Wilson disease mutations associated with uncommon haplotypes in mediterranean patients

This study reports 12 novel mutations of the Wilson disease (WD) gene which have been detected by the molecular analysis of 29 patients of Mediterranean descent carrying uncommon chromosomal haplotypes at the WD locus. These mutations include two nonsense, one splice site and nine missense. The missense mutations lie in regions of the WD gene critical for its function, such as the transmembrane region, the transduction domain and the ATP loop and ATP-binding domain, indicating that they are disease-causing mutations. These new findings improve our knowledge for the role played by functional domains on the ATP7B function. Received: 20 March 1996     

Analysis of intragenic polymorphic markers of the CFTR gene in cystic fibrosis patients and health donors from Bashkorostan

The differences in the polymorphic allele frequency distribution patterns of the biallelic (M470 and TUB20) and microsatellite (IVS6aGATT, IVS8CA, and IVS17CA) markers within the CFTR gene between normal and delF508 chromosomes have been established. For most of the marker loci similar distribution of the allele frequencies on normal and mutant chromosomes without delF508 was demonstrated. Certain polymorphic alleles displayed substantial linkage disequilibrium with the delF508 mutation. Analysis of the IVS6aGATT-IVS8CA-M470-IVS17CA-TUB20 haplotypes association on normal and mutant chromosomes provided identification of the delF508 ancestral haplotype. It was suggested that delF508 mutant chromosomes were introduced into the modern Bashkir gene pool as a result of Slavic migrations from the Eastern Europe. The IVS6aGATT-IVS8CA-M470-IVS17CA-TUB20 major haplotype (77272) revealed was statistically significantly most frequently found on the mutant chromosomes without the delF508 mutation. This finding suggests that the Bashkir cystic fibrosis patients, mostly belonging to the Turkic-speaking families, possessed specific CF gene defect associated with the given haplotype.     

Phylogenetic signals from point mutations and polymorphic Alu

Allelic frequency data derived from five polymorphic Alu insertion loci and five point mutation polymorphic loci were compared to determine their ability to infer phylogenetic relationships among human populations. While point mutation polymorphisms inferred a monophyletic Caucasian clade that is corroborated by other studies, these data failed to support the generally accepted monophyly of Orientals with native Americans. In addition, there is less statistical bootstrap support for the maximum-likelihood tree derived from the point mutation polymorphisms as compared to those generated from either the Alu insertion data or the combined Alu insertion+point mutation data. The Alu data and the combined Alu insertion+point mutation data inferred a monophyletic relationship among the Oriental and native American populations. The Alu insertion data and the combined Alu insertion+point mutation data also displayed two separate, well defined, tight clusters of the Caucasian and the Oriental+native American populations which was not inferred from the point mutation data. These findings indicate greater phylogenetic information contained in Alu insertion frequencies than in allelic frequencies derived from point-mutations. This revised version was published online in July 2006 with corrections to the Cover Date.     

Isolation and characterization of new highly polymorphic DNA markers from the Huntington disease region.

The defect causing Huntington disease (HD) has been mapped to 4p16.3, distal to the DNA marker D4S10. Subsequently, additional polymorphic markers closer to the HD gene have been isolated, which has led to the establishment of predictive testing programs for individuals at risk for HD. Approximately 17% of persons presenting to the Canadian collaborative study for predictive testing for HD have not received any modification of risk, in part because of limited informativeness of currently available DNA markers. Therefore, more highly polymorphic DNA markers are needed, which will further increase the accuracy and availability of predictive testing, specifically for families with complex or incomplete pedigree structures. In addition, new markers are urgently needed in order to refine the breakpoints in the few known recombinant HD chromosomes, which could allow a more accurate localization of the HD gene within 4p16.3 and, therefore, accelerate the cloning of the disease gene. In this study we present the identification and characterization of nine new polymorphic DNA markers, including three markers which detect highly informative multiallelic VNTR-like polymorphisms with PIC values of up to .84. These markers have been isolated from a cloned region of DNA which has been previously mapped approximately 1,000 kb from the 4p telomere.     

Adult polycystic kidney disease: prenatal diagnosis with DNA polymorphic markers.

A prenatal diagnosis of adult polycystic kidney disease (ADPKD) by DNA testing is reported. Evidence showing a linkage between the disease and the DNA markers on chromosome 16 was obtained in the family by linkage analysis and homogeneity testing with Italian families of the linked type. Prenatal diagnosis was performed either by polymerase chain reaction (PCR) of GGG1 fragment either by Southern blotting analysis of the others chromosome 16 markers. Diagnostic results were available by PCR analysis in a few hours and then were confirmed by Southern blotting of the others probes. The foetus was monitored by ultrasounds. At 26th week the foetal kidney were enlarged with small cysts and, at birth, the newborn had bilateral renal cysts, confirming the foetal genotype prediction based on flanking markers.     

Cystic fibrosis mutations and associated haplotypes in Turkish cystic fibrosis patients.

Identification of mutations causing cystic fibrosis (CF) in the Turkish population is essential for assessment of the molecular basis of CF in Turkey and the development of strategies for prenatal diagnosis and genetic counseling. Here, we present an updated report of mutations found in the Turkish CF population from an extensive screening study of the entire coding region, including exon-intron boundaries and the promoter region. Cases for which mutations could not be identified were also screened for previously defined large alterations and (TG)mTn-M470V loci. This study revealed a total of 27 different mutations accounting for almost 60% of disease genes in the Turkish population. In this study, we also identified the haplotypes associated with 17 mutations and those associated with unknown mutations. The mutation spectrum of CF in Turkey and its associated haplotypes indicated the presence of a major Mediterranean component in the contemporary Turkish population.     

Heterogeneity of haplotypes among patients with severe Cooley disease in Eastern Sicily

Summary There is a large variation of clinical severity among thalassemic patients in Sicily. A heterogeneous molecular basis has already been demonstrated among the patients presenting with thalassemia intermedia. The same approach, based mostly on linked haplotypes of the gene cluster polymorphisms and in some cases on the demonstration of the molecular defect itself, was used to investigate 55 patients presenting with severe Cooley anemia, all maintained under permanent transfusion regimen. A large heterogeneity was demonstrated in the observed haplotypes, and only a limited overlap with those already found in thalassemia intermedia. It has been noted that many of the patients are compound heterozygotes, the various observed associations making the antenatal diagnosis at the DNA level difficult in the near future.     

Analysis of cystic fibrosis gene mutations and associated haplotypes in the Croatian population

The aim of this study was to reveal the CFTR gene mutation status in the Croatian population as well as to establish the haplotypes associated with cystic fibrosis (CF) and those associated with specific gene mutations. A total of 48 unrelated CF patients from Croatia were examined. Among 96 tested alleles, we found nine different mutations: DeltaF508, 58.33%; G542X, 3.12%; N1303K, 2.08%; R1162X; 621 + 1G --> T; G85E; Y569C; E585X; and S466X, 1.04%. Analysis of three polymorphic loci revealed 15 different haplotypes. Two of them (21-23-13 and 21-17-13) occurred with a higher frequency (40% and 24%). Both of these haplotypes also carried a CFTR gene mutation (DeltaF508 or G542X) on 27 out of 32 chromosomes. Among 12 (of all together 29) CF alleles on which no mutations were found, we detected 10 different haplotypes. Because there are still no published data on the distribution of polymorphic loci in Croatia, nor haplotypes associated with mutations in the CFTR gene, our results greatly contribute to knowledge regarding the genetic background of CF in this region.     

Analysis of expansion of the triplet repeat (CTG)n in myotonic dystrophy patients from Bashkir

A method was elaborated for simple and rapid diagnosis of myotonic dystrophy (MD). The method consists in estimating expansion of the CTG repeat in the myotonin protein kinase gene by means of PCR amplification of a gene fragment from genomic DNA and Southern hybridization of the amplified fragments with probe (CTG)9. Bashkir patients with Rossolimo-Steinert-Batten-Kurshmann MD were examined with this method.     

Accuracy of marker-assisted selection with single markers and marker haplotypes in cattle

A key question for the implementation of marker-assisted selection (MAS) using markers in linkage disequilibrium with quantitative trait loci (QTLs) is how many markers surrounding each QTL should be used to ensure the marker or marker haplotypes are in sufficient linkage disequilibrium (LD) with the QTL. In this paper we compare the accuracy of MAS using either single markers or marker haplotypes in an Angus cattle data set consisting of 9323 genome-wide single nucleotide polymorphisms (SNPs) genotyped in 379 Angus cattle. The extent of LD in the data set was such that the average marker-marker r2 was 0.2 at 200 kb. The accuracy of MAS increased as the number of markers in the haplotype surrounding the QTL increased, although only when the number of markers in the haplotype was 4 or greater did the accuracy exceed that achieved when the SNP in the highest LD with the QTL was used. A large number of phenotypic records (>1000) were required to accurately estimate the effects of the haplotypes.     

Inferring haplotypes from genotypes on a pedigree with mutations, genotyping errors and missing alleles

Inferring the haplotypes of the members of a pedigree from their genotypes has been extensively studied. However, most studies do not consider genotyping errors and de novo mutations. In this paper, we study how to infer haplotypes from genotype data that may contain genotyping errors, de novo mutations, and missing alleles. We assume that there are no recombinants in the genotype data, which is usually true for tightly linked markers. We introduce a combinatorial optimization problem, called haplotype configuration with mutations and errors (HCME), which calls for haplotype configurations consistent with the given genotypes that incur no recombinants and require the minimum number of mutations and errors. HCME is NP-hard. To solve the problem, we propose a heuristic algorithm, the core of which is an integer linear program (ILP) using the system of linear equations over Galois field GF(2). Our algorithm can detect and locate genotyping errors that cannot be detected by simply checking the Mendelian law of inheritance. The algorithm also offers error correction in genotypes/haplotypes rather than just detecting inconsistencies and deleting the involved loci. Our experimental results show that the algorithm can infer haplotypes with a very high accuracy and recover 65%-94% of genotyping errors depending on the pedigree topology.     

Isolation and characterization of polymorphic DNA microsatellite markers from Schistosoma japonicum

The ability of microsatellite loci to reveal genetic diversity within the trematode Schistosoma japonicum is demonstrated. Eleven novel microsatellite markers were isolated, assessing variability within 80 S. japonicum individuals from three Chinese and one Philippine population. Novel primers were also tested upon S. mansoni and S. haematobium. Eight primers showed polymorphic amplification from all S. japonicum groups, three amplified S. mansoni DNA, but none amplified S. haematobium DNA. Only six of 27 previously isolated S. mansoni‐specific primers amplified S. japonicum DNA. Allelic diversity and observed heterozygosity ranged from 4 to 21 and 0.05 to 0.82, respectively, suggesting high variability.     

Analysis of deletions in the dystrophin gene in patients with Duchenne muscular dystrophy in the Bashkir Republic]

The deletion spectrum and distribution of deletion breakpoints (DBs) in 36 patients with Duchenne muscular dystrophy (DMD) from 33 families and in three patients with Becker muscular dystrophy (BMD) from one family from Bashkortostan were studied by amplifying 20 exons of the dystrophin gene by multiplex polymerase chain reaction (mPCR). Eight out of 34 unrelated DMD (BMD) patients (23.2%) were shown to carry a deletion varying in size from one to seven exons. Most DBs (15 out of 16, 93.7%) were in the distal region of the gene, commonly between exons 44-45, 45-47, and 50-52. Thus, high-polymorphic intergenic markers located in introns 44 (STR 44), 45 (STR 45), 49 (STR 49), and 50 (STR 50) can be used for indirect or direct carrier detection among women closely related to DMD patients that carry a deletion with DB located between exons 44-45, 45-47, and 50-52. Prenatal diagnosis of DMD is also possible in these families.     

Analysis of polymorphic DNA markers cosegregation with arterial blood pressure in ISIAH hypertensive rats]

A search for DNA markers of hereditary arterial hypertension in ISIAH rats was performed by means of contemporary molecular genetic approaches. The backcross rat population used for the analyses was derived from a cross of the Wistar x ISIAH F1 progeny with the Wistar rats. Hybridization of the HaeIII-digested DNA samples with the (CAC)5 microsatellite probe revealed cosegregation of the basal arterial pressure value with the 4.8-kb polymorphic DNA fragment. Examination of the DNA polymorphism by means of polymerase chain reaction with arbitrary primers showed an association of the 700-bp polymorphic DNA fragment with the increase of arterial blood pressure under conditions of emotional stress.     

Spectrum of phenylketonuria mutations in Western Europe and North Africa,and their relation to polymorphic DNA haplotypes at the phenylalanine hydroxylase locus

Summary A total of 252 chromosomes from 126 patients with phenylalanine hydroxylase (PAH) deficiencies were analyzed for both mutant genotypes and restriction fragment length polymorphism (RFLP) haplotypes at the PAH locus. The mutant genes studied originated either from Western Europe (116 alleles) or from Mediterranean countries (136 alleles). Only 27% of all mutant alleles were found to carry identified mutations, particularly mutations at codon 252 (2.3%), 261 (7.5%), 280 (6.3%), 408 (3.5%) and at the splice donor site of intron 12 (6.3%). The mutant genotypes were associated with RFLP haplotypes 7, 1, 38, 2 and 3 at the PAH locus respectively. Except for the splice mutation of intron 12, these associations were preferential, but not exclusive, since the other four mutations were found on the background of at least two RFLP haplotypes. These results, together with the observation that 85% of PAH deficient patients are heterozygotes for their mutant genotypes, emphasize the great heterogeneity of PAH deficiencies in Mediterranean countries and hamper systematic DNA testing for carrier status in this population.     

Distribution of beta-thalassemia mutations in south China and their association with haplotypes.

DNA from 93 Chinese beta-thalassemia chromosomes were hybridized to eight different mutant oligomers to determine their specific mutation. Four mutations accounted for 87% of the chromosomes; in descending frequencies, these mutations were codon 41/42, IVS-2 nt654, codon 17, and -28. Since codon 41/42 mutation can be associated with multiple beta-thalassemia haplotypes, codon 41/42 is probably a hot spot for the 4-bp deletion. The distributions of these mutations were mapped to various regions in south China. These data are useful for the planning of prenatal diagnosis programs in other Chinese communities worldwide.     

Phenylketonuria in Spain: RFLP haplotypes and linked mutations

In order to investigate the molecular basis of phenylketonuria (PKU) in Spain, we analyzed the restriction fragment length polymorphism (RFLP) haplotypes and common mutations in the phenylalanine hydroxylase (PAH) gene in 32 unrelated Spanish PKU families. The distribution of RFLP haplotypes differs from that of northern Europe. Mutant haplotypes 2 and 3 were completely absent in our sample. Approximately 65% of the mutant alleles are confined to three RFLP haplotypes, namely haplotypes 1, 6 and 9, also frequently found in other Mediterranean populations. We screened for previously described PKU mutations using the polymerase chain reaction and allele-specific oligonucleotides, and found IVS10,165T, E280K and P281L as the major mutations, representing 41% of the PKU alleles. Other mutations found were Y414C, and a new one, P244L. Mutations R408W and IVS12, prevalent in northern Europe, as well as others present in southern European populations (R252W, R261Q, L249F) were not detected in our sample. Our results reveal the genetic heterogeneity present in the Spanish PKU population, which shows similarities to others of Mediterranean origin.     

Variability of polymorphic gene markers in Buryat and Russian newborns from Ulan-Ude]

Variability of ten polymorphic loci (ABO, RhD, PGD, ACP, PGM1, GLO, ESD, ADA, GC, TF) was studied in 326 Buryat and 310 Russian newborns from Ulan-Ude city. Marked differences between two groups were observed in the distributions of allelic frequencies of ABO, RhD, PGD, ACP, PGM1, GLO, ESD, GC loci. Genetic similarities between Buryat and other mongoloids were estimated. Close similarity was observed between Buryat, Mongols, Yakut and Kyzyl.     

Functional effects of mutations identified in patients with multiminicore disease

Multiminicore disease is a recessive congenital myopathy characterized by the presence of small cores or areas lacking oxidative enzymes, in skeletal muscle fibres. From a clinical point of view, the condition is widely heterogeneous and at least four phenotypes have been identified; genetic analysis has revealed that most patients with the classical form of multiminicore characterized by rigidity of the spine, early onset and respiratory impairment harbour recessive mutations in the SEPN1 gene, whereas the majority of patients belonging to the other categories, including patients with ophthalmoplegia or patients with a phenotype similar to central core disease, carry recessive mutations in the RYR1. In the present review we discuss the most recent findings on the functional effect of mutations in SEPN1 and RYR1 and discuss how they may adversely affect muscle function and lead to the clinical phenotype.     

Usefulness of polymorphic markers in exclusion of BRCA1/BRCA2 mutations in families with aggregation of breast/ovarian cancers

Founder mutations can account for a large proportion of BRCA1/BRCA2 gene abnormalities in a given population. However there is still a need to study the entire gene in many families, even in countries where founder mutations have been identified. It is possible to decrease the number of cases which are studied by complex and expensive sequencing/Southern blot analyses of BRCA1/BRCA2 genes by exclusion of common BRCA1/BRCA2 alleles in a given family by using polymorphic dinucleotide markers. The goal of o ur study was to assess the effectiveness of this method in exclusion of BRCA1/BRCA2 constitutional mutations. In each family, blood samples for genetic analyses were taken from two affected relatives from the same generation. Six polymorphic microsatellite markers linked to BRCA1/BRCA2 genes were analysed. Results obtained with these markers were verified by applying BRCA1 testing for the most common founder mutations in Poland and using exon by exon" sequencing of coding fragments of the BRCA2 gene. Polymorphic markers useful in BRCA1/BRCA2 analyses included only 3 of 6 examined - D17S855, D13S260 and D13S267. Occurrence of commoalleles of BRCA1 was excluded in 3 families and BRCA2 in 5 out of 30 families. Results obtained by testing for BRCA1 Polish founder mutations and BRCA2 sequencing were in agreement with BRCA1 findings based on polymorphic markers. The only exception was family 994 with BRCA1 exon 5 300T/G mutation, in which BRCA1 mutation carrier was excluded by using D17S855. Among 14 families without BRCA1 Polish founder mutations in this gene were excluded in 2 families and BRCA2 mutation was excluded in one family.