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At least 127 records · Page 7Linked to original sources

Clinical comparison of Alzheimer's disease in pedigrees with the codon 717 Val-->Ile mutation in the amyloid precursor protein gene.

Alzheimer's disease (AD) is the most common cause of dementia (32). Although the majority of cases of AD are sporadic, the most consistent risk factor detected in several epidemiological studies has been a positive family history of the disease (14,21). In addition, many large pedigrees have been described in which AD appears to be inherited as an autosomal dominant disorder. In one such pedigree (F23) a point mutation within the beta-amyloid precursor protein (APP) gene at codon 717 was identified and hypothesized to be pathogenic (10). The mutation results in a valine to isoleucine change in APP (APP717 Val-->Ile). Subsequent screening has revealed four other pedigrees, detailed in this study, in which this mutation co-segregates with AD (13,26,37). In addition, one other pedigree (Tor3) with this mutation has been described (15) and detailed clinical, neuropsychological, and neuropathological data are reported. Tor3 is discussed below in comparison to the findings in the families in this study. The five families we report with the mutation were identified in Britain (1 family), the United States (1 family), and Japan (3 families). The mutation has not been reported in the general population of any of these countries (3,13,26,33). On this basis alone it seems this mutation is pathogenic. Other APP codon 717 mutations have been identified which co-segregate with the disease (4,25). Also, a double mutation in APP at codons 670/671 has been shown to cosegregate with the disease in two large Swedish pedigrees (22). In all cases, there is complete co-segregation of the APP mutation with early onset AD, providing overwhelming statistical evidence that these mutations are pathogenic. We present the clinical features and limited neuropathology of AD in these families with the APP 717 Val-->Ile mutation.

Adult↗

Estimation of genotype error rate using samples with pedigree information--an application on the GeneChip Mapping 10K array.

Currently, most analytical methods assume all observed genotypes are correct; however, it is clear that errors may reduce statistical power or bias inference in genetic studies. We propose procedures for estimating error rate in genetic analysis and apply them to study the GeneChip Mapping 10K array, which is a technology that has recently become available and allows researchers to survey over 10,000 SNPs in a single assay. We employed a strategy to estimate the genotype error rate in pedigree data. First, the "dose-response" reference curve between error rate and the observable error number were derived by simulation, conditional on given pedigree structures and genotypes. Second, the error rate was estimated by calibrating the number of observed errors in real data to the reference curve. We evaluated the performance of this method by simulation study and applied it to a data set of 30 pedigrees genotyped using the GeneChip Mapping 10K array. This method performed favorably in all scenarios we surveyed. The dose-response reference curve was monotone and almost linear with a large slope. The method was able to estimate accurately the error rate under various pedigree structures and error models and under heterogeneous error rates. Using this method, we found that the average genotyping error rate of the GeneChip Mapping 10K array was about 0.1%. Our method provides a quick and unbiased solution to address the genotype error rate in pedigree data. It behaves well in a wide range of settings and can be easily applied in other genetic projects. The robust estimation of genotyping error rate allows us to estimate power and sample size and conduct unbiased genetic tests. The GeneChip Mapping 10K array has a low overall error rate, which is consistent with the results obtained from alternative genotyping assays.

Computer Simulation↗

Extensive investigation of a large Brazilian pedigree of 11778/haplogroup J Leber hereditary optic neuropathy.

PURPOSE: To conduct systematic epidemiologic, neuro-ophthalmologic, psychophysical, and mitochondrial DNA (mtDNA) genetic examinations on a newly identified pedigree with Leber hereditary optic neuropathy (LHON). DESIGN: Observational population cohort study. METHODS: A prospective investigation of an entire Brazilian LHON family. SETTING: A field investigation by an international team conducted in a remote part of Brazil. STUDY POPULATION: We evaluated 265 (both eyes) of the 328 living family members of this LHON pedigree. Only members of this pedigree were studied. Those entering the pedigree as spouses were used as controls. OBSERVATION PROCEDURES: We conducted epidemiologic interviews emphasizing possible environmental risk factors, comprehensive neuro-ophthalmologic examinations, psychophysical tests, Humphrey visual field studies, fundus photography, and blood testing for mitochondrial genetic analysis. RESULTS: We reconstructed a seven-generation maternal lineage descended from a common ancestor dating to the 1870s. All maternally related family members were invariably homoplasmic 11778 with a haplogroup J mtDNA, 33 being affected, of which 22 are still living. With each subsequent generation, there was a progressive decrease of penetrance, and only males were affected in the last two generations. A significant exposure (greater than 95% confidence intervals) to a variety of environmental risk factors characterized the affected individuals, with smoking as the most common (P <.01). Both affected and carriers (95% confidence intervals) presented with a significantly lower incidence of hypertension and high cholesterol compared with the control group (P <.05). CONCLUSIONS: Almost 95% of a 328-living-member pedigree with LHON 11778/J haplogroup was comprehensively studied. Our initial results indicate the strong influence of environmental risk factors. The remarkably reduced incidence of cardiovascular risk in the maternal lineage is discussed. Further genetic analysis may reveal a role for the nuclear genome.

Adolescent↗

Clinical features of five pedigrees genetically linked to the juvenile glaucoma locus on chromosome 1q21-q31.

BACKGROUND: Primary juvenile glaucoma is a rare form of glaucoma that typically affects individuals between 3 and 20 years of ages and is inherited as an autosomal dominant trait. One gene responsible for this condition has been localized to the 1q21-q31 region of chromosome 1. To investigate the clinical features of this form of glaucoma, the authors have examined the affected members of five pedigrees demonstrating genetic linkage to the 1q21-q31 locus. METHODS: Clinical characterization of 23 affected patients was performed. Genetic linkage to the 1q21-q31 locus was confirmed by segregation of the disease trait in each pedigree with genetic markers located in the 1q21-q31 region. RESULTS: The clinical features of affected members of the five pedigrees presented are generally homogeneous. The average age of diagnosis was 18.5 years (range, 5-30 years), and the average initial intraocular pressure was 38.5 mmHg (range, 30-53 mmHg). Eighty-seven percent of affected individuals were myopic and 83% of affected individuals required surgical treatment for glaucoma. There were no uniformly associated systemic or ocular conditions. One possible nonpenetrant carrier was identified and a difference in phenotypic expression of the presumed disease gene was observed in a pair of affected monozygotic twins. We also identified two pedigrees with juvenile glaucoma and three pedigrees affected by the pigment dispersion syndrome that are not genetically linked to the 1q21-q31 region. CONCLUSION: The form of juvenile glaucoma caused by a gene located in the q21-q31 region of chromosome 1 is generally phenotypically homogeneous. The severe elevation of intraocular pressure typically seen in affected patients suggests the product of the predisposing gene may participate in the outflow function of the eye.

Adolescent↗

An algorithm for sampling descent graphs in large complex pedigrees efficiently.

No exact method for determining genotypic and identity-by-descent probabilities is available for large complex pedigrees. Approximate methods for such pedigrees cannot be guaranteed to be unbiased. A new method is proposed that uses the Metropolis-Hastings algorithm to sample a Markov chain of descent graphs which fit the pedigree and known genotypes. Unknown genotypes are determined from each descent graph. Genotypic probabilities are estimated as their means. The algorithm is shown to be unbiased for small complex pedigrees and feasible and consistent for moderately large complex pedigrees.

Algorithms↗

Pedigree-assisted genotype imputation enables cost-effective genomic prediction in Penaeus vannamei.

Genomic selection in Penaeus vannamei has long been constrained by the high cost of dense genotyping. To address this limitation, we evaluated genotype imputation from a low-density 1&#xa0;K panel to a medium-density 55&#xa0;K panel of the "Yellow Sea Array No. 1" and examined its impact on genomic prediction for harvest body weight in P. vannamei. A four-generation pedigree including 30 great-grandparents, 39 grandparents, 100 parents, and 608 offspring was genotyped using the 55&#xa0;K panel. A two-step experimental design was implemented to (i) assess the performance of different imputation algorithms under reference population scenarios with varying proportions of siblings, and (ii) compare six alternative reference population structures incorporating parents, ancestors, and siblings. Genotype imputation using the pedigree-based method FImpute v3.0 consistently achieved higher accuracy than the population-based method Beagle v5.5. Using this pedigree-assisted approach, imputation accuracy increased from 0.73 when only parental genotypes were used to 0.84 with the inclusion of 10% siblings, and subsequently plateaued at 0.87-0.90 when sibling representation reached 20%. Across the six reference population structures, imputation accuracy was primarily driven by the availability of parental genotypes, ranging from 0.50 to 0.56 in the absence of parents to 0.88-0.89 when both parents and ancestral generations were included. Accuracy remained high when both parents were available (0.84-0.87 with siblings; 0.73 without siblings) but declined substantially when only one parent was genotyped (0.65-0.68). Imputation accuracy was positively associated with both minor allele frequency (MAF) and linkage disequilibrium (max r2LD), with LD exerting the stronger influence. Heritability estimates derived from imputed 55&#xa0;K genotypes were highly consistent with those obtained from the original 55&#xa0;K data (0.39&#x2009;&#xb1;&#x2009;0.14 vs. 0.41&#x2009;&#xb1;&#x2009;0.14), indicating that genotype imputation did not compromise variance component estimation. In predictive ability analyses, pedigree-based BLUP (PBLUP) achieved higher predictive ability than genomic BLUP (GBLUP) based on the 1&#xa0;K panel, with predictive abilities of 0.42-0.44 for PBLUP compared with 0.34-0.35 for GBLUP. Using imputed genotypes for genomic prediction further improved predictive ability relative to the true 1&#xa0;K panel, yielding values ranging from 0.35 to 0.47. Notably, when parental genotypes were included in the reference population, GBLUP based on imputed genotypes surpassed the predictive ability of PBLUP and approached that achieved with the original 55&#xa0;K genotypes (0.45-0.47). Collectively, these results provide the first empirical evidence that low- to medium-density genotype imputation, combined with pedigree information, can effectively support genomic prediction in P. vannamei. This study establishes a cost-efficient and scalable framework for implementing genomic selection in P. vannamei and provides a practical reference for the application of genomic selection in other aquaculture species with constrained breeding budgets.

Animals↗

Genome scan stratified by the presence of anti-double-stranded DNA (dsDNA) autoantibody in pedigrees multiplex for systemic lupus erythematosus (SLE) establishes linkages at 19p13.2 (SLED1) and 18q21.1 (SLED2).

Anti-double-stranded DNA (anti-dsDNA) is arguably one of the most specific autoantibodies in systemic lupus erythematosus (SLE). This antibody is associated with more severe SLE and with glomerulonephritis. From 196 pedigrees multiplex for SLE, we selected those that had any SLE affected positive for anti-dsDNA by the Crithidia luciliae kinetoplast imunofluorescence assay. This stratification strategy tested the hypothesis that anti-dsDNA would identify a more genetically homogeneous group of pedigrees, in which previously undetected linkage effects could be established. A genome screen data for linkage to SLE was available at 307 microsatellite markers for this selected group of 71 pedigrees: 37 European-American, 29 African-American, and five others. The most significant results were obtained at 19p13.2 (LOD(max) = 4.93), named SLED1, in the 37 European-American pedigrees using a dominant model with mixed penetrances (92% for females and 49% for males) at 100% homogeneity (theta = 0). A second linkage effect, SLED2, was established in the 29 African-American pedigrees at 18q21.1 (LOD(max) = 3.40) using a recessive model with 100% penetrance (theta = 0.1). Parametric and non-parametric multipoint analyses were performed, which provided further evidence and support of susceptibility genes residing in these regions. In conclusion, two powerful linkages have been detected with SLE based on the presence of anti-dsDNA. These findings show SLE to be a richly complicated disease phenotype that is now ripe for important new discovery through a genetic approach.

Animals↗

An analysis of clinical characteristics in genetically linked migraine-affected pedigrees.

Migraine is a common complex disorder characterized by severe recurrent headache and usually accompanied by nausea and vomiting. Previous studies in our laboratory have utilized three large multigenerational Australian pedigrees affected with migraine to indicate that the disease is genetically heterogeneous, with linkage results implicating genomic susceptibility regions on both chromosomes 19p and Xq. The present study explores the possibility of a correlation between genetic and clinical heterogeneity in these affected pedigrees. Specifically, the clinical characteristics of migraine including subtype, age of onset, frequency, duration, and disease symptoms were compared between the migraine pedigrees, and gender differences were also assessed. Our exploratory analyses revealed no significant differences in any of the clinical characteristics tested between the chromosome 19-linked family and the two X-linked families. Also, we did not detect any differences in male vs. female clinical features for these pedigrees. In conclusion, migraine is considered to be a clinically and genetically heterogeneous disorder; however, our study provided no conclusive evidence that variation in genomic susceptibility region is related to heterogeneity at the clinical level in these migraine-affected pedigrees.

Adolescent↗

Multipoint quantitative-trait linkage analysis in general pedigrees.

Multipoint linkage analysis of quantitative-trait loci (QTLs) has previously been restricted to sibships and small pedigrees. In this article, we show how variance-component linkage methods can be used in pedigrees of arbitrary size and complexity, and we develop a general framework for multipoint identity-by-descent (IBD) probability calculations. We extend the sib-pair multipoint mapping approach of Fulker et al. to general relative pairs. This multipoint IBD method uses the proportion of alleles shared identical by descent at genotyped loci to estimate IBD sharing at arbitrary points along a chromosome for each relative pair. We have derived correlations in IBD sharing as a function of chromosomal distance for relative pairs in general pedigrees and provide a simple framework whereby these correlations can be easily obtained for any relative pair related by a single line of descent or by multiple independent lines of descent. Once calculated, the multipoint relative-pair IBDs can be utilized in variance-component linkage analysis, which considers the likelihood of the entire pedigree jointly. Examples are given that use simulated data, demonstrating both the accuracy of QTL localization and the increase in power provided by multipoint analysis with 5-, 10-, and 20-cM marker maps. The general pedigree variance component and IBD estimation methods have been implemented in the SOLAR (Sequential Oligogenic Linkage Analysis Routines) computer package.

Computer Simulation↗

Handling marker-marker linkage disequilibrium: pedigree analysis with clustered markers.

Single-nucleotide polymorphisms (SNPs) are rapidly replacing microsatellites as the markers of choice for genetic linkage studies and many other studies of human pedigrees. Here, we describe an efficient approach for modeling linkage disequilibrium (LD) between markers during multipoint analysis of human pedigrees. Using a gene-counting algorithm suitable for pedigree data, our approach enables rapid estimation of allele and haplotype frequencies within clusters of tightly linked markers. In addition, with the use of a hidden Markov model, our approach allows for multipoint pedigree analysis with large numbers of SNP markers organized into clusters of markers in LD. Simulation results show that our approach resolves previously described biases in multipoint linkage analysis with SNPs that are in LD. An updated version of the freely available Merlin software package uses the approach described here to perform many common pedigree analyses, including haplotyping and haplotype frequency estimation, parametric and nonparametric multipoint linkage analysis of discrete traits, variance-components and regression-based analysis of quantitative traits, calculation of identity-by-descent or kinship coefficients, and case selection for follow-up association studies. To illustrate the possibilities, we examine a data set that provides evidence of linkage of psoriasis to chromosome 17.

Algorithms↗

A deep intronic mutation in CDKN2A is associated with disease in a subset of melanoma pedigrees.

Germline mutations of CDKN2A at 9p21 have been shown to predispose to disease in melanoma pedigrees worldwide. However, there remains a significant proportion of melanoma pedigrees with evidence of linkage to 9p21 in which mutations in CDKN2A have not been detected. Investigation of other potential tumour suppressor genes at 9p21 and the promotor of CDKN2A has been unable to explain genetic predisposition to melanoma in these pedigrees. Here we describe a mutation, IVS2-105 A/G, deep in intron 2 of CDKN2A, detected in six English melanoma pedigrees. The mutation creates a false GT splice donor site 105 bases 5' of exon 3 and has been demonstrated to result in aberrant splicing of the mRNA. This is the most common mutation identified in English families to date. The presence of this deep intronic mutation in a relatively large number of kindreds, indicates that it may account for a significant proportion of 9p21-linked melanoma pedigrees with no detectable mutations in the coding region of CDKN2A. In addition, the identification of one deep intronic mutation in CDKN2A indicates the possibility of the existence of other similar splicing mutations located elsewhere in the CDKN2A introns.

Alleles↗

Sampling genotypes on complex pedigrees with phenotypic constraints: the origin of the B allele among the Polar Eskimos.

Exact probability calculations are often infeasible on large complex pedigrees. Conditional independences, however, occurring as a natural consequence of Mendelian inheritance of genetic traits, define a locally dependent Markov random field on the state space of all genotypic configurations on the pedigree. The underlying Markov chain is irreducible for most traits determined by a diallelic locus. For a given pedigree and a known genetic model, the Gibbs sampler can be used to obtain good estimates of the posterior distribution of genotypes given the observed data. The areas of pedigree analysis to which such an approach would be most directly relevant include genetic counselling and selective animal breeding, together with questions about ancestral genotypes and the ancestral paths of rare alleles. The method is illustrated by tracing the ancestral paths of a rare allele in a simple diallelic system on a highly complex Eskimo pedigree.

ABO Blood-Group System↗

Simulating realistic zero loop pedigrees using a bipartite Prufer code and graphical modelling.

Graph algorithms previously developed by the authors are adapted to simulate pedigrees similar to those used in genetic linkage studies which associate disease phenotypes with specific genomic locations. Pedigrees are chosen uniformly at random from the set of those with specified numbers of individuals and matings and which contain no loops. Summary statistics from pedigrees generated in this way can be used to check real pedigrees for anomalies due to biased sampling or phenotypic effects on the pedigree structure.

Algorithms↗

The ascertainment of multiplex schizophrenia pedigrees from Daghestan genetic isolates (Northern Caucasus, Russia).

This article describes the preliminary ascertainment of multiplex schizophrenia pedigrees from the isolated mountain region of Daghestan (Northern Caucasus, Russia). Daghestan has a population of two million people and contains 26 aboriginal ethnic groups. Many of the ethnic groups reside in remote mountain villages that can be classified as 'primary isolates'. Prolonged reproductive isolation and severe environmental conditions in the highlands have created diverse, genetically isolated ethnic populations in Daghestan. A number of the isolates in this region contain large extended multiplex schizophrenia pedigrees that are ideal for genetic analyses. During summer expeditions of 1996 and 1997, 14 separate large multiplex schizophrenia pedigrees were ascertained from 14 different mountain villages. Of the 14 kindreds, one had 50 schizophrenic cases available for ascertainment, one had 32, and another had 24. Seven of the remaining pedigrees had between 11 and 23 living cases. Within the kindreds, the number of males with chronic schizophrenia was at least twice that of females. The average age of onset of schizophrenia is 21.2 years for offspring of consanguineous marriages and 17.4 years for offspring of nonconsanguineous marriages (P = 0.033). Although the pedigrees ascertained from the remote mountain villages may not be representative of the general population, they are unique kindreds for mapping schizophrenia susceptibility genes.

Ethnicity↗

Software for constructing and verifying pedigrees within large genealogies and an application to the Old Order Amish of Lancaster County.

This paper describes PedHunter, a software package that facilitates creation and verification of pedigrees within large genealogies. A frequent problem in medical genetics is to connect distant relatives with a pedigree. PedHunter uses methods from graph theory to solve two versions of the pedigree connection problem for genealogies as well as other pedigree analysis problems. The pedigrees are produced by PedHunter as files in LINKAGE format ready for linkage analysis. PedHunter uses a relational database of genealogy data, with tables in specified format, for all calculations. The functionality and utility of PedHunter are illustrated by examples using the Amish Genealogy Database (AGDB), which was created for the Old Order Amish community of Lancaster County, Pennsylvania.

Christianity↗

Finding consistent gene transmission patterns on large and complex pedigrees.

A heuristic algorithm for finding gene transmission patterns on large and complex pedigrees with partially observed genotype data is proposed. The method can be used to generate an initial point for a Markov chain Monte Carlo simulation or to check that the given pedigree and the genotype data are consistent. In small pedigrees, the algorithm is exact by exhaustively enumerating all possibilities, but, in large pedigrees, with a considerable amount of unknown data, only a subset of promising configurations can actually be checked. For that purpose, the configurations are ordered by combining the approximative conditional probability distribution of the unknown genotypes with the information on the relationships between individuals. We also introduce a way to divide the task into subparts, which has been shown to be useful in large pedigrees. The algorithm has been implemented in a program called APE (Allelic Path Explorer) and tested in three different settings with good results.

Algorithms↗

Clinical heterogeneity in two pedigrees with the 3243 bp tRNA(Leu(UUR)) mutation of mitochondrial DNA.

We studied two pedigrees with a mutation at the nucleotide 3243 of mitochondrial DNA (mtDNA). The proband from the first pedigree had clinically defined MELAS plus maternally transmitted insulin-dependent diabetes mellitus (IDDM). The propositus of the other pedigree had exercise intolerance, lactic acidosis and ragged-red fibers (RRF). In the first pedigree, both the mother and the sister's proband harbored the point mutation in their muscle. The mother had 40% of mutant mitochondrial genomes and the sister 70%. In the second pedigree, the mutation was present in both muscle and blood from the proband as well as in blood from all other members studied. Proportion of mutant mtDNA was 90% in muscle and ranged from 40% to 90% in blood.

Adult↗

Familial amyloidotic polyneuropathy in Sweden: a pedigree analysis.

Extended genealogical studies were performed on the heredity patterns in Swedish patients with familial amyloidotic polyneuropathy (FAP) using Swedish historical archives. The population studied included 239 patients: 109 patients were linked to five large pedigrees and 80 patients belonged to 30 smaller pedigrees or nuclear families. In the remaining 50 cases, no genealogical links were found. Differences in mean ages of onset between the different pedigrees were found, although a considerable variation within the pedigrees was also present. There was a tendency for later ages of onset among older generations than younger ones: descendants of affected mothers seem to be more prone to anticipation in age of onset than descendants of affected fathers. Furthermore, there seems to be a tendency for earlier ages of onset among patients with a carrier mother than a carrier father. Some extended pedigrees, from the Skellefteå and Piteå areas, are presented in detail. The former go back into the middle of the 17th century. One important conclusion is that the mutational event may have occurred in late mediaeval times.

Adult↗