On computation of p-values in parametric linkage analysis
(2004) In Human Heredity 57(4). p.207-219- Abstract
- Parametric linkage analysis is usually used to find chromosomal regions linked to a disease (phenotype) that is described with a specific genetic model. This is done by investigating the relations between the disease and genetic markers, that is, well-characterized loci of known position with a clear Mendelian mode of inheritance. Assume we have found an interesting region on a chromosome that we suspect is linked to the disease. Then we want to test the hypothesis of no linkage versus the alternative one of linkage. As a measure we use the maximal lod score Z(max). It is well known that the maximal lod score has asymptotically a (2 ln 10)(-1) x (1/2 chi(2)(0) + 1/2 chi(2)(1)) distribution under the null hypothesis of no linkage when only... (More)
- Parametric linkage analysis is usually used to find chromosomal regions linked to a disease (phenotype) that is described with a specific genetic model. This is done by investigating the relations between the disease and genetic markers, that is, well-characterized loci of known position with a clear Mendelian mode of inheritance. Assume we have found an interesting region on a chromosome that we suspect is linked to the disease. Then we want to test the hypothesis of no linkage versus the alternative one of linkage. As a measure we use the maximal lod score Z(max). It is well known that the maximal lod score has asymptotically a (2 ln 10)(-1) x (1/2 chi(2)(0) + 1/2 chi(2)(1)) distribution under the null hypothesis of no linkage when only one point ( one marker) on the chromosome is studied. In this paper, we show, both by simulations and theoretical arguments, that the null hypothesis distribution of Z(max) has no simple form when more than one marker is used ( multipoint analysis). In fact, the distribution of Z(max) depends on the number of families, their structure, the assumed genetic model, marker denseness, and marker informativity. This means that a constant critical limit of Z(max) leads to tests associated with different significance levels. Because of the above-mentioned problems, from the statistical point of view the maximal lod score should be supplemented by a p-value when results are reported. Copyright (C) 2004 S. Karger AG, Basel. (Less)
Please use this url to cite or link to this publication:
https://lup.lub.lu.se/record/257974
- author
- Kurbasic, Azra LU and Hossjer, O
- organization
- publishing date
- 2004
- type
- Contribution to journal
- publication status
- published
- subject
- keywords
- pointwise/genomewide p-value, linkage analysis, lod score distribution
- in
- Human Heredity
- volume
- 57
- issue
- 4
- pages
- 207 - 219
- publisher
- Karger
- external identifiers
-
- wos:000226013000006
- pmid:15583427
- scopus:10844237959
- ISSN
- 1423-0062
- DOI
- 10.1159/000081448
- language
- English
- LU publication?
- yes
- id
- 00ac8464-50ab-498f-b3d6-33a3a6260f44 (old id 257974)
- date added to LUP
- 2016-04-01 11:59:16
- date last changed
- 2022-01-26 21:11:43
@article{00ac8464-50ab-498f-b3d6-33a3a6260f44,
abstract = {{Parametric linkage analysis is usually used to find chromosomal regions linked to a disease (phenotype) that is described with a specific genetic model. This is done by investigating the relations between the disease and genetic markers, that is, well-characterized loci of known position with a clear Mendelian mode of inheritance. Assume we have found an interesting region on a chromosome that we suspect is linked to the disease. Then we want to test the hypothesis of no linkage versus the alternative one of linkage. As a measure we use the maximal lod score Z(max). It is well known that the maximal lod score has asymptotically a (2 ln 10)(-1) x (1/2 chi(2)(0) + 1/2 chi(2)(1)) distribution under the null hypothesis of no linkage when only one point ( one marker) on the chromosome is studied. In this paper, we show, both by simulations and theoretical arguments, that the null hypothesis distribution of Z(max) has no simple form when more than one marker is used ( multipoint analysis). In fact, the distribution of Z(max) depends on the number of families, their structure, the assumed genetic model, marker denseness, and marker informativity. This means that a constant critical limit of Z(max) leads to tests associated with different significance levels. Because of the above-mentioned problems, from the statistical point of view the maximal lod score should be supplemented by a p-value when results are reported. Copyright (C) 2004 S. Karger AG, Basel.}},
author = {{Kurbasic, Azra and Hossjer, O}},
issn = {{1423-0062}},
keywords = {{pointwise/genomewide p-value; linkage analysis; lod score distribution}},
language = {{eng}},
number = {{4}},
pages = {{207--219}},
publisher = {{Karger}},
series = {{Human Heredity}},
title = {{On computation of p-values in parametric linkage analysis}},
url = {{http://dx.doi.org/10.1159/000081448}},
doi = {{10.1159/000081448}},
volume = {{57}},
year = {{2004}},
}