Whole-genome scan, in a complex disease, using 11,245 single-nucleotide polymorphisms: comparison with microsatellites

Abstract

Despite the theoretical evidence of the utility of single-nucleotide polymorphisms (SNPs) for linkage analysis, no whole-genome scans of a complex disease have yet been published to directly compare SNPs with microsatellites. Here, we describe a whole-genome screen of 157 families with multiple cases of rheumatoid arthritis (RA), performed using 11,245 genomewide SNPs. The results were compared with those from a 10-cM microsatellite scan in the same cohort. The SNP analysis detected HLA*DRB1, the major RA susceptibility locus (P=.00004), with a linkage interval of 31 cM, compared with a 50-cM linkage interval detected by the microsatellite scan. In addition, four loci were detected at a nominal significance level (P<.05) in the SNP linkage analysis; these were not observed in the microsatellite scan. We demonstrate that variation in information content was the main factor contributing to observed differences in the two scans, with the SNPs providing significantly higher information content than the microsatellites. Reducing the number of SNPs in the marker set to 3,300 (1-cM spacing) caused several loci to drop below nominal significance levels, suggesting that decreases in information content can have significant effects on linkage results. In contrast, differences in maps employed in the analysis, the low detectable rate of genotyping error, and the presence of moderate linkage disequilibrium between markers did not significantly affect the results. We have demonstrated the utility of a dense SNP map for performing linkage analysis in a late-age-at-onset disease, where DNA from parents is not always available. The high SNP density allows loci to be defined more precisely and provides a partial scaffold for association studies, substantially reducing the resource requirement for gene-mapping studies.

Figure A

Multipoint NPL scores for SNPs (green) and microsatellites (orange) for all 23 chromosomes.

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.

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).

Figure B

Comparison of multipoint NPL scores for SNPs, using NCBI genome builds 31 (orange) and 33 (green).

Figure C

Comparison of multipoint NPL scores for SNPs, using the deCODE (green) and Marshfield (orange) genetic maps for interpolation of SNP marker positions.

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.

Figure D

Multipoint entropy plots for SNPs (green) versus microsatellites (orange), as calculated using Merlin.

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.

Figure E

Changes in multipoint NPL scores for all SNPs (green) and the removal of all but one SNP in LD (orange).

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.