretoria, Pretoria, South Africa Section of Maxillo-Facial Radiology, School of Dentistry, University of Limpopo (Medunsa Campus), Pretoria, South Africa Department of Oral Pathology, School of Dentistry, University of Limpopo (Medunsa Campus), Pretoria, South Africa

A plate method for demonstrating the breakdown of heparin and chrondroitin sulphate by bacteria

Abstract A plate method for demonstrating the breakdown of heparin and chondroitin sulphate by bacteria is described. The medium contained phytone, yeast extract and either heparin or chondroitin sulphate as organic nutrients. Sulphate, which is released by the breakdown of heparin or chondroitin sulphate, combined with barium chloride in the medium to form a white precipitate of barium sulphate on the plates.

Effect of novobiocin on gamma-radiation-induced dna repair in human lymphocyte subpopulations

1. DNA repair was measured in 3 Gy gamma-irradiated human peripheral lymphocyte subpopulations by means of nucleoid sedimentation. 2. The influence of the antibiotic, novobiocin (an inhibitor of inter alia topoisomerase II) on the repair process was investigated. 3. Repair of 33 37% of the DNA lesions induced by gamma-irradiation in enriched B lymphocyte fractions, was retarded by novobiocin. 4. Repair in enriched T lymphocyte fractions was unaffected by novobiocin.