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PubMedDate not supplied

False-positive seroreactions for syphilis as a harbinger of disease revisited.

A cohort of 59 initially healthy subjects with chronic false-positive seroreactions for syphilis was followed for 3 to 19 years (mean 13 years) by data linkage to computerized population registry and to national hospital discharge registry using a unique personal identification number. One subject had moved abroad, but all others were known to be alive at the end of the follow-up period. Four subjects developed systemic lupus erythematosus and two developed rheumatoid arthritis. One subject was admitted to hospital because of protracted substernal pain, but a myocardial infarction could not be verified. This case corresponds to the expected number of cardiovascular events in the cohort. A chronic false positive seroreaction for syphilis was calculated to represent a hundred-fold risk for the development of systemic lupus, but such seroreactions did not seem to predict an excess of cardiovascular diseases.

Adolescent↗
PubMed1989

[In-situ hybridization on chorionic villi chromosomes].

Novel techniques for the prenatal diagnosis of inherited defects are currently being developed. The long-range aim is to be able to predict precisely, at an early stage of fetal development, the tendency of the fetus to develop multiple genetic, congenital or acquired diseases. We adapted the technique of gene mapping by in-situ hybridization for use with chromosomes from fetal chorionic villi sampling (CVS). Refined mapping of the genes coding for cholinesterase (CHE) in comparison with the haptoglobin and the transferrin receptor genes on CVS chromosomes Nos. 3 and 16 revealed 3 CHE genes in positions 3q21, 3q26, and 16q12. In view of genetic linkage data, at least 2 of these appear to be potentially active. These findings demonstrate that genes, for which molecularly cloned DNA probes are available, may be localized on CVS chromosomes by comparing their localization with that of known genes after in-situ hybridization. The implications for prenatal diagnosis are promising.

Cholinesterases↗
PubMed1987

Genetics of stomach and ocular alcohol dehydrogenase and aldehyde dehydrogenase in the mouse.

Activity variants of the stomach and ocular isozyme of aldehyde dehydrogenase (AHD-4) were observed among inbred strains of mice. The phenotypes were inherited in a normal mendelian fashion, with two alleles showing codominant expression at a single locus (Ahd-4). Linkage data indicated that Ahd-4 is localized on chromosome 11 near Hba (alpha hemoglobin locus), and segregated independently of Adh-3, encoding the stomach and ocular isozyme of alcohol dehydrogenase (ADH-C2).

Alcohol Dehydrogenase↗
PubMed1982

Genetic mapping: chromosomes 6-22.

Using a method that considers physical assignments and the distribution of chiasmata, as well as linkage data, genetic maps are constructed for chromosomes 6, 9, 13, and 16, and unassigned markers are tested for inclusion in these linear maps.

Centromere↗
PubMed1994

The gene encoding eIF-2 beta in S. cerevisiae maps to chromosome XVI.

The gene encoding the beta subunit of the translation initiation factor eIF-2 in the yeast Saccharomyces cerevisiae was mapped by physical methods to the distal part of the left arm of chromosome XVI, adjacent to the HSP90 locus. This assignment was confirmed by genetic linkage data with the GAL4 locus.

Chromosome Mapping↗
PubMed1995

Myotubular myopathy in a girl with a deletion at Xq27-q28 and unbalanced X inactivation assigns the MTM1 gene to a 600-kb region.

A young girl with a clinically moderate form of myotubular myopathy was found to carry a cytogenetically detectable deletion in Xq27-q28. The deletion had occurred de novo on the paternal X chromosome. It encompasses the fragile X (FRAXA) and Hunter syndrome (IDS) loci, and the DXS304 and DXS455 markers, in Xq27.3 and proximal Xq28. Other loci from the proximal half of Xq28 (DXS49, DXS256, DXS258, DXS305, and DXS497) were found intact. As the X-linked myotubular myopathy locus (MTM1) was previously mapped to Xq28 by linkage analysis, the present observation suggested that MTM1 is included in the deletion. However, a significant clinical phenotype is unexpected in a female MTM1 carrier. Analysis of inactive X-specific methylation at the androgen receptor gene showed that the deleted X chromosome was active in approximately 80% of leukocytes. Such unbalanced inactivation may account for the moderate MTM1 phenotype and for the mental retardation that later developed in the patient. This observation is discussed in relation to the hypothesis that a locus modulating X inactivation may lie in the region. Comparison of this deletion with that carried by a male patient with a severe Hunter syndrome phenotype but no myotubular myopathy, in light of recent linkage data on recombinant MTM1 families, led to a considerable refinement of the position of the MTM1 locus, to a region of approximately 600 kb, between DXS304 and DXS497.

Adult↗
PubMed1993

BLH1 codes for a yeast thiol aminopeptidase, the equivalent of mammalian bleomycin hydrolase.

We have cloned the BLH1 gene of the yeast Saccharomyces cerevisiae coding for a peptidase with significant homology to rabbit bleomycin hydrolase. Bleomycin is a glycopeptide antibiotic used for the treatment of human cancers. The antitumor activity of the drug is limited by its metabolic inactivation caused by bleomycin hydrolase, a member of the cysteine protease family. The open reading frame of BLH1 consists of 1,449 base pairs encoding a 55.4-kDa protein consistent with the molecular mass found in sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The consensus sequence within the active site region of cysteine proteases is conserved in the yeast enzyme. Biochemical studies on the purified enzyme confirm its classification as a thiol protease. The nonvacuolar enzyme has a molecular mass of 220 kDa, suggesting a homotetrameric structure. It exhibits an aminopeptidase activity with broad substrate specificity. Biochemical and genetic linkage data give evidence that the BLH1 and the LAP3 (Trumbly, R. J., and Bradley, G. (1983) J. Bacteriol. 156, 36-48) encoded aminopeptidases are identical. Deletion of the BLH1 gene is not lethal under normal growth conditions. However, blh1 mutants show hypersensitivity to bleomycin, indicating that bleomycin hydrolase is able to inactivate bleomycin in vivo and to protect cells from bleomycin-induced toxicity.

Amino Acid Sequence↗
PubMed1997

German family study on hereditary breast and/or ovarian cancer: germline mutation analysis of the BRCA1 gene.

Women harboring BRCA1 germline mutations carry an 85% lifetime risk of developing breast cancer and a 63% risk of ovarian cancer. In this first systematic study of familial breast and/or ovarian cancer in Germany we investigated 29 families for germline mutations in the BRCA1 gene. We identified mutations in three breast cancer families and in four breast-ovarian cancer families. The mutations include one missense mutation, one frameshift mutation, one splice mutation, and four nonsense mutations cosegregating with breast and/or ovarian susceptibility in five of ten (50%) families showing positive evidence of linkage to chromosome band 17q21 and in two of 19 (11%) families where linkage data was not available. Two apparently unrelated families carried the same nonsense mutation at codon 1835 and three families harbored a C to T transition at nucleotide 49 of the untranslated exon 4. Allelotyping of the markers D17S855, D17S1322, D17S1323, and D17S1327 located within or near BRCA1 revealed that all affected individuals in the two families harboring the mutation at codon 1835 shared at least one allele indicating a founder mutation. With respect to the overall mutation spectrum, no mutations were identified in exon 11 (0/7) in this set of German families. These findings differed significantly from those in British (17/32)(P = 0.012) and Southern Swedish (13/15) (P < 0.001) families. The lack of BRCA1 mutations in exon 11 which represents 61% of the entire coding sequence may provide additional insight into BRCA1 associated breast and ovarian tumor development.

BRCA1 Protein↗
PubMed1997

Development of an HIV clinical and research database for South Africa.

Health service restructuring in South Africa provides an opportunity to introduce appropriate Health Information System (HIS) technology. This is particularly relevant given the emerging HIV epidemic and the need to capture, translate and disseminate new experiences in HIV/AIDS care, support and clinical research. In 1994, a number of clinicians and health-care providers working in South Africa had begun to establish basic computerized databases to assist in research on HIV, but no standardized nomenclature or framework for collaboration was created. This paper describes a clinical and research database that could be used as an example for a standardized system by clinicians working in South Africa. The authors, with assistance from the National AIDS Research Programme of the Medical Research Council, created a prototype relational database using Microsoft Access. To test the prototype, 1057 HIV-positive patients from the infectious Disease Clinic at Johannesburg General Hospital were entered.

Databases, Factual↗
PubMed2002

Web-based detection of genotype errors in pedigree data.

For linkage analysis using pedigree data, it is important to eliminate contradictions concerning Mendelian inheritance from genotypic data. Such contradictions may derive from either genotyping errors or pedigree errors. We implemented an error-checking algorithm in a World Wide Web-based program that can be used through the Internet even by computer nonspecialists. This program, named Checkfam, uses two error-checking algorithms to detect and report contradictions concerning Mendelian inheritance. With this program, users can guess the causes of genotype errors (technical problems in genotyping, pedigree misrecording, or errors in input data concerning familial relationships). The present program will be useful to researchers for checking genotypic data and for preparing correct input files for linkage analysis.

Algorithms↗
PubMedDate not supplied

Probabilistic linkage of large public health data files.

Probabilistic linkage technology makes it feasible and efficient to link large public health databases in a statistically justifiable manner. The problem addressed by the methodology is that of matching two files of individual data under conditions of uncertainty. Each field is subject to error which is measured by the probability that the field agrees given a record pair matches (called the m probability) and probabilities of chance agreement of its value states (called the u probability). Fellegi and Sunter pioneered record linkage theory. Advances in methodology include use of an EM algorithm for parameter estimation, optimization of matches by means of a linear sum assignment program, and more recently, a probability model that addresses both m and u probabilities for all value states of a field. This provides a means for obtaining greater precision from non-uniformly distributed fields, without the theoretical complications arising from frequency-based matching alone. The model includes an iterative parameter estimation procedure that is more robust than pre-match estimation techniques. The methodology was originally developed and tested by the author at the U.S. Census Bureau for census undercount estimation. The more recent advances and a new generalized software system were tested and validated by linking highway crashes to Emergency Medical Service (EMS) reports and to hospital admission records for the National Highway Traffic Safety Administration (NHTSA).

Adult↗
PubMed1990

A genetic map of chromosome 1: comparison of different data sets and linkage programs.

We have used 22 chromosome 1 loci to construct a genetic linkage map of this autosome using the Venezuelan Reference Pedigree. These markers formed two linkage groups separated by an interval of more than 30 cM. Linkage maps were constructed separately using the computer programs LINKAGE and MAPMAKER to determine their relative speed, efficiency, and accuracy. We found that both programs generated maps with the same order and distances, although the LINKAGE program derived more information from the data, allowing placement of one additional marker. Many of the probes have previously been mapped using the CEPH pedigrees. However, the current map is generated from a different data set and so can be used to increase the certainty of locus order and map position. Ultimately, the generation and confirmation of a 1-cM map of this chromosome will require such multiple data sets.

Alleles↗
PubMed2005

Comparison of marker types and map assumptions using Markov chain Monte Carlo-based linkage analysis of COGA data.

We performed multipoint linkage analysis of the electrophysiological trait ECB21 on chromosome 4 in the full pedigrees provided by the Collaborative Study on the Genetics of Alcoholism (COGA). Three Markov chain Monte Carlo (MCMC)-based approaches were applied to the provided and re-estimated genetic maps and to five different marker panels consisting of microsatellite (STRP) and/or SNP markers at various densities. We found evidence of linkage near the GABRB1 STRP using all methods, maps, and marker panels. Difficulties encountered with SNP panels included convergence problems and demanding computations.

Alcoholism↗
PubMed1997

[Linking of individual data. Methods of linkage].

This paper gives an overview of linking methods of personal data computed in different files as registers and administrative or medical records. Epidemiological and demographic examples are studied, then the successive steps of record linkage are described:definition and choice of identifiants, searching and comparing pairs of records to determine whether they should be linked. A special mention is made to probability matching and methods optimizing the matching procedures. The discussion envisages the advantages of record linkage:better use of health statistics, new types of epidemiologic studies. The ethical problems and the need for evaluation are also discussed.

Epidemiologic Methods↗
PubMed2003

Multipoint and single point non-parametric linkage analysis with imperfect data.

We used simulation to explore the impact of common data imperfections (i.e., missing parents, genotyping error, map error, and missing genotypes) upon the performance of multipoint and single point linkage analysis in the analyses of linkage data from pairs of siblings affected with an idealized complex trait. The performance of single point and multipoint linkage was similar under an unrealistic best case scenario; however, when four data imperfections were combined, the performance of single point linkage analysis appeared to be superior to multipoint. The absence of parental genotypes in the presence of 1% genotype error led to marked degradation of linkage signal, particularly for multipoint analyses.

Computer Simulation↗
PubMed1984

Genetic Analysis Workshop II: segregation and three-locus linkage analysis.

Data stimulated for Genetic Analysis Workshop II were analyzed using PAP. Segregation analysis showed a simple recessive mode of inheritance for data set 2 while no conclusions could be made about the mode of inheritance for data set 3. Pairwise linkage analysis suggested three linkage groups, but three-locus analysis did not provide strong evidence for the gene order within these groups. For three of the four three-locus comparisons performed, three-locus analysis suggested the simulated order. In only one case did the pairwise analysis suggest the simulated order, indicating the necessity for multi-locus analysis for gene order.

Chromosome Mapping↗
PubMed2005

Statistical Viewer: a tool to upload and integrate linkage and association data as plots displayed within the Ensembl genome browser.

BACKGROUND: To facilitate efficient selection and the prioritization of candidate complex disease susceptibility genes for association analysis, increasingly comprehensive annotation tools are essential to integrate, visualize and analyze vast quantities of disparate data generated by genomic screens, public human genome sequence annotation and ancillary biological databases. We have developed a plug-in package for Ensembl called "Statistical Viewer" that facilitates the analysis of genomic features and annotation in the regions of interest defined by linkage analysis. RESULTS: Statistical Viewer is an add-on package to the open-source Ensembl Genome Browser and Annotation System that displays disease study-specific linkage and/or association data as 2 dimensional plots in new panels in the context of Ensembl's Contig View and Cyto View pages. An enhanced upload server facilitates the upload of statistical data, as well as additional feature annotation to be displayed in DAS tracts, in the form of Excel Files. The Statistical View panel, drawn directly under the ideogram, illustrates lod score values for markers from a study of interest that are plotted against their position in base pairs. A module called "Get Map" easily converts the genetic locations of markers to genomic coordinates. The graph is placed under the corresponding ideogram features a synchronized vertical sliding selection box that is seamlessly integrated into Ensembl's Contig- and Cyto- View pages to choose the region to be displayed in Ensembl's "Overview" and "Detailed View" panels. To resolve Association and Fine mapping data plots, a "Detailed Statistic View" plot corresponding to the "Detailed View" may be displayed underneath. CONCLUSION: Features mapping to regions of linkage are accentuated when Statistic View is used in conjunction with the Distributed Annotation System (DAS) to display supplemental laboratory information such as differentially expressed disease genes in private data tracks. Statistic View is a novel and powerful visual feature that enhances Ensembl's utility as valuable resource for integrative genomic-based approaches to the identification of candidate disease susceptibility genes. At present there are no other tools that provide for the visualization of 2-dimensional plots of quantitative data scores against genomic coordinates in the context of a primary public genome annotation browser.

Chromosome Mapping↗