Whole-Genome Scan, in a Complex Disease, Using 11,245 Single-Nucleotide Polymorphisms: Comparison with Microsatellites Sally John, Neil Shephard, Guoying.

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Presentation transcript:

Whole-Genome Scan, in a Complex Disease, Using 11,245 Single-Nucleotide Polymorphisms: Comparison with Microsatellites Sally John, Neil Shephard, Guoying Liu, Eleftheria Zeggini, Manqiu Cao, Wenwei Chen, Nisha Vasavda, Tracy Mills, Anne Barton, Anne Hinks, Steve Eyre, Keith W. Jones, William Ollier, Alan Silman, Neil Gibson, Jane Worthington, Giulia C. Kennedy The American Journal of Human Genetics Volume 75, Issue 1, Pages 54-64 (July 2004) DOI: 10.1086/422195 Copyright © 2004 The American Society of Human Genetics Terms and Conditions

Figure 1 Multipoint NPL scores on chromosome 6 for SNPs (solid line) and microsatellites (dashed line). HLA*DRB1 maps directly under the SNP maximum NPL score. Vertical lines indicate 1-LOD intervals. The lower panel indicates regions of LD defined by clusters of SNPs where all pairwise correlations were >0.4. The American Journal of Human Genetics 2004 75, 54-64DOI: (10.1086/422195) Copyright © 2004 The American Society of Human Genetics Terms and Conditions

Figure 2 Multipoint NPL scores for chromosomes 12, 13, 21, and X, demonstrating differences observed in allele sharing between SNPs (solid line) and microsatellites (dashed line). The American Journal of Human Genetics 2004 75, 54-64DOI: (10.1086/422195) Copyright © 2004 The American Society of Human Genetics Terms and Conditions

Figure 3 Entropy values calculated in Merlin for the whole cohort for SNPs (solid line) and microsatellites (dashed line) for chromosomes 6, 12, 13, 21, and X. The American Journal of Human Genetics 2004 75, 54-64DOI: (10.1086/422195) Copyright © 2004 The American Society of Human Genetics Terms and Conditions

Figure 4 Pairwise LD for 106 SNPs mapping to a 40-cM (35–75 cM) region on chromosome 6 under the peak of linkage at HLA*DRB1. Measures of r2 are shown in the upper triangle, and measures of D′ are shown in the lower triangle. The American Journal of Human Genetics 2004 75, 54-64DOI: (10.1086/422195) Copyright © 2004 The American Society of Human Genetics Terms and Conditions

Figure 5 Linkage and association in the HLA region. ♦ = single-point association; ▪ = haplotype association in region of LD. The lower panel indicates regions of LD defined by clusters of SNPs where all pairwise correlations were >0.4. The American Journal of Human Genetics 2004 75, 54-64DOI: (10.1086/422195) Copyright © 2004 The American Society of Human Genetics Terms and Conditions

Figure A Multipoint NPL scores for SNPs (green) and microsatellites (orange) for all 23 chromosomes. The American Journal of Human Genetics 2004 75, 54-64DOI: (10.1086/422195) Copyright © 2004 The American Society of Human Genetics Terms and Conditions

Figure B Comparison of multipoint NPL scores for SNPs, using NCBI genome builds 31 (orange) and 33 (green). The American Journal of Human Genetics 2004 75, 54-64DOI: (10.1086/422195) Copyright © 2004 The American Society of Human Genetics Terms and Conditions

Figure C Comparison of multipoint NPL scores for SNPs, using the deCODE (green) and Marshfield (orange) genetic maps for interpolation of SNP marker positions. The American Journal of Human Genetics 2004 75, 54-64DOI: (10.1086/422195) Copyright © 2004 The American Society of Human Genetics Terms and Conditions

Figure D Multipoint entropy plots for SNPs (green) versus microsatellites (orange), as calculated using Merlin. The American Journal of Human Genetics 2004 75, 54-64DOI: (10.1086/422195) Copyright © 2004 The American Society of Human Genetics Terms and Conditions

Figure E Changes in multipoint NPL scores for all SNPs (green) and the removal of all but one SNP in LD (orange). The American Journal of Human Genetics 2004 75, 54-64DOI: (10.1086/422195) Copyright © 2004 The American Society of Human Genetics Terms and Conditions