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At least 343 records · Page 19Linked to original sources
PubMed2005

A comparison of univariate, bivariate, and trivariate whole-genome linkage screens of genetically correlated electrophysiological endophenotypes.

We used a maximum-likelihood based multipoint linkage approach implemented in SOLAR to examine simultaneously linkage for three electrophysiological endophenotypes from the Collaborative Study of the Genetics of Alcoholism: TTTH1, TTTH2, and TTTH3. These endophenotypes have been identified as markers of alcohol dependence susceptibility. Data were from 905 individuals in 143 families. Measured covariates considered included sex, age at electrophysiology data collection, habitual smoking status, and the maximum number of drinks consumed in a 24-hour period. Comparisons were made among genome-wide univariate, bivariate, and trivariate linkage analyses using genotypes based on microsatellite markers supplied by the Center for Inherited Disease Research, and genotypes based on single-nucleotide polymorphism markers provided by Illumina. All LODs were corrected to a standard equivalent to 1 degree of freedom. Using the trivariate approach and the microsatellite-based genotypes, we estimated a maximum multipoint linkage signal of LOD = 2.66 on chromosome 7q at 157 cM. Analyses using the Illumina SNP genotypes produced similar results, yielding a maximum multipoint LOD of 2.95 on 7q at 174 cM. These regions of interest correspond to those identified in the univariate and bivariate linkage screens. Our results suggest that trivariate multipoint linkage analyses have utility in the further characterization of chromosomal regions potentially containing genes influencing the phenotypes being examined. Based on a comparison of the number of LOD scores achieving statistical significance, our results suggest that the microsatellite- and Illumina SNP-based genotypes have similar utility for detecting genomic regions of interest.

Chromosome Mapping↗
PubMed2003

Investigation of seven proposed regions of linkage in multiple sclerosis: an American and French collaborative study.

Multiple sclerosis (MS) is a demyelinating autoimmune disease with a strong yet complex genetic component. To date only the HLA-DR locus, and specifically the HLA-DR15 allele, has been identified and confirmed as influencing the risk of developing MS. Genomic screens on several datasets have been performed and have identified several chromosomal regions with interesting results, but none have yet been confirmed. We tested seven of the most-promising regions (on chromosomes 1p, 2p, 3p, 3q, 5q, 19q, and Xp) identified from several genomic screens in a dataset of 98 multiplex MS families from the United States and 90 multiplex MS families from France. The results did not confirm linkage to 2p, 3q, 5q, or Xp in the overall dataset, or in subsets defined by geographic origin or HLA-DR15 status. Regions on 1p34, 3p14, and 19q13 produced lod scores >0.90 in at least one subset of the data, suggesting that these regions should be examined in more detail.

Chromosomes, Human, Pair 1↗
PubMedDate not supplied

Genome-wide screening of genes showing altered expression in liver metastases of human colorectal cancers by cDNA microarray.

In spite of intensive and increasingly successful attempts to determine the multiple steps involved in colorectal carcinogenesis, the mechanisms responsible for metastasis of colorectal tumors to the liver remain to be clarified. To identify genes that are candidates for involvement in the metastatic process, we analyzed genome-wide expression profiles of 10 primary colorectal cancers and their corresponding metastatic lesions by means of a cDNA microarray consisting of 9121 human genes. This analysis identified 40 genes whose expression was commonly upregulated in metastatic lesions, and 7 that were commonly downregulated. The upregulated genes encoded proteins involved in cell adhesion, or remodeling of the actin cytoskeleton. Investigation of the functions of more of the altered genes should improve our understanding of metastasis and may identify diagnostic markers and/or novel molecular targets for prevention or therapy of metastatic lesions.

Biomarkers, Tumor↗
PubMed2003

Horizontally transferred genes in plant-parasitic nematodes: a high-throughput genomic approach.

BACKGROUND: Published accounts of horizontally acquired genes in plant-parasitic nematodes have not been the result of a specific search for gene transfer per se, but rather have emerged from characterization of individual genes. We present a method for a high-throughput genome screen for horizontally acquired genes, illustrated using expressed sequence tag (EST) data from three species of root-knot nematode, Meloidogyne species. RESULTS: Our approach identified the previously postulated horizontally transferred genes and revealed six new candidates. Screening was partially dependent on sequence quality, with more candidates identified from clustered sequences than from raw EST data. Computational and experimental methods verified the horizontal gene transfer candidates as bona fide nematode genes. Phylogenetic analysis implicated rhizobial ancestors as donors of horizontally acquired genes in Meloidogyne. CONCLUSIONS: High-throughput genomic screening is an effective way to identify horizontal gene transfer candidates. Transferred genes that have undergone amelioration of nucleotide composition and codon bias have been identified using this approach. Analysis of these horizontally transferred gene candidates suggests a link between horizontally transferred genes in Meloidogyne and parasitism.

Amino Acid Sequence↗
PubMed2007

Screening of genomic imbalances in glioblastoma multiforme using high-resolution comparative genomic hybridization.

Comparative genomic hybridization (CGH) is a molecular cytogenetic technique that allows the genome-wide analysis of DNA sequence copy number differences. We applied conventional CGH and the recently developed high-resolution CGH (HR-CGH) to tumour samples from 18 patients with glioblastoma multiforme (GBM) in order to compare the sensitivity of CGH and HR-CGH in the screening of chromosomal abnormalities. The abnormalities were studied in topologically different central and peripheral tumour parts. A total of 78 different changes were observed using CGH (0-16 per tumour, median 3.5) and 154 using HR-CGH (0-21 per tumour, median 6). Using HR-CGH, losses were more frequent than gains. The representation of the most prominent changes revealed by both methods was similar and was comprised of the amplification of 7q12 and 12q13-q15, the gain of 7, 3q and 19, and the loss of 10, 9p, and 13q. However, HR-CGH detected certain other abnormalities (the loss of 6, 14q, 15q and 18q, and the gain of 19), which were rarely revealed by CGH. Using HR-CGH, the numbers and types of chromosomal changes detected in the central and peripheral parts of GBM were almost the same. The loss of chromosomes 10 and 9p and the gain of chromosomes 7 and 19 were the most frequent chromosomal alterations in both tumour parts. Our results from the GBM analysis show that HR-CGH technology can reveal new, recurrent genetic alterations involving the genes known to participate in tumorigenesis and in the progression of several human malignancies, thus allowing for a more accurate genetic characterization of these tumours.

Adult↗
PubMed2006

The genome-wide screening of yeast deletion mutants to identify the genes required for tolerance to ethanol and other alcohols.

A set of homozygous diploid deletion mutants of the yeast Saccharomyces cerevisiae was screened for the genes required for tolerance to aliphatic alcohols. The screen identified 137, 122 and 48 deletion mutants sensitive to ethanol, 1-propanol and 1-pentanol, respectively. A number of the genes required for ethanol tolerance were those also required for tolerance to other alcohols. Numerous mutants with defective genes encoding for vacuolar H+ -ATPase (V-ATPase) were cosensitive to these alcohols. A global screening approach of yeast deletion library mutants was useful in elucidating the mechanisms of alcohol tolerance based on different lipophilicities.

1-Propanol↗
PubMed2005

Identification of a novel locus on 2q for autosomal dominant high-grade myopia.

PURPOSE: Myopia, or nearsightedness, is a visual disorder of high and growing prevalence in the United States and in other countries. Pathologic high myopia, or myopia of </=-6.00 D, predisposes individuals to retinal detachment, macular degeneration, cataracts, and glaucoma. Autosomal dominant (AD) nonsyndromic high-grade myopia has been mapped to loci on 18p11.31, 12q21-q23, 17q21-q23, and 7q36. This is the report of significant linkage to a novel locus on the long arm of chromosome 2 in a large, multigenerational family with AD high-grade myopia. METHODS: The family contains 31 participating members (14 affected). The average spherical refractive error for affected individuals was -14.46 D (range, -7.25 to -27.00). Before a genome screening was undertaken, linkage to intragenic or flanking markers for the myopic genetic syndromes of Stickler syndrome types I, II, and III; Marfan syndrome; and juvenile glaucoma were ruled out. In addition, no linkage was found to the known AD high-grade myopia loci listed above. A full genome screen of the family was performed with 382 microsatellite markers with an average intermarker distance of 10 cM. SimWalk2 software was used for multipoint linkage analysis based on an AD model with a penetrance of 90% and a disease allele frequency of 0.01. RESULTS: Fine-point mapping with an additional nine custom-made and five commercial markers yielded a maximum two-point lod score of 5.67 at marker D2S2348. Results of multipoint analysis indicate that the 1-unit support intervals for this new locus spans approximately 9.1 cM from (238.7 to 247.8 cM) on the chromosome 2 genetic map at q37.1. CONCLUSIONS: A novel locus for AD high-grade myopia has been determined, providing further evidence of genetic heterogeneity for this disorder.

Adolescent↗
PubMed2006

Whole genome RNAi screens for increased longevity: important new insights but not the whole story.

This article discusses the pros and cons of using RNAi screening to identify longevity genes in Caenorhabditis elegans. The discussion will focus on the results of two large-scale longevity RNAi screens that were recently published. The two screens revealed largely non-overlapping sets of candidate longevity genes. The possible reasons for such differences and their implications will be discussed.

Aging↗
PubMed2006

Paternal relatives and family history of breast cancer.

BACKGROUND: Reported family medical history may be the most widely accessible genomics screen currently available. The worth of any population-screening tool may be measured by parameters such as sensitivity and specificity. There is some evidence and theory suggesting that family history of breast cancer may be more frequently communicated about maternal (versus paternal) lines. If true, a discrepancy in reporting family history of breast cancer could mean suboptimal accuracy for this genomics-screening tool. METHODS: A cross-sectional analysis of reported family history of breast cancer was conducted beginning in early fall 2005 of data collected from April 2003 to March 2005. Study participants were Women's Health Clinic patients without breast cancer aged at least 40 years. The number of women reporting extended paternal relatives (e.g., aunts, grandmothers) with breast cancer was compared to the number of women reporting maternal relatives. RESULTS: More women reported a maternal relative with breast cancer (16%) compared to those reporting paternal relatives (10%) (McNemar odds ratio = 1.71, 95% confidence interval = 1.26 to 2.34). A discrepancy remained in analyses adjusting for potential covariates (race/ethnicity, awareness of breast cancer, family communication about breast cancer, and perceived risk). CONCLUSIONS: Self-reported family history of breast cancer may not optimally capture inherited risk from the father's side of the family. Further research is needed to look for modifiable contributors to this discrepancy to optimize screening for familial breast cancer.

Adult↗
PubMed2001

Linkage analysis suggests a region of importance for multiple sclerosis in 3p14-13.

Four genomic screens for linkage in multiple sclerosis (MS) have been reported. They confirmed the established role of the human leucocyte antigen (HLA) complex genes in MS and, in addition, suggested the importance of a few other chromosomal segments. Here we report evidence for the importance of 3p14-13 region identified by suggestive linkage in genomic screens from Canada and the United Kingdom. When studying 146 Nordic MS multiplex families, mostly affected sib-pairs, with eight microsatellite markers, spanning a 36-cM region, we observed a two-point non-parametric linkage (NPL) score of 2.39 (P = 0.007) by the GENEHUNTER package for marker D3S1285 and a multipoint NPL score of 1.20 in the same region. Association studies in Swedish MS patients revealed modest allelic associations of uncertain significance not supported by transmission analysis. Analysis of the trinucleotide repeat sequence of the SCA7 gene in Swedish index cases did not reveal expansions. We conclude that support was obtained for the location of a gene or genes with importance for MS susceptibility in 3p14-13 region.

Alleles↗
PubMed1998

What is the evidence of genetic factors in the etiology of Graves' disease? A brief review.

Graves' disease (GD) is generally thought of as a multifactorial disorder in which genetic susceptibility interacts with environmental and endogenous factors to cause disease. The importance of genetic factors is suggested by the clustering of GD within families and by a higher concordance rate for disease in monozygotic than in dizygotic twins. This has, however, recently been shown to be less pronounced than previously thought. During the last decade much effort has been put into characterization of the genetic background of GD. Until recently, most studies have examined associations between GD and the human leukocyte antigen (HLA) region, but recent advances in molecular techniques have opened the way for whole genome screening. A number of HLA and non-HLA candidate genes have been proposed, but despite several large investigations within multiplex families no major susceptibility genes have been identified. This brief review discusses relevant articles published from 1940 through 1997 regarding the influence of genetic factors in the etiology of GD. Ongoing studies focus on whole genome screening in multiplex families as well as population-based twin studies. However, the possibility of GD being a heterogeneous disease without a single well-defined genotype and phenotype should be left open.

Genetic Markers↗
PubMed2002

Phenotypic homogeneity provides increased support for linkage on chromosome 2 in autistic disorder.

Autistic disorder (AutD) is a neurodevelopmental disorder characterized by significant disturbances in social, communicative, and behavioral functioning. A two-stage genomic screen analysis of 99 families with AutD revealed suggestive evidence for linkage to chromosome 2q (D2S116 nonparametric sib-pair LOD score [MLS] 1.12 at 198 cM). In addition, analysis of linkage disequilibrium for D2S116 showed an allele-specific P value of <.01. Recently, linkage to the same region of 2q was reported in an independent genome screen. This evidence for linkage increased when analysis was restricted to the subset of patients with AutD who had delayed onset (>36 mo) of phrase speech (PSD). We similarly classified our data set of 82 sib pairs with AutD, identifying 45 families with AutD and PSD. Analysis of this PSD subset increased our support for linkage to 2q (MLS 2.86 and HLOD 2.12 for marker D2S116). These data support evidence for a gene on chromosome 2 contributing to risk of AutD, and they suggest that phenotypic homogeneity increases the power to find susceptibility genes for AutD.

Age of Onset↗
PubMed1998

What is the evidence of genetic factors in the etiology of Graves' disease? A brief review.

Graves' disease (GD) is generally thought of as a multifactorial disorder in which genetic susceptibility interacts with environmental and endogenous factors to cause disease. The importance of genetic factors is suggested by the clustering of GD within families and by a higher concordance rate for disease in monozygotic than dizygotic twins. This has, however, recently been shown to be less pronounced than previously thought. During the last decade, much effort has been put into characterization of the genetic background of GD. Until recently most studies have examined associations between GD and the human leukocyte antigen (HLA) region, but recent advances in molecular techniques have opened the way for whole-genome screening. A number of HLA and non-HLA candidate genes have been proposed, but despite several large investigations within multiplex families no major susceptibility genes have been identified. This brief review discusses relevant articles published from 1940 through 1997 regarding the influence of genetic factors in the etiology of GD. Ongoing studies will focus on whole genome screening in multiplex families as well as population based twin studies. However, the possibility of GD being a heterogeneous disease without a single well-defined genotype and phenotype should be left open.

Genetic Markers↗
PubMed2002

Sharing of a conserved haplotype suggests a susceptibility gene for multiple sclerosis at chromosome 17p11.

Multiple sclerosis (MS) is a chronic inflammatory disease resulting in demyelination in the central nervous system (CNS). Increasing evidence supports that genetic factors confer susceptibility to MS. One locus, the HLA complex (6p21), has been identified as important in MS, but no other loci have been clearly implicated, neither by a candidate gene approach, nor by a genomic screen strategy. Here, we studied a genetically isolated population in the northern-most part of Sweden, which demonstrates a high incidence of MS, using haplotype sharing analysis. Genealogical analysis demonstrated that 22 MS patients originate from a single common ancestral couple in the eighteenth century. Five affected individuals from four nuclear families were selected for an initial genomic screen with 390 microsatellite markers. Seven shared haplotypes in six different chromosomal regions were observed. After genotyping for these haplotypes with the same and additional markers in 15 MS patients and healthy relatives, some portion of a conserved haplotype spanning 10 cM at 17p11 was found to be shared by 12 of 15 affected individuals. The statistical analysis revealed a significant excess of transmission of alleles of three markers to affected individuals (P<0.05) by the transmission/disequilibrium test (TDT). An identical four-marker haplotype was shared by six of 15 patients (40%; P<0.01). Surprisingly, DR-typing revealed no significant sharing of the HLA region. In conclusion, our data suggests a novel susceptibility gene for MS in chromosome 17p11.

Chromosomes, Human, Pair 17↗
PubMed2004

Comparison of microsatellites versus single-nucleotide polymorphisms in a genome linkage screen for prostate cancer-susceptibility Loci.

Prostate cancer is one of the most common cancers among men and has long been recognized to occur in familial clusters. Brothers and sons of affected men have a 2-3-fold increased risk of developing prostate cancer. However, identification of genetic susceptibility loci for prostate cancer has been extremely difficult. Although the suggestion of linkage has been reported for many chromosomes, the most promising regions have been difficult to replicate. In this study, we compare genome linkage scans using microsatellites with those using single-nucleotide polymorphisms (SNPs), performed in 467 men with prostate cancer from 167 families. For the microsatellites, the ABI Prism Linkage Mapping Set version 2, with 402 microsatellite markers, was used, and, for the SNPs, the Early Access Affymetrix Mapping 10K array was used. Our results show that the presence of linkage disequilibrium (LD) among SNPs can lead to inflated LOD scores, and this seems to be an artifact due to the assumption of linkage equilibrium that is required by the current genetic-linkage software. After excluding SNPs with high LD, we found a number of new LOD-score peaks with values of at least 2.0 that were not found by the microsatellite markers: chromosome 8, with a maximum model-free LOD score of 2.2; chromosome 2, with a LOD score of 2.1; chromosome 6, with a LOD score of 4.2; and chromosome 12, with a LOD score of 3.9. The LOD scores for chromosomes 6 and 12 are difficult to interpret, because they occurred only at the extreme ends of the chromosomes. The greatest gain provided by the SNP markers was a large increase in the linkage information content, with an average information content of 61% for the SNPs, versus an average of 41% for the microsatellite markers. The strengths and weaknesses of microsatellite versus SNP markers are illustrated by the results of our genome linkage scans.

Chromosome Mapping↗
PubMed2005

A genome-wide screen on the genetics of atopy in a multiethnic European population reveals a major atopy locus on chromosome 3q21.3.

BACKGROUND: Dissecting complex diseases in underlying distinct traits and studying these for their genetic basis might enhance the power as well as the specificity, of detection of disease genes. These phenotypes are known as intermediate phenotypes. OBJECTIVE: We were interested in the atopic basis of asthma, and used the sensitization to mite (Dermatophagoides pteronyssinus) allergens as a pathophysiologically important intermediate phenotype. METHODS: This time we performed a genome-wide scan based on the same already used multiethnic European population consisting of 82 nuclear families with at least two affected siblings. We carried out nonparametric as well as parametric MOD-score analyses based on the genotypes of 603 microsatellite markers. RESULTS: In comparison with our first genome-wide candidate region search three novel regions additionally appeared to be significant. We obtained significant results for the region 2p12 with a MOD score of 3.35 and for the region 16q21 with a MOD score of 4.18. The most significant result was found for the region 3q21.3 with the same microsatellite marker, which showed significant linkage to atopic dermatitis (AD) in another study with a MOD score of 4.51 and an nonparametric linkage analysis (NPL) of 4.00. CONCLUSION: Our findings indicate that atopy, allergic asthma, allergic rhinitis and AD on the one hand are distinct traits on both the clinical and genetic basis, but on the other hand, our results also underline that these traits are closely related diseases concerning the atopic basis of the traits.

Antigens, Dermatophagoides↗
PubMed2003

Familial idiopathic scoliosis: evidence of an X-linked susceptibility locus.

STUDY DESIGN: A genomic screen and statistical linkage analysis of a large sample of families with individuals having idiopathic scoliosis was performed. OBJECTIVES: To identify an X-linked susceptibility locus involved in the expression of familial idiopathic scoliosis. SUMMARY OF BACKGROUND DATA: A large sample of families with individuals having idiopathic scoliosis (202 families; 1198 individuals) were diagnosed through physical examination and radiographic criteria, and genomic screening and genetic linkage analyses were performed. METHODS: Model-independent linkage analysis was used to screen genotyping data from 15 X-linked markers in 202 families (1198 individuals). Families were stratified based on the ratio of the likelihood of an X-linked dominant (XLD) inheritance model relative to that of an autosomal dominant (AD) model. Both model-independent and model-dependent linkage analyses were used to identify potential candidate regions. RESULTS: When the entire set of families were analyzed with model-independent methods, no result was significant at the 0.05 level for any of the markers. However, when the families were stratified based on the ratio of the likelihood of the X-linked dominant to autosomal dominant mode of inheritance, results from model-dependent linkage analysis of 15% of the families most likely to have X-linked dominant inheritance showed six adjacent markers with positive lod score values and a maximum lod score of 1.69 (theta = 0.2) at marker GATA172D05. A lod score of 2.23 at this same marker was found in a single family with six affected individuals. CONCLUSION: The results suggest that a region on the X chromosome may be linked to the expression of familial idiopathic scoliosis in a subset of these families.

Alleles↗
PubMed1997

Effectiveness of extreme discordant sib pairs to detect oligogenic disease loci.

A method for the genomic screening of quantitative traits using extreme discordant sib pairs (EDSPs) has recently been described by Risch and Zhang [1995; 1996]. For many models relevant to common, genetically complex diseases, EDSPs are the most powerful siblings for detecting linkage. Thus, if such siblings can be identified and collected, powerful studies with reasonable genotyping budgets can be conducted. Using a subset of the GAW10 data, we have simulated a genomic screen using EDSPs. From the 4,780 total families in the first 20 replicates of 239 families, there were 100, 104, 155, 107, and 180 EDSP families for Q1, Q2, Q3, Q4, and Q5, respectively. EDSP data were analyzed for each trait using a modified version of MAPMAKER/SIBS capable of handling extreme discordant sib pairs. Four regions, one for Q1, one for Q2, and two for Q4, were able to exceed a threshold for linkage corresponding to a 0.001 pointwise significance level. In three cases, maximum lod score (MLS) peaks occurred within 3.8 cM of a major gene. In the fourth case, the MLS peak occurred 28.4 cM from a major gene. Omission of parents and an alternative definition of EDSP were also investigated.

Chromosome Mapping↗