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At least 703 records · Page 39Linked to original sources
PubMed1997

An extension of affected-pedigree-member analyses to triads of relatives.

The affected third-degree relatives method ("cousins method"-CM) shares key features with the affected-sibling method, but it groups first cousins in triads, with the hope of requiring fewer individuals to be typed. The aim is to provide an efficient and computationally convenient method of genome screening, capitalizing on the vast number of highly informative markers mapped in recent years. The nonparametric CM statistic measures increased marker similarity, making no assumptions concerning how the disease is inherited; this can be advantageous when dealing with complex diseases for which the mode of inheritance is difficult to determine. This article presents a brief statistical development of the CM method and describes the results of applying the method to one replicate of the simulated extended family data set.

Alleles↗
PubMed1999

Genetic aspects of multiple sclerosis.

A large body of immunological, epidemiological, and genetic data indicate that tissue injury in multiple sclerosis (MS) results from an abnormal immune response to one or more myelin antigens that develops in genetically susceptible individuals after exposure to an as-yet undefined causal agent. A genetic component in MS is indicated by an increased relative risk to siblings compared to the general population, and an increased concordance rate in monozygotic compared to dizygotic twins. The past few years have seen real progress in defining the genetic basis of MS setting the stage for new approaches for the final characterization of the genes involved in MS susceptibility and pathogenesis. Whole genome screens conducted in different populations identified discrete chromosomal regions potentially harboring MS susceptibility genes, however, with the exception of the Major Histocompatibility Complex (MHC) on 6p21, no single locus generated overwhelming evidence of linkage. These results suggest a complex genetic etiology, including multiple genes of small to moderate effect and probable genetic heterogeneity. The identification and characterization of MS susceptibility genes and their correlation with disease phenotypes is likely to define the basic etiology of the disease, improve risk assessment, and influence therapeutics.

Demyelinating Diseases↗
PubMed2003

A genomewide screen of 345 families for autism-susceptibility loci.

We previously reported a genomewide scan to identify autism-susceptibility loci in 110 multiplex families, showing suggestive evidence (P <.01) for linkage to autism-spectrum disorders (ASD) on chromosomes 5, 8, 16, 19, and X and showing nominal evidence (P <.05) on several additional chromosomes (2, 3, 4, 10, 11, 12, 15, 18, and 20). In this follow-up analysis we have increased the sample size threefold, while holding the study design constant, so that we now report 345 multiplex families, each with at least two siblings affected with autism or ASD phenotype. Along with 235 new multiplex families, 73 new microsatellite markers were also added in 10 regions, thereby increasing the marker density at these strategic locations from 10 cM to approximately 2 cM and bringing the total number of markers to 408 over the entire genome. Multipoint maximum LOD scores (MLS) obtained from affected-sib-pair analysis of all 345 families yielded suggestive evidence for linkage on chromosomes 17, 5, 11, 4, and 8 (listed in order by MLS) (P <.01). The most significant findings were an MLS of 2.83 (P =.00029) on chromosome 17q, near the serotonin transporter (5-hydroxytryptamine transporter [5-HTT]), and an MLS of 2.54 (P =.00059) on 5p. The present follow-up genome scan, which used a consistent research design across studies and examined the largest ASD sample collection reported to date, gave either equivalent or marginally increased evidence for linkage at several chromosomal regions implicated in our previous scan but eliminated evidence for linkage at other regions.

Autistic Disorder↗
PubMed2005

A genome-wide screen and linkage mapping for a large pedigree with episodic ataxia.

Episodic ataxias are ion channel disorders characterized by attacks of incoordination. The authors performed a genome-wide screen in a large pedigree segregating a novel episodic ataxia and found significant linkage on 1q42 with a multipoint lod score of 3.65. Haplotype analysis and fine mapping yielded a peak 2-point lod score of 4.14 and indicated a 4-cM region on 1q42 that is likely to harbor an episodic ataxia gene.

Adolescent↗
PubMed1999

Functional analysis of human FEN1 in Saccharomyces cerevisiae and its role in genome stability.

The flap endonuclease, FEN1, is an evolutionarily conserved component of DNA replication from archaebacteria to humans. Based on in vitro results, it processes Okazaki fragments during replication and is involved in base excision repair. FEN1 removes the last primer ribonucleotide on the lagging strand and it cleaves a 5' flap that may result from strand displacement during replication or during base excision repair. Its biological importance has been revealed largely through studies in the yeast Saccharomyces cerevisiae where deletion of the homologous gene RAD27 results in genome instability and mutagen sensitivity. While the in vivo function of Rad27 has been well characterized through genetic and biochemical approaches, little is understood about the in vivo functions of human FEN1. Guided by our recent results with yeast RAD27, we explored the function of human FEN1 in yeast. We found that the human FEN1 protein complements a yeast rad27 null mutant for a variety of defects including mutagen sensitivity, genetic instability and the synthetic lethal interactions of a rad27 rad51 and a rad27 pol3-01 mutant. Furthermore, a mutant form of FEN1 lacking nuclease function exhibits dominant-negative effects on cell growth and genome instability similar to those seen with the homologous yeast rad27 mutation. This genetic impact is stronger when the human and yeast PCNA-binding domains are exchanged. These data indicate that the human FEN1 and yeast Rad27 proteins act on the same substrate in vivo. Our study defines a sensitive yeast system for the identification and characterization of mutations in FEN1.

Amino Acid Sequence↗
PubMed1999

Mapping alcoholism genes using linkage/linkage disequilibrium analysis.

Using a recently developed semiparametric method for combined linkage/linkage-disequilibrium analysis, we analyzed the Collaborative Study on the Genetics of Alcoholism data subset developed for Genetic Analysis Workshop 11 (GAW11). This semiparametric approach estimates recombination fractions for linkage, marker log odds ratios for linkage-disequilibrium, their product for combined linkage/linkage-disequilibrium, and corresponding z-scores. We used two outcomes: alcohol dependence and "alcoholism-free" and a genome-wide significance level of 4.1 (which corresponds to a genome-wide lod score of 3.6). For the alcohol dependence outcome, we observed significant linkage signals at D1S1588-D1S1631, D1S547, D2S399, D2S425, D4S2361, D7S1796, and D7S1824. We also found significant linkage-disequilibrium signals at D1S547 and D7S1795. For the "alcoholism-free" outcome, we found significant linkage signals at D4S2457, D41651 (both flank ADH3), D11S2359, and D16S47 and significant linkage-disequilibrium signals at D4S2361, FABP2, D11S2359, D19S431 and D19S47-D19S198-D19S601.

Alcoholism↗
PubMed2001

Genetic factors underlying gluten-sensitive enteropathy.

Genetic epidemiology clearly has shown that there is a genetic predisposition to gluten-sensitive enteropathy (GSE), or celiac disease. The strong genetic component, as determined by the lambda sib (lambda s), has been calculated to lie in the range of 7.5 to 30, based on a 5% to 10% recurrence risk for siblings. Ninety-five percent of northern European patients with GSE carry a particular HLA-DQ alpha beta heterodimer. Studies support the concept that the HLA-DQ gene acts as a dominant gene, and they also found that, in addition to HLA-DQ, a second locus within the major histocompatibility complex (MHC) is involved in the predisposition to GSE in the Dutch population. Genome scans conducted so far suggest that MHC and non-MHC loci collectively contribute to disease susceptibility. Since one, and probably even two, gene(s) from the MHC region itself determine at least 40% to 50% of the genetic predisposition to GSE, it is expected that the other loci each contribute only a little to the total genetic variation. The exact role of these additional genes (i.e., whether they are involved in the initiation or the progression of the disease) remains to be determined.

Celiac Disease↗
PubMed2002

Genome-wide linkage analysis of the acute coronary syndrome suggests a locus on chromosome 2.

A positive family history is a recognized cardiovascular risk factor, and genome-wide scans may reveal susceptibility loci for coronary artery disease. The acute coronary syndrome, consisting of myocardial infarction and unstable angina, is the most important manifestation of coronary disease and is characterized by atherosclerotic plaque disruption and coronary thrombosis. From approximately 6000 hospital admissions to cardiology units, we identified affected sibling pairs (n=61) who had documented acute coronary syndrome before the age of 70 years. A 10-cM resolution genetic map and MAPMAKER/SIBS were used for genome-wide linkage analysis. One locus on chromosome 2q36-q37.3 showed linkage with a lod score of 2.63 (P<0.0001). Separate multipoint fine-mapping of this locus with independent markers replicated the linkage results (lod 2.64). Two other regions on chromosomes 3q26-q27 and 20q11-q13 showed lod scores in excess of 1.5 (P<0.005). This genome scan in acute coronary syndrome suggests 1 locus that encompasses the gene encoding the insulin receptor substrate-1 gene. Two other potential loci were identified. These data imply that a limited number of potent susceptibility genes exist for the acute coronary syndrome. Such genes are likely to be relevant to the combined processes of atherosclerosis, plaque instability, and coronary thrombosis.

Acute Disease↗
PubMed2001

CTLA-4 and not CD28 is a susceptibility gene for thyroid autoantibody production.

One of the hallmarks of the human autoimmune thyroid diseases (AITDs) is the production of high titers of autoantibodies against thyroglobulin and thyroid peroxidase that often precedes the development of clinical disease. A high percentage of family members of patients with AITDs have significant titers of thyroid antibodies (TAbs), suggesting a genetic predisposition for their development, and segregation analyses have favored a dominant mode of inheritance. The aim of the present study was to identify the susceptibility genes for TAb production. We completed a genome-wide scan in 56 multiplex families (323 individuals) in which all family members with AITDs and/or detectable TAbs were considered affected. The highest 2-point logarithm of odds (LOD) score of 3.6 was obtained for marker D2S325 on chromosome 2q33 at 210.9 centimorgans. This locus showed no evidence for linkage to Graves' disease or Hashimoto's thyroiditis (2-point LOD scores, 0.42 for Graves' disease and -0.60 for Hashimoto's thyroiditis), demonstrating that the gene in this region conferred susceptibility to TAbs, but that clinical disease development required additional genetic and/or environmental factors. We then fine-mapped the region linked with TAbs using 11 densely spaced microsatellite markers. Multipoint linkage analysis using these markers showed a maximum LOD score of 4.2 obtained for marker D2S155 at 209.8 centimorgans (with heterogeneity, alpha = 0.41). As the linked region contained the CTLA-4 and CD28 genes, we then tested whether they were the susceptibility genes for TAbs on chromosome 2q33. The CD28 gene was sequenced in 15 individuals, and a new C/T single nucleotide polymorphism (SNP) was identified in intron 3. Analysis of this SNP revealed no association with TAbs in the probands of the linked families (families that were linked with D2S155) compared with controls. The CTLA-4 gene was analyzed using the known A/G(49) SNP, and the results showed a significantly increased frequency of the G allele in the probands of the linked families compared with the probands of the unlinked families or with controls (P = 0.02). We concluded that 1) a major gene for thyroid autoantibody production was located on chromosome 2q33; 2) the TAb gene on chromosome 2q33 was most likely the CTLA-4 gene and not the CD28 gene; and 3) CTLA-4 contributed to the genetic susceptibility to TAb production, but there was no evidence that it contributed specifically to Graves' or Hashimoto's diseases.

Abatacept↗
PubMed2000

Genetic susceptibility to tuberculosis in Africans: a genome-wide scan.

Human genetic variation is an important determinant of the outcome of infection with Mycobacterium tuberculosis. We have conducted a two-stage genome-wide linkage study to search for regions of the human genome containing tuberculosis-susceptibility genes. This approach uses sibpair families that contain two full siblings who have both been affected by clinical tuberculosis. For any chromosomal region containing a major tuberculosis-susceptibility gene, affected sibpairs inherit the same parental alleles more often than expected by chance. In the first round of the screen, 299 highly informative genetic markers, spanning the entire human genome, were typed in 92 sibpairs from The Gambia and South Africa. Seven chromosomal regions that showed provisional evidence of coinheritance with clinical tuberculosis were identified. To identify whether any of these regions contained a potential tuberculosis-susceptibility gene, 22 markers from these regions were genotyped in a second set of 81 sibpairs from the same countries. Markers on chromosomes 15q and Xq showed suggestive evidence of linkage (lod = 2.00 and 1.77, respectively) to tuberculosis. The potential identification of susceptibility loci on both chromosomes 15q and Xq was supported by an independent analysis designated common ancestry using microsatellite mapping. These results indicate that genome-wide linkage analysis can contribute to the mapping and identification of major genes for multifactorial infectious diseases of humans. An X chromosome susceptibility gene may contribute to the excess of males with tuberculosis observed in many different populations.

Adolescent↗
PubMed2004

Genetics of essential hypertension.

Essential hypertension affects 1 billion people worldwide and its genetic basis is well established. For this review we surveyed the literature on the genetics of hypertension during the past 18 months and we now report the highlights. There has been publication of the two largest genome scans for blood pressure and new loci including significant linkage to chromosome 6q have been reported. The molecular basis of Gordon's syndrome has been partially unravelled with a dual function for WNK4 in ion transport regulation being discovered. There has also been progress in narrowing rodent quantitative trait loci using congenic approaches and several linkage peaks have now been demonstrated to have more than one loci. We also report some of the initial findings from pharmacogenetic studies.

Animals↗
PubMed1999

Incorporating larger families in identity-by-descent based linkage analysis.

Genome scans for alcoholism susceptibility genes were carried out using identity-by-descent-based statistics for qualitative traits. We compared the results when 1) multipoint information was used for all families, where some had to be truncated, 2) multipoint information was used only for small families while large (untruncated) pedigrees were analyzed with a single-point approach, and 3) single-point analysis was used for all pedigrees. Differences between the methods were observed, but neither method could identify regions related to the susceptibility for alcoholism.

Alcoholism↗
PubMed2004

Genomic organization and mutation analysis of three candidate genes for hereditary neuralgic amyotrophy.

Hereditary neuralgic amyotrophy (HNA) is an autosomal-dominant inherited recurrent focal neuropathy affecting mainly the brachial plexus. In this study we report the genomic structure and mutation analysis of three candidate genes: sphingosine kinase 1 (SPHK1); tissue inhibitor of metalloproteinase 2 (TIMP2); and cytoglobin (CYGB). We did not find any disease-associated mutations, indicating that HNA is not caused by point mutations in these genes. However, we identified several sequencing errors in the cDNA of SPHK1 as well as seven novel single-nucleotide polymorphisms.

Amino Acid Substitution↗
PubMed2003

A whole genome screen for association with multiple sclerosis in Portuguese patients.

Multiple sclerosis (MS) is common in Europe affecting up to 1:500 people. In an effort to identify genes influencing susceptibility to the disease, we have performed a population-based whole genome screen for association. In this study, 6000 microsatellite markers were typed in separately pooled DNA samples from MS patients (n=188) and matched controls (n=188). Interpretable data was obtained from 4661 of these markers. Refining analysis of the most promising markers identified 10 showing potential evidence for association.

Adolescent↗
PubMed2002

Information overload: assigning genetic functionality in the age of genomics and large-scale screening.

As more and more genome sequences are completed, it is becoming increasingly evident that our understanding of the function of most bacterial gene products is lacking. This is frustrating, particularly in the study of pathogens, where an understanding of the role of individual gene products would probably facilitate the development of novel antimicrobials and vaccines. Recently, we devised a technique known as virulence-attenuated pool (VAP) screening to help assign genetic functionality to gene products that the pathogen Vibrio cholerae requires for colonization. This screen and potential new applications of the VAP technique are discussed here.

Bacteria↗
PubMed2002

Genetic evidence for a novel thymidylate synthase in the halophilic archaeon Halobacterium salinarum and in Campylobacter jejuni.

A search of the complete genome sequence of the halophilic archaeon Halobacterium salinarum failed to identify a gene homologous to the thymidylate synthase (thyA) gene present in the closely related Haloferax volcanii. To understand the source of thymidine synthesis in Hbt. salinarum, a genomic library of Hbt. salinarum was constructed and used to complement a Hfx. volcanii thyA deletion mutation. The Hbt. salinarum ORF that complemented the thyA mutation shares sequence homology with ORFs found in numerous microorganisms that lack a thyA gene, including the recently discovered thyX of Helicobacter pylori. We also show that a homolog of the Hbt. salinarum ORF is present in Campylobacter jejuni and is able to complement an Escherichia coli thyA mutant under oxygen-limiting conditions.

Campylobacter jejuni↗
PubMed2001

A dominant gene for developmental dyslexia on chromosome 3.

Developmental dyslexia is a neurofunctional disorder characterised by an unexpected difficulty in learning to read and write despite adequate intelligence, motivation, and education. Previous studies have suggested mostly quantitative susceptibility loci for dyslexia on chromosomes 1, 2, 6, and 15, but no genes have been identified yet. We studied a large pedigree, ascertained from 140 families considered, segregating pronounced dyslexia in an autosomal dominant fashion. Affected status and the subtype of dyslexia were determined by neuropsychological tests. A genome scan with 320 markers showed a novel dominant locus linked to dyslexia in the pericentromeric region of chromosome 3 with a multipoint lod score of 3.84. Nineteen out of 21 affected pedigree members shared this region identical by descent (corrected p<0.001). Previously implicated genomic regions showed no evidence for linkage. Sequencing of two positional candidate genes, 5HT1F and DRD3, did not support their role in dyslexia. The new locus on chromosome 3 is associated with deficits in all three essential components involved in the reading process, namely phonological awareness, rapid naming, and verbal short term memory.

Adolescent↗
PubMed1999

Niemann-Pick C1 disease: the I1061T substitution is a frequent mutant allele in patients of Western European descent and correlates with a classic juvenile phenotype.

Niemann-Pick type C (NPC) disease is an autosomal recessive lipid-storage disorder usually characterized by hepatosplenomegaly and severe progressive neurological dysfunction, resulting from mutations affecting either the NPC1 gene (in 95% of the patients) or the yet-to-be-identified NPC2 gene. Our initial study of 25 patients with NPC1 identified a T3182-->C transition that leads to an I1061T substitution in three patients. The mutation, located in exon 21, affects a putative transmembrane domain of the protein. PCR-based tests with genomic DNA were used to survey 115 unrelated patients from around the world with all known clinical and biochemical phenotypes of the disease. The I1061T allele constituted 33 (14.3%) of the 230 disease-causing alleles and was never found in controls (>200 alleles). The mutation was particularly frequent in patients with NPC from Western Europe, especially France (11/62 alleles) and the United Kingdom (9/32 alleles), and in Hispanic patients whose roots were in the Upper Rio Grande valley of the United States. The I1061T mutation originated in Europe and the high frequency in northern Rio Grande Hispanics results from a founder effect. All seven unrelated patients who were homozygous for the mutation and their seven affected siblings had a juvenile-onset neurological disease and severe alterations of intracellular LDL-cholesterol processing. The mutation was not found (0/40 alleles) in patients with the severe infantile neurological form of the disease. Testing for this mutation therefore has important implications for genetic counseling of families affected by NPC.

Adolescent↗