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At least 307 records · Page 17Linked to original sources

PubMed2005

Dysferlin mutation in a Chinese pedigree with Miyoshi myopathy.

OBJECTIVES: Mutations in the dysferlin gene cause two autosomal recessive forms of muscular dystrophy: Miyoshi myopathy and limb-girdle muscular dystrophy type 2B. The purpose of this study was to diagnose a Chinese pedigree with the autosomal recessive form of muscular dystrophy and conduct mutational screening. METHODS: The pedigree was diagnosed accurately by using two-point linkage analysis and multi-Western blot analysis. Mutations were determined by reverse transcriptase polymerase chain reaction (RT-PCR) followed by DNA sequencing. RESULTS: Two-point linkage analysis showed significant LOD scores with makers from chromosome 2p13. Multi-Western blot analysis confirmed dysferlin deficiency of muscle specimen from the propositus. Mutation analysis of the dysferlin gene revealed a novel mutation, 6429delG, on exon 53. CONCLUSIONS: We identified an inbred Chinese pedigree with Miyoshi myopathy caused by the 6429delG mutation in the dysferlin gene. This mutation is predicted to result in premature termination of translation contributing to Miyoshi myopathy.

Asian People↗

PubMed2002

Creatine depletion in a new case with AGAT deficiency: clinical and genetic study in a large pedigree.

Arginine:glycine amidinotransferase (AGAT, EC 2.1.4.1) deficiency is a recently recognized autosomal recessive inborn error of creatine biosynthesis, characterized by mental retardation and severe language impairment. We extensively investigated a third 5-year-old patient with AGAT deficiency, discovered in the pedigree of the same Italian family as the two index cases. At the age of 2 years he presented with psychomotor and language delay, and autistic-like behavior. Brain MRI was normal, but brain 1H-MRS disclosed brain creatine depletion, which almost completely normalized following creatine monohydrate supplementation. A remarkable clinical improvement paralleled the restoration of brain creatine concentration. AGAT and GAMT (guanidinoacetate:methyltransferase) genes were analyzed in the proband and in 26 relatives, including the two cousins with AGAT deficiency. Sequencing of the proband's AGAT gene disclosed the same homozygous mutation at nt position 9093 converting a tryptophan (TGG) to a stop codon (TAG) at residue 149 (W149X), as already described in the two previously reported cases. The proband's parents and 10 additional subjects of the pedigree were carriers for this mutation. AGAT deficiency was further confirmed by undetectable AGAT activity in the patient's lymphoblasts. Mutation analysis of the GAMT gene revealed a sequence variation in exon 6 (T209M), not in the proband, but in 15 additional subjects from the pedigree. The silent nature of this sequence variation is supported by its homozygosity in one AGAT deficient cousin and in one asymptomatic adult, both with normal GAMT activity.

Amidinotransferases↗

PubMed1990

Incorporation of twins in the regressive logistic model for pedigree disease data.

Segregation and twin disease concordance analyses have assumed a theoretical underlying liability following a multivariate normal distribution. For reasons of computation, of incorporation of measured explanatory variables, and of testing of fit and assumptions, newer analytical methods are being developed. The regressive logistic model (RLM) relies on expressing the pedigree likelihood as a product of conditional probabilities, one for each individual. In addition to logistic regression modelling of measured epidemiological variables on disease prevalence, there is modelling of vertical transmission, of transmission of unmeasured genotypes and of sibship environment. This paper discusses methods for the analysis of binary traits in twins and in pedigrees. Some extensions to the RLM for pedigrees which include twins are proposed. These enable exploration of twin concordance in the context of the twins' common parenthood, the sibship similarities within the family, and the twins' similarity in age, sex, genes and environment.

Asthma↗

PubMed2003

Haplotypic QTL mapping in an outbred pedigree.

An offspring genome can be viewed as a mosaic of chromosomal segments or haplotypes contributed by multiple founders in any quantitative trait locus (QTL) detection study but tracing these is especially complex to achieve for outbred pedigrees. QTL haplotypes can be traced from offspring back to individual founders in outbred pedigrees by combining founder-origin probabilities with fully informative flanking markers. This haplotypic method was illustrated for QTL detection using a three-generation pedigree for a woody perennial plant, Pinus taeda L. Growth rate was estimated using height measurements from ages 2 to 10 years. Using simulated and actual datasets, power of the experimental design was shown to be efficient for detecting QTLs of large effect. Using interval mapping and fully informative markers, a large QTL accounting for 11.3% of the phenotypic variance in the growth rate was detected. This same QTL was expressed at all ages for height, accounting for 7.9-12.2% of the phenotypic variance. A mixed-model inheritance was more appropriate for describing genetic architecture of growth curves in P. taeda than a strictly polygenic model. The positive QTL haplotype was traced from the offspring to its contributing founder, GP3, then the haplotypic phase for GP3 was determined by assaying haploid megagametophytes. The positive QTL haplotype was a recombinant haplotype contributed by GP3. This study illustrates the combined power of fully informative flanking markers and founder origin probabilities for (1) estimating QTL haplotype magnitude, (2) tracing founder origin and (3) determining haplotypic transmission frequency.

Haplotypes↗

PubMed2002

Attention-deficit/hyperactivity disorder (ADHD): feasibility of linkage analysis in a genetic isolate using extended and multigenerational pedigrees.

Segregation analyses converge in explaining the predisposition to attention-deficit/hyperactivity disorder (ADHD) as the consequence of a major gene and exclude purely environmental or cultural transmission. As a result of the ADHD phenotype restrictions, collection of extended families or design of linkage studies using families has been extremely difficult and thus currently linkage studies have been performed using only concordant or discordant sib-pairs rather than large families. On the other hand, intergenerational studies are represented by the transmission disequilibrium test (TDT) using trios. We collected pedigree data on ADHD from the Paisa community from Antioquia, Colombia, a genetic isolate. The goal of this study was to genetically map a putative gene predisposing to ADHD in a set of 27 multigenerational Paisa families. Here we present the results of a power simulation using SIMLINK to detect linkage of ADHD. ADHD was assumed to be a dichotomous trait with incomplete penetrance and a phenocopy rate of 3% in males and 0.2% in females. We simulated cosegregation of the trait and a marker locus in our pedigrees. We assumed Hardy-Weinberg and linkage equilibrium, equally frequent marker alleles and evaluated power at several recombination fractions between the trait and marker loci. Also, the ADHD trait was assumed to be genetically heterogeneous and different functions of age-dependent penetrance were simulated. We found exceptionally good power to detect linkage (expected LOD > 14 if theta is 0.1 or less), and that the presence of heterogeneity up to 50% does not affect substantially the projected LOD scores even for a theta recombination value of 0.05 (eLOD > 5.87). Having now obtained blood samples and confirmatory interviews in five families (representing 20% of the projected number of families), we performed a new analysis. The expected mean LOD in these five families reached values close to 10 and remained invariant when heterogeneity and different penetrance models were considered. We discuss the relative benefits of using extended and multigenerational families for genetic mapping studies as opposed to using nuclear families, affected sib pairs or sporadic cases which require the collection of over 1000 analytical units to get the same power exhibited by the small number of pedigrees described here.

Adult↗

PubMedDate not supplied

Close linkage of c-Harvey-ras-1 and the insulin gene to affective disorder is ruled out in three North American pedigrees.

Affective disorder (AD) is one of the major forms of functional psychoses. Although the mode of transmission is uncertain, family, twin and adoption studies strongly suggest a genetic involvement. Because a basic biochemical abnormality is not known, direct analysis of the disease using a probe for the defective gene is not possible. However, a specific locus can be tested for its relevance to the aetiology of AD by genetic linkage, using restriction fragment length polymorphisms (RFLPs). Using probes for the c-Ha-ras-1 oncogene and the insulin gene, Gerhard et al. and Egeland et al. found convincing evidence for close linkage between these markers and a locus for AD in a large Old Order Amish pedigree. In an attempt to confirm this finding, we examined three bipolar pedigrees outside the Amish population. Our results indicate the absence of linkage from 0 to 15% recombination frequency between AD and the insulin gene-HRAS1 region in these pedigrees.

Bipolar Disorder↗

PubMed2002

Segregation analysis of HDL cholesterol in the NHLBI Family Heart Study and in Utah pedigrees.

We investigated the genetic determination of high-density-lipoprotein cholesterol (HDL-C) levels in the NHLBI Family Heart Study by segregation analysis. Included was a total of 3755 subjects from 560 randomly selected nuclear families and 522 families selected due to a high family risk of coronary heart disease (CHD). In the whole dataset, there was no evidence for an allele at a major gene locus responsible for HDL-C levels lower than the population mean or even for significant bimodality for low levels of HDL-C. However, we observed evidence for a recessive allele that was associated with higher HDL-C levels than average. This evidence for a recessive major gene was independent of triglyceride concentrations and was most strongly observed in families recruited for CHD. The environmental model was rejected (P=0.0027) while the codominant and recessive models were not rejected (P=0.085 and P=0.133, respectively). The dominant model was also rejected (P<0.0001). In the recessive segregation model, the means of those inferred to be homozygous for the high HDL-C allele and those without the high HDL-C allele were separated by about 25 mg/dl HDL-C (73.9+/-1.99 vs 48.2+/-0.36 mg/dl). Because these results were unexpected, segregation was tested in a separate sample of 2013 individuals in 85 large pedigrees ascertained for early heart disease deaths, early stroke deaths, and early hypertension in Utah. Similar evidence for an allele at a major gene locus for high HDL-C was found. In summary, we did not find evidence for an allele at a major gene locus associated with low HDL-C levels segregating in pedigrees recruited for the NHLBI Family Heart Study, or in pedigrees ascertained in Utah for early CHD or related phenotypes. Instead we found some evidence for the segregation of an allele associated with high HDL-C. d

Alleles↗

PubMed2005

High-throughput pedigree drawing.

Family trees have long been a valuable visual tool for geneticists in identifying clusters of inherited traits and genotypes. As more data are collected, drawing the graphs by hand becomes impractical and, for this reason, we have developed the pedigree software CraneFoot. It can process any family graph with minimal computational cost by making a pedigree transformation that enables the use of a linear node positioning algorithm. The program is designed for automated drawing to printed media and efficient visual classification of genetically interesting families from large data sets. It also incorporates a robust pedigree topology check with detailed error messages.

Algorithms↗

PubMed2000

A pedigree-based study of mitochondrial D-loop DNA sequence variation among Arabian horses.

Through DNA sequence comparisons of a mitochondrial D-loop hypervariable region, we investigated matrilineal diversity for Arabian horses in the United States. Sixty-two horses were tested. From published pedigrees they traced in the maternal line to 34 mares acquired primarily in the mid to late 19th century from nomadic Bedouin tribes. Compared with the reference sequence (GenBank X79547), these samples showed 27 haplotypes with altogether 31 base substitution sites within 397 bp of sequence. Based on examination of pedigrees from a random sampling of 200 horses in current studbooks of the Arabian Horse Registry of America, we estimated that this study defined the expected mtDNA haplotypes for at least 89% of Arabian horses registered in the US. The reliability of the studbook recorded maternal lineages of Arabian pedigrees was demonstrated by haplotype concordance among multiple samplings in 14 lines. Single base differences observed within two maternal lines were interpreted as representing alternative fixations of past heteroplasmy. The study also demonstrated the utility of mtDNA sequence studies to resolve historical maternity questions without access to biological material from the horses whose relationship was in question, provided that representatives of the relevant female lines were available for comparison. The data call into question the traditional assumption that Arabian horses of the same strain necessarily share a common maternal ancestry.

Animals↗

PubMed1999

Relative efficiencies of the chi-square recombination models for gene mapping with human pedigree data.

In the paper by Goldstein et al. (Genomics, 1995), the authors carried out a simulation study to investigate the relative efficiencies of a no interference linkage analysis to an analysis with certain models that allow for interference. They showed that, for completely informative and independent recombination data, the analysis with the no interference model was inefficient, in the present of interference. In practice, the assumption of completely informative markers is unrealistic with data from human pedigrees. We report the results of a study investigating whether this conclusion still holds for gametes arising within pedigrees. We consider the same two mapping problems as Goldstein et al.: exclusion mapping and gene ordering. The results obtained were consistent with their findings, although the efficiency gains for analyses using the chi-square model were not as great in some cases. This is not unexpected with less than fully informative data. These results point to the need for research of developing new statistical and computational methods to incorporate interference into multipoint linkage mapping using pedigree data. This would make efficient use of available, but sometimes scarce data, especially in disease gene mapping.

Alleles↗

PubMed2001

Mapping loci causing susceptibility to anal atresia in pigs, using a resource pedigree.

BACKGROUND/PURPOSE: Very little information on the genetic background for anal atresia (anorectal malformations; AA) in humans has been described. A strikingly similar natural anomaly occurs in piglets. The authors have used this as an animal model for various research purposes. The affected piglets were treated surgically soon after birth, raised, and used for breeding. The authors have generated a resource pedigree segregating for this naturally occurring nonsyndromal AA and describe here the first attempt to map susceptibility loci by marker analysis. METHODS: A pig pedigree with a high incidence of AA has been established by selective breeding using 3 probands from the Landrace and Large White breeds. It has been maintained by intrafamilial crossing for more than 15 years. A backcross pedigree has now been generated by mating 4 AA females to an unaffected male from the Chinese Meishan breed. F(1) animals were both intercrossed and backcrossed to affected AA animals. A genome scan was carried out using the F(0), F(1), and affected backcross progeny. Ninety-two microsatellite loci were analyzed using fluorescently labelled primers and an ABI377 sequencer. Linkage analysis was done with the CRI-MAP 2.4 software. RESULTS: Crossing affected parents increased the incidence of abnormalities from 30% to 61.9%. All 39 F(1) pigs were unaffected. In the F(1) intercross, only 3 of 205 (1.5%) were affected, whereas 42 of 523 (8.0%) backcross progeny were affected. The marked difference in the incidence of affected progeny in the F(1) intercross and in the backcross indicates the presence of multiple genes causing AA. The genome scan showed suggestive evidence for the presence of a susceptibility locus on pig chromosome 15 (lod score 2.7 for a pig microsatellite marker SW2072). CONCLUSIONS: The results clearly show that AA has a oligogenic or polygenic background. The genome scan showed one suggestive locus causing AA on pig chromosome 15. The long-term goal is to identify causative genes for this malformation by comparative positional candidate cloning. This study provides, for the first time, linkage mapping of nonsyndromal anorectal malformations with a polygenic inheritance.

Animals↗

PubMed1999

Delineation of the critical interval of Bardet-Biedl syndrome 1 (BBS1) to a small region of 11q13, through linkage and haplotype analysis of 91 pedigrees.

Bardet-Biedl syndrome (BBS) is a genetically heterogeneous recessive disease characterized primarily by atypical retinitis pigmentosa, obesity, polydactyly, hypogenitalism, and mental retardation. Despite the presence of at least five loci in the human genome, on chromosomes 2q, 3p, 11q, 15q and 16q, as many as 50% of the mutations appear to map to the BBS1 locus on 11q13. The recessive mode of inheritance and the genetic heterogeneity of the syndrome, as well as the inability to distinguish between different genetic loci by phenotypic analyses, have hindered efforts to delineate the 11q13 region as a first step toward cloning the mutated gene. To circumvent these difficulties, we collected a large number of BBS pedigrees of primarily North American and European origin and performed genetic analysis, using microsatellites from all known BBS genomic regions. Heterogeneity analysis established a 40.5% contribution of the 11q13 locus to BBS, and haplotype construction on 11q-linked pedigrees revealed several informative recombinants, defining the BBS1 critical interval between D11S4205 and D11S913, a genetic distance of 2.9 cM, equivalent to approximately 2.6 Mb. Loss of identity by descent in two consanguineous pedigrees was also observed in the region, potentially refining the region to 1.8 Mb between D11S1883 and D11S4944. The identification of multiple recombinants at the same position forms the basis for physical mapping efforts, coupled with mutation analysis of candidate genes, to identify the gene for BBS1.

Bardet-Biedl Syndrome↗

PubMed2000

Power comparison of parametric and nonparametric linkage tests in small pedigrees.

When the mode of inheritance of a disease is unknown, the LOD-score method of linkage analysis must take into account uncertainties in model parameters. We have previously proposed a parametric linkage test called "MFLOD," which does not require specification of disease model parameters. In the present study, we introduce two new model-free parametric linkage tests, known as "MLOD" and "MALOD." These tests are defined, respectively, as the LOD score and the admixture LOD score, maximized (subject to the same constraints as MFLOD) over disease-model parameters. We compared the power of these three parametric linkage tests and that of two nonparametric linkage tests, NPLall and NPLpairs, which are implemented in GENEHUNTER. With the use of small pedigrees and a fully informative marker, we found the powers of MLOD, NPLall, and NPLpairs to be almost equivalent to each other and not far below that of a LOD-score analysis performed under the assumption the correct genetic parameters. Thus, linkage analysis is not much hindered by uncertain mode of inheritance. The results also suggest that both parametric and nonparametric methods are suitable for linkage analysis of complex disorders in small pedigrees. However, whether these results apply to large pedigrees remains to be answered.

Chromosome Mapping↗

PubMed2001

Genomewide multipoint linkage analysis of seven extended Palauan pedigrees with schizophrenia, by a Markov-chain Monte Carlo method.

Palauans are an isolated population in Micronesia with lifetime prevalence of schizophrenia (SCZD) of 2%, compared to the world rate of approximately 1%. The possible enrichment for SCZD genes, in conjunction with the potential for reduced etiological heterogeneity and the opportunity to ascertain statistically powerful extended pedigrees, makes Palauans a population of choice for the mapping of SCZD genes. We have used a Markov-chain Monte Carlo method to perform a genomewide multipoint analysis in seven extended pedigrees from Palau. Robust multipoint parametric and nonparametric linkage (NPL) analyses were performed under three nested diagnostic classifications-core, spectrum, and broad. We observed four regions of interest across the genome. Two of these regions-on chromosomes 2p13-14 (for which, under core diagnostic classification, NPL=6.5 and parametric LOD=4.8) and 13q12-22 (for which, under broad diagnostic classification, parametric LOD=3.6, and, under spectrum diagnostic classification, parametric LOD=3.5)-had evidence for linkage with genomewide significance, after correction for multiple testing; with the current pedigree resource and genotyping, these regions are estimated to be 4.3 cM and 19.75 cM in size, respectively. A third region, with intermediate evidence for linkage, was identified on chromosome 5q22-qter (for which, under broad diagnostic classification, parametric LOD=2.5). The fourth region of interest had only borderline suggestive evidence for linkage (on 3q24-28; for this region, under broad diagnostic classification, parametric LOD=2.0). All regions exhibited evidence for genetic heterogeneity. Our findings provide significant evidence for susceptibility loci on chromosomes 2p13-14 and 13q12-22 and support both a model of genetic heterogeneity and the utility of a broader set of diagnostic classifications in the population from Palau.

Chromosome Mapping↗

PubMed2001

Statistics for nonparametric linkage analysis of X-linked traits in general pedigrees.

We have compared the power of several allele-sharing statistics for "nonparametric" linkage analysis of X-linked traits in nuclear families and extended pedigrees. Our rationale was that, although several of these statistics have been implemented in popular software packages, there has been no formal evaluation of their relative power. Here, we evaluate the relative performance of five test statistics, including two new test statistics. We considered sibships of sizes two through four, four different extended pedigrees, 15 different genetic models (12 single-locus models and 3 two-locus models), and varying recombination fractions between the marker and the trait locus. We analytically estimated the sample sizes required for 80% power at a significance level of.001 and also used simulation methods to estimate power for a sample size of 10 families. We tried to identify statistics whose power was robust over a wide variety of models, with the idea that such statistics would be particularly useful for detection of X-linked loci associated with complex traits. We found that a commonly used statistic, S(all), generally performed well under various conditions and had close to the optimal sample sizes in most cases but that there were certain cases in which it performed quite poorly. Our two new statistics did not perform any better than those already in the literature. We also note that, under dominant and additive models, regardless of the statistic used, pedigrees with all-female siblings have very little power to detect X-linked loci.

Alleles↗

PubMed2002

myotilin Mutation found in second pedigree with LGMD1A.

Limb-girdle muscular dystrophy 1A (LGMD1A [MIM 159000]) is an autosomal dominant form of muscular dystrophy characterized by adult onset of proximal weakness progressing to distal muscle weakness. We have reported elsewhere a mutation in the myotilin gene in a large, North American family of German descent. Here, we report the mutation screening of an additional 86 families with a variety of neuromuscular pathologies. We have identified a new myotilin mutation in an Argentinian pedigree with LGMD1 that is predicted to result in the conversion of serine 55 to phenylalanine (S55F). This mutation has not been found in 392 control chromosomes and is located in the unique N-terminal domain of myotilin, only two residues from the T57I mutation reported elsewhere. Both T57I and S55F are located outside the alpha-actinin and gamma-filamin binding sites within myotilin. The identification of two independent pedigrees with the same disease, each bearing a different mutation in the same gene, has long been the gold standard for establishing a causal relationship between defects in a gene and the resultant disease. As a description of the second known pedigree with LGMD1A, this finding constitutes that gold standard of proof that mutations in the myotilin gene cause LGMD1A.

Argentina↗

PubMed2003

Polymorphisms at the G72/G30 gene locus, on 13q33, are associated with bipolar disorder in two independent pedigree series.

Linkage evidence suggests that chromosome 13 (13q32-33) contains susceptibility genes for both bipolar disorder and schizophrenia. Recently, genes called "G72" and "G30" were identified, and polymorphisms of these overlapping genes were reported to be associated with schizophrenia. We studied two series of pedigrees with bipolar disorder: the Clinical Neurogenetics (CNG) pedigrees (in which linkage to illness had been previously reported at 13q32-33), with 83 samples from 22 multiplex families, and the National Institute of Mental Health (NIMH) Genetics Initiative pedigrees, with 474 samples from 152 families. Sixteen single-nucleotide polymorphisms (SNPs) were genotyped at and around the G72/G30 locus, which covered a 157-kb region encompassing the entire complementary DNA sequences of G72 and G30. We performed transmission/disequilibrium testing (TDT) and haplotype analysis, since a linkage-disequilibrium block was present at this gene locus. In the CNG and NIMH data sets, the results of global TDT of the entire haplotype set were significant and consistent (P=.0004 and P=.008, respectively). In the CNG series, the associated genotypes divided the families into those with linkage and those without linkage (partitioned by the linkage evidence). Analysis of the decay of haplotype sharing gave a location estimate that included G72/G30 in its 95% confidence interval. Although statistically significant association was not detected for individual SNPs in the NIMH data set, the same haplotype was consistently overtransmitted in both series. These data suggest that a susceptibility variant for bipolar illness exists in the vicinity of the G72/G30 genes. Taken together with the earlier report, this is the first demonstration of a novel gene(s), discovered through a positional approach, independently associated with both bipolar illness and schizophrenia.

Alternative Splicing↗

PubMed2003

Genomic imprinting and linkage test for quantitative-trait Loci in extended pedigrees.

Genomic imprinting is a mechanism in which only one of the two copies of a gene is expressed. Some genes that affect development and behavior in mammals are known to be imprinted. Deregulation of imprinted genes has been found in a number of human diseases. Incorporating imprinting information into linkage analysis results in a more powerful test for linkage. Here, we propose an efficient method to test for linkage and imprinting of quantitative traits in extended pedigrees. We compared the results obtained by using the extended-pedigree-analysis approach proposed in this study with other existing approaches. We found that the proposed method is more powerful and uses extended-pedigree information most efficiently.

Female↗