Robust genetic linkage analysis based on a score test of homogeneity: The weighted pairwise correlation statistic

Commenges, Daniel

doi:10.1002/gepi.1370110208

Cited by 71 publications

(77 citation statements)

References 17 publications

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“…Therefore, the identification of additional putative loci that could be involved in the control of intensity of infection by S. mansoni will require the use of nonparametric linkage methods which do not need to specify the major gene model. The weighted pairwise correlation method, 38,39 which is a nonparametric linkage method for general pedigrees, appears to be the method of choice for the Brazilian population studied here, and we could use a recent twolocus extension of this method 40 which will allow us to test for the presence of a second locus taking into account the 5q31-q33 locus. The role of these regions will also be assessed by replication studies performed in other populations.…”

Section: Discussionmentioning

confidence: 99%

Full results of the genome-wide scan which localises a locus controlling the intensity of infection by Schistosoma mansoni on chromosome 5q31–q33

et al. 1999

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Three hundred million individuals are at risk of infection by schistosomes, and thousands die each year of severe hepatic disease. Previous studies have shown that the intensity of infection by Schistosoma mansoni in a Brazilian population is controlled by a major gene, denoted as SM1. We report here the full results of a genome-wide search that was performed on this population to localise SM1. Two hundred and forty-six microsatellites were used for the primary map, and only one region in 5q31-q33 provided significant evidence of linkage. SM1 was subsequently mapped to this region, which contains several genes encoding cytokines or cytokine receptors which are involved in protection against schistosomes. Three additional regions, 1p22.2, 7q36 and 21q22-22-qter, yielded promising, although not significant, lod-score values. These regions contain candidate genes encoding cytokines or molecules relevant to anti-schistosome immunity.

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Section: Discussionmentioning

confidence: 99%

Full results of the genome-wide scan which localises a locus controlling the intensity of infection by Schistosoma mansoni on chromosome 5q31–q33

et al. 1999

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“…Other non-parametric methods, which take non-affected individuals into consideration (e.g. Blackwelder et al, 1985, Commenges, 1994, Green and Montasser, 1988 are bound to run into the same difficulty of siblings with different phenotypes who share the same markers around the trait locus.…”

Section: Discussionmentioning

confidence: 99%

Genetic Linkage Analysis in the Presence of Germline Mosaicism

Weissbrod¹,

Geiger²

2011

Statistical Applications in Genetics and Molecular Biology

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Germline mosaicism is a genetic condition in which some germ cells of an individual contain a mutation. This condition violates the assumptions underlying classic genetic analysis and may lead to failure of such analysis. In this work we extend the statistical model used for genetic linkage analysis in order to incorporate germline mosaicism. We develop a likelihood ratio test for detecting whether a genetic trait has been introduced into a pedigree by germline mosaicism. We analyze the statistical properties of this test and evaluate its performance via computer simulations. We demonstrate that genetic linkage analysis has high power to identify linkage in the presence of germline mosaicism when our extended model is used. We further use this extended model to provide solid statistical evidence that the MDN syndrome studied by Genzer-Nir et al. has been introduced by germline mosaicism.

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“…Zhu et al [1997] described several types of transformations based on regression models including nonparametric and parametric models. See also, for example, Commenges [1994], Dawson et al [1990], Blangero and Elston [1989], Elston and George [1989] and Elston [1973]. The approach developed here may be seen as extending the logistic and proportional hazards regression statistics so that they are not confounded by population admixture.…”

Section: Discussionmentioning

confidence: 99%

Association Tests for Traits with Variable Age at Onset

2000

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This paper is concerned with testing association between marker genotypes and traits with variable age at onset. Two methods are proposed, one which makes use of both age-at-ascertainment and age-at-onset information, and one which may be applied when only age-at-ascertainment information is available. (Here, by age-at-ascertainment, is meant the subject’s age when presence of onset and age at onset are determined; for subjects who have died or are otherwise censored before ascertainment, the censoring time should be used instead). Adjustment for confounding due to population stratification is carried out by conditioning on observed traits and parental genotypes, or, if complete parental genotypes are not available, by conditioning on observed traits and the minimal sufficient statistics under the null hypothesis for the parental genotypes. Proportional hazards regression models and logistic regression models are used to motivate the methods, but correct type I error rates result even if the models are not correct. An illustrative example is described.

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Robust genetic linkage analysis based on a score test of homogeneity: The weighted pairwise correlation statistic

Cited by 71 publications

References 17 publications

Full results of the genome-wide scan which localises a locus controlling the intensity of infection by Schistosoma mansoni on chromosome 5q31–q33

Full results of the genome-wide scan which localises a locus controlling the intensity of infection by Schistosoma mansoni on chromosome 5q31–q33

Genetic Linkage Analysis in the Presence of Germline Mosaicism

Association Tests for Traits with Variable Age at Onset

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