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PubMed2003

Data integration and warehousing: coordination between newborn screening and related public health programs.

At birth, patient demographic and health information begin to accumulate in varied databases. There are often multiple sources of the same or similar data. New public health programs are often created without considering data linkages. Recently, newborn hearing screening (NHS) programs and immunization programs have virtually ignored the existence of newborn dried blood spot (DBS) newborn screening databases containing similar demographic data, creating data duplication in their 'new' systems. Some progressive public health departments are developing data warehouses of basic, recurrent patient information, and linking these databases to other health program databases where programs and services can benefit from such linkages. Demographic data warehousing saves time (and money) by eliminating duplicative data entry and reducing the chances of data errors. While newborn screening data are usually the first data available, they should not be the only data source considered for early data linkage or for populating a data warehouse. Birth certificate information should also be considered along with other data sources for infants that may not have received newborn screening or who may have been born outside of the jurisdiction and not have birth certificate information locally available. This newborn screening serial number provides a convenient identification number for use in the DBS program and for linking with other systems. As a minimum, data linkages should exist between newborn dried blood spot screening, newborn hearing screening, immunizations, birth certificates and birth defect registries.

Birth Certificates↗
PubMed2006

Matching waveform audio files with toxicall data: Record linkage in a poison control center.

Analysis of coded communications and electronic patient record data present a unique opportunity for nursing knowledge discovery, the integration of communication content with clinical data. However, joint analysis of coded communications and clinical data depends on the ability to link waveform audio files with patient records. A procedure has been developed to link waveform audio files with Toxicall patient records, using date/time stamps and station identification numbers.

Communication↗
PubMed2001

Adding value to clinical data by linkage to a public death registry.

We describe the methodology and impact of merging detailed statewide mortality data into the master patient index tables of the clinical data repository (CDR) of the University of Virginia Health System (UVAHS). We employ three broadly inclusive linkage passes (designed to result in large numbers of false positives) to match the patients in the CDR to those in the statewide files using the following criteria: a) Social Security Number; b) Patient Last Name and Birth Date; c) Patient Last Name and Patient First Name. The results from these initial matches are refined by calculation and assignment of a total score comprised of partial scores depending on the quality of matching between the various identifiers. In order to validate our scoring algorithm, we used those patients known to have died at UVAHS over the eight year period as an internal control. We conclude that we are able to update our CDR with 97% of the deaths from the state source using this scheme. We illustrate the potential of the resulting system to assist caregivers in identification of at-risk patient groups by description of those patients in the CDR who were found to have committed suicide. We suggest that our approach represents an efficient and inexpensive way to enrich hospital data with important outcomes information.

Death Certificates↗
PubMed2006

A cohort study of 20,822 young drivers: the DRIVE study methods and population.

BACKGROUND AND OBJECTIVE: Research on young drivers directly linking risk factors to serious injury and death outcomes is required. The DRIVE Study was established to facilitate this aim. This paper outlines the study methods and describes the population that has been recruited, in order to demonstrate that the necessary heterogeneity in risk factors has been attained. DESIGN, SETTING AND PARTICIPANTS: Drivers aged 17-24 years holding their first-stage provisional driver's licence from New South Wales, Australia, were recruited into a prospective cohort study. The participants were contacted by mail and asked to complete the study questionnaire at an online site or via a mailed questionnaire. Baseline data collection involved a questionnaire with questions to drivers about their training, risk perception, driver behavior, sensation-seeking behavior and mental health. Participants gave consent for prospective data linkage to their data on licensing, crashes and injuries, held in routinely collected databases. RESULTS: 20 822 drivers completed the baseline questionnaire, of whom 45.4% were men, 74.3% resided in capital cities and 25.7% in regional or remote areas. The recruited study population showed a wide variation in the risk factors under examination. For example, almost 40% of drivers reported drinking alcohol at hazardous levels and about 32% of participants seemed to be at a high or very high risk of psychological distress. Participants reported a mean of 67.3 h (median 60 h) of supervised driver training while holding their learner's permit. CONCLUSIONS: The DRIVE Study has a robust study design aimed at minimizing bias in the collection of outcome data. Analyses of baseline data showed substantial heterogeneity of risk factors in the study population. Subsequent prospective linkages comparing relative differences in exposures at baseline with the outcomes of interest have the potential to provide important new information needed to develop targeted interventions aimed at young drivers.

Accidents, Traffic↗
PubMed1976

Methods for detecting teratogenic agents in man.

At a multidiscipline international meeting sponsored by L'Institut de la Vie held at Guadeloupe in January 1974, current methods for detecting teratogenic agents were outlined and discussed. Recommendations of the participants of the conference were: recognize the limitations of the present defenses against teratogenic agents; educate the public and medical profession about the known human teratogenic agents; select for animal teratogenicity screening among new and existing agents by emphasizing substances to which the entire population will be exposed, agents to which pregnant women are exposed, viruses which are found to persist in the human fetus, and agents which have become suspect from clinical experience; recognize that nearly all compounds have a fetotoxic dose but that this does not imply teratogenicity; encourage the development of new, quick in vitro testing methods for detecting teratogenic agents; monitor for sudden increases in the frequency of specific malformations in newborn infants and in aborted fetuses; assure that expert multidiscipline committees are available to evaluate the threat when suspected teratogens are reported; improve teratology information storage and retrieval systems by record linkage of clinical data, linkage between computer systems, and universal identifier system for chemical compounds and congenical malformations; foster the exchange of data, particularly those held by the pharmaceutical industry.

Amniocentesis↗
PubMed2002

Regional meta-analysis of published data supports linkage of autism with markers on chromosome 7.

Although the concept of meta-analysis of multiple linkage scans of a genetic trait is not new, it can be difficult to apply to published data given the lack of consistency in the presentation of linkage results. In complex inheritance common diseases, there are many instances where one or two studies meet genome-wide criteria for significant or suggestive linkage but several other studies do not show even nominally significant results with the same region. One possibility for resolving differences between study results would be to combine an available result parameter of several studies. We describe here a method of regional meta-analysis, the multiple-scan probability (MSP), which can be used on published results. It combines the reported P-values of individual studies, after correcting each value for the size of the region containing a minimum P-value. Analyses of the power of MSP and of its type I error rates are presented. The type I error rate is at least as low as that for a single genome scan and thus genome-wide significance criteria may be applied. We also demonstrate appropriate criteria for this type of meta-analysis when the most significant study is included, and when that study is used to define a region of interest and then excluded. In our simulations, meta-analysis is at least as powerful as pooling data. Finally, we apply this method of meta-analysis to the evidence for linkage of autism susceptibility loci and demonstrate evidence for a susceptibility locus at 7q.

Algorithms↗
PubMed1999

Summary of analyses of problem 2 simulated data for GAW11.

The simulated data for Problem 2 of the 11th Genetic Analysis Workshop (GAW11) consisted of family linkage data and disease data from three populations, each population with different genetic parameters. The disease was simulated such that there were two genetically distinct diseases, one caused by a single locus with three alleles and the other by two epistatically interacting loci. The two diseases were clinically identical. Each of the diseases had a severe and mild form. One of the diseases was influenced by an environmental factor and one by an allele at one of the marker loci (association). Linkage data consisted of 300 polymorphic markers. Investigators analyzed these data in a myriad of ways, using most currently available linkage techniques and association analysis methods. In addition, investigators also tested newly developed methods, some of which took advantage of the existence of the environmental component. Other types of analyses included meta-analyses, methods of combining data from different studies, questions of replication, how much information is available in a single data set, and analyses for gene x gene and gene x environment interaction.

Computer Simulation↗
PubMed1993

Integration of the classical and molecular linkage maps of tomato chromosome 6.

In the past, a classical map of the tomato genome has been established that is based on linkage data from intraspecific Lycopersicon esculentum crosses. In addition, a high density molecular linkage map has recently been constructed using a L. esculentum x L. pennellii cross. As the respective maps only partially match, they provide limited information about the relative positions of classical and molecular markers. In this paper we describe the construction of an integrated linkage map of tomato chromosome 6 that shows the position of cDNA-, genomic DNA- and RAPD markers relative to 10 classical markers. Integration was achieved by using a L. esculentum line containing an introgressed chromosome 6 from L. pennellii in crosses to a variety of L. esculentum marker lines. In addition, an improved version of the classical linkage map is presented that is based on a combined analysis of new linkage data for 16 morphological markers and literature data. Unlike the classical map currently in use, the revised map reveals clustering of markers into three major groups around the yv, m-2 and c loci, respectively. Although crossing-over rates are clearly different when comparing intraspecific L. esculentum crosses with L. esculentum x L. pennellii crosses, the clusters of morphological markers on the classical map coincide with clusters of genomic- and cDNA-markers on the molecular map constructed by Tanksley and coworkers.

Chromosome Mapping↗
PubMedDate not supplied

Linkage analysis under locus heterogeneity: behaviour of the A-test in complex analyses.

The admixture test (A-test) is a popular method for the analysis of linkage data when locus heterogeneity is suspected. It can be applied on pairwise linkage data, multipoint data and even for the simultaneous analysis of data from multiple dispersed candidate regions. However, very little is known about the conditions for the use of the method under these divergent circumstances. By performing analytical evaluations, we demonstrate that the A-test is inconsistent if there is a relationship between the phenotype and the probability of being linked. Biased estimates of the recombination fraction (theta) and the proportion of linked families (alpha) may occur if the actual frequency of linked families is not identical among small and large families. We conclude that the A-test should be used with caution if the phenotype and the probability of developing the phenotype at a certain age cannot be shown to be equal for family members of linked and unlinked families. If dissimilarities in family size cannot be ruled out, the extent of bias should be considered and size specific alpha-values should be used in risk calculations.

Bias↗
PubMed1989

The new standard environmental inventory questionnaire for estimation of indoor concentrations.

Several investigators have developed indoor air quality questionnaires for use in field studies. The approach used in many of them have numerous features in common, but most of them are unique in their content (wording, format, item selection). It is thought that indoor air quality research could be greatly advanced if the primary or fundamental questions and instruments could be consolidated. The use of a basic set of "standard" questions would permit intercomparison of results from different research studies. It is generally agreed that environmental inventory questionnaires (EIQ) help to classify, at least in screening, relative concentration estimates, which precede exposure estimation. Thus, such instruments are not equivalent to monitoring for exposure assessment. However, data linkage and mega data bases are important for some comparative analyses of exposure assessment and exposure-response relationships. Standard instruments such as the EIQ are useful as a screening device to precede other tests to allow identification of potentially high exposure situations. They can also amplify information from other tests. General usage of standard questionnaires and protocols can lead to cumulative improvements in data collection, specificity and effectiveness. This has been the rationale for the present efforts by investigators to form a standardized environmental inventory questionnaire, under the auspices of the U.S. Environmental Protection Agency (EPA), Gas Research Institute (GRI), and Electric Power Research Institute (EPRI).

Air↗
PubMed1992

Linkage analysis of keratosis follicularis spinulosa decalvans, and regional assignment to human chromosome Xp21.2-p22.2.

Keratosis follicularis spinulosa decalvans (KFSD) is a rare X-chromosomal disorder. It consists of follicular hyperkeratosis of the skin, scarring alopecia of the scalp, absence of the eyebrows, and corneal degeneration. There is photophobia in childhood, but the symptoms tend to diminish after puberty, and prognosis for vision is good. Some heterozygotes do show clinical symptoms. In a large Dutch pedigree we performed DNA analysis in order to localize the KFSD gene. In 54 individuals, including 21 affected males, RFLP analysis was done using DNA probes covering the X chromosome. Two-point linkage analyses with 19 informative DNA markers revealed significant linkage to DNA probes on Xp21.1-p22.3. The highest lod scores of 5.70 and 4.38 were obtained with DXS41 and DXS16 at a recombination fraction of zero and 4 cM, respectively. Multipoint linkage data place KFSD between DXS16 and DXS269. Our data confirm X linkage of KFSD in this family and tentatively map the gene on Xp22.2-p21.2. Combined with clinical investigation, RFLP analysis may become an important tool in carrier detection.

Chromosome Mapping↗
PubMed1998

Health registers as a feasible means of measuring health status in childhood--a 7-year follow-up of the 1987 Finnish birth cohort.

Follow-up studies on health have usually been based on ad hoc cohort studies in which detailed information is collected specifically for research purposes on a certain group of people. The increasing collection of routine health data provides an alternative method of gathering follow-up data. In this study, the feasibility of using routinely collected health-register data and data linkages to follow up children's health was investigated. Five nationwide registers, 18 regional registers of intellectually disabled children and school administration data in one county were found to be of use for our follow-up and were combined with the 1987 Finnish Medical Birth Register (n = 60,254 births). In the follow-up, 62 children were untraced (0.1%), 327 were stillborn (0.5%), 440 died after birth (0.7%) and 287 emigrated (0.5%) before the age of 7 years. The cumulative incidences for all diseases (8.9% of all children living in Finland at the age of 7 years), for diabetes (3.0/1000), for epilepsy (6.8/1000) and for asthma (34.2/1000) correspond to the estimates of other studies, but our estimate for intellectual disabilities (18.0/1000, of whom 18% were reported to have an IQ of 70 or less) seems to be an underestimate. Our data collection did not provide reliable information on institutionalised children or children taken into care. Data collection conducted by using health registers is a feasible method, and it saves both time and financial resources compared with cohort studies. Potential problems with data linkage studies are variation in the content of data and in data quality of different registers and data protection issues.

Adolescent↗
PubMed1990

[A clinical study of a family affected with HLA-linked hereditary spinocerebellar ataxia].

The gene locus of hereditary olivopontocerebellar atrophy (OPCA) has been mapped to the short arm of chromosome 6. This locus has been termed as SCA 1 and it is linked to HLA locus. Linkage for OPCA locus to HLA was first been reported by Yakura et al. We had a chance to re-investigate the original family reported by them. Among the members affected, 6 cases were autopsied and their clinical and pathological features were reported by Fujimoto et al. Kudoh et al, and Ikeda. We clinically studied 2 additional patients in this pedigree. The clinical features of these patients, including 6 previously reported cases, were characterized by 1) cerebellar ataxia predominating throughout clinical course; 2) pyramidal tract involvement, characterized by pathological reflexes, with hyper-reflexia or terminal hyporeflexia; 3) generalized muscle atrophy; 4) slow eye movement; 5) facial and tongue atrophy; 6) optic disc pallor; 7) terminal external ophthalmoparesis; 8) mydriasis and sluggish light reflex; 9) mild peripheral neuropathy; 10) mild reduction of deep sense; 11) bulbar symptom; 12) emotional lability, irritation, or euphoria dominating terminally. Clinically, there are certain similarities between this pedigree and other reported pedigrees of which linkage for OPCA locus to HLA have been proved. Furthermore, clinico-pathological reports of hereditary OPCA showing slow eye movement share numbers of clinical characteristics observed in the patients of this pedigree. Accumulating linkage data suggest that hereditary OPCA might be heterogenous disorder genetically. Whether there are any correlation between linkage data and clinico-pathological findings is essential to establish disease entities, and to re-classify hereditary OPCA and its related disorders.

Adolescent↗
PubMed1982

Subtyping of phosphoglucomutase locus 1 (PGM1) polymorphism in some populations of Rwanda: description of variant phenotypes, "haplotype" frequencies, and linkage disequilibrium data.

Some populations of Rwanda (South Twa Pygmies, Hutu, and Tutsi) have been analyzed by acid starch gel electrophoresis for the subtyping of PGM1 polymorphism. The new polymorphic third PGM11 allele, the PGM1(1Twa), which we recently detected in Twa Pygmies from North Rwanda, has not been found in this survey, whereas the rare PGM1(6) allele attains subpolymorphic frequencies in all groups. Comparison between the various populations of Rwanda shows that they differ significantly from each other with the exception of South Twa Pygmies and Tutsi. A relatively low frequency (9.6%) of the PGM1(2S) allele appears to be typical of North Twa Pygmies; a low frequency of PGM1(2F) (1.2%-3.6%) has been found in all these groups but not in the Hutu (6.4%); and a particularly high incidence of the PGM1(1F) allele (the highest so far reported) has been observed in the South Twa Pygmies (20%) and in the Tutsi (18%). The PGM1(1Twa) and PGM1(6) enzymes, which in acid starch gel are not distinguishable, can be clearly differentiated by isoelectric focusing. In addition, the same technique has shown that the rare PGM1(7) allele observed in one Hutu is different from that found at polymorphic frequency in the Japanese and from a rare PGM1(7) allele found in Germany. On the very likely hypothesis that the PGM1(1S), PGM1(1F), PGM1(2S), and PGM1(2F) result from variations at two different polymorphic sites, 1/2 and F/S, within the PGM1 structural gene, all the available population data have been analyzed to investigate whether preferential combinations (haplotypes) were identifiable. Whereas Caucasians show a prevalence of 2F and 1S combination with an 8.02% mean value of linkage disequilibrium expressed as % Dmax, from the very few and scattered African data, it is impossible to draw any inference at present.

Alleles↗
PubMed1992

Linkage and association studies with C8A and C8B RFLPs on chromosome 1.

Linkage relations for the C8A and C8B BamHI RFLPs have been investigated. A peak lod score of 4.52 at recombination fraction zero was obtained between the two C8 genes. Combined with our previously obtained linkage data (Rogde et al. 1986) the maximum lod score is 7.53 at recombination fraction zero. The compiled C8-PGM1 linkage data from this and the previous study gave a maximum lod score of 22.02 at recombination fraction 0.11 (0.07-0.16) with no sex difference. A chromosome 1p reference marker, D1S57, has been applied in this linkage study. A maximum lod score of 5.06 between the C8 cluster and D1S57 at theta = 0.18 (0.11-0.28) was recorded. The linkage analyses and triply informative families gave evidence that the C8 loci are situated about halfway between PGM1 and D1S57 on the short arm of chromosome 1. There was no evidence of allelic association between the C8A and C8B BamHI RFLPs in 62 unrelated haplotypes.

Chromosome Mapping↗
PubMed2001

Single region linkage analyses of asthma: description of data sets.

Linkage (genotypic) data from the 5q31-33 candidate region for asthma were contributed to Genetic Analysis Workshop 12 by members of the International Consortium on Asthma Genetics (COAG). Data came from five independent studies sampled from five countries. Genotypic data for a total of 26 markers were available, although the number of markers typed in each data set varied. Phenotypic and genotypic data was available from a total of 569 families and 3,175 subjects. The phenotypic data available varied among the studies; however information regarding physician-diagnosed asthma and total serum IgE levels was available in all five studies. This paper describes the ascertainment, data collection methods, phenotypic data, and genotypic data available for the single linkage region analyses undertaken for Genetic Analysis Workshop 12.

Adolescent↗
PubMed1986

Linkage analysis of Von Recklinghausen neurofibromatosis: chromosomes 4 and 19.

This report describes a study that examines the hypotheses of genetic linkage between the autosomal dominant disorder neurofibromatosis (NF) and loci on human chromosomes 4 and 19. Twelve Utah families were evaluated for evidence of possible linkage of NF to six known markers on chromosome 4 and five markers on chromosome 19. Due to previous reports suggesting tight linkage of NF to the GC locus on chromosome 4 and the C3 (linked to myotonic dystrophy) locus on chromosome 19, these two markers were of particular interest. For the Utah families the cumulative LOD score for GC was -4.81 (r = 0.05). Cumulative LOD scores were -0.90 (r = 0.05) and -1.01 (r = 0.05) for C3 serum determinations and a C3 DNA polymorphism respectively. Linkage data is also included on all individual informative families for the GC and C3 loci to specifically address the question of heterogeneity. Linkage data is consistent with, but does not strongly support, the existence of heterogeneity implicating both the GC locus on chromosome 4 and the C3 locus on chromosome 19. A compilation of cumulative LOD scores from this and other current linkage studies produces values that in the absence of heterogeneity refute previous reports for tight linkage of NF to GC and to C3.

Adolescent↗