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Results for “haplotype analysis”

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PubMed1986

Further data supporting linkage between cystic fibrosis and the met oncogene and haplotype analysis with met and pJ3.11.

The linkage of cystic fibrosis (CF) and the polymorphic DNA markers pJ3.11, met, 7C22, DOCR1-917, COL1A2, and TCRB have jointly localized the mutation causing CF to chromosome 7q2.1-3.1. We report further linkage data with two polymorphic markers at the met oncogene locus, pmetH and pmetD, which supports the tight linkage found by White et al. between CF and met. One family shows evidence for meiotic recombination between CF and met. Analysis of haplotypes in CF pedigrees collected for linkage studies combined with data from single affected families requesting prenatal diagnosis (Farrall et al., Lancet i:1402-1404, 1986) shows CF and met to be in linkage equilibrium in our population while pJ3.11-CF haplotypes show a deviation from the equilibrium frequencies.

Cystic Fibrosis↗
PubMed1998

Prenatal diagnosis of Fukuyama type congenital muscular dystrophy in eight Japanese families by haplotype analysis using new markers closest to the gene.

We conducted prenatal diagnosis by haplotype analysis, using newly developed microsatellite markers, in eight Fukuyama type congenital muscular dystrophy (FCMD) families. In addition to six new families, two previously reported families were reexamined by haplotype analysis including detection of an ancestral founder haplotype (138-183-301) for 3 microsatellite markers closest to the FCMD gene, designated D9S2105-D9S2107-D9S172, the distances of which from the FCMD gene are presumed to be approximately 140, approximately 20, and approximately 280 kb, respectively. Five fetuses from five families were diagnosed as nonaffected, and were subsequently confirmed to be healthy. Three fetuses of the other three families were diagnosed as having a high probability of being affected by FCMD. In the prenatal diagnosis conducted for these eight families, the ancestral founder allele was observed in 13 of 16 (81%) FCMD-bearing chromosomes. Detection of the ancestral haplotype facilitated achieving accurate prenatal diagnosis of FCMD. The brains of all three fetuses prenatally diagnosed as FCMD-affected showed the initial stage of cortical dysplasia, strong evidence of FCMD.

Brain↗
PubMed2005

ATM mutations, haplotype analysis, and immunological status of Russian patients with ataxia telangiectasia.

Mutations in the ATM gene are responsible for the autosomal recessive disorder, ataxia telangiectasia (A-T). Mutations in different ethnic groups are distributed along the entire length of the large, 66 exon ATM gene. In this study, A-T patients from 16 Russian families were assessed for immunological status and ATM haplotype analysis, and screened for ATM mutations. Haplotype analysis was performed to enhance the efficiency of mutation detection. Mutations predicted to cause disease were identified in 19 of 32 alleles (59%), including a truncating mutation (c.5932G>T) that was identified in 8/32 (25%) alleles both by haplotype analysis and mutation screening. This mutation has been found in low abundance in other European A-T cohorts suggesting that this founder-effect mutation may be of Russian origin. The abundance of this mutation may allow for large-scale screening of cancer patients to help clarify the role of ATM in breast and other cancers. Nine of the remaining mutations were previously unreported, and add to the multitude of unique mutations found throughout the gene.

Adolescent↗
PubMedDate not supplied

Extended haplotype analysis reveals an association of TNF polymorphisms with susceptibility to systemic lupus erythematosus beyond HLA-DR3.

OBJECTIVE: To study the relative contribution of tumour necrosis factor (TNF) and HLA-DRB1 polymorphisms to the genetic susceptibility to systemic lupus erythematosus (SLE) via an extended haplotype analysis. METHODS: We performed an association study in 205 unrelated German Caucasian patients with SLE fulfilling the 1997 revised American College of Rheumatology (ACR) criteria. Healthy age-, ethnically- and sex-matched individuals (n = 157) served as controls. HLA-DRB1 typing was performed by a sequence-specific oligonucleotide hybridisation assay. Two TNF single nucleotide polymorphisms (SNPs) and two multiallelic microsatellites were analysed by mutagenically separated polymerase chain reaction (PCR) or fragment length analysis, respectively. Extended haplotypes were reconstructed with the PHASE software. RESULTS: Alleles for all polymorphic loci studied and the most frequent haplotypes showed a significantly different distribution between SLE patients and controls. The alleles HLA-DR2, DR3, TNFd1, TNF2, TNFB*1, and TNFa2, designated as risk alleles, and the extended haplotypes DR3-TNFd1-TNF2-TNFB*1-TNFa2 and DR2-TNFd3-TNF1-TNFB*2-TNFa11 prevailed in SLE patients. TNF risk alleles were strongly positively linked with HLA-DR3 and negatively linked with HLA-DR2. Thus, in HLA-DR3 haplotypes individual effects of TNF polymorphisms could not be resolved. By contrast, HLA-DR2 showed an association with SLE independently of TNF risk alleles, while the risk increased further when they were present. In haplotypes lacking HLA-DR2 and DR3, the alleles TNFdl and TNF2 contributed independently to SLE susceptibility. CONCLUSION: Extended haplotype analysis revealed HLA-DR3 independent associations of TNF polymorphisms with susceptibility to SLE. Haplotypes that have been shown to be associated with different TNF-alpha production capacity may prevail in different disease subgroups.

Adolescent↗
PubMed2003

[Fibrillin-1 gene mutation in Chinese patients with Marfan syndrome and its gene diagnosis by haplotype analysis].

OBJECTIVE: To analyze fibrillin-1 (FBN(1)) gene mutation in Chinese patients with Marfan syndrome(MFS) and to make a gene diagnosis by haplotype analysis for MFS. METHODS: Nine MFS families were analysed with single strand conformation polymorphism(SSCP) and DNA sequencing. With the use of four primers designed in the flanking sequences of each short-sequence tandem-repeat region in FBN(1) gene, the haplotype-segregation analysis for MFS(B) was performed. RESULTS: In MFS(A)II(1), PCR-SSCP detected SSCP band alterations in exon 25 of FBN(1) gene; direct sequencing showed a small 13bp deletion, the deleted sequence being gcctctgcaccca at base 3243-3456 of cDNA. This mutation caused a frame-shift which was never seen in any unaffected members of the family, and it was a heterozygous mutation; neither of them was identified in 100 chromosomes from 50 normal control individuals. Haplotype-segregation analysis suggested that the disease was passed from Subject I(2) to Subject II(2), Subject II(3), Subject II(5) with the same allele in MFS B family, the proband's daughter also inherited the allele. These data indicated that MFS(B) family was linked to FBN(1) gene, the proband's daughter was an asymptomatic patient. CONCLUSION: The combination of mutation analysis and haplotype analysis can provide more evidence for gene diagnosis.

Base Sequence↗
PubMed2003

Haplotype analysis of aldosterone synthase gene (CYP11B2) polymorphisms shows association with essential hypertension.

OBJECTIVE: The CYP11B2 locus is an important candidate region in essential hypertension (HT). We therefore investigated CYP11B2 polymorphisms T-344C, T4986C and A6547G for association with essential HT. This included haplotype analysis and measurement of plasma aldosterone levels. METHODS: The three single nucleotide polymorphisms were genotyped by polymerase chain reaction-restriction fragment length polymorphism analysis of genomic DNA from 146 HT and 291 normotensive (NT) white subjects of Anglo-Celtic descent, in whom parental blood pressure status was the same as the subjects'. Genotype and allele frequencies in HTs and NTs were compared by chi2 analysis. Linkage disequilibrium and haplotype frequencies were estimated by the program 'snphap'. Phenotype-genotype relationships were tested using one-way analysis of variance. RESULTS: The T-344C variant was associated with HT (chi2 = 7.4, P = 0.0064). This association was confined to female HTs (P = 0.0061 for genotypes, P = 0.0013 for alleles). A strong association with HT was also seen for the A6547G variant (P = 0.0015), being greatest in females (P < 0.0001). No association was seen for the T4986C variant. Haplotype analysis of the three single nucleotide polymorphisms across eight different haplotype combinations showed a significant association with HT (chi2 = 24, seven degrees of freedom, P < 0.001). No significant tracking of plasma aldosterone with genotype was observed. CONCLUSION: The T-344C and A6547G, but not the T4986C, variants of the aldosterone synthase gene are associated with HT in females of the Anglo-Celtic population studied. This was reinforced by haplotype analysis.

Adult↗
PubMed2004

Y-chromosome haplotype analysis in Antioquia (Colombia).

Allele frequencies and haplotype analysis have been performed for eight Y-chromosome STRs (DYS19, DYS385 I and II, DYS389 I and II, DYS390, DYS391, DYS392, DYS393). Population data was obtained from a sample of 400 unrelated individuals living in Antioquia (Colombia). A total of 270 different haplotypes were found, and the haplotype diversity was 0.989. The first and second most frequent haplotypes where shared by 8 and 6% of the individuals, respectively.

Chromosomes, Human, Y↗
PubMed1995

Haplotype analysis in autosomal dominant polycystic kidney disease.

Haplotype analysis was performed in 35 autosomal dominant polycystic kidney disease (ADPKD) families typed with 13 markers close to the PKD1 locus. The identification of recombinants close to the PKD1 gene on chromosome 16p indicates that PKD1 lies between CMM65 distally and 26-6 proximally. In addition, three unlinked (PKD2) families and two families with potential new mutation were identified.

Adult↗
PubMed2003

Detection of the four sequence variations of MDR1 gene using TaqMan MGB probe based real-time PCR and haplotype analysis in healthy Japanese subjects.

OBJECTIVES: P-glycoprotein (P-gp) is significant from the viewpoint of pharmacokinetics/pharmacodynamics (PK/PD). MDR1 gene encodes P-gp and has a wide variety of SNPs. As the SNPs may be one of the factors that induce pharmacogenetic individual difference, haplotype analysis is necessary to evaluate the PK/PD. DESIGN AND METHODS: The SNPs of the detected MDR1 were -129T>C, 325G>A, 2677G>T/A, and 3435C>T. For the analysis of linkage disequilibrium (LD) and haplotype analysis, and for the reconstruction of the haplotype pair, ARLEQUIN and PHASE were employed. RESULTS: The result of the chi(2) test detected significant LD between -129 and 2677, -129 and 3435, and 2677 and 3435. There were 9 haplotypes: T-G-C, T-T-C, C-T-C, T-A-C, C-A-C, T-G-T, T-T-T, C-G-T, and C-T-T. CONCLUSIONS: LD was found among the positions -129, 2677 and 3435. As a result, 9 haplotypes exists in the Japanese population. These results suggest that it would be necessary to give consideration to haplotype for the purpose of evaluating the PK/PD of the drugs transported by P-gp.

Adult↗
PubMed2005

Calpainopathy (LGMD2A) in Croatia: molecular and haplotype analysis.

AIM: To determine types and frequency of CAPN3 mutations in 29 unrelated Croatian families, analyzed during 6-year prospective and ongoing genetic and epidemiological study of muscular dystrophies in Croatia. METHODS: Mutation analysis included allele-specific polymerase chain reaction (PCR) or combination of PCR and restriction fragment length polymorphisms (RFLP) methods. Haplotype analysis was performed by PCR and DNA electrophoresis using 5 highly polymorphic markers flanking CAPN3 gene locus. RESULTS: Mutation analysis revealed the presence of 6 different CAPN3 mutations (550delA, R541W, P82L, delFWSAL, R49H, Y537X), accounting for 94.8% of CAPN3 chromosomes in the studied population. 550delA was the most frequent mutation, found in 43/58 (74%) CAPN3 chromosomes, whereas the frequency of other five mutations ranged from 2-9%. Haplotype analysis of 38 chromosomes carrying 550delA mutation showed the presence of the same haplotype on 66% of analyzed chromosomes. CONCLUSIONS: The present data, together with our previously published results, explain the frequency and the distribution of the 550delA mutation in Croatia by founder effect and genetic drift. Results of haplotype study are in favor of the hypothesis that 550delA is an old, rather than a recurrent mutation. The findings are important for effective diagnostic screening of CAPN3 gene in Croatia and neighboring countries, as well as for accurate genetic counseling.

Calpain↗
PubMed1995

Haplotype analysis in Australian hemochromatosis patients: evidence for a predominant ancestral haplotype exclusively associated with hemochromatosis.

Hemochromatosis (HC), an inherited disorder of iron metabolism, shows a very strong founder effect in Australia, with the majority of patients being of Celtic (Scots/Irish) origin. Australian HC patients thus provide an ideal group in which to examine HC-gene-region haplotypes, to analyze the extent of linkage disequilibrium and genetic heterogeneity in HC. We have analyzed chromosomes from 26 multiply affected HC pedigrees, and we were able to assign HC status unambiguously to 107 chromosomes--64 as affected and 43 as unaffected. The haplotypes examined comprise the following highly polymorphic markers: the serological marker HLA-A and the microsatellites D6S248, D6S265, HLA-F, and D6S105. All show highly significant allelic association with HC and no evidence of separation from the disease locus by recombination. Analysis identified a predominant ancestral haplotype comprising alleles 5-1-3-2-8 (marker order: D6S248-D6S265-HLA-A-HLA-F-D6S105), present in 21 (33%) of 64 affected chromosomes, and exclusively associated with HC (haplotype relative risk 903). No other common haplotype was significantly associated with HC. Haplotype analysis in Australian HC patients thus provides strong evidence for (a) the introduction of HC into this population on an ancestral haplotype, (b) a common mutation associated with HC in Australian patients, and (c) a candidate HC-gene region extending between and including D6S248 and D6S105.

Australia↗
PubMed1992

Diagnosis of familial hypercholesterolemia using DNA haplotype analysis in three large families with two hyperlipidemic parents.

Since the cloning of the human LDL receptor (LDLR) gene, familial hypercholesterolemia (FH) can be diagnosed by recombinant DNA technology either using restriction enzyme mapping to detect major rearrangements of the gene or using restriction fragment length polymorphisms (RFLPs) and linkage analysis in family studies. Genotypes and haplotypes of four RFLPs (StuI, ApaII 5', PvuII, NcoI) were used to study the inheritance of the detective LDLR gene in three families. Diagnosis of FH based on the lipid levels alone was not possible because in these kindreds both parents exhibit elevated lipid levels. However, in two families using haplotype analysis, elevated cholesterol levels in certain relatives could be attributed to the inheritance of a defective LDRL gene and thereby distinguished from hypercholesterolemia due to familial combined hyperlipidemia. In the third family where both hypercholesterolemic parents carried a defective LDLR gene, a case of homozygous FH could be excluded in a child by demonstrating the inheritance of a normal LDLR gene.

Adult↗
PubMed1998

Efficient localization of mutations by interval haplotype analysis.

We have developed a mathematical algorithm to implement a method for localizing mutations using haplotype analysis. Our strategy infers haplotypes based on the determination of genotypes of a proximal and a distal marker for 21 chromosomal intervals distributed across the mouse genome (corresponding to two intervals for Chromosomes (Chrs) 1 and 2 and one for the remaining 17 autosomes). To simulate the analysis of mice homozygous for recessive mutations, we tested the efficacy of our method on over 200 data sets generated from two independent mapping panel data sets containing the genotypes of 46 F2 progeny of an intercross and 94 F2 progeny of a backcross. In all cases we were able to identify the chromosomal interval carrying the recessive mutation despite the fact that some of the data sets consisted of as few as 10 meioses. Our strategy proved sensitive and expedient, since the simulated genome-wide screen could be executed by genotype analysis of 40 microsatellite markers in small numbers of intercross or backcross progeny.

Algorithms↗
PubMed1994

DNA haplotype analysis of Huntington disease reveals clues to the origins and mechanisms of CAG expansion and reasons for geographic variations of prevalence.

This study of allelic association using three intra- and two extragenic markers within 150 kb of the Huntington disease (HD) mutation has provided evidence for linkage disequilibrium for four of five markers. Haplotype analysis of 67 HD families using markers in strong linkage disequilibrium with HD identified two haplotypes underlying 77.6% of HD chromosomes. Normal chromosomes with these two haplotypes had a mean number of CAG repeats significantly larger than and an altered distribution of CAG repeats compared with other normal chromosomes. Furthermore, haplotype analysis of five new mutation families reveals that HD has arisen on these same two chromosomal haplotypes. These findings suggest that HD arises more frequently on chromosomes with specific DNA haplotypes and higher CAG repeat lengths. We then studied CAG and CCG repeat lengths in the HD gene on 896 control chromosomes from different ancestries to determine whether the markedly reduced frequency of HD in Finland, Japan, China and African Blacks is associated with an altered frequency of DNA haplotypes and subsequently lower CAG lengths on control chromosomes compared to populations of Western European descent. The results show a highly significant inverse relationship between CAG and CCG repeat lengths. In populations with lowered prevalence rates of HD, CAG repeat lengths are smaller and the distribution of CCG alleles is markedly different from Western European populations. These findings suggest that, in addition to European emigration, new mutations make a contribution to geographical variation of prevalence rates and is consistent with a multistep model of HD developing from normal chromosomes with higher CAG repeat lengths.

Africa↗
PubMed2005

Haplotype analysis improves molecular diagnostics of autosomal recessive polycystic kidney disease.

BACKGROUND: Autosomal recessive polycystic kidney disease (ARPKD) is characterized by wide phenotypic variability, ranging from in utero detection with enlarged, echogenic kidneys to an adult presentation with congenital hepatic fibrosis. The ARPKD gene, PKHD1 , covers about 470 kb of DNA (67 exons), and mutation studies have found marked allelic heterogeneity with a high level of novel missense changes and neutral polymorphisms. To improve the prospects for molecular diagnostics and to study the origin of some relatively common mutations, the authors have developed a strategy for improved ARPKD haplotyping. METHODS: A protocol of multiplex PCR and fluorescence genotyping in a single capillary has been developed to assay 7 highly informative simple sequence repeat (SSR) markers that are intragenic or closely flanking PKHD1. RESULTS: Examples in which haplotype analysis, used in combination with mutation screening, improved the utility of molecular diagnostics, especially in families in which just a single PKHD1 mutation has been identified, are illustrated. The new markers also allow screening for larger DNA deletions, detecting unknown consanguinity and exploring the disease mechanism. Analysis of 8 recurring mutations has shown likely common haplotypes for each, and the divergence from the ancestral haplotype, by recombination, can be used to trace the history of the mutation. The common mutation, T36M, was found to have a single European origin, about 1,225 years ago. CONCLUSION: Improved haplotype analysis of ARPKD complements mutation-based diagnostics and helps trace the history of common PKHD1 mutations.

3' Flanking Region↗
PubMed2004

Haplotype analysis in multiple crosses to identify a QTL gene.

Identifying quantitative trait locus (QTL) genes is a challenging task. Herein, we report using a two-step process to identify Apoa2 as the gene underlying Hdlq5, a QTL for plasma high-density lipoprotein cholesterol (HDL) levels on mouse chromosome 1. First, we performed a sequence analysis of the Apoa2 coding region in 46 genetically diverse mouse strains and found five different APOA2 protein variants, which we named APOA2a to APOA2e. Second, we conducted a haplotype analysis of the strains in 21 crosses that have so far detected HDL QTLs; we found that Hdlq5 was detected only in the nine crosses where one parent had the APOA2b protein variant characterized by an Ala61-to-Val61 substitution. We then found that strains with the APOA2b variant had significantly higher (P < or = 0.002) plasma HDL levels than those with either the APOA2a or the APOA2c variant. These findings support Apoa2 as the underlying Hdlq5 gene and suggest the Apoa2 polymorphisms responsible for the Hdlq5 phenotype. Therefore, haplotype analysis in multiple crosses can be used to support a candidate QTL gene.

Amino Acid Sequence↗
PubMed2001

The advantages of haplotype analysis of the promoter region of the human apolipoprotein E gene.

Polymorphisms in the regulatory region of the human apolipoprotein E gene (gene, APOE; protein, apoE) have been implicated in Alzheimer's disease. Here we describe in detail the advantages of a simple method for haplotype analysis of this region (at -491 and -427 bases relative to the transcription start site of the gene). The promoter region of the APOE gene was amplified by polymerase chain reaction (PCR) and this fragment was then used as a template for PCR with "nested" primers to generate a 228-bp product incorporating both the -491 and the -427 loci. PCR products were then digested with DraI and AluI together and subjected to polyacrylamide gel electrophoresis. The distinct pattern of bands appearing on the gel was then used to ascribe [-491,-427] haplotypes to each subject, from which -491 and -427 genotypes were inferred. -491 and -427 genotypes were also confirmed by digestion with DraI alone or AluI alone. Haplotype analysis was successful in all 20 samples analyzed and was 100% consistent with genotyping. We suggest that this is a reliable, time-saving method that the will be useful in large-scale APOE promoter genotyping studies.

Adult↗