scholarly journals Evaluation of a Fine-mapping Method Exploiting Linkage Disequilibrium in Livestock Populations: Simulation Study

2006 ◽  
Vol 19 (12) ◽  
pp. 1702-1705 ◽  
Author(s):  
JongJoo Kim ◽  
Frederic Farnir
Keyword(s):  
Linkage Disequilibrium ◽  
Fine Mapping ◽  
Simulation Study ◽  
Mapping Method

scholarly journals Linkage disequilibrium fine mapping of quantitative trait loci: A simulation study

2003 ◽  
Vol 35 (6) ◽  
Author(s):  
Jihad M Abdallah ◽  
Bruno Goffinet ◽  
Christine Cierco-Ayrolles ◽  
Miguel Pérez-Enciso
Keyword(s):  
Linkage Disequilibrium ◽  
Quantitative Trait Loci ◽  
Fine Mapping ◽  
Simulation Study ◽  
Quantitative Trait ◽  
Trait Loci

scholarly journals Multitrait Fine Mapping of Quantitative Trait Loci Using Combined Linkage Disequilibria and Linkage Analysis

Genetics ◽  
2003 ◽  
Vol 163 (1) ◽  
pp. 405-410 ◽  
Author(s):  
M S Lund ◽  
P Sørensen ◽  
B Guldbrandtsen ◽  
D A Sorensen
Keyword(s):  
Linkage Disequilibrium ◽  
Linkage Analysis ◽  
Fine Mapping ◽  
First Generation ◽  
Mapping Method ◽  
Linkage Disequilibria ◽  
Identical By Descent ◽  
Pleiotropic Qtl ◽  
Marker Information ◽  
Qtl Effects

Abstract A novel multitrait fine-mapping method is presented. The method is implemented by a model that treats QTL effects as random variables. The covariance matrix of allelic effects is proportional to the IBD matrix, where each element is the probability that a pair of alleles is identical by descent, given marker information and QTL position. These probabilities are calculated on the basis of similarities of marker haplotypes of individuals of the first generation of genotyped individuals, using “gene dropping” (linkage disequilibrium) and transmission of markers from genotyped parents to genotyped offspring (linkage). A small simulation study based on a granddaughter design was carried out to illustrate that the method provides accurate estimates of QTL position. Results from the simulation also indicate that it is possible to distinguish between a model postulating one pleiotropic QTL affecting two traits vs. one postulating two closely linked loci, each affecting one of the traits.

scholarly journals The Decay of Disease Association with Declining Linkage Disequilibrium: A Fine Mapping Theorem

2016 ◽  
Author(s):  
Mehdi Maadooliat ◽  
Naveen K. Bansal ◽  
Jiblal Upadhya ◽  
Manzur R. Farazi ◽  
Zhan Ye ◽  
...  
Keyword(s):  
Monte Carlo ◽  
Linkage Disequilibrium ◽  
Fine Mapping ◽  
Disease Model ◽  
Disease Association ◽  
Simple Relationship ◽  
Locus System ◽  
Using Data ◽  
Relationship Of ◽  
The Relationship

AbstractSeveral important and fundamental aspects of disease genetics models have yet to be described. One such property is the relationship of disease association statistics at a marker site closely linked to a disease causing site. A complete description of this two-locus system is of particular importance to experimental efforts to fine map association signals for complex diseases. Here, we present a simple relationship between disease association statistics and the decline of linkage disequilibrium from a causal site. A complete derivation of this relationship from a general disease model is shown for very large sample sizes. Quite interestingly, this relationship holds across all modes of inheritance. Extensive Monte Carlo simulations using a disease genetics model applied to chromosomes subjected to a standard model of recombination are employed to better understand the variation around this fine mapping theorem due to sampling effects. We also use this relationship to provide a framework for estimating properties of a non-interrogated causal site using data at closely linked markers. We anticipate that understanding the patterns of disease association decay with declining linkage disequilibrium from a causal site will enable more powerful fine mapping methods.

scholarly journals Comparing Linkage Disequilibrium-Based Methods for Fine Mapping Quantitative Trait Loci

Genetics ◽  
2004 ◽  
Vol 166 (3) ◽  
pp. 1561-1570 ◽  
Author(s):  
L. Grapes ◽  
J. C. M. Dekkers ◽  
M. F. Rothschild ◽  
R. L. Fernando
Keyword(s):  
Linkage Disequilibrium ◽  
Quantitative Trait Loci ◽  
Fine Mapping ◽  
Quantitative Trait ◽  
Trait Loci

Selection of Genes and Single Nucleotide Polymorphisms for Fine Mapping Starting From a Broad Linkage Region

2007 ◽  
Vol 10 (6) ◽  
pp. 871-885 ◽  
Author(s):  
An Windelinckx ◽  
Robert Vlietinck ◽  
Jeroen Aerssens ◽  
Gaston Beunen ◽  
Martine A. I. Thomis
Keyword(s):  
Linkage Disequilibrium ◽  
Candidate Gene ◽  
Candidate Genes ◽  
Fine Mapping ◽  
Complex Disease ◽  
Gene Selection ◽  
Candidate Gene Approach ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Selection Of

AbstractFine mapping of linkage peaks is one of the great challenges facing researchers who try to identify genes and genetic variants responsible for the variation in a certain trait or complex disease. Once the trait is linked to a certain chromosomal region, most studies use a candidate gene approach followed by a selection of polymorphisms within these genes, either based on their possibility to be functional, or based on the linkage disequilibrium between adjacent markers. For both candidate gene selection and SNP selection, several approaches have been described, and different software tools are available. However, mastering all these information sources and choosing between the different approaches can be difficult and time-consuming. Therefore, this article lists several of these in silico procedures, and the authors describe an empirical two-step fine mapping approach, in which candidate genes are prioritized using a bioinformatics approach (ENDEAVOUR), and the top genes are chosen for further SNP selection with a linkage disequilibrium based method (Tagger). The authors present the different actions that were applied within this approach on two previously identified linkage regions for muscle strength. This resulted in the selection of 331 polymorphisms located in 112 different candidate genes out of an initial set of 23,300 SNPs.

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