ArticleBMC genetics2005
Microsatellites versus single-nucleotide polymorphisms in linkage analysis for quantitative and qualitative measures.
Article in BMC genetics, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- ACN9 and alcohol dependence: family-based association analysis in multiplex alcohol dependence families.American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics · 2015Article
- Risk of nasopharyngeal carcinoma associated with polymorphic lactotransferrin haplotypes.Medical oncology (Northwood, London, England) · 2012Article
- Multi-species data integration and gene ranking enrich significant results in an alcoholism genome-wide association study.BMC genomics · 2012Article
- Linkage analyses of cannabis dependence, craving, and withdrawal in the San Francisco family study.American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics · 2010Article
- Molecular genetics of alcohol dependence and related endophenotypes.Current genomics · 2008Article
- A Systematic single nucleotide polymorphism screen to fine-map alcohol dependence genes on chromosome 7 identifies association with a novel susceptibility gene ACN9.Biological psychiatry · 2008Article
- Genomewide linkage scan of 409 European-ancestry and African American families with schizophrenia: suggestive evidence of linkage at 8p23.3-p21.2 and 11p13.1-q14.1 in the combined sample.American journal of human genetics · 2006Article
- Multipoint identity-by-descent computations for single-point polymorphism and microsatellite maps.BMC genetics · 2005Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundGenetic maps based on single-nucleotide polymorphisms (SNP) are increasingly being used as an alternative to microsatellite maps. This study compares linkage results for both types of maps for a neurophysiology phenotype and for an alcohol dependence phenotype. Our analysis used two SNP maps on the Illumina and Affymetrix platforms. We also considered the effect of high linkage disequilibrium (LD) in regions near the linkage peaks by analysing a "sparse" SNP map obtained by dropping some markers in high LD with other markers in those regions.
resultsThe neurophysiology phenotype at the main linkage peak near 130 MB gave LOD scores of 2.76, 2.53, 3.22, and 2.68 for the microsatellite, Affymetrix, Illumina, and Illumina-sparse maps, respectively. The alcohol dependence phenotype at the main linkage peak near 101 MB gave LOD scores of 3.09, 3.69, 4.08, and 4.11 for the microsatellite, Affymetrix, Illumina, and Illumina-sparse maps, respectively.
conclusionThe linkage results were stronger overall for SNPs than for microsatellites for both phenotypes. However, LOD scores may be artificially elevated in regions of high LD. Our analysis indicates that appropriately thinning a SNP map in regions of high LD should give more accurate LOD scores. These results suggest that SNPs can be an efficient substitute for microsatellites for linkage analysis of both quantitative and qualitative phenotypes.
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