Programs for pedigree analysis: Mendel, Fisher, and dGene

Lange, Kenneth; Weeks, Daniel E.; Boehnke, Michael; MacCluer, Jean W.

doi:10.1002/gepi.1370050611

Cited by 558 publications

(369 citation statements)

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“…The analysis was conducted by using a multivariate normal model for pedigree analysis as described by Lange et al 35,36 with the software FISHER, which also performed tests of goodness of fit of the underlying multinormal distribution. The general models assumed that the studied trait was the result of the sum of three independent random components: a polygenic component (G) representing additive genetic factors, household factors common to individuals within a family (H) and unmeasured environmental factors particular to an individual (including measurement error) (E) with the hypothesis of equality of their effect in the four groups of relatives.…”

Section: Discussionmentioning

confidence: 99%

Heritability of serum hs-CRP concentration and 5-year changes in the Stanislas family study: association with apolipoprotein E alleles

et al. 2007

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We aimed at estimating additive genetic heritability, household component effect and the influence of common alleles of the apolipoprotein E gene (APOE) on serum high-sensitivity C-reactive protein (hs-CRP) concentrations and the subsequent changes over 5 years. A sub-sample of 320 nuclear families was randomly selected from the Stanislas Family Study. Serum hs-CRP concentration was measured by immunonephelometry at entrance and after 5 years. APOE alleles were determined by restriction fragment length polymorphism. After adjustment for covariates, the number of the e4 allele was negatively associated with serum concentration of hs-CRP in the whole sample, at entrance and 5 years later, without significant interaction with sex by generation groups (P ¼ 0.003 and P ¼ 0.0003, respectively). However, no significant association was found between e4 allele and 5-year changes in hs-CRP concentration. Using a variance component analysis, no significant genetic influence was shown in family aggregation of both hs-CRP measurements and 5-year changes; the household common component was between 6.5 and 12.8%. In addition, after adjustment for APOE gene polymorphisms, degrees of resemblance were almost unchanged. In the Stanislas Family Study, e4 allele of the APOE gene was associated with lower hs-CRP concentration, but not with 5-year changes. However, variance component analysis did not evidence a significant polygenic effect.

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Section: Discussionmentioning

confidence: 99%

Heritability of serum hs-CRP concentration and 5-year changes in the Stanislas family study: association with apolipoprotein E alleles

et al. 2007

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“…For the evaluation of specific familial correlations, maximum likelihood techniques, as implemented in FISHER (Lange et al 1988), were used to choose the estimate of the correlation coefficient that provided the greatest likelihood of observing the data. This approach used the complete pedigree information and allowed for the simultaneous estimation of covariate effects.…”

Section: Population Materials and Methodsmentioning

confidence: 99%

Genetic epidemiology of fecal egg excretion during Schistosoma mansoni infection in an endemic area in Minas Gerais, Brazil

Bethony

Gazzinelli

Lopes

et al. 2001

Mem. Inst. Oswaldo Cruz

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“…93 Linkage analysis Pairwise LOD scores (H-LODs) were calculated under the assumption of heterogeneity using the program MENDEL. 96 The parameters used have been published, 34 and we have kept these parameters constant for all work to date except where noted. We have made no attempts to increase the significance of the findings by using additional programs or by varying the parameters or conditions of the analy- …”

Section: Genotyping and Error Checkingmentioning

confidence: 99%

Genome-wide scans of three independent sets of 90 Irish multiplex schizophrenia families and follow-up of selected regions in all families provides evidence for multiple susceptibility genes

et al. 2002

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From our linkage study of Irish families with a high density of schizophrenia, we have previously reported evidence for susceptibility genes in regions 5q21-31, 6p24-21, 8p22-21, and 10p15-p11. In this report, we describe the cumulative results from independent genome scans of three a priori random subsets of 90 families each, and from multipoint analysis of all 270 families in ten regions. Of these ten regions, three (13q32, 18p11-q11, and 18q22-23) did not generate scores above the empirical baseline pairwise scan results, and one (6q13-26) generated a weak signal. Six other regions produced more positive pairwise and multipoint results. They showed the following maximum multipoint H-LOD (heterogeneity LOD) and NPL scores: 2p14-13: 0.89 (P = 0.06) and 2.08 (P = 0.02), 4q24-32: 1.84 (P = 0.007) and 1.67 (P = 0.03), 5q21-31: 2.88 (P = 0.0007), and 2.65 (P = 0.002), 6p25-24: 2.13 (P = 0.005) and 3.59 (P = 0.0005), 6p23: 2.42 (P = 0.001) and 3.07 (P = 0.001), 8p22-21: 1.57 (P = 0.01) and 2.56 (P = 0.005), 10p15-11: 2.04 (P = 0.005) and 1.78 (P = 0.03). The degree of 'internal replication' across subsets differed, with 5q, 6p, and 8p being most consistent and 2p and 10p being least consistent. On 6p, the data suggested the presence of two susceptibility genes, in 6p25-24 and 6p23-22. Very few families were positive on more than one region, and little correlation between regions was evident, suggesting substantial locus heterogeneity. The levels of statistical significance were modest, as expected from loci contributing to complex traits. However, our internal replications, when considered along with the positive results obtained in multiple other samples, suggests that most of these six regions are likely to contain genes that influence liability to schizophrenia.

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Programs for pedigree analysis: Mendel, Fisher, and dGene

Cited by 558 publications

References 0 publications

Heritability of serum hs-CRP concentration and 5-year changes in the Stanislas family study: association with apolipoprotein E alleles

Heritability of serum hs-CRP concentration and 5-year changes in the Stanislas family study: association with apolipoprotein E alleles

Genetic epidemiology of fecal egg excretion during Schistosoma mansoni infection in an endemic area in Minas Gerais, Brazil

Genome-wide scans of three independent sets of 90 Irish multiplex schizophrenia families and follow-up of selected regions in all families provides evidence for multiple susceptibility genes

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