Sets of short tandem repeat polymorphisms for efficient linkage screening of the human genome

Dubovsky, Jan; Sheffield, Val C.; Duyk, Geoffrey M.; Weber, James L.

doi:10.1093/hmg/4.3.449

Cited by 75 publications

(49 citation statements)

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“…Genotypic data used were identical to those in previous reports (13,18). In brief, 503 autosomal microsatellite markers were typed in the laboratory of J. Weber at the Marshfield Medical Research Foundation (19). An additional 13 markers were typed at GlaxoWellcome.…”

Section: Methodsmentioning

confidence: 99%

Genome-Wide Linkage Analysis of Serum Adiponectin in the Pima Indian Population

et al. 2003

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Adiponectin is a circulating protein secreted by adipocytes and is thought to have insulin-sensitizing effects. We present genetic analysis of adiponectin levels in 517 Pima Indians without diabetes (from 162 families, 750 sib-pairs). Adiponectin concentrations were heritable, with 39% of the variance of age-and sex-adjusted adiponectin potentially accounted for by additive genetic influences in this population. In genome-wide linkage analyses, suggestive linkage (logarithm of odds [LOD] ‫؍‬ 3.0) of adiponectin adjusted for age and sex was found on chromosome 9p at 18 cM. Linkage was also present after inclusion of adiponectin concentrations of siblings with type 2 diabetes not treated pharmacologically (total siblings 582, 182 families, 860 sib-pairs: LOD ‫؍‬ 3.5). Tentative evidence of linkage was also found on chromosomes 2 (LOD ‫؍‬ 1.7 at 89 cM), 3 (LOD ‫؍‬ 1.9 at 124 cM), and 10 (LOD ‫؍‬ 1.7 at 70 cM), offering some support to findings of a previous genome-wide scan of adiponectin. Our data suggest that quantitative trait loci on chromosomes 2, 3, 9, and 10 may influence circulating adiponectin concentrations in the Pima population.

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Section: Methodsmentioning

confidence: 99%

Genome-Wide Linkage Analysis of Serum Adiponectin in the Pima Indian Population

et al. 2003

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“…Genome-wide linkage analysis. A total of 516 autosomal microsatellite markers were previously typed in a genome-wide linkage scan (14), of which 503 were typed in the laboratory of J. Weber at Marshfield Medical Research Foundation (20,21), and 13 were typed at Glaxo-Wellcome. For duplicate samples, the median rate of agreement was 97%, and no marker had an agreement rate Ͻ90%.…”

Section: Methodsmentioning

confidence: 99%

Genome-Wide Linkage Analyses to Identify Loci for Diabetic Retinopathy

et al. 2007

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Hyperglycemia and long duration of diabetes are widely recognized risk factors for diabetic retinopathy, but inherited susceptibility may also play a role because retinopathy aggregates in families. A genome-wide linkage analysis was conducted in 211 sibships in which >2 siblings had diabetes and retinal photographs were available from a longitudinal study. These sibships were a subset of 322 sibships who had participated in a previous linkage study of diabetes and related traits; they comprised 607 diabetic individuals in 725 sibpairs. Retinal photographs were graded for presence and severity of diabetic retinopathy according to a modification of the Airlie House classification system. The grade for the worse eye was adjusted for age, sex, and diabetes duration and analyzed as a quantitative trait. Heritability of diabetic retinopathy in this group was 18% (95% CI 2-36). A genome-wide linkage analysis using variance components modeling found evidence of linkage on chromosome 1p. Using single-point analysis, the peak logarithm of odds (LOD) was 3.1 for marker D1S3669 (34.2 cM), whereas with multipoint analysis the peak LOD was 2.58 at 35 cM. No other areas of suggestive linkage were found. We propose that an area on chromosome 1 may harbor a gene or genes conferring susceptibility to diabetic retinopathy.

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“…Methods for the genome-wide scan are described in Rioux et al 29 Briefly, a modified version of the Cooperative Human Linkage Centre (CHLC) Screening Set, version 6.0, 30 that also included Généthon markers 31 was used to create panels containing either 310 or 378 microsatellite markers with an average intermarker spacing of 11.1 and 8.7 cM, respectively, and average heterozygosity of approximately 75%. Fluorescently labeled markers (Research Genetics) were detected with ABI 377 and 3700 DNA analyzers.…”

Section: Study Cohortmentioning

confidence: 99%