ArticleAmerican journal of human genetics2004
Whole-genome scan, in a complex disease, using 11,245 single-nucleotide polymorphisms: comparison with microsatellites.
Article in American journal of human genetics, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 84 papers, 2 of them syntheses that pooled it.
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Who cites it
84 citing papers in PubMed, 2 syntheses or guidelines pooled it, 226 citations in OpenAlex.
- Meta-analysis of genome-wide linkage studies across autoimmune diseases.European journal of human genetics : EJHG · 2009Pooled it
- Genome-wide meta-analysis for rheumatoid arthritis.Human genetics · 2006Pooled it
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- High-Throughput Transcriptome Profiling in Drug and Biomarker Discovery.Frontiers in genetics · 2020Review
- MMP-2 gene polymorphisms are associated with type A aortic dissection and aortic diameters in patients.Medicine · 2016Observational
- The IL-33-ST2L pathway is associated with coronary artery disease in a Chinese Han population.American journal of human genetics · 2013Article
- Hunting human disease genes: lessons from the past, challenges for the future.Human genetics · 2013Review
- A genome-wide analysis of 'Bounty' descendants implicates several novel variants in migraine susceptibility.Neurogenetics · 2012Article
- Genome-wide linkage analysis of QTL for growth and body composition employing the PorcineSNP60 BeadChip.BMC genetics · 2012Article
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- A powerful approach for association analysis incorporating imprinting effects.Bioinformatics (Oxford, England) · 2011Article
- Integrated genomic analysis of sézary syndrome.Genetics research international · 2011Article
- Bayesian mixture models for the incorporation of prior knowledge to inform genetic association studies.Genetic epidemiology · 2010Article
- A comparison of SNPs and microsatellites as linkage mapping markers: lessons from the zebra finch (Taeniopygia guttata).BMC genomics · 2010Article
- Detection of parent-of-origin effects using general pedigree data.Genetic epidemiology · 2010Article
- Use of supplementary phenotype to identify additional rheumatoid arthritis loci in a linkage analysis of 342 UK affected sibling pair families.BMC medical genetics · 2009Article
- Genome wide high density SNP-based linkage analysis of childhood absence epilepsy identifies a susceptibility locus on chromosome 3p23-p14.Epilepsy research · 2009Article
- Finding common susceptibility variants for complex disease: past, present and future.Briefings in functional genomics & proteomics · 2009Review
- Article
24 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
17 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.