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A general method for linkage disequilibrium correction for multipoint linkage and association.

Kurbasic, Azra LU and Hössjer, Ola (2008) In Genetic Epidemiology 32(7). p.647-657
Abstract
Lately, many different methods of linkage, association or joint analysis for family data have been invented and refined. Common to most of those is that they require a map of markers that are in linkage equilibrium. However, at the present day, high-density single nucleotide polymorphisms (SNPs) maps are both more inexpensive to create and they have lower genotyping error. When marker data is incomplete, the crucial and computationally most demanding moment in the analysis is to calculate the inheritance distribution at a certain position on the chromosome. Recently, different ways of adjusting traditional methods of linkage analysis to denser maps of SNPs in linkage disequilibrium (LD) have been proposed. We describe a hidden Markov model... (More)
Lately, many different methods of linkage, association or joint analysis for family data have been invented and refined. Common to most of those is that they require a map of markers that are in linkage equilibrium. However, at the present day, high-density single nucleotide polymorphisms (SNPs) maps are both more inexpensive to create and they have lower genotyping error. When marker data is incomplete, the crucial and computationally most demanding moment in the analysis is to calculate the inheritance distribution at a certain position on the chromosome. Recently, different ways of adjusting traditional methods of linkage analysis to denser maps of SNPs in linkage disequilibrium (LD) have been proposed. We describe a hidden Markov model which generalizes the Lander-Green algorithm. It combines Markov chain for inheritance vectors with a Markov chain modelling founder haplotypes and in this way takes account for LD between SNPs. It can be applied to association, linkage or combined association and linkage analysis, general phenotypes and arbitrary score functions. We also define a joint likelihood for linkage and association that extends an idea of Kong and Cox (1997 Am. J. Hum. Genet. 61: 1179-1188) for pure linkage analysis. Genet. Epidemiol. 2008. (c) 2008 Wiley-Liss, Inc. (Less)
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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
hidden Markov model • linkage • association • linkage disequilibrium • SNPs
in
Genetic Epidemiology
volume
32
issue
7
pages
647 - 657
publisher
John Wiley & Sons
external identifiers
  • wos:000260871600007
  • pmid:18481794
  • scopus:58849166616
ISSN
0741-0395
DOI
10.1002/gepi.20339
language
English
LU publication?
yes
id
5aaa1ad6-bd79-4102-bbad-636144a2096a (old id 1154103)
date added to LUP
2009-05-06 14:15:41
date last changed
2017-05-14 03:37:59
@article{5aaa1ad6-bd79-4102-bbad-636144a2096a,
  abstract     = {Lately, many different methods of linkage, association or joint analysis for family data have been invented and refined. Common to most of those is that they require a map of markers that are in linkage equilibrium. However, at the present day, high-density single nucleotide polymorphisms (SNPs) maps are both more inexpensive to create and they have lower genotyping error. When marker data is incomplete, the crucial and computationally most demanding moment in the analysis is to calculate the inheritance distribution at a certain position on the chromosome. Recently, different ways of adjusting traditional methods of linkage analysis to denser maps of SNPs in linkage disequilibrium (LD) have been proposed. We describe a hidden Markov model which generalizes the Lander-Green algorithm. It combines Markov chain for inheritance vectors with a Markov chain modelling founder haplotypes and in this way takes account for LD between SNPs. It can be applied to association, linkage or combined association and linkage analysis, general phenotypes and arbitrary score functions. We also define a joint likelihood for linkage and association that extends an idea of Kong and Cox (1997 Am. J. Hum. Genet. 61: 1179-1188) for pure linkage analysis. Genet. Epidemiol. 2008. (c) 2008 Wiley-Liss, Inc.},
  author       = {Kurbasic, Azra and Hössjer, Ola},
  issn         = {0741-0395},
  keyword      = {hidden Markov model • linkage • association • linkage disequilibrium • SNPs},
  language     = {eng},
  number       = {7},
  pages        = {647--657},
  publisher    = {John Wiley & Sons},
  series       = {Genetic Epidemiology},
  title        = {A general method for linkage disequilibrium correction for multipoint linkage and association.},
  url          = {http://dx.doi.org/10.1002/gepi.20339},
  volume       = {32},
  year         = {2008},
}