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PubMed1993

A user-friendly Hypercard interface for human linkage analysis.

The availability of a large number of highly informative genetic markers has made human linkage analysis faster and easier to perform. However, current linkage analysis software does not provide an organizational database into which a large body of linkage data can be easily stored and manipulated. This manual entry and editing of linkage data is often time consuming and prone to typing errors. In addition, the large number of alleles in many of these markers must be reduced in order to perform linkage analysis with multiple loci across large genetic distances. This reduction in allele number is often difficult and confusing, especially in large pedigrees. We have taken advantage of the Macintosh-based Hypercard program to develop an interface with which linkage data can be easily stored, retrieved and edited. For each family, the components of the pedigree, including ID numbers, sex and affection status, only need to be entered once. The program (Linkage Interface) retrieves this information each time the data from a new polymorphic marker is entered. Linkage Interface has flexible editing capabilities that allow the user to change any portion of the pedigree, including the addition or deletion of family members, without affecting previously entered genotype data. Linkage Interface can also analyze both the pedigree and marker data and will detect any inconsistencies in inheritance patterns. In addition, the program can reduce the number of alleles for a polymorphic marker. Linkage Interface will then compare the 'reduced' data to the original marker data and assists in maintaining all informative meioses by pointing out which meioses have become non-informative.(ABSTRACT TRUNCATED AT 250 WORDS)

Female↗
PubMed1999

Effect of the worldwide epidemic on HIV prevalence in the United Kingdom: record linkage in anonymous neonatal seroprevalence surveys.

OBJECTIVE: To assess the impact of the worldwide HIV/AIDS epidemic on the prevalence of HIV in women in the United Kingdom (UK), particularly in the large immigrant and ethnic minority communities. METHOD: Unlinked anonymous neonatal seroprevalence survey with electronic record linkage of data from child health computers (maternal age and ethnic status) and birth registration (parent's country of birth). RESULTS: Of a total 137456 samples collected in 1997-1998, 188 (0.14%) were anti-HIV-1 seropositive. Seroprevalence was highest in women born in East Africa (2.3%) and Central Africa (1.9%). 76.4% of seropositive newborns were delivered to mothers born in sub-Saharan Africa; a further 6.0% had fathers from sub-Saharan Africa. However, there was little evidence of HIV in women born in Southern Asia [prevalence 0.0081%; 95% confidence interval (CI) 0-0.04], and none within UK-born Asian communities. Prevalence among the UK-born Black African community was low (0.14%; 95% CI 0-0.6). Among infants with both parents known to be born in the UK, seroprevalence was 0.023% (95% CI 0.01-0.04) in London, and zero (95% CI 0-0.007) in non-Metropolitan areas. Irrespective of mother's region of birth, seroprevalence was 4.2 times higher (95% CI 3.0-5.8) in newborns whose father's details were not recorded at birth registration, a marker for single unsupported mothers. CONCLUSION: The risk of HIV among pregnant women from sub-Saharan Africa has been recognized. However, in southern England, HIV is very rare in women from Southern Asia and in UK-born women in ethnic minority communities, in spite of cultural and travel ties to high-prevalence countries. Data linkage in anonymous surveys assists in monitoring the impact of the worldwide epidemic on prevalence and incidence locally.

Adult↗
PubMed1995

The severe perinatal form of autosomal recessive polycystic kidney disease maps to chromosome 6p21.1-p12: implications for genetic counseling.

Autosomal recessive polycystic kidney disease (ARPKD) is a one of the most common hereditary renal cystic diseases in children. Its clinical spectrum is widely variable with most cases presenting in infancy. Most affected neonates die within the first few hours of life. At present, prenatal diagnosis relies on fetal sonography, which is often imprecise in detecting even the severe form of the disease. Recently, in a cohort of families with mostly milder ARPKD phenotypes, an ARPKD locus was mapped to a 13-cM region of chromosome 6p21-cen. To determine whether severe perinatal ARPKD also maps to chromosome 6p, we have analyzed the segregation of seven microsatellite markers from the ARPKD interval in 22 families with the severe phenotype. In the majority of the affected infants, ARPKD was documented by histopathology. Our data confirm linkage and refine the ARPKD region to a 3.8-cM interval, delimited by the markers D6S465/D6S427/D6S436/D6S272 and D6S466. Taken together, these results suggest that, despite the wide variability in clinical phenotypes, there is a single ARPKD gene. These linkage data and the absence of genetic heterogeneity in all families tested to date have important implications for DNA-based prenatal diagnoses as well as for the isolation of the ARPKD gene.

Amniocentesis↗
PubMed1999

[Molecular-genetic approach to congenital malformation syndromes].

The causes of congenital malformation syndromes had long remained obscure, because their biochemical bases were unknown. However, with recently developed reverse-genetic and/or Human Genome Project-derived technology, we have been able to approach such disorders. These new methods include positional cloning techniques, candidate gene approach and positional candidate strategies. Among them, positional cloning has become most reliable nowadays, and three ways are mainly available to obtain position information of disease genes, i.e., data from linkage analysis of disease families; comparative maps between different species; breakpoints of disease-related de novo chromosomal translocations. I present here some examples for each strategy: a large kindred with mesomelic dysplasia Kantaputra type for linkage data, and its seemingly allelic bone dysplasia associated with t (2; 8) for positional cloning that starts from a chromosomal translocation; Waardenburg syndrome for candidate gene approach; and the p57KIP2 gene for positional candidate approach to Wiedemann-Beckwith syndrome. I finally emphasize that a human link composed of general physicians, molecular geneticists and clinical researchers is essential to reach a goal of reverse genetics. Without such a goal, we can neither understand the genesis of diseases nor develop their therapy.

Beckwith-Wiedemann Syndrome↗
PubMed2005

No genetic association of the human prolyl endopeptidase gene in the Dutch celiac disease population.

Celiac disease (CD) is a complex genetic disorder of the small intestine. The DQ2/DQ8 human leucocyte antigen (HLA) genes explain approximately 40% of the genetic component of the disease, but the remaining non-HLA genes have not yet been identified. The key environmental factor known to be involved in the disease is gluten, a major protein present in wheat, barley, and rye. Integrating microarray data and linkage data from chromosome 6q21-22 revealed the prolyl endopeptidase (PREP) gene as a potential CD candidate in the Dutch population. Interestingly, this gene encodes for the only enzyme that is able to cleave the proline-rich gluten peptides. To investigate the role of the human PREP gene as a primary genetic factor in CD, we conducted gene expression, sequence analysis, and genetic association studies of the PREP gene and determined PREP enzyme activity in biopsies from CD patients and controls. Sequence analysis of the coding region of the PREP gene revealed two novel polymorphisms. Genetic association studies using two novel polymorphisms and three known PREP variants excluded a genetic association between PREP and CD. Determination of PREP activity revealed weak but significant differences between treated and untreated CD biopsies (P < 0.05). Our results from the association study indicate that PREP is not a causative gene for CD in the Dutch population. These are further supported by the activity determinations in which we observed no differences in PREP activity between CD patients and controls.

Adolescent↗
PubMed2004

Overdose in young people using heroin: associations with mental health, prescription drug use and personal circumstances.

OBJECTIVE: To identify patterns of mental health, prescription drug use and personal circumstances associated with heroin overdose in young people. DESIGN: Linkage of data on use of Pharmaceutical Benefits Scheme (PBS) prescription drugs with data from a self-report questionnaire. SETTING: Inner metropolitan Melbourne, Australia. SUBJECTS: 163 young people, 15-30 years, using heroin. MAIN OUTCOME MEASURES: Personal circumstances, mental health (as measured by various scales), and PBS-listed prescription drug use. RESULTS: Young people using heroin reported high rates of feelings of hopelessness, depression, antisocial behaviour, self-harm and diagnosed mental illness. A prior history of overdose was associated with previous mental illness, which in turn was associated with being female, having poor social support, being dissatisfied with relationships, and living alone or in temporary accommodation. While feelings of hopelessness and antisocial behaviour were strongly associated with overdose history, the number of PBS prescription drugs used had a very strong relationship with overdose, particularly benzodiazepines, other opioids, tricyclic antidepressants and tranquillisers. CONCLUSIONS: Further research to explore causal relationships between prescription drugs and heroin overdose is warranted. Improved data linkage to PBS records for general practitioners may facilitate safer prescribing practices.

Adolescent↗
PubMed2005

[National public health information system].

Information production and its communication being a key public health activity, developing modern information systems is a precondition for its fulfilling these assignments. A national public health information system (NPHIS) is a set of human resources combined with computing and communication technologies. It enables data linkage and data coverage as well as undertaking information production and dissemination in an effective, standardized and safe way. The Croatian Institute of Public Health LAN/WAN modules are under development. Health Safety System, Health Workers Registry, and Digital Library are among the Institute's developmental priorities. Communication between NPHIS participants would unfold over the Internet by using every relevant data protection method. Web technology-based applications would be run on special servers. Between individual applications, use would be made of the transaction module of communication through an exchange of the HL7 standard-based xml messages. In the conditions of transition, the health system must make an optimal use of the resources, which is not feasible without applying modern information and communication technologies.

Croatia↗
PubMed1998

Determining first admissions in a hospital discharge file via record linkage.

The aim of this study was to identify first admissions in a public hospital discharge file with the greatest possible accuracy. Computerised data linkage was used to link injury events. This involved the use of "internal" data linkage (unduplication) which, in data linkage terms, is equivalent to matching two identical files. Admission status indicators obtained from deterministic and probabilistic linkages were compared with those obtained from a manual review. Small absolute reductions in error were obtained using a probabilistic linkage over a deterministic linkage. However, these reflected large relative reductions in error. A validity check confirmed initial results and discounted against possible bias due to the subjective nature of the probabilistic linking procedure.

Humans↗
PubMed1990

[Properties of the cell surface of normal and malignant cells: investigations on polysialic acid and terminal sialic acid residues in specific linkages].

Data are reported to demonstrate the usefulness of a monoclonal anti-polysialic acid antibody for (i) the visualization of immature and mature neural elements in human teratomas, and (ii) the distinction of small cell lung carcinoma from bronchial carcinoids as well as squamous cell and adenocarcinomas of the lung. Lectins which discriminate between the various types of sialylated sequences, such as the Sambucus nigra L. I lectin specific for Neu5Ac alpha 2,6 Gal/GalNAc and the leukoagglutinin from Maackia amurensis (MAL) specific for Neu5Ac alpha 2,3 Gal beta 1,4 GlcNAc have been applied to the study of human colonic mucosa. The Neu5Ac alpha 2,3 Gal beta 1,4 GlcNAc sequence was detectable in normal and transitional mucosa and carcinomas, whereas the Neu5Ac alpha 2,6 Gal/GalNAc sequence was found in carcinomas. The lectin Amaranthin reacts with Gal beta 1,3 GalNAc-alpha (the T antigen) and NeuAc alpha 2,3 Gal beta 1,3 GalNAc-alpha (the cryptic T antigen). It stained normal and transitional colonic mucosa as well as carcinoma. The reactivity was solely due to the cryptic T antigen and indicates that the T antigen may not represent a general carcinoma autoantigen.

Cell Membrane↗
PubMed2005

Estimating the incidence of hospitalized injurious falls: impact of varying case definitions.

AIM: To assess the validity of widely used approaches to estimate the incidence of hospitalized falls. METHODS: Internal probabilistic data linkage of the 2000-01 New South Wales Inpatient Statistics Collection was used to identify first admissions for injurious falls. RESULTS: Using data linkage techniques, a total of 20,883 (93.9%, 95% CI 93.5 to 94.2) cases were identified as first admission for injurious falls corresponding to an incidence rate of 1161.4 per 100,000. The exclusion of non-acute admissions approach provided the best estimate of incidence (1185.4 per 100,000 people). When comparing the performance of different approaches to identifying first admissions to that of the data linkage "gold standard", the method based on the transfer variable performed best in terms of sensitivity and specificity. CONCLUSIONS: All the examined approaches have relatively low specificity raising questions about their use. The introduction of a unique patient identifier and the date of injury in hospital discharge datasets would facilitate the identification of incident cases of fall related hospitalizations.

Accidental Falls↗
PubMed1999

Chromosome Workshop: chromosomes 11, 14, and 15.

This report describes linkage data presented at the Workshop on Chromosomes 11, 14, and 15 at the Sixth World Congress of Psychiatric Genetics in Bonn, Germany, together with relevant linkage data submitted to the chair and co-chair, and it is presented in the context of the previous literature concerning these chromosomes. We have attempted to collate current linkage data to provide a guide to potentially interesting findings on chromosomes 11, 14, and 15 for the phenotypes of bipolar disorder, schizophrenia, alcoholism, autism, and spelling and reading disability. We discuss methodological limitations and provide chromosome ideograms and tables summarizing findings to date. The most promising region currently appears to be 15q13-q15 in the region of the alpha 7 nicotinic receptor for the phenotype of schizophrenia (and, perhaps, more generally for functional psychosis). Additionally, 15q11-q13 in the region of GABRB3 holds interest as a potential site of a susceptibility gene for autism. Two regions on chromosome 11, 11p15 in the region of tyrosine hydroxylase gene and 11q22-q23 in the region of DRD2, continue to retain some interest for functional psychosis.

Alcoholism↗
PubMed1995

Health and Environment Analysis for Decision-Making (HEADLAMP): field study in Accra, Ghana.

This field study assesses the feasibility of routine data linkage of health and environmental indicators in Accra, Ghana. In Accra, as in most low-income developing countries, there is no coherent management information system available covering environmental, demographic and health aspects of the city. These categories of data are, however, collected either routinely or on an ad hoc basis by different agencies within the city. These data bases, even though of variable quality, can be adapted for the purpose of health and environment data linkage. A number of studies have already been undertaken within Accra linking health and environment data with a good measure of success. These include: an intra-urban environment and health differentials study using mortality data; a household survey of environmental problems and the urban household in which morbidity data and environmental data were linked, also indicating intra-urban differentials together with the isolation of high risk factors from a logistical regression analysis; simple cholera mapping; and an initiative to pilot-test a community-based environmental management information system in a low-income community in which health and environmental data will be linked. All these studies have created a greater awareness of the need for such data linkage and of the value of such studies for the sustainable management of the city.

Adolescent↗
PubMed1992

There is more than one way to collect data for linkage analysis. What a study of epilepsy can tell us about linkage strategy for psychiatric disease.

The most popular strategy for finding genes in psychiatric diseases has been to focus on large pedigrees with many affected members. While this strategy has sound advantages, it also has drawbacks that have seldom been addressed. The strategy of using smaller families also has its place in a linkage analysis. To illustrate the point, I discuss herein the successful search for a gene for another common complex disease, namely, idiopathic primary generalized epilepsy. There, investigators in the Los Angeles (Calif) Epilepsy Program used mostly nuclear families who were chosen through a proband with highly specific characteristics. An independent study, using a different strategy but one still focused on small families, then confirmed the linkage. However, investigators of both epilepsy projects put much care into determining which clinical characteristics would be used to define the index cases. The implications for the study of psychiatric disease are as follows: (1) careful attention must be paid to clinical presentation, and (2) there is room for both large-pedigree and small-family strategies in designing linkage studies.

Data Collection↗
PubMed2003

Genesis and evolution of the Evx and Mox genes and the extended Hox and ParaHox gene clusters.

BACKGROUND: Hox and ParaHox gene clusters are thought to have resulted from the duplication of a ProtoHox gene cluster early in metazoan evolution. However, the origin and evolution of the other genes belonging to the extended Hox group of homeobox-containing genes, that is, Mox and Evx, remains obscure. We constructed phylogenetic trees with mouse, amphioxus and Drosophila extended Hox and other related Antennapedia-type homeobox gene sequences and analyzed the linkage data available for such genes. RESULTS: We claim that neither Mox nor Evx is a Hox or ParaHox gene. We propose a scenario that reconciles phylogeny with linkage data, in which an Evx/Mox ancestor gene linked to a ProtoHox cluster was involved in a segmental tandem duplication event that generated an array of all Hox-like genes, referred to as the 'coupled' cluster. A chromosomal breakage within this cluster explains the current composition of the extended Hox cluster (with Evx, Hox and Mox genes) and the ParaHox cluster. CONCLUSIONS: Most studies dealing with the origin and evolution of Hox and ParaHox clusters have not included the Hox-related genes Mox and Evx. Our phylogenetic analyses and the available linkage data in mammalian genomes support an evolutionary scenario in which an ancestor of Evx and Mox was linked to the ProtoHox cluster, and that a tandem duplication of a large genomic region early in metazoan evolution generated the Hox and ParaHox clusters, plus the cluster-neighbors Evx and Mox. The large 'coupled' Hox-like cluster EvxHox/MoxParaHox was subsequently broken, thus grouping the Mox and Evx genes to the Hox clusters, and isolating the ParaHox cluster.

Animals↗
PubMed2001

Pooling data and linkage analysis in the chromosome 5q candidate region for asthma.

We investigated a variety of methods for pooling data from eight data sets (n = 5,424 subjects) to validate evidence for linkage of markers in the cytokine cluster on chromosome 5q31-33 to asthma and asthma-associated phenotypes. Chromosome 5 markers were integrated into current genetic linkage and physical maps, and a consensus map was constructed to facilitate effective data pooling. To provide more informative phenotypes with better distributional properties, variance component models were fitted using Gibbs sampling methods in order to generate residual additive genetic effects, or sigma-squared-A-random-effects (SSARs), which were used as derived phenotypes in subsequent linkage analyses. Multipoint estimates of alleles shared identically by descent (IBD) were computed for all full sibling pairs. Linkage analyses were performed with a new Haseman-Elston method that uses generalized-least-squares and a weighted combination of the mean-corrected trait-sum squared and trait-difference squared as the dependent variable. Analyses were performed with all data sets pooled together, and also separately with the resulting linkage statistics pooled by several meta-analytic methods. Our results provide no significant evidence that loci conferring susceptibility to asthma affection or atopy, as measured by total serum IgE levels, are present in the 5q31-33 region. This study has provided a clearer understanding of the significance, or lack of significance, of the 5q31-33 region in asthma genetics for the phenotypes studied.

Adult↗
PubMed2004

Genetics of familial combined hyperlipidemia and risk of coronary heart disease.

Coronary heart disease is the leading cause of death in developed countries. This alarming statistic is partly attributable to lifestyle, and partly due to the genetic factors that make humans highly susceptible to atherosclerotic vascular disease. The principal metabolic causes of atherosclerosis include hyperlipidemia, hypertension, obesity, insulin resistance and diabetes mellitus. Here we discuss the aetiology of familial combined hyperlipidemia (FCHL), a highly atherogenic disorder affecting 1-2% of the Western world. Genome-wide linkage studies indicate that more than three genes contribute to the pernicious lipid profile of FCHL, and that these genes reside within the 1q21-23, 11p14.1-q12.1 and 16q22-24.1 chromosomal regions. Other loci include 1p31, 6q16.1-16.3 and 8p23.3-22, but the linkage data for these are not yet persuasive. Combined linkage and association analyses provide compelling evidence for the involvement of two distinct alleles at the APOA1/C3/A4/A5 gene cluster in the transmission of FCHL. An important lesson arising from the study of a complex genetic disorder, such as FCHL, that lacks a consensus on diagnostic criteria, is that an understanding of complex genetic disorders can derive from comparative analyses of genome-wide linkage data generated from conditions that share phenotypic overlap. The identification of potential genetic overlap between FCHL and the Metabolic Syndrome, which is estimated to affect 47 million Americans, promises to deliver new targets for reducing the risk of important conditions such as cardiovascular disease and stroke.

Alleles↗
PubMed1997

Utility of linked markers in genetic counseling: estimation of carrier risks in X-linked ocular albinism.

We apply a method proposed by Rogatko et al. [1995: Am J Med Genet 59:24-32] to estimate carrier risks using genetic linkage data. The method is illustrated for X-linked ocular albinism. Linkage data from pedigrees were combined with genome mapping data to compute carrier risks for individuals with unknown carrier status based on pedigree data alone. We considered two situations. First, a linkage map with some ambiguity in the gene order was considered. This analysis allows us to examine the effect of incomplete genetic map information on risk computations. Second, published physical and meiotic mapping information was used to derive a linkage map that could be assumed known without ambiguity. In both situations, the mean and median estimate of carrier risk differed significantly from that obtained using pedigree relationships only, in that the computed risk was significantly different from the a priori value of 0.5. The 95% CI's associated with point estimates of risk made using the known map or an map with ambiguity did not overlap in some cases. These results suggest that the risk estimate and the confidence with which a risk estimate can be imparted may depend on the genetic map and marker data used in the risk estimation procedure. We conclude that the method presented here can be used to estimate genetic risk under a variety of analytical conditions.

Albinism, Ocular↗
PubMed1997

Chromosomal localization of six bovine microsatellite markers.

Six lambda genomic clones containing polymorphic microsatellite (MS) markers were assigned to bovine chromosomes 1, 3, 5, 7, 13 and 24 by fluorescence in situ hybridization (FISH). Linkage data for four MS markers were presented earlier and linkage data for the remaining two on chromosome 7 and 24 are presented here. All assignments either orient or confirm the orientation of linkage groups relative to the centromere. A comparison of physical assignments and linkage intervals was possible on chromosome 5 (three loci, 38 cM) and 13 (two loci, 6 cM).

Animals↗