Extended haplotype studies in South African and Dutch variegate porphyria families carrying the recurrent p.R59W mutation confirm a common ancestry.

BACKGROUND: Variegate porphyria (VP) is due to a partial deficiency of protoporphyrinogen oxidase (PPOX), the seventh enzyme in the haem biosynthetic pathway. Clinically, VP is characterized by photosensitivity and acute neurovisceral attacks that can manifest separately or together in affected individuals. The disease is inherited in an autosomal dominant fashion with incomplete penetrance and PPOX gene mutations associated with VP are usually unique to patients and their families. In South Africa, however, VP is highly prevalent as the result of a founder mutation, designated p.R59W. Previous genealogical and haplotype studies showed a link between South African and Dutch carriers of p.R59W and it was suggested that this mutation was introduced to South Africa by Dutch settlers at the end of the 17th century. OBJECTIVES: To perform extended haplotype analysis in six South African and Dutch VP families with the p.R59W mutation. METHODS: Haplotyping of 13 microsatellite markers flanking the PPOX gene on chromosome 1q22-23 and five informative single nucleotide polymorphisms within and around the gene. RESULTS: A core haplotype cosegregated in all families studied. CONCLUSIONS: Our data deliver further confirmation that the South African and Dutch VP families carrying mutation p.R59W shared a common ancestor.

Population genetic structure of economically important Tortricidae (Lepidoptera) in South Africa: a comparative analysis.

Comparative studies of the population genetic structures of agricultural pests can elucidate the factors by which their population levels are affected, which is useful for designing pest management programs. This approach was used to provide insight into the six Tortricidae of major economic importance in South Africa. The population genetic structure of the carnation worm E. acerbella and the false codling moth T. leucotreta, analyzed using amplified fragment length polymorphism (AFLP) analysis, is presented here for the first time. These results were compared with those obtained previously for the codling moth Cydia pomonella, the oriental fruit moth Grapholita molesta, the litchi moth Cryptophlebia peltastica and the macadamia nut borer T. batrachopa. Locally adapted populations were detected over local geographic areas for all species. No significant differences were found among population genetic structures as result of population history (whether native or introduced) although host range (whether oligophagous or polyphagous) had a small but significant effect. It is concluded that factors such as dispersal ability and agricultural practices have the most important effects on genetically structuring populations of the economically important Tortricidae in South Africa.

Functional analysis of the 5' regulatory region of the 5-aminolevulinate synthase (ALAS1) gene in response to estrogen.

Genetic defects in the heme synthesis enzymes lead to a group of heterogeneous disorders termed the porphyrias. Numerous factors influence the clinical expression of porphyrias, primarily by altering the rate of heme synthesis. To date, no genotype-phenotype correlation has been made to explain the variable penetrance observed in variegate porphyria (VP) and other acute hepatic porphyrias. As first and rate determining gene in the heme pathway, 5-aminolevulinate synthase-1 (ALAS1), appears to be an ideal candidate modifier. Previous studies established critical mechanisms for ALAS1 regulation and a direct transcriptional response to drugs by defined drug-responsive enhancer sequences (ADRES). To identify possible functional variants within the 5' region of ALAS1, selected regulatory regions, including the ADRES elements, were screened by DNA sequencing analysis in 26 VP patients heterozygous for the causative R59W mutation in the protoporphyrinogen oxidase (PPOX) gene. Two novel variants, -853C>T and -1253T>A were identified. In silico analyses indicated that the -853C>T transition is located immediately 5' to a half-palindromic putative estrogen receptor binding site. Co-transfection experiments with an estrogen receptor-alpha (ERalpha) expression vector in HepG2 cells, suggest that this region mediates an increased transcriptional response in the presence of estrogen (E2) and ERalpha. The wild-type -853C/-1253T allele induced a 47% increase in transcription, while the -853T/-1253A double mutant allele showed a 35% increase in transcription compared to expression in the absence of E2. The highest induction was observed for the mutant -853T/1253T allele that generated an increase of 66%. We conclude that the -853T variant functions as an enhancer in the presence of estrogen and speculates that the -1253A variant reduces transcription activity.

Gene flow among Cydia pomonella (Lepidoptera: Tortricidae) geographic and host populations in South Africa.

Information on gene flow among geographic and host populations of C. pomonella (L.) (Lepidoptera: Tortricidae) in South Africa is lacking, despite the importance of these measures for the success of control practices such as chemical control and sterile insect release, which are affected by the amount of gene flow among populations. Therefore, populations collected from nine geographically distant regions in South Africa from apples, pears, and stone fruit were compared using amplified fragment length polymorphism with five selective primer pairs. Results showed that although populations from different hosts were not genetically differentiated, significant evidence for population substructure was apparent between geographic populations. Over local scales, it was possible to distinguish between populations collected from orchards situated <1 km apart. These results suggest that although extensive gene flow occurs among populations from different hosts, gene flow among local geographic C. pomonella populations may be limited and is explained in terms of limited moth flight, the relative isolation of pome fruit production areas, and the absence of wild hosts.

Two novel point mutations causing receptor-negative familial hypercholesterolemia in a South African Indian homozygote.

Two novel point mutations have been identified in the low density lipoprotein receptor (LDLR) gene of a South African Indian patient with a clinical diagnosis of homozygous familial hypercholesterolemia (FH). The patient is a compound heterozygote, whose paternally-inherited allele has a single base substitution of A to T at position + 1. This conversion of the initiation codon ATG (methionine) to TTG (leucine) would abolish initiation of translation at the normal site, and consequently the synthesis of any normal LDLR molecules. The second mutation identified is a C to A base change at nucleotide position 1176 in exon 8, which creates a stop codon at cysteine-371. Except for previously-described polymorphisms in specific regions of the LDLR gene, the mutations identified in exons 1 and 8 were the only variants observed by screening enzymatically amplified genomic DNA comprising the entire coding and promoter region of the LDLR gene by combined heteroduplex-single-strand conformation polymorphism analysis and by direct sequencing. Cultured cells from the proband expressed no functional LDLR activity and contained no receptor protein that could be detected by antibody binding. These findings are consistent with the nature of the two base changes identified and provide evidence that the mutations cause FH in the proband and his affected family members. The mutations, designated M-21L and C371X, were absent in 17 apparently unrelated Indian hypercholesterolemics and 200 normal chromosomes screened.

Psychiatric genetics in South Africa: cutting a rough diamond.

Psychiatric disorders place a considerable healthcare burden on South African society. Incorporating genetic technologies into future treatment plans offers a potential mechanism to reduce this burden. This review focuses on psychiatric genetic research that has been performed in South African populations with regards to obsessive-compulsive disorder, schizophrenia and bipolar disorder. Preliminary findings from these studies suggest that data obtained in developed countries cannot necessarily be extrapolated to South African population groups. Psychiatric genetic studies in South Africa seem to involve relatively low-cost methodologies and only a limited number of large national collaborative studies. Future research in South Africa should therefore aim to incorporate high-throughput technologies into large scale psychiatric studies through the development of collaborations. On a global level, the vast majority of psychiatric genetic studies have been performed in non-African populations. South Africa, as the leading contributor to scientific research in Africa, may provide a foundation for addressing this disparity and strengthening psychiatric genetic research on the continent. Although the elucidation of the genetic architecture of psychiatric disorders has proved challenging, examining the unique genetic profiles found in South African populations could provide valuable insight into the genetics of psychiatric disorders.

Genetic diversity of woolly apple aphid Eriosoma lanigerum (Hemiptera: Aphididae) populations in the Western Cape, South Africa.

The woolly apple aphid Eriosoma lanigerum (Hausmann) is one of the most damaging apple pests in South Africa. Information on its genetic diversity is lacking and this study, in which the genetic structure of parthenogenetic E. lanigerum populations was characterized in the Western Cape Province of South Africa, represents the first local study of its kind. A total of 192 individuals from four different regions were collected and analysed using amplified fragment length polymorphism (AFLP). Using five selective AFLP primer pairs, 250 fragments were scored for analysis. Results indicated that a low level of genetic variation was apparent in E. lanigerum populations in the Western Cape (H = 0.0192). Furthermore, populations collected from geographically distant regions were very closely related, which can partly be explained by the fact that agricultural practices were responsible for dissemination of populations from a common ancestor to geographically distant areas. The low level of variation found indicated that the possibility of controlling E. lanigerum in the Western Cape using host plant resistance is favourable. This is the first report of AFLP being used to characterize the genetic structure of an aphid species. Results indicate that this marker may be useful for analysis of other aphid species.

Analysis of the three common mutations in the CARD15 gene (R702W, G908R and 1007fs) in South African colored patients with inflammatory bowel disease.

The caspase recruitment domain-containing protein 15 gene (CARD15) was recently identified as an important susceptibility gene for Crohn's disease (CD). The purpose of this study was to assess the likelihood that the three most common CARD15 mutations, R702W, G908R and 1007fs, contribute to inflammatory bowel disease (IBD) susceptibility in the South African colored population. The study cohort included 76 IBD patients, 41 with CD and 35 with ulcerative colitis (UC), and 100 population-matched controls. Mutations R702W, G908R and 1007fs were present at relatively low frequencies (<20%) in our study population. No statistically significant differences were furthermore, observed for these mutations between UC and CD patients or when compared with normal control individuals. Two additional mutations were identified, one novel (A661P) and one previously described (A725G), with the latter being identified in 4 of 35 (11%) UC patients. Statistically significant differences were obtained between UC and control individuals when comparing both allele (p<0.004, chi2 with Yates' correction=8.01) and genotype frequencies (p<0.004, chi2 with Yates' correction=8.14) for the A725G mutation, suggesting a possible role for this variant in disease expression.

Dinucleotide repeat polymorphism at the D5S99 locus on chromosome 5q33-34.

We report a highly polymorphic, sequence-tagged microsatellite site (STMS) at the D5S99 locus that was previously identified by a less informative restriction fragment length polymorphism (RFLP). This marker, which was also localized to the physical map of chromosome 5q by fluorescent in situ hybridization (FISH), should assist in the precision mapping of genes in the area 5q33-34.

Highly informative dinucleotide repeat polymorphism at the D11S29 locus on chromosome 11q23.

The informativeness of locus D11S29 as a genetic marker was improved by the identification of a highly polymorphic (GT)n repeat within the locus. Ten alleles were identified in parents of 40 Centre d'Etude du Polymorphisme Humain families and the polymorphism information content (PIC) was 0.77. The increased PIC value thus enables refinement of the linkage map of 11q23.

Molecular characterisation of a low-frequency mutation in exon 8 of the human low-density lipoprotein receptor gene.

The prevalence of familial hypercholesterolaemia (FH), an autosomal dominant disease characterised by raised low-density lipoprotein (LDL) cholesterol levels, is at least five times higher in the white Afrikaner population than in most other population groups in the world. A founder gene effect has been suggested to explain this abnormally high frequency. Detection of a polymorphic Stu I site in the 5' region of the LDL receptor gene and association of both restriction fragment length polymorphism alleles with FH in Afrikaners, indicated the existence of at least two founder members for the disease in this population. DNA from a hetero-allelic FH homozygote from this South African group has been analysed through genomic cloning and sequencing. The DNA polymorphic site is caused by a single guanine to adenine transition within exon 8 of the LDL receptor gene and can be used in the determination of haplotype-associated defects.

Significance of novel endothelin-B receptor gene polymorphisms in Hirschsprung's disease: predominance of a novel variant (561C/T) in patients with co-existing Down's syndrome.

Several genes have been implicated in the pathogenesis of Hirschsprung's disease (HSCR). In a previous study performed, five novel (V202M, E480K, IVS10-2A/G, D771N, IVS19-9C/T) mutations and one previously described mutation (P937L) have been identified in the RET proto-oncogene in 20% of the study population. To further investigate the involvement of other genes, mutation analysis of the endothelin-B receptor (EDNRB) gene was performed in 52 unrelated sporadic HSCR patients, including 38 non-syndromic and 14 patients with HSCR and Down's syndrome. Six novel (178G/A, 552C/T, 561C/T, 702C/T, IVS3-6C/T and IVS4 + 3A/G) sequence variants and one previously described (831G/A) polymorphism were identified. Statistically significant differences were achieved for six (178G/A, 552C/T, 561C/T, 702C/T, IVS3-6C/T and 831G/A) of these variants. The T-allele of the 561C/T polymorphism was over represented in the HSCR/Down's syndrome patient group (36% representing 5 of 14) compared to normal controls (6% representing 5 of 84) (p < 0.002, chi(2) with Yates correction = 12.14), suggesting that the 561C/T variant is associated with a low penetrance effect in patients with this complex phenotype. Detection of the 178G/A polymorphism in only non-syndromic HSCR patients, provide further support for an important role of specific sequence variants in the EDNRB gene in the HSCR/Down's syndrome phenotype.

Detection of a frequent polymorphism in exon 10 of the low-density lipoprotein receptor gene.

DNA sequencing of enzymatically-amplified exons of the low-density lipoprotein receptor gene from several individuals revealed a polymorphism in exon 10 of the gene. The codon for arginine 450 was converted from AGG to AGA in some alleles.

An exon 4 mutation identified in the majority of South African familial hypercholesterolaemics.

The prevalence of familial hypercholesterolaemia (FH) is significantly higher in the Afrikaans speaking population (Afrikaners) of South Africa than reported in most other populations. A founder gene effect has been proposed to explain the high FH frequency, implying that the same low density lipoprotein (LDL) receptor gene defect is present in the majority of affected Afrikaners. By using DNA amplification and sequence determination, we have detected a point mutation in DNA from two Afrikaner FH homozygotes. A cytosine to guanine base substitution at nucleotide position 681 of the LDL receptor cDNA results in an amino acid change from aspartic acid to glutamic acid at residue 206 in the cysteine rich ligand binding domain of the LDL receptor. Since three previously mapped transport deficient alleles of the LDL receptor were also traced to cysteine rich repeats of the protein, these results suggest that the mutation is responsible for the receptor defective mutation predominantly found in Afrikaner FH homozygotes. The mutation gives rise to an additional DdeI restriction site in DNA of affected subjects and segregation of the mutation with the disease was confirmed in five large Afrikaner FH families. We predict that 65% of affected South African Afrikaners carry this particular base substitution. Amplification of genomic DNA, using the polymerase chain reaction method, and restriction enzyme analysis now permit accurate diagnosis of the mutation in subjects with FH.

The molecular basis and diagnosis of familial hypercholesterolaemia in South African Afrikaners.

Three different point mutations were recently identified in South African familial hypercholesterolaemics. These mutations result in the modification of recognition sites of specific restriction endonucleases. This study describes rapid methods for presymptomatic detection of these defects based on restriction enzyme analysis or allele-specific hybridization of enzymatically amplified genomic DNA. These methods were used to determine the frequencies of the three known low-density lipoprotein (LDL) receptor gene mutations in 138 chromosomes of Afrikaner FH patients. It has been shown that a common mutation at the 3' end of exon 4 (base 681) of the LDL receptor gene is present in about 70% of alleles, while the mutations in exons 9 (base 1285) and 4 (base 523) of the gene are present in about 20 and 10% respectively of the genes studied. These mutations were found in approximately 95% of Afrikaner familial hypercholesterolaemic patients studied, indicating at least three founder members for the disease in this population of South Africa.

Regional localization of alpha-galactosidase (GLA) to Xpter----q22, hexosaminidase B (HEXB) to 5q13----qter, and arylsulfatase B (ARSB) to 5pter----q13.

Two series of somatic cell hybrids were made by fusion of human cells with karyotypes 46,X,t(X;2;15)(q22;p12;p12) and 46,XX,t(5;7)(q13;p15) and rodent cells. Chromosome and isozyme analysis of human chromosomes and gene products in the hybrids localized GLA to Xpter----q22, HEXB to 5q13----qter, in both cases narrowing the regional assignments, and ARSB to 5pter----q13.

Variegate porphyria in Western Australian Aboriginal patients.

BACKGROUND: Survivors of shipwrecks along the Western Australian coast may have introduced a mutation for variegate porphyria into the Aboriginal population prior to first settlement. AIMS: To assess the mutations responsible for variegate porphyria in Western Australian Aboriginal patients, particularly the R59W mutation, which is the most common cause of variegate porphyria in South Africa. METHODS: New cases of porphyria were diagnosed by biochemical separation of porphyrin subtypes. Single-stranded conformation polymorphism analysis and DNA sequencing of the protoporphyrinogen oxidase gene was performed on Aboriginal patients to define possible causative mutation sites. RESULTS: Of the 296 new cases of porphyria diagnosed in Western Australia from 1978 to 1998, six had biochemically proven variegate porphyria. Three of those cases occurred in Aboriginal patients. Evidence for a possible fourth Aboriginal case of variegate porphyria is described. The R59W founder mutation responsible for over 90% of variegate porphyria in South Africa was excluded. Two new mutations that predicted amino acid substitutions with significant effects on enzyme function were detected in conserved regions of the protoporphyrinogen oxidase gene in one Aboriginal variegate porphyria patient and the possible fourth case. CONCLUSION: Results suggest that the mutations causing variegate porphyria in the Western Australian Aboriginal population occur sporadically and were not inherited from shipwrecked sailors.

Mapping of the variegate porphyria (VP) gene: contradictory evidence for linkage between VP and microsatellite markers at chromosome 14q32.

The gene for variegate porphyria (VP), an autosomal dominant disease with a high prevalance in South Africa, evidently due to a founder effect, was previously mapped to chromosome 14q32. In the current study this localization was evaluated by linkage and haplotype analyses using microsatellite markers spanning a region of more than 20 cM on chromosome 14q32. In many recent studies linkage disequilibrium between disease and marker loci has been utilized to map genes in founder populations, but we could not find any association between VP and the markers used in this study. Our data suggest that the allocation of VP to chromosome 14q32 may be incorrect.

Molecular diagnosis of hereditary hemochromatosis: application of a newly-developed reverse-hybridization assay in the South African population.

A recently developed strip-assay for hemochromatosis provides a rapid method for simultaneous detection of multiple mutations, which among others includes the HFE gene mutations V53M, V59M, H63D, H63H, S65C, Q127H, E168Q, and C282Y, previously detected in the general South African population using gel-based mutation-screening methods. The objective of the study was to determine the frequency of the relatively rare mutations in samples selected for altered iron parameters or a family history of hereditary hemochromatosis (HH) as part of the validation process of the assay for routine diagnostic purposes. The study population consisted of 451 individuals previously screened for mutations C282Y and H63D by restriction enzyme analysis in order to confirm or possibly exclude a diagnosis of HH. These individuals were subjected to mutation screening using the commercially available hemochromatosis strip-assay. Previous positive results for mutations C282Y and H63D in 233 individuals confirmed the accuracy of the reverse-hybridization assay. Mutation S65C was detected in 13 Caucasians, including three compound heterozygotes. These constituted 2% (13/600) of the chromosomes without mutations C282Y or H63D. The African-specific HFE mutation V53M was detected in one out of 11 (9%) African subjects screened. Mutation E168Q was detected in a single Caucasian individual together with mutation H63D. Our data demonstrate the value of the strip-based technology in providing a rapid and reliable comprehensive test for simultaneous analysis of multiple mutations.

A microsatellite-based index map of human chromosome 11.

We have constructed a continuous index map of 25 microsatellite markers on human chromosome 11. The markers have been typed in 40 CEPH families, have heterozygosities of 69% or higher and can be typed by PCR. The odds against inversion of adjacent marker loci order are at least 10(5):1. The sex average map covers a total of 162 cM with no gap exceeding 15 cM. Total lengths for female and male maps are 205 and 123 cM, respectively. By use of a hybrid cell panel or by in situ hybridization, 16 of the markers have also been mapped cytogenetically, providing a good correlation of the index map with the cytogenetic map. The map will facilitate high resolution mapping of additional polymorphic loci and of disease genes on chromosome 11.