Linkage disequilibrium and linkage analysis of the glucose-6-phosphatase gene

1998 ◽  
Vol 103 (2) ◽  
pp. 199-203 ◽  
Author(s):  
L.-J. C. Wong ◽  
Min-Hui Liang ◽  
Wuh-Liang Hwu ◽  
Ching-Wan Lam
Keyword(s):  
Linkage Disequilibrium ◽  
Linkage Analysis

Joint Linkage and Linkage Disequilibrium Mapping of Quantitative Trait Loci in Natural Populations

Genetics ◽  
2002 ◽  
Vol 160 (2) ◽  
pp. 779-792 ◽  
Author(s):  
Rongling Wu ◽  
Chang-Xing Ma ◽  
George Casella
Keyword(s):  
Linkage Disequilibrium ◽  
Quantitative Trait Loci ◽  
Linkage Analysis ◽  
Quantitative Trait ◽  
Genome Mapping ◽  
Linkage Disequilibrium Mapping ◽  
Allelic Association ◽  
Mapping Strategy ◽  
Trait Loci ◽  
New Strategy

AbstractLinkage analysis and allelic association (also referred to as linkage disequilibrium) studies are two major approaches for mapping genes that control simple or complex traits in plants, animals, and humans. But these two approaches have limited utility when used alone, because they use only part of the information that is available for a mapping population. More recently, a new mapping strategy has been designed to integrate the advantages of linkage analysis and linkage disequilibrium analysis for genome mapping in outcrossing populations. The new strategy makes use of a random sample from a panmictic population and the open-pollinated progeny of the sample. In this article, we extend the new strategy to map quantitative trait loci (QTL), using molecular markers within the EM-implemented maximum-likelihood framework. The most significant advantage of this extension is that both linkage and linkage disequilibrium between a marker and QTL can be estimated simultaneously, thus increasing the efficiency and effectiveness of genome mapping for recalcitrant outcrossing species. Simulation studies are performed to test the statistical properties of the MLEs of genetic and genomic parameters including QTL allele frequency, QTL effects, QTL position, and the linkage disequilibrium of the QTL and a marker. The potential utility of our mapping strategy is discussed.

scholarly journals Examining the effect of linkage disequilibrium on multipoint linkage analysis

BMC Genetics ◽  
2005 ◽  
Vol 6 (Suppl 1) ◽  
pp. S83 ◽  
Author(s):  
Qiqing Huang ◽  
Sanjay Shete ◽  
Michael Swartz ◽  
Christopher I Amos
Keyword(s):  
Linkage Disequilibrium ◽  
Linkage Analysis ◽  
Multipoint Linkage Analysis ◽  
Multipoint Linkage

scholarly journals Human P2X7 Pore Function Predicts Allele Linkage Disequilibrium

2006 ◽  
Vol 52 (6) ◽  
pp. 995-1004 ◽  
Author(s):  
Loren C Denlinger ◽  
Douglas B Coursin ◽  
Kathleen Schell ◽  
Giuditta Angelini ◽  
Dawn N Green ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Linkage Analysis ◽  
Whole Blood ◽  
Interleukin 10 ◽  
Genomic Variation ◽  
Loss Of Function ◽  
Roc Curve Analysis ◽  
Activity Data ◽  
Diagnostic Threshold ◽  
Sequence Variations

Abstract Background: Innate immune response amplification is achieved by leukocyte expression of the purinergic nucleotide receptor P2X7, an extracellular nucleotide-gated pore. Previously, low P2X7 pore activity in whole blood was associated with loss-of-function genotypes in correlation with a decreased ratio of lipopolysaccharide-stimulated tumor necrosis factor-α to interleukin-10, of relevance to a variety of infectious and inflammatory disorders. We hypothesized that evaluation of participants with discordance between the P2X7 genotype and pore status would disclose additional alleles, linkage disequilibrium, and novel functional correlates of genotype to phenotype. Methods: Comparison of whole-blood pore results with restriction fragment length polymorphism data for known loss-of-function genotypes from 200 healthy participants optimized the diagnostic threshold for low pore activity by ROC curve analysis. We identified novel alleles and inferred haplotypes by sequencing outlier genomic templates and by linkage analysis. Results: With a refined threshold of low activity, a normal pore result had only a 2% probability of association with known loss-of-function variants. By contrast, the positive predictive value of low pore activity was 59% for identifying known alleles. DNA samples from this discordant group contained 28 P2X7 sequence variations. Linkage analysis demonstrated that A1513C, T1729A, and G946A are inherited independently from one another, although these loss-of-function variants are in disequilibrium with other alleles. When we segregated pore activity data according to genotypes, nonsynonymous sequence variations (G474A and A1405G) appeared to exhibit modulatory effects on P2X7 pore activity. Conclusions: Direct analysis of pore activity demonstrates functional interactions between P2X7 alleles. The performance characteristics of the whole-blood pore assay enables correlation of genomic variation with concomitant investigation of functional performance in clinical studies.

Identification of Susceptibility Genes for Tuberculosis in Southern and West Africans Using Family-Based Linkage Analysis and Linkage Disequilibrium Mapping

2003 ◽  
Vol 104 (s49) ◽  
pp. 56P-56P
Author(s):  
Graham Cooke ◽  
Sarah Campbell ◽  
Richard Bellamy ◽  
Christian Lienhardt ◽  
Oumou Sow ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Linkage Analysis ◽  
Susceptibility Genes ◽  
Linkage Disequilibrium Mapping ◽  
West Africans ◽  
Family Based
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