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Understanding the clinical and economic outcomes of HIV therapy: the Johns Hopkins HIV clinical practice cohort.

The Johns Hopkins AIDS Service is the principal provider of medical care for HIV-infected patients in Maryland, a state in which the majority of HIV-infected patients live in an urban environment. A component of the HIV service at Johns Hopkins Medical Center is an information system that is used to track longitudinally the ambulatory and inpatient care of HIV-infected patients. Enrollment into this database coincides with first enrollment into the HIV Service. Extensive laboratory, diagnostic, clinical, and pharmaceutical information is collected at enrollment and is updated every 6 months. Outpatient and inpatient medical records, Johns Hopkins Health System automated databases, supplemental medical records from outside facilities, vital records, and patient and provider interviews are all used to obtain the detailed data that are stored on the database. The database also includes an economic component, which was added in 1994. This component links all Maryland state Medicaid claims data to that relating to patients who are insured by the Maryland Medical Assistance program, who account for approximately 60% of patients using the Johns Hopkins HIV Service. This data linkage facilitates detailed quantification of the costs of medical care for the HIV-infected patient throughout the course of the infection. We currently have data on about 3,000 HIV-infected patients representing a heterogeneous mix by race, sex, socioeconomic status, and risk factors for HIV transmission. Our data have been used to address a variety of issues regarding access to, utilization of, and clinical outcomes of HIV therapeutics. Clinical practice data such as ours will be increasingly important as the number and types of antiretroviral and other drugs for HIV infection continue to increase.

Adolescent↗

Linkage between the fragile X and F9, DXS52 (St14), DXS98 (4D-8) and DXS105 (cX55.7).

Linkage data using the markers F9, DXS105 (cX55.7), DXS98 (4D-8) and DXS52 (St14) are presented from 22 kindreds segregating with the fragile X. Two-point linkage analysis was carried out taking into account cytogenetic results and penetrance classes defined by mental impairment status of mothers. Recombination frequencies (theta) corresponding to the maximum z scores (z) were obtained between F9 (z = 3.48, theta = 0.18), DXS105 (z = 5.06, theta = 0.07), DXS98 (z = 4.79, theta = 0.01) and DXS52 (z = 6.44, theta = 0.09) and the fragile X. Recombination frequencies between marker loci in fragile X families are also presented. These recombination frequencies need to be combined with those from other studies in order to determine the best estimates of map distances for use in genetic counselling, until markers closer to the fragile X, or at the fragile X, can be used. Most potential fra(X) heterozygotes were informative for flanking markers using the above 4 probes. Carrier risks were determined by 3-point analysis using informative flanking markers, taking into account cytogenetic results. Low level fra(X) expression occurred in 2 probable non-carriers; emphasising the need for extreme caution in the interpretation of low rates of expression.

Factor IX↗

Multipoint mapping of the central core disease locus.

A linkage analysis with 12 DNA markers from proximal 19q was performed in eight families with central core disease (CCO). Two-point analysis gave a peak lod score of Z = 4.95 at theta = 0.00 for the anonymous marker D19S190 and of Z = 2.53 at theta = 0.00 for the ryanodine receptor (RYR1) candidate gene. Multipoint linkage data place the CCO locus at 19q13.1, flanked proximally by D19S191/D19S28 and distally by D19S47. This map location includes the RYR1 gene. The results of the linkage study present no evidence for genetic heterogeneity of CCO.

Animals↗

Genetic testing for breast cancer susceptibility: frequency of BRCA1 and BRCA2 mutations.

Genetic testing for breast cancer susceptibility became a reality after two cancer predisposition genes, BRCA1 and BRCA2, were identified. Mutations in these two genes were predicted to account for 85% to 90% of hereditary breast and ovarian cancer syndromes. We present results of mutation analysis of the coding sequence of these two genes in 110 consecutive non-Jewish breast cancer patients with a positive family history of breast and/or ovarian cancer. The individuals were identified in various cancer risk evaluation centers in the country. Twenty-two (20%) mutations in the BRCA1 gene and 8 mutations (7%) in the BRCA2 gene were detected. We also analyzed 52 Ashkenazi Jewish breast cancer patients for mutations in the BRCA1 and BRCA2 genes. Eleven Jewish individuals (21%) carried either one of the two common mutations, 185delAG and 5382InsC, in the BRCA1 gene and 4 individuals (8%) had the 6174delT mutation in the BRCA2 gene. The frequency of mutations in BRCA genes in affected people in this ethnic group was not significantly different from the non-Jewish population. On further analysis, the data demonstrate that neither age of onset nor phenotype of the disease had any significant predictive value for the frequency of mutations in these genes. These data confirm the lower prevalence of mutations in either of the BRCA genes in clinical families when compared to high-risk families used for obtaining linkage data in a research setting.

Adult↗

A consensus linkage map for sugi (Cryptomeria japonica) from two pedigrees, based on microsatellites and expressed sequence tags.

A consensus map for sugi (Cryptomeria japonica) was constructed by integrating linkage data from two unrelated third-generation pedigrees, one derived from a full-sib cross and the other by self-pollination of F1 individuals. The progeny segregation data of the first pedigree were derived from cleaved amplified polymorphic sequences, microsatellites, restriction fragment length polymorphisms, and single nucleotide polymorphisms. The data of the second pedigree were derived from cleaved amplified polymorphic sequences, isozyme markers, morphological traits, random amplified polymorphic DNA markers, and restriction fragment length polymorphisms. Linkage analyses were done for the first pedigree with JoinMap 3.0, using its parameter set for progeny derived by cross-pollination, and for the second pedigree with the parameter set for progeny derived from selfing of F1 individuals. The 11 chromosomes of C. japonica are represented in the consensus map. A total of 438 markers were assigned to 11 large linkage groups, 1 small linkage group, and 1 nonintegrated linkage group from the second pedigree; their total length was 1372.2 cM. On average, the consensus map showed 1 marker every 3.0 cM. PCR-based codominant DNA markers such as cleaved amplified polymorphic sequences and microsatellite markers were distributed in all linkage groups and occupied about half of mapped loci. These markers are very useful for integration of different linkage maps, QTL mapping, and comparative mapping for evolutional study, especially for species with a large genome size such as conifers.

Base Sequence↗

Physical localization of 70 polymorphic markers to human chromosome 5 by fluorescence in situ hybridization.

We used fluorescence in situ hybridization (FISH) to prepare a cytogenetic framework map of 21 polymorphic markers that had been used previously to construct a genetic linkage anchor map of chromosome 5. In addition, we localized 49 other markers that have been genotyped on CEPH families. This study demonstrates that FISH can be used to confirm genetic linkage data, and that it can provide a means of determining the cytogenetic locations and relative order of markers whose order could not be assigned by genetic linkage analysis alone. The cytogenetic map prepared by FISH may help to identify probes of interest for regional mapping studies.

Chromosome Mapping↗

Meta-analysis of whole-genome linkage scans of bipolar disorder and schizophrenia.

Badner and Gershon (2001) presented a technique of meta-analysis of linkage data that could be applied to published genome scans. It combines the reported P-values of individual studies, after correcting each value for the size of the region containing a minimum P-value. Simulations demonstrated that the type I error rate was at least as low as that for a single genome scan and thus genome-wide significance criteria may be applied. Power to detect linkage was at least as high as the power of pooling the data from all the studies. We applied this method to all the published genome scans for bipolar disorder and schizophrenia. We found the strongest evidence for susceptibility loci on 13q (P < 6 x 10(-6)) and 22q (P < 1 x 10(-5)) for bipolar disorder, and on 8p (P < 2 x 10(-4)), 13q (P < 7 x 10(-5)), and 22q (P < 9 x 10(-5)) for schizophrenia.

Bipolar Disorder↗

Evidence of genetic heterogeneity in Romano-Ward long QT syndrome. Analysis of 23 families.

BACKGROUND: The Romano-Ward long-QT Syndrome (LQTS) is an autosomal dominant inherited trait characterized by prolonged QT interval on ECG, life-threatening arrhythmias, syncope, and sudden death in affected individuals. A gene responsible for this disorder has been shown to be linked to the Harvey ras-1 locus (H-ras-1) DNA marker on the short arm of chromosome 11 (11p) in 7 families. The purpose of this study was to determine, by analyzing 23 families with LQTS for linkage to chromosome 11p, whether evidence exists for more than one gene causing LQTS (ie, locus heterogeneity). METHODS AND RESULTS: Twenty-three families (262 family members) were clinically evaluated using medical histories, ECGs, and Holter recordings. Each corrected QT interval (QTc) were determined using Bazett's formula. Blood for DNA extraction and cell line immortalization was obtained after informed consent. Southern blotting and polymerase chain reaction were performed, and linkage analysis carried out using the LINKAGE computer program (v 5.03). Genetic heterogeneity was determined using the HOMOG 2 (v 2.51) computer program. Twenty-three families were studied for evidence of linkage to chromosome 11p using the H-ras-1 locus probe pTBB-2 and multiple flanking markers, including tyrosine hydroxylase (TH). Two-point linkage analysis using pTBB-2 and TH markers was consistent with linkage in 15 of 23 families, with the maximum single-family LOD score of +3.038 occurring at theta = 0. However, 8 of 23 families had negative LOD scores, with the values in 4 families being less than -2 at theta = 0, consistent with exclusion of linkage. Analysis with the HOMOG program was consistent with genetic heterogeneity (P < .0001). Multipoint linkage data using pTBB-2 and TH were also examined for evidence of heterogeneity. HOMOG analysis of multipoint LOD scores from 100 cM surrounding the H-ras-1 locus also supported heterogeneity (P < .001). CONCLUSIONS: In the 23 families with LQTS analyzed for linkage to the H-ras-1 locus on chromosome 11p15.5, 15 of 23 families had LOD scores consistent with linkage. The remaining 8 of 23 families had negative LOD scores, 4 of which were definitively excluded from linkage. Thus, genetic heterogeneity is definitively (P < .001) demonstrated for this disorder.

Base Sequence↗

The epidemiology of mental retardation: challenges and opportunities in the new millennium.

There are a number of problems and challenges in relating the science of epidemiology to mental retardation (MR). These relate to how MR is defined and classified and how these definitions may change over time. These as well as other differences in ascertainment sources and methods need to be considered when comparing MR prevalence over time and place. On the other hand, advances in technology also provide new and efficient methods of data collection both by data linkage and by use of web-based methods to study rare diseases. While prevalence studies have not been individually reviewed, we have examined the range of data including recent studies relating to how prevalence differs according to age, gender, social class and ethnicity. Some problems with available etiological classification systems have been identified. Recent etiological studies, most of which use different classification systems, have been reviewed and explanations have been postulated to account for differences in results. Individual risk factors for MR are considered whilst the option of considering a population as opposed to a high risk strategy to MR prevention is raised. This might well involve improving the social milieu surrounding the occurrence of individual risk factors. The impact of biotechnological advances such as antenatal and neonatal screening and assisted reproduction on MR are discussed. The issue of how inequalities in access to technology may impact on case identification and even have the potential to further widen inequalities is raised. The importance of extending the use of epidemiological tools to study the social, health and economic burden of MR is also emphasized. However, in order to apply to MR the "prevention-intervention-research" cycle, which surely underpins all epidemiology, it is vital to ensure that the methodological challenges we raise are adequately addressed.

Adolescent↗

Linkage analyses in British pedigrees suggest a single locus for Darier disease and narrow the location to the interval between D12S105 and D12S129.

Darier disease is a dominantly inherited skin disorder in which there appears to be abnormal adhesion between keratinocytes. We and others have shown that the disease in some British pedigrees is closely linked to markers mapping to 12q23-q24.1. In the present study we have defined crossovers that enable us to narrow the location of the disease gene to the interval between the D12S105 and the D12S129 markers. This interval may be expected to be on the order of about 4 cM on the basis of linkage data obtained using the primary CEPH reference families. Our data provide further evidence for locus homogeneity: each of four large British pedigrees, two of which have previously been subjected to preliminary characterization, shows statistically significant evidence for linkage to markers mapping to 12q23-q24.1.

Chromosome Mapping↗

The relational database model and multiple multicenter clinical trials.

The Southwest Oncology Group (SWOG) chose to use a relational database management system (RDBMS) for the management of data from multiple clinical trials because of the underlying relational model's inherent flexibility and the natural way multiple entity types (patients, studies, and participants) can be accommodated. The tradeoffs to using the relational model as compared to using the hierarchical model include added computing cycles due to deferred data linkages and added procedural complexity due to the necessity of implementing protections against referential integrity violations. The SWOG uses its RDBMS as a platform on which to build data operations software. This data operations software, which is written in a compiled computer language, allows multiple users to simultaneously update the database and is interactive with respect to the detection of conditions requiring action and the presentation of options for dealing with those conditions. The relational model facilitates the development and maintenance of data operations software.

Clinical Trials as Topic↗

Linkage of cystic fibrosis to the pro alpha 2(I) collagen gene, COL1A2, on chromosome 7.

A linkage has been detected between the locus for cystic fibrosis (CF) and the pro alpha 2(I) collagen gene (COL1A2) which is located in the region q21.3----q22.1 of chromosome 7. Based on the combined linkage data derived from 50 informative two-generation nuclear families collected in Canada and Denmark, the distance between COL1A2 and CF is estimated to be 19 centiMorgans. Close linkage has also been detected between COL1A2 and the DNA marker D7S15 (formerly D0CRI-917) and the serum enzyme activity marker paraoxonase (PON), both of which have previously been found linked to CF. The results of the two-point and three-point linkage analyses indicate that the most probable order of these four genetic loci is COL1A2-D7S15 - PON - CF.

Chromosomes, Human, 6-12 and X↗

Development of record linkage of hospital discharge data for the study of neonatal readmission.

Computerized record linkage has been used increasingly in epidemiologic studies. We developed a multistage, deterministic matching algorithm using various combinations of key variables. Then, from the records for March 1, 1993, to March 31, 1996, contained in the discharge abstract database of the Canadian Institute for Health Information (CIHI), we examined the relation between length of hospital stay at birth and neonatal readmission. A combined use of province/territory of occurrence, 6-digit postal code of residence, date of birth and sex (step 1) matched 88.5% of 26,629 eligible neonatal readmission records with their birth records. Additional use of institution code and chart number or health card number combined with date of birth and sex (step 2 and step 3) increased the matching rate to 93.0%. Compared with the gold standard, step 1 correctly matched 94.4% of the records. We conclude that this deterministic matching algorithm is a feasible and convenient approach to data linkage for the study of neonatal readmission. The linkage strategy may also be helpful in epidemiologic studies of other short-term events

Algorithms↗

Autosomal dominant retinitis pigmentosa: a new multi-allelic marker (D3S621) genetically linked to the disease locus (RP4).

We report the characterization of a new eight-allele microsatellite (D3S621) isolated from a human chromosome 3 library. Two-point and multi-locus genetic linkage analysis have shown D3S621 to co-segregate with the previously mapped RP4 (theta m = 0.12, Zm = 4.34) and with other genetic markers on the long arm of the chromosome, including D3S14 (R208) (theta m = 0.00, Zm = 15.10), D3S47 (C17) (theta m = 0.11, Zm = 4.95), Rho (theta m = 0.07, Zm = 1.37), D3S21 (L182) (theta m = 0.07, Zm = 2.40) and D3S19 (U1) (theta m = 0.13, Zm = 2.78). This highly informative marker, with a polymorphic information content of 0.78, should be of considerable value in the extension of linkage data for autosomal dominant retinitis pigmentosa with respect to locii on the long arm of chromosome 3.

Alleles↗

Linkage analysis and physical mapping near the gene for X-linked agammaglobulinemia at Xq22.

The gene for X-linked agammaglobulinemia (XLA) has been mapped to Xq22. No recombinations have been reported between the gene and the probe p212 at DXS178; however, this probe is informative in only 30-40% of women and the reported flanking markers, DXS3 and DXS94, are 10-15 cM apart. To identify additional probes that might be useful in genetic counseling, we examined 11 polymorphisms that have been mapped to the Xq21.3-q22 region in 13 families with XLA. In addition, pulsed-field gel electrophoresis and yeast artificial chromosomes (YACs) were used to further characterize the segment of DNA within which the gene for XLA must lie. The results demonstrated that DXS366 and DXS442, which share a 430-kb pulsed-field fragment, could replace DXS3 as proximal flanking markers. Probes at DXS178 and DXS265 identified the same 145-kb pulsed-field fragment, and both loci were contained within a 200-kb YAC identified with the probe p212. A highly polymorphic CA repeat (DXS178CA) was isolated from one end of this YAC and used in linkage analysis. Probes at DXS101 and DXS328 shared several pulsed-field fragments, the smallest of which was 250 kb. No recombinations were seen between XLA and the DXS178-DXS265-DXS178CA complex, DXS101, DXS328, DXS87, or the gene for proteolipid protein (PLP). Key crossovers, when combined with the linkage data from families with Alport syndrome, suggested the following order of loci: cen-DXS3-DXS366-DXS442-(PLP, DXS101, DXS328, DXS178-DXS265-DXS178CA complex, XLA)-(DXS87, DXS94)-DXS327-(DXS350, DXS362)-tel.(ABSTRACT TRUNCATED AT 250 WORDS)

Agammaglobulinemia↗

Linkage of Wiskott-Aldrich syndrome with three marker loci, DXS426, SYP and TFE3, which map to the Xp11.3-p11.22 region.

Linkage analysis was performed in 19 families segregating for the Wiskott-Aldrich syndrome (WAS) and in 1 family with X-linked thrombocytopenia using nine polymorphic DNA markers spanning the interval DXS7-DXS14. The results confirm close linkage of WAS to the DXS7, TIMP, OATL1, DXS255, DXS146, and DXS14 loci and reveal three additional marker loci, DXS426, SYP, and TFE3, to be closely linked to WAS. The linkage data are also consistent with the localization of X-linked thrombocytopenia to the same chromosomal region as WAS and support localization of the WAS gene between the TIMP and DXS146 loci. However, the data were insufficient for positioning these disease genes with respect to the four marker loci that map within this latter interval. Analysis of recombination events between the marker loci place the TFE3 gene distal to DXS255 and favor the marker loci order Xpter-DXS7-(DXS426, TIMP)-(OATL1, SYP, TFE3)-DXS255-DXS146-DXS14.

Base Sequence↗

X-linked Charcot-Marie-Tooth disease. A linkage study in a large family by using 12 probes of the pericentromeric region.

Linkage analysis was performed on 41 subjects belonging to a large family with a recurrence of X-linked Charcot-Marie-Tooth disease (CMTX), by using 12 restriction fragment length polymorphism markers mapping in p11-q13. The results are in agreement with previous linkage data. Three new markers that are potentially useful for genetic analysis of CMTX families are described. A more precise estimate of the localization of the disease locus was attempted by multipoint linkage analysis.

Blotting, Southern↗

Dependence of linkage of alleles on their physical distance in natural transformation of Acinetobacter sp. strain ADP1.

The interdependence of genetic linkage in transformation and physical distance was studied in the bacterium Acinetobacter sp. strain ADP1. Transformation experiments were performed using 17 strains containing different mutations within the 21-kb pca-qui-pob gene cluster as recipients for the DNA of one of two strains carrying a mutation causing a temperature-sensitive phenotype. The different phenotypes of the transformants (temperature-sensitive or wild-type-like) were used to evaluate linkage. Combination of the recipient and donor strains resulted in physical distances ranging from 2 bp to 10,533 bp. A logarithmic relationship of decreasing linkage and increasing distance was observed, thus leading to calibration of a system for analysis of physical distance derived from linkage data. Limitations of this application are described here: Certain mutations (3 out of 17 mutations used in this study) are an exception to the observed relationship and result in much lower linkage than expected. Observed DNA sequence repetitions leading to DNA rearrangements may be the cause of this anomaly.

Acinetobacter↗