Gonçalo R. Abecasis, Janis E. Wigginton

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Presentation transcript:

Handling Marker-Marker Linkage Disequilibrium: Pedigree Analysis with Clustered Markers Gonçalo R. Abecasis, Janis E. Wigginton The American Journal of Human Genetics Volume 77, Issue 5, Pages 754-767 (November 2005) DOI: 10.1086/497345 Copyright © 2005 The American Society of Human Genetics Terms and Conditions

Figure 1 Schematic representation of the standard Lander-Green algorithm. The American Journal of Human Genetics 2005 77, 754-767DOI: (10.1086/497345) Copyright © 2005 The American Society of Human Genetics Terms and Conditions

Figure 2 Schematic representation of the Lander-Green algorithm, with clustering of neighboring markers. The American Journal of Human Genetics 2005 77, 754-767DOI: (10.1086/497345) Copyright © 2005 The American Society of Human Genetics Terms and Conditions

Figure 3 Founder allele graphs used to identify possible haplotype states for a pedigree. A, Summary of the observed genotype data for two markers. B, Possible inheritance vector or genetic descent graph. Genotyped alleles are shown in gray, and the connections they induce between founder alleles are denoted with dashed lines. C, Representation of the founder allele graph corresponding to panels A and B. D, Possible haplotype states, calculated as the Cartesian product of possible states for each founder allele graph component. The American Journal of Human Genetics 2005 77, 754-767DOI: (10.1086/497345) Copyright © 2005 The American Society of Human Genetics Terms and Conditions

Figure 4 Analysis of affected sibship data with one parent genotyped, with and without the modeling of LD. This simulated data set included 500 sibships, each with three affected siblings and one genotyped parent. The American Journal of Human Genetics 2005 77, 754-767DOI: (10.1086/497345) Copyright © 2005 The American Society of Human Genetics Terms and Conditions

Figure 5 Analysis of exemplary psoriasis data set The American Journal of Human Genetics 2005 77, 754-767DOI: (10.1086/497345) Copyright © 2005 The American Society of Human Genetics Terms and Conditions