title: 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.
authors.affiliation: University of Manchester, Manchester, United Kingdom.
authors.forename: Sally
authors.initials: S
authors.lastname: John
authors.forename: Neil
authors.initials: N
authors.lastname: Shephard
authors.forename: Guoying
authors.initials: G
authors.lastname: Liu
authors.forename: Eleftheria
authors.initials: E
authors.lastname: Zeggini
authors.forename: Manqiu
authors.initials: M
authors.lastname: Cao
authors.forename: Wenwei
authors.initials: W
authors.lastname: Chen
authors.forename: Nisha
authors.initials: N
authors.lastname: Vasavda
authors.forename: Tracy
authors.initials: T
authors.lastname: Mills
authors.forename: Anne
authors.initials: A
authors.lastname: Barton
authors.forename: Anne
authors.initials: A
authors.lastname: Hinks
authors.forename: Steve
authors.initials: S
authors.lastname: Eyre
authors.forename: Keith W
authors.initials: KW
authors.lastname: Jones
authors.forename: William
authors.initials: W
authors.lastname: Ollier
authors.forename: Alan
authors.initials: A
authors.lastname: Silman
authors.forename: Neil
authors.initials: N
authors.lastname: Gibson
authors.forename: Jane
authors.initials: J
authors.lastname: Worthington
authors.forename: Giulia C
authors.initials: GC
authors.lastname: Kennedy
mesh_terms: D001172:Arthritis, Rheumatoid / Q000235:genetics*; D002874:Chromosome Mapping; D015331:Cohort Studies; D004247:DNA / Q000235:genetics; D005190:Family; D005260:Female; D008040:Genetic Linkage; D020022:Genetic Predisposition to Disease / Q000235:genetics*; D015894:Genome, Human; D005838:Genotype; D006801:Humans; D008285:Major Histocompatibility Complex / Q000235:genetics; D008297:Male; D018895:Microsatellite Repeats / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*
chemical_list: D004247:DNA