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At least 145 records · Page 8Linked to original sources
PubMed2005

Inheritance of total serum IgE in the isolated Tangier Island population from Virginia: complexities associated with genealogical depth of pedigrees in segregation analyses.

OBJECTIVES: This study was aimed at performing a segregation analysis of total serum immunoglobulin E (tIgE) in an isolated population using maximal genealogical information permitted by current software and computer capacities, while assessing the reliability of the best-fitting model of inheritance for tIgE through simulations. METHODS: All current Tangier Island, VA, residents (n = 664) belonged to one large extended pedigree (n = 3,501) spanning 13 generations, with an average inbreeding coefficient of 0.009. Phenotype data were obtained on 453 (68.2%) of the residents using a population-based recruitment scheme. Due to computational limitations resulting from the extremely complex pedigree structure, analysis on only two pedigree reconstructions was feasible: a reduced pedigree retaining all phenotyped individuals and their parents as 57 distinct families, and 922 nuclear families. RESULTS: Familial correlations and heritability calculations reveal a significant genetic component to tIgE in these data (heritability = 26%). The most parsimonious model to explain tIgE distribution indicated by the reduced pedigree structure was a two-distribution Mendelian model. However, larger and non-genetic models could not be rejected. Simulations over 200 replicates performed to evaluate the reliability of this model, indicated that using restricted genealogical information had minimal impact on results of segregation analyses performed here.

Adolescent↗
PubMed2005

SimPed: a simulation program to generate haplotype and genotype data for pedigree structures.

With the widespread availability of SNP genotype data, there is great interest in analyzing pedigree haplotype data. Intermarker linkage disequilibrium for microsatellite markers is usually low due to their physical distance; however, for dense maps of SNP markers, there can be strong linkage disequilibrium between marker loci. Linkage analysis (parametric and nonparametric) and family-based association studies are currently being carried out using dense maps of SNP marker loci. Monte Carlo methods are often used for both linkage and association studies; however, to date there are no programs available which can generate haplotype and/or genotype data consisting of a large number of loci for pedigree structures. SimPed is a program that quickly generates haplotype and/or genotype data for pedigrees of virtually any size and complexity. Marker data either in linkage disequilibrium or equilibrium can be generated for greater than 20,000 diallelic or multiallelic marker loci. Haplotypes and/or genotypes are generated for pedigree structures using specified genetic map distances and haplotype and/or allele frequencies. The simulated data generated by SimPed is useful for a variety of purposes, including evaluating methods that estimate haplotype frequencies for pedigree data, evaluating type I error due to intermarker linkage disequilibrium and estimating empirical p values for linkage and family-based association studies.

Computer Simulation↗
PubMed2006

Increase in linkage information by stratification of pedigree data into gold-standard and standard diagnoses: application to the NIMH Alzheimer Disease Genetics Initiative Dataset.

Patients diagnosed with a standard clinical method (subject to misclassification error) are often combined with patients diagnosed with a gold-standard method (with zero or very small misclassification error) in family-based studies of complex disease. For example, non-autopsied patients (NAP) are often included along with autopsy-proven (AP) patients in family-based studies of complex diseases, such as Alzheimer's disease (AD). Theoretical and simulation studies suggest that certain misclassification errors can result in severe reduction of power in genetic linkage and association analyses and that phenotype (or diagnostic) error can produce misleading results. Morton's test for heterogeneity can identify genomic regions where error may have led to loss in power. We applied this test to pedigree data from the NIMH Alzheimer's Disease Genetics Initiative Database separated into AP and NAP pedigrees. Morton's test identified one highly significant region of heterogeneity on chromosome 2. The source of the heterogeneity was due to significant indication of linkage in the AP pedigrees at position 109 cM (p value = 6.68 x 10(-5)) with no indication in the NAP pedigrees. Furthermore, Morton's test showed no evidence for heterogeneity on chromosome 19 in early-onset pedigrees that showed highly significant evidence for linkage in other published reports. These results suggest that supplementing linkage analysis with Morton's test can be usefully applied to genetic data sets that have AP and NAP samples, or other sample mixtures that include a 'gold standard' subgroup with reduced error rate, to increase power to detect linkage in the presence of diagnostic misclassification.

Alzheimer Disease↗
PubMed1983

Extensions to pedigree analysis. V. Optimal calculation of Mendelian likelihoods.

Mendelian likelihoods are computed from human pedigree data for purposes of gene mapping, risk prediction in genetic counseling, and hypothesis testing in genetic epidemiology. The Mendelian likelihood of an extended pedigree can be written as a sum of products, the sum ranging over all possible genotypic combinations for the individuals in the pedigree. Exclusion of genotypes incompatible with the phenotypic information and pedigree structure reduces the ranges of summation and simplifies the likelihood calculation. To evaluate the likelihood with the fewest possible arithmetic operations requires carrying out the summations over one individual at a time and the intervening multiplications in some appropriate order. Each such removal of an individual reduces the likelihood evaluation to another evaluation of the same numerical form. Greedy-type algorithms are suggested for determining an order in which the summations and multiplications may be carried out. The greedy methods are fast and appear to generate good removal sequences. They are shown to work well when applied to a large, complex pedigree.

ABO Blood-Group System↗
PubMedDate not supplied

Adequacy of single-locus approximations for linkage analyses of oligogenic traits: extension to multigenerational pedigree structures.

When a disease is controlled by two or more mendelian loci acting epistatically, it can be modeled in a linkage analysis as a single-locus mendelian disease with reduced penetrance. Previous work has demonstrated the reliability of such approximation for nuclear families, but not for extended pedigrees. We simulated extended pedigrees under two-locus models, in which one of the two disease loci was linked to a marker, and analyzed them both under the correct two-locus models and under single-locus approximations. The single-locus approximations provided results that were very close to the correct two-locus results. This held true, whether we ascertained pedigrees based on the presence of at least one affected individual, or based on the presence of at least five affected individuals. While a simulation study cannot guarantee that extrapolation of the results to models other than those examined is justified, our findings strongly suggest that single-locus linkage analysis can be reliably used in analyzing two-locus disorders in extended pedigrees. We also found striking confirmation of the importance of performing linkage analyses under both dominant and recessive models when the mode of inheritance is unknown, for extended pedigrees ascertained through multiple affected individuals.

Chromosome Mapping↗
PubMed2007

Two pedigrees segregating Duane's retraction syndrome as a dominant trait map to the DURS2 genetic locus.

PURPOSE: The genetic bases of Duane's retraction syndrome (DRS) were investigated to determine its molecular etiologies. In prior studies, the transcription factors SALL4 and HOXA1 were identified as the genes mutated in DRS with radial anomalies, and in DRS with deafness, vascular anomalies, and cognitive deficits, respectively. Less is known, however, about the genetic etiology of DRS when it occurs in isolation, and only one genetic locus for isolated DRS, the DURS2 locus on chromosome 2, has been mapped to date. Toward the goal of identifying the DURS2 gene, two pedigrees have been ascertained that segregate DRS as a dominant trait. METHODS: Members of two large dominant DRS pedigrees were enrolled in an ongoing study of the genetic basis of the congenital cranial dysinnervation disorders, and linkage analysis was conducted to determine whether their DRS phenotype maps to the DURS2 locus. RESULTS: By haplotype analysis, the DRS phenotype in each family cosegregates with markers spanning the DURS2 region. Linkage analysis reveals maximum lod scores >2, establishing that the DRS phenotype in these two pedigrees maps to the DURS2 locus. CONCLUSIONS: These two pedigrees double the published pedigrees known to map to the DURS2 locus and can thus contribute toward the search for the DURS2 gene. The affected members represent a genetically defined population of DURS2-linked DRS individuals, and hence studies of their clinical and structural features can enhance understanding of the DURS2 phenotype, as described in the companion paper.

Chromosome Mapping↗
PubMed1992

Pedigree analysis of children with phonology disorders.

This study examined 87 pedigrees of individuals with histories of preschool phonology disorders. Results confirmed previous reports that speech and language disorders aggregate in families, with a higher incidence of males affected than females. Significantly more family members with dyslexia and learning disabilities, but not stuttering or hearing impairment, were found in pedigrees of individuals with phonology disorders than in pedigrees of nondisabled individuals. Probands with and without additional language problems did not differ in the incidence of affected family members. Nuclear family members demonstrated a higher incidence of disorders than when all family members were considered, with brothers of probands most often affected. Pedigrees of female probands had more affected members in their nuclear families than pedigrees of male probands.

Adolescent↗
PubMed2025

Whole-exome sequencing uncovers the genetic basis of hereditary concomitant exotropia in ten Chinese pedigrees.

PURPOSE: To explore possible pathogenic genes for concomitant exotropia using whole-exome sequencing. METHODS: In this study, 47 individuals from 10 concomitant exotropia (including intermittent exotropia and constant exotropia) pedigrees were enrolled. Whole-exome sequencing was used to screen mutational profiles in 25 affected individuals and 10 unaffected individuals. Sanger sequencing and in silico analysis were performed for all participants. Two target genes were used to capture the sequences of 220 sporadic samples. RESULTS: All 10 concomitant exotropia pedigrees presented autosomal dominant inheritance with childhood onset (3.35 ± 1.51 years old). Eleven different missense variants were identified among seven potential pathogenic genes (COL4A2, SYNE1, LOXHD1, AUTS2, GTDC2, HERC2 and CDH3) that cosegregated with pedigree members. All variants were predicted to be deleterious and had low frequencies in the general population. Distinct variants of COL4A2 were present in three pedigrees, and distinct variants of SYNE1 were present in two pedigrees. Fifteen variants in AUTS2 and four variants in GTDC2 were identified in 220 patients with sporadic concomitant exotropia using a target-capture sequencing approach. CONCLUSION: This is the first study to explore the genetic mechanism of concomitant exotropia and identify seven associated genes (COL4A2, SYNE1, LOXHD1, AUTS2, GTDC2, HERC2 and CDH3) that may be candidate genes causing concomitant exotropia. More samples and in-depth studies are needed to verify these findings.

Adult↗
PubMed2004

Conditional probability methods for haplotyping in pedigrees.

Efficient haplotyping in pedigrees is important for the fine mapping of quantitative trait locus (QTL) or complex disease genes. To reconstruct haplotypes efficiently for a large pedigree with a large number of linked loci, two algorithms based on conditional probabilities and likelihood computations are presented. The first algorithm (the conditional probability method) produces a single, approximately optimal haplotype configuration, with computing time increasing linearly in the number of linked loci and the pedigree size. The other algorithm (the conditional enumeration method) identifies a set of haplotype configurations with high probabilities conditional on the observed genotype data for a pedigree. Its computing time increases less than exponentially with the size of a subset of the set of person-loci with unordered genotypes and linearly with its complement. The size of the subset is controlled by a threshold parameter. The set of identified haplotype configurations can be used to estimate the identity-by-descent (IBD) matrix at a map position for a pedigree. The algorithms have been tested on published and simulated data sets. The new haplotyping methods are much faster and provide more information than several existing stochastic and rule-based methods. The accuracies of the new methods are equivalent to or better than those of these existing methods.

Animals↗
PubMed2005

Approximating identity-by-descent matrices using multiple haplotype configurations on pedigrees.

Identity-by-descent (IBD) matrix calculation is an important step in quantitative trait loci (QTL) analysis using variance component models. To calculate IBD matrices efficiently for large pedigrees with large numbers of loci, an approximation method based on the reconstruction of haplotype configurations for the pedigrees is proposed. The method uses a subset of haplotype configurations with high likelihoods identified by a haplotyping method. The new method is compared with a Markov chain Monte Carlo (MCMC) method (Loki) in terms of QTL mapping performance on simulated pedigrees. Both methods yield almost identical results for the estimation of QTL positions and variance parameters, while the new method is much more computationally efficient than the MCMC approach for large pedigrees and large numbers of loci. The proposed method is also compared with an exact method (Merlin) in small simulated pedigrees, where both methods produce nearly identical estimates of position-specific kinship coefficients. The new method can be used for fine mapping with joint linkage disequilibrium and linkage analysis, which improves the power and accuracy of QTL mapping.

Algorithms↗
PubMed1989

[A computer program that draws pedigree charts for inbred strains of animals].

We produced a computer program that draws pedigree charts for inbred strains of animals such as mice or rats. This program is composed of four subprograms, which are (1) inputting the data, (2) drawing pedigree charts, (3) listing the data which have been input, and (4) backup of the system and the data. Pedigree charts and lists of data can be displayed on a TV screen and printed out on the papers. Using this program, we drew the pedigree charts of the inbred strains of rats which we are maintaining by brother-sister inbreeding in our institute and found that there were three sublines in one of the strains, WKAH/Hkm, because of unsuitable maintenance. This program is very convenient to draw the pedigree charts and useful for checking the maintenance of inbred strains or the strains of animal models of human diseases.

Animals↗
PubMed1990

Effects of errors in pedigree on three methods of estimating breeding value for litter size, backfat and average daily gain in swine.

Estimated breeding value (EBV) was calculated based on either individual phenotype (SP), an index of individual phenotype and full- and half-sib family averages (SI) or Best Linear Unbiased Prediction (BLUP). Calculations were done with correct data or data with 5, 10, 15 or 20% of the records per generation containing pedigree errors. Traits considered were litter size (LS), backfat (BF) and average daily gain (ADG). When data were correct, BLUP resulted in an advantage in expected genetic gain over SP of 22, 7.2 or 30.8% for LS, BF and ADG, respectively, and over SI of 9.6, 3.8 or 21.4%. When sire and dam pedigrees were incorrect for 20% of the pigs each generation, genetic gain using SI was reduced by 7, 2.5 or 6.5% and genetic gain using BLUP was reduced by 9.3, 3.2 or 12.4% for LS, BF and ADG, respectively. With 20% of the pedigrees in error, the advantages in genetic gain of using BLUP over SP, the method unaffected by errors in pedigree, were 10.5, 3.8 and 14.6% for LS, BF and ADG, respectively. These results suggest that, although BLUP is affected to a greater degree by pedigree errors than SP or SI, selection of swine using BLUP still would improve response to selection over the use of SP or SI.

Adipose Tissue↗
PubMed1995

Influences of amount of pedigree information on computing time and of model assumptions on restricted maximum-likelihood estimates of population parameters in Swiss black-brown mountain sheep.

Average daily gain between birth and 30 d of age of 42,644 lambs of Swiss Black-Brown Mountain Sheep were used in this analysis. The influence of amount of pedigree information on computing time and on REML estimates of population parameters was investigated on a subset of 7,848 lambs. If all available pedigree information was used, 89.4% of the lambs had at least four complete generations of known ancestors. For the reduced pedigree information, only parents and grandparents of a lamb were included. In the data set with complete pedigree information, 2,616 additional animals (without records) caused 19.4% more equations, 4.6 times the number of non-zero elements in the system of equations, and 21.2 times the computing time to reach convergence. The difference in amount of pedigree information had only a marginal influence on the estimates of direct heritability (h2), maternal heritability (m2), permanent environmental effects, and on the genetic correlation between direct and maternal effect (rAM). The complete data set of 42,644 recorded lambs was randomly split into four subsets to save computing time. In a fifth subset of 27,787 lambs (Set C) all combinations of recorded grandparents and grand-offspring were accumulated because they contain information on the covariance between direct and maternal effects (cov[AM]). Including cov(AM) in the model assumptions increased estimates of h2 and m2 in all subsets. Estimates from Set C were smallest but showed the same trend. The estimate of rAM was always strongly negative, < or = -.64.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed2001

Efficient computation of genotype probabilities for loci with many alleles: II. Iterative method for large, complex pedigrees.

An algorithm for computing genotype probabilities for marker loci with many alleles in large, complex pedigrees with missing marker data is presented. The algorithm can also be used to calculate grandparental origin probabilities, which summarize the segregation pattern and are useful for mapping quantitative trait loci. The algorithm is iterative and is based on peeling on alleles instead of the traditional peeling on genotypes. This makes the algorithm more computationally efficient for loci with many alleles. The algorithm is approximate in pedigrees that contain loops, including loops generated by full sibs. The algorithm has no restrictions on pedigree structure or missing marker phenotypes, although together those factors affect the degree of approximation. In livestock pedigrees with dense marker data, the degree of approximation may be minimal. The algorithm can be used with an incomplete penetrance model for marker loci. Thus, it takes into account the possibility of marker scoring errors and helps to identify them. The algorithm provides a computationally feasible method to analyze genetic marker data in large, complex livestock pedigrees.

Alleles↗
PubMed2002

[Screening for mitochondrial DNA mutation in two pedigrees with nonsyndromic inherited sensorineural hearing loss].

OBJECTIVE: To investigate the genetic mechanism of maternal nonsyndromic inherited sensorineural hearing loss(SNHL), to identify the incidence of the 7445(G) mutation in such pedigrees and sporadic patients with SNHL, and to provide the theoretical evidence for the diagnosis of this disease. METHODS: Blood samples were obtained from 2 pedigrees and 14 sporadic patients with SNHL. DNA was extracted from the isolated leukocytes. The mitochondrial DNA (mtDNA) fragments were amplified by PCR. The 1555(G), 3243(G) and 7445(G) mutation was detected by Alw 26 I, Apa I and Xba I restriction endonuclease digestion respectively. The sequence of 12S rRNA, tRNA(Leu(UUR)) and tRNA(Ser(UCN)) was examined. RESULTS: Restriction endonuclease digestion analysis showed that 12 individuals from 2 pedigrees carried homoplasmic 7445(G) mutation, which was of maternal inheritance. Six individuals from 2 pedigrees and 14 sporadic patients did not have 7445(G) mutation. All individuals did not have 1555(G) and 3243(G) mutation. The sequence analysis further showed that none of them carried homoplasmic 1555(G) and 3243(G) mutation, 12 individuals had (nt)7445 A--> G substitution in tRNA(Ser(UCN)) gene. CONCLUSION: The incidence of 7445(G) mutation in such pedigrees is higher than that in sporadic patients. Screening for mtDNA 7445(G) mutation combined with 1555(G) examination is of much value to clinical use.

DNA Mutational Analysis↗
PubMed2002

[Molecular analysis of two pedigrees with hereditary F VII deficiency].

OBJECTIVE: To identify the mutation of coagulation factor VII (F VII) gene in two pedigrees with hereditary F VII deficiency. METHODS: F VII gene mutations were analysed in two propositi and their family members by direct DNA sequencing. Allele specific PCR and PCR combined with restricted enzyme digestion were used to confirm the detected mutations. RESULTS: Two gene mutations were detected in the propositus of pedigree A: G to C transition at position 6390 resulting in Trp40Cys and G to A at 11496 resulting in Arg353Gln, both are heterozygotes. The heterozygosity for polymorphism Arg353Gln was confirmed with the restriction enzyme Msp I digestion in his mother. In the propositus of pedigree B, there was a T to G transition at position 11482 resulting in His348Gln, heterozygosity of which was confirmed with Nsp I digestion in the propositus and his daughter. G to T transition at position 11514 resulting in Thr359Met was also found in the propositus of pedigree B, and the heterozygosity for Thr359Met was confirmed with allele specific PCR in the propositus and his son. CONCLUSION: Three missense mutations were found in two pedigrees with hereditary F VII deficiency. A novel Trp40Cys mutation was reported for the first time.

Factor VII↗
PubMed2002

Clinical and gene mutation studies on a Chinese pedigree with glucocorticoid-remediable aldosteronism.

OBJECTIVE: To report the clinical characteristics, biochemical profiles, diagnosis and treatment of one Chinese pedigree with glucocorticoid-remediable aldosteronism (GRA) and to study its molecular mechanism. METHODS: Plasma and urinary aldosterone, cortisol and plasma renin activities were dynamically tested and diagnostic therapy with dexamethasone was undergone in 3 affected subjects. Long-distance PCR as well as DNA sequencing were applied to detect the fusion gene in this pedigree. RESULTS: In this GRA pedigree, there were 4 affected subjects who had hypertension, hypokalemia and low basic and provoked renin activity. Three patients were given dexamethasone treatment, and had a significant decrease in plasma aldosterone concentrations (PACs) (from 192 +/- 9 ng/L to 87 +/- 7ng/L, P < 0.05) after 5 days. Among them, one patient (II -3) responded quite satisfactorily to the therapy, with serum K(+) rising from baseline value of 2.5 to 2.9, 3.8 and 4.15 mEq/L on the 10th, 28th and 35th days after treatment respectively. Three weeks later, his blood pressure decreased from its original level of 146.3 +/- 1 0.7/94.6 +/- 5.3 mm Hg to 138.3 +/- 3.1/87.3 +/- 6.1 mm Hg (P < 0.05). The other 2 members (III -2 and III -4) showed modest improvement although their PACs decreased significantly. Using long-distance PCR, we found a 3.9 kb band in all 4 affected individuals, which was absent in 5 unaffected members from this pedigree or 8 patients with aldosterone-producing adenoma (APA) or idiopathic hyperaldosteronism (IHA). By DNA sequence analysis, we found that the breakpoint of "unequal crossing-over" is both within intron 2 of the 11beta-hydroxylase gene (CYP11B1) and the aldosterone synthase gene (CYP11B2). CONCLUSIONS: The excess of mineralocorticoid in patients with GRA can be inhibited by exogenous glucocorticoids. The fusion gene resulting from unequal crossing-over between the 11beta-hydroxylase gene and the aldosterone synthase gene is the pathogenesis of this Chinese GRA pedigree.

Adrenocorticotropic Hormone↗
PubMed2002

[KCNQ4 gene mutations affected a pedigree with autosomal dominant hereditary hearing loss].

OBJECTIVE: To investigate if the KCNQ4 gene contributes to a Chinese non-syndromic hearing loss pedigree and to detect the gene mutations in the pedigree using candidate approach. METHODS: PCR-SSCP and clone sequencing were performed to identify the mutations and polymorphism in PCR products of KCNQ4 coding sequence in the six-generations pedigree of autosomal dominant hereditary hearing loss. RESULTS: Mutations and polymorphism detection were performed on the KCNQ4 coding sequence in 36 family members of the pedigree. A molecular polymorphism marker located in the exon2 and exon3 intron sequence, which resulted from a copy variation of 47 base pairs insertion or deletion, was found in KCNQ4 sequence. CONCLUSION: A new molecular polymorphism marker with different genotypes was proved to locate at the intron sequence between at exon2 and exon3. The correlation between genotype and phenotype was analyzed. Deaf individuals were accompanied by the increase of the intron copies in the family. These findings suggest that the changes of the copies of intron between exon2 and exon3 of KCNQ4 might be a specific marker for the hearing loss of the pedigree.

Exons↗