Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “haplotype analysis”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 415 records · Page 23Linked to original sources
PubMed2005

The effect of missing data on linkage disequilibrium mapping and haplotype association analysis in the GAW14 simulated datasets.

We used our newly developed linkage disequilibrium (LD) plotting software, JLIN, to plot linkage disequilibrium between pairs of single-nucleotide polymorphisms (SNPs) for three chromosomes of the Genetic Analysis Workshop 14 Aipotu simulated population to assess the effect of missing data on LD calculations. Our haplotype analysis program, SIMHAP, was used to assess the effect of missing data on haplotype-phenotype association. Genotype data was removed at random, at levels of 1%, 5%, and 10%, and the LD calculations and haplotype association results for these levels of missingness were compared to those for the complete dataset. It was concluded that ignoring individuals with missing data substantially affects the number of regions of LD detected which, in turn, could affect tagging SNPs chosen to generate haplotypes.

Chromosome Mapping↗
PubMed2003

FBN1 mutation in Chinese patients with Marfan syndrome and its gene diagnosis using haplotype linkage analysis.

OBJECTIVES: To analyze the FBN1 mutations in Chinese patients with Marfan syndrome (MFS) and to make a genetic diagnosis based on haplotype linkage analysis for MFS. METHODS: Nine MFS families (17 patients) were analyzed with single strand conformation polymorphism (SSCP) and sequencing. Four primers were designed for the flanking sequences of FBN1 gene and used for haplotype-segregation analysis of MFS(B). RESULTS: SSCP band alteration was detected in the PCR products for exon 25 in MFS(A) II:1. Direct sequencing revealed a small 13 bp deletion; the deleted sequence is gccTc Tgcaccca at bases 3243-3456 of the cDNA in exon 25. This mutation was novel. MFS(B) families were analyzed using the haplotype linkage technique. The data suggested that MFS(B) families were linked to the FBN1 gene. The proband's daughter was an asymptomatic patient. CONCLUSION: The combination of mutation detection and chromosome haplotype analysis can provide better evidence for a genetic diagnosis of MFS.

Fibrillin-1↗
PubMed2005

Haplotype interaction analysis of unlinked regions.

Genetically complex diseases are caused by interacting environmental factors and genes. As a consequence, statistical methods that consider multiple unlinked genomic regions simultaneously are desirable. Such consideration, however, may lead to a vast number of different high-dimensional tests whose appropriate analysis pose a problem. Here, we present a method to analyze case-control studies with multiple SNP data without phase information that considers gene-gene interaction effects while correcting appropriately for multiple testing. In particular, we allow for interactions of haplotypes that belong to different unlinked regions, as haplotype analysis often proves to be more powerful than single marker analysis. In addition, we consider different marker combinations at each unlinked region. The multiple testing issue is settled via the minP approach; the P value of the "best" marker/region configuration is corrected via Monte-Carlo simulations. Thus, we do not explicitly test for a specific pre-defined interaction model, but test for the global hypothesis that none of the considered haplotype interactions shows association with the disease. We carry out a simulation study for case-control data that confirms the validity of our approach. When simulating two-locus disease models, our test proves to be more powerful than association methods that analyze each linked region separately. In addition, when one of the tested regions is not involved in the etiology of the disease, only a small amount of power is lost with interaction analysis as compared to analysis without interaction. We successfully applied our method to a real case-control data set with markers from two genes controlling a common pathway. While classical analysis failed to reach significance, we obtained a significant result even after correction for multiple testing with our proposed haplotype interaction analysis. The method described here has been implemented in FAMHAP.

Algorithms↗
PubMed2006

Multiple hypothesis testing strategies for genetic case-control association studies.

The genetic case-control association study of unrelated subjects is a leading method to identify single nucleotide polymorphisms (SNPs) and SNP haplotypes that modulate the risk of complex diseases. Association studies often genotype several SNPs in a number of candidate genes; we propose a two-stage approach to address the inherent statistical multiple comparisons problem. In the first stage, each gene's association with disease is summarized by a single p-value that controls a familywise error rate. In the second stage, summary p-values are adjusted for multiplicity using a false discovery rate (FDR) controlling procedure. For the first stage, we consider marginal and joint tests of SNPs and haplotypes within genes, and we construct an omnibus test that combines SNP and haplotype analysis. Simulation studies show that when disease susceptibility is conferred by a SNP, and all common SNPs in a gene are genotyped, marginal analysis of SNPs using the Simes test has similar or higher power than marginal or joint haplotype analysis. Conversely, haplotype analysis can be more powerful when disease susceptibility is conferred by a haplotype. The omnibus test tracks the more powerful of the two approaches, which is generally unknown. Multiple testing balances the desire for statistical power against the implicit costs of false positive results, which up to now appear to be common in the literature.

Case-Control Studies↗
PubMed2006

Association of sequence variations in the gene encoding adiponectin receptor 1 (ADIPOR1) with body size and insulin levels. The Finnish Diabetes Prevention Study.

AIMS/HYPOTHESIS: Adiponectin is a circulating peptide derived from adipose tissue. It mediates its insulin-sensitising and anti-atherogenic effects on target tissues through two known receptors, adiponectin receptors 1 and 2 (ADIPOR1; ADIPOR2), which are encoded by the genes ADIPOR1 and ADIPOR2. Our aim was to study the association of ADIPOR1 gene variations with body size and risk of type 2 diabetes in subjects with impaired glucose tolerance, who participated in the Finnish Diabetes Prevention Study (DPS). SUBJECTS AND METHODS: We selected seven single nucleotide polymorphisms (SNPs) of the ADIPOR1 gene to perform association studies with anthropometrics and metabolic parameters at baseline, and with the risk of type 2 diabetes during the 3-year follow-up in the DPS study population. Both single SNP analysis and haplotype effects were studied. RESULTS: Three out of seven markers studied (rs10920534, rs22757538 and rs1342387) were significantly associated with various body size measurements including weight, height, waist and hip circumference, sagittal diameter and body mass index. Furthermore, three markers (rs10920534, rs12045862 and rs7539542), of which two were different from those associating with body size, were linked to fasting and 2-h insulin levels, particularly in men at baseline. The haplotype analysis with five markers revealed seven major haplotypes in the DPS study population. The haplotype effects on body size measures were in line with those of single SNP analysis. However, none of the markers were associated with the risk of type 2 diabetes. CONCLUSIONS/INTERPRETATION: Our findings suggest that ADIPOR1 has a putative role in the development of body size, and that traits for central adiposity and insulin resistance may be dissociated from each other.

Body Size↗
PubMed2005

Haplotype sharing analysis using mantel statistics.

OBJECTIVE: The potential value of haplotypes has attracted widespread interest in the mapping of complex traits. Haplotype sharing methods take the linkage disequilibrium information between multiple markers into account, and may have good power to detect predisposing genes. We present a new approach based on Mantel statistics for spacetime clustering, which is developed in order to improve the power of haplotype sharing analysis for gene mapping in complex disease. METHODS: The new statistic correlates genetic similarity and phenotypic similarity across pairs of haplotypes for case-only and case-control studies. The genetic similarity is measured as the shared length between haplotypes around a putative disease locus. The phenotypic similarity is measured as the mean-corrected cross-product based on the respective phenotypes. We analyzed two tests for statistical significance with respect to type I error: (1) assuming asymptotic normality, and (2) using a Monte Carlo permutation procedure. The results were compared to the chi(2) test for association based on 3-marker haplotypes. RESULTS: The results of the type I error rates for the Mantel statistics using the permutational procedure yielded pointwise valid tests. The approach based on the assumption of asymptotic normality was seriously liberal. CONCLUSION: Power comparisons showed that the Mantel statistics were better than or equal to the chi(2) test for all simulated disease models.

Case-Control Studies↗
PubMed2001

The I1307K APC polymorphism: prevalence in non-Ashkenazi Jews and evidence for a founder effect.

A missense mutation within the APC gene, I1307K, was described in Ashkenazi individuals at risk for colorectal cancer (CRC) and in the general population. The anecdotal reporting of the occurrence of this mutation in some non-Ashkenazi individuals led us to hypothesize that within the Jewish people, the I1307K polymorphism may reflect a founder mutation, and that the mutation is not restricted to ethnic Ashkenazis. To test that notion, and to establish the occurrence rate of the I1307K polymorphism in non-Ashkenazi Jewish populations, we screened Iraqi and Moroccan Jews and consecutive Jewish CRC patients and performed haplotype analysis with APC-linked markers in two I1307K carrier families. We analyzed Jewish individuals: 210 Moroccans, 160 Iraqis, 148 Ashkenazi, and 349 CRC patients (227 Ashkenazi and 122 non-Ashkenazi). The mutation detection scheme included PCR followed by denaturing gradient gel electrophoresis (DGGE) or modified restriction analysis (MRA). Haplotypes were assessed using three intragenic and three flanking markers. The I1307K polymorphism was detected in 29/227 Ashkenazi (12.8%), 2/122 (1.6%) non-Ashkenazi CRC patients, and in 2 individuals each (approximately 1%) within the Moroccan and Iraqi populations. Allelic pattern analysis in all our I1307K carriers, revealed a common haplotype for the three intragenic markers tested, in all mutation carriers, regardless of ethnic origin. The I1307K polymorphism, therefore, exists in all ethnic Jewish populations: Ashkenazi and non-Ashkenazi, with or without colon cancer. Jewish I1307K mutation carriers share a common allelic pattern with APC-linked markers. This strongly supports the notion of a founder mutation for I1307K.

Adenocarcinoma↗
PubMed2025

A Swedish genome-wide haplotype association analysis identifies novel candidate loci associated with endometrial cancer risk.

Genome-wide association studies [GWAS] have identified a limited number of endometrial cancer risk loci by analyzing single nucleotide polymorphisms [SNPs]. We hypothesized that analyzing haplotypes rather than SNPs could provide novel and more detailed information on genetic cancer susceptibility loci. To examine the association of a SNP or haplotype with endometrial cancer risk we performed a two-stage haplotype GWAS. The discovery GWAS included a sub-cohort of 1,116 Swedish endometrial cancer cases and 5,021 controls from previously published GWAS data. A sliding window analysis was employed with window sizes of 1-25 SNPs using a logistic regression model. The Swedish haplotype analysis identified 15 novel candidate risk loci (2q31.1, 4p16.1, 4p15.31, 6q13, 7p21.1, 9p13.3, 10q26.3, 11q21, 12q13.11, 13q12.11, 15q13.3, 16q24.3, 19q13.32, 20p12.3 and 22q13.2) with OR ranging from 1.6 to 3.3 and p-values from 4.25 × 10-8 to 9.86 × 10-15. A second replication haplotype analysis of the Swedish novel loci was performed using two cohorts from Belgium and Germany. In spite of small sample sizes in the replication cohorts, there was still support for most loci with positive ORs. In addition, the findings in the two European cohorts motivates further studies to search for founder haplotypes. These novel findings suggested that endometrial cancer loci, identified through haplotype analysis, conferred a higher risk compared to previous single-variant GWAS.

Humans↗
PubMed2003

Evolutionary-based association analysis using haplotype data.

Association studies, both family-based and population-based, can be powerful means of detecting disease-liability alleles. To increase the information of the test, various researchers have proposed targeting haplotypes. The larger number of haplotypes, however, relative to alleles at individual loci, could decrease power because of the additional degrees of freedom required for the test. An optimal strategy would focus the test on particular haplotypes or groups of haplotypes, much as is done with cladistic-based association analysis. First suggested by Templeton et al. ([1987] Genetics 117:343-351), such analyses use the evolutionary relationships among haplotypes to produce a limited set of hypothesis tests and to increase the interpretability of these tests. To more fully utilize the information contained in the evolutionary relationships among haplotypes and in the sample, we propose generalized linear models (GLM) for the analysis of data from family-based and population-based studies. These models fully account for haplotype phase ambiguity and allow for covariates. The models are encoded into a software package (the Evolutionary-Based Haplotype Analysis Package, EHAP), which also provides for various kinds of exploratory data analysis. The exploratory analyses, such as error checking, estimation of haplotype frequencies, and tools for building cladograms, should facilitate the implementation of cladistic-based association analysis with haplotypes.

Genetic Predisposition to Disease↗
PubMed1999

Hybrid survival motor neuron genes in Japanese patients with spinal muscular atrophy.

Spinal muscular atrophy (SMA) is a frequently occurring autosomal recessive disease, characterized by the degeneration of spinal cord anterior horn cells, leading to muscular atrophy. Most SMA patients carry homozygous deletions of the telomeric survival motor neuron gene (SMN) exons 7 and 8. In the study presented here, we examined 20 Japanese SMA patients and found that 4 of these patients were lacking in telomeric SMN exon 7, but retained exon 8. In these 4 patients, who exhibited all grades of disease severity, direct sequencing analysis demonstrated the presence of a hybrid SMN gene in which centromeric SMN exon 7 was adjacent to telomeric SMN exon 8. In an SMA family, a combination of polymerase chain reaction and enzyme-digestion analysis and haplotype analysis with the polymorphic multicopy marker Agl-CA indicated that the patient inherited the hybrid gene from her father. In conclusion, hybrid SMN genes can be present in all grades of disease severity and inherited from generation to generation in an SMA family.

Adult↗
PubMed2005

Haplotype association analysis of human disease traits using genotype data of unrelated individuals.

Haplotype inference has become an important part of human genetic data analysis due to its functional and statistical advantages over the single-locus approach in linkage disequilibrium mapping. Different statistical methods have been proposed for detecting haplotype - disease associations using unphased multi-locus genotype data, ranging from the early approach by the simple gene-counting method to the recent work using the generalized linear model. However, these methods are either confined to case - control design or unable to yield unbiased point and interval estimates of haplotype effects. Based on the popular logistic regression model, we present a new approach for haplotype association analysis of human disease traits. Using haplotype-based parameterization, our model infers the effects of specific haplotypes (point estimation) and constructs confidence interval for the risks of haplotypes (interval estimation). Based on the estimated parameters, the model calculates haplotype frequency conditional on the trait value for both discrete and continuous traits. Moreover, our model provides an overall significance level for the association between the disease trait and a group or all of the haplotypes. Featured by the direct maximization in haplotype estimation, our method also facilitates a computer simulation approach for correcting the significance level of individual haplotype to adjust for multiple testing. We show, by applying the model to an empirical data set, that our method based on the well-known logistic regression model is a useful tool for haplotype association analysis of human disease traits.

Computer Simulation↗
PubMedDate not supplied

M385T polymorphism in the factor V gene, but not Leiden mutation, is associated with placental abruption in Finnish women.

This study determines whether genetic variability in the gene encoding factor V contributes to differences in susceptibility to placental abruption. Allele and genotype frequencies of three single nucleotide polymorphisms (SNPs) in the factor V gene leading to nonsynonymous changes (M385T in exon 8, and R485K and R506Q [Leiden mutation] in exon 10) were studied in 116 Caucasian women with placental abruption and 112 healthy controls. Single-point analysis was expanded to haplotype analysis and haplotype frequencies were estimated using an expectation-maximisation (EM) algorithm. Comparison of single-point allele and genotype distributions of SNPs in exon 8 and exon 10 of the factor V gene revealed statistically significant differences in M385T allele (P = 0.021) and genotype ( P = 0.013) frequencies between the patients and the control subjects. The C allele of SNP M385T was significantly less frequent among the patients (7%) vs. the control subjects (13%), at an odds ratio of 0.48 (95% CI 0.25-0.91). Allele and genotype differences between the patients and control subjects as regards R485K and Leiden mutation were not significant. In haplotype estimation analysis, there was a significantly lower frequency of haplotype T-R-R encoding the T385-R485-R506 variant in the group with placental abruption vs. the control group (P = 0.038) at an odds ratio of 0.519 (95% CI 0.272-0.987). We conclude that T385 is less frequent among the patient group than in the control group. The M385T variant in the factor V gene other than the Leiden mutation may play a role in disease susceptibility.

Abruptio Placentae↗
PubMed2004

Susceptibility to pre-eclampsia in Finnish women is associated with R485K polymorphism in the factor V gene, not with Leiden mutation.

This study determines whether genetic variability in the gene-encoding factor V contributes to differences in pre-eclampsia susceptibility. Allele and genotype frequencies of three single-nucleotide polymorphisms (SNPs) in the factor V gene leading to nonsynonymous changes (M385T in exon 8, and R485K and R506Q (Leiden mutation) in exon 10) were studied in 133 Caucasian women with pre-eclampsia and 112 healthy controls. Single-point analysis was expanded to haplotype analysis, and haplotype frequencies were estimated using an expectation-maximization algorithm. Comparison of single-point allele and genotype distributions of SNPs in exons 8 and 10 of the factor V gene revealed statistically significant differences in R485K allele (P=0.003) and genotype (P=0.03) frequencies between the patients and the control subjects. The A allele of SNP R485K was over-represented among the patients (12%) vs the control subjects (4%), at an odds ratio (OR) of 2.8 (95% confidence interval (CI) 1.2-6.2) for combined A genotypes (GA+AA vs GG). Allele and genotype differences between the patients and control subjects as regards M385T and Leiden mutation were not significant. In haplotype estimation analysis, there was a significantly elevated frequency of haplotype T-A-G encoding the M385-K485-R506 variant in the pre-eclamptic group vs the control group (P=0.01), at an OR of 2.6 (95% CI 1.2-5.5). We conclude that the T-A-G haplotype was more frequent among the patient group than in the control group, and genetic variations in the factor V gene other than the Leiden mutation may play a role in disease susceptibility.

Arginine↗
PubMed2006

Medullary cystic kidney disease type 1: mutational analysis in 37 genes based on haplotype sharing.

Medullary cystic kidney disease type 1 (MCKD1) is an autosomal dominant, tubulo-interstitial nephropathy that causes renal salt wasting and end-stage renal failure in the fourth to seventh decade of life. MCKD1 was localized to chromosome 1q21. We demonstrated haplotype sharing and confirmed the telomeric border by a recombination of D1S2624 in a Belgian kindred. Since the causative gene has been elusive, high resolution haplotype analysis was performed in 16 kindreds. Clinical data and blood samples of 257 individuals (including 75 affected individuals) from 26 different kindreds were collected. Within the defined critical region mutational analysis of 37 genes (374 exons) in 23 MCKD1 patients was performed. In addition, for nine kindreds RT-PCR analysis for the sequenced genes was done to screen for mutations activating cryptic splice sites. We found consistency with the haplotype sharing hypothesis in an additional nine kindreds, detecting three different haplotype subsets shared within a region of 1.19 Mb. Mutational analysis of all 37 positional candidate genes revealed sequence variations in 3 different genes, AK000210, CCT3, and SCAMP3, that were segregating in each affected kindred and were not found in 96 healthy individuals, indicating, that a single responsible gene causing MCKD1 remains elusive. This may point to involvement of different genes within the MCKD1 critical region.

Chromosome Mapping↗
PubMed2003

CDKN2A region polymorphism and genetic susceptibility to melanoma in the melim swine model of familial melanoma.

Some herds of miniature swine are genetically predisposed to cutaneous melanoma. To test if swine melanoma susceptibility could be linked to the CDKN2A gene, which is involved in a proportion of 9p21-linked human familial melanoma, we performed a genetic analysis of miniature pigs of the MeLiM strain. F(1) and backcross animals were generated by crossing 1 MeLiM boar with healthy Duroc sows. We isolated the swine CDKN2A gene and characterized a linked informative microsatellite marker, the S0644 marker. Using this marker and 2 flanking markers, we analyzed the segregation of the CDKN2A gene in a 3-generation pedigree. Allelic association, linkage analysis and haplotype analysis of these data led to exclusion of the CDKN2A gene as a candidate for melanoma susceptibility. Nonetheless, this analysis suggests an association with the swine 1q25 chromosomal region, which is homologous to the human 9p21 region.

Alleles↗
PubMed1993

A single polymorphic STR system in the human phenylalanine hydroxylase gene permits rapid prenatal diagnosis and carrier screening for phenylketonuria.

Phenylketonuria (PKU) is an autosomal recessive genetic disorder caused by phenylalanine hydroxylase (PAH) deficiency. Individuals afflicted with PKU develop irreversible mental retardation that can be largely prevented by the administration of a low-phenylalanine diet. A number of restriction fragment-length polymorphisms (RFLPs) have been identified in the PAH gene. Combinations of RFLPs constitute unique haplotypes that can be used to identify mutant PAH chromosomes for prenatal diagnostic purpose in PKU families. Unfortunately, the utility of haplotype analysis is limited in populations with a single predominant haplotype. We have identified a novel short tandem repeat (STR) within the PAH gene that has an average level of heterozygosity of about 75% in Orientals and about 80% in European Caucasian populations. This single marker is as informative as haplotype analysis in Europeans and nearly twice as informative as haplotype analysis in Orientals. Although there is statistically significant disequilibrium between STR alleles and RFLP-based haplotypes, there is a relatively low degree of disequilibrium between STR alleles and certain RFLP sites. Nevertheless, the combined use of the STR and RFLP haplotype systems increases the informativity of linkage-based tests for prenatal diagnosis and carrier screening in PKU families.

Alleles↗
PubMed1994

Molecular genetic detection of Xp21 muscular dystrophy carriers in Cyprus.

Multiplex Polymerase Chain Reaction (PCR) for 18 different exons of the dystrophin gene was used to characterize the mutations in 29 Cypriot families with Duchenne or Becker Muscular Dystrophy. Deletions were detected in 21 out of 28 families from which DNA was available for an affected patient (75%). Quantitative Multiplex PCR further enabled the identification of a duplication in one of our families (3.6%). Quantitative Multiplex PCR also enabled carrier diagnosis in families where a deletion or a duplication was detectable in an affected patient. Out of 69 at-risk females examined in these families, 20 were shown by Quantitative Multiplex PCR to be carriers, including three obligatory carriers. In the remaining six families with a surviving patient, carrier diagnosis was based on haplotype analysis using microsatellite polymorphisms from the 5'- and 3'-ends of the dystrophin gene. Haplotype analysis was informative in three of the above families (10.7%). Thus, deletions or duplications were detected in 78.6% of our families with a surviving patient, while carrier diagnosis was possible in 89.3% of these families. In the single family without a surviving patient, Quantitative Multiplex PCR indicated the absence of a deletion or duplication in the mother, while haplotype analysis could not be carried out in the absence of an affected patient. The high rate of new mutations in the dystrophin gene of which only about 80% are directly detectable by Quantitative Multiplex PCR, and the difficulty of haplotype analysis in some of our families, restricts the usefulness of these techniques to about 90% of our families.

Cyprus↗
PubMed1994

[Indirect genetic diagnosis of cystic fibrosis].

The diagnosis cystic fibrosis was made in a three years old girl. Her older brother and her mother's sister both had minor symptoms and signs suggestive of this disease. None of 17 mutations in the gene locus for cystic fibrosis was identified in the patient by DNA-analyses. By haplotype analyses her brother, but not her aunt, was shown to share the proband's haplotypes. This family is used as an example of the general diagnostic potential of indirect diagnosis of genetic disease by haplotype analysis. The prerequisite for haplotype analysis is the availability of DNA from both the patient and the patient's relatives, stressing the need for a DNA bank of material from persons with inherited disorders, for future use.

Child, Preschool↗