Microsatellites versus single-nucleotide polymorphisms in linkage analysis for quantitative and qualitative measures.
- Authors
- Dunn, Gerald; Hinrichs, Anthony L; Bertelsen, Sarah; Jin, Carol H; Kauwe, John S K; Suarez, Brian K; Bierut, Laura J
- Year
- 2005
- Journal
- BMC genetics
- PMID
- 16451580
- DOI
- 10.1186/1471-2156-6-S1-S122
- PMCID
- PMC1866815
BACKGROUND: Genetic 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. RESULTS: The 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. CONCLUSION: The 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.
No figures extracted from this document.
No entities extracted from this document yet.
No uploaded files.
In this knowledge base
External
| Title | Authors | Journal | Year | Link |
|---|---|---|---|---|
| ACN9 and alcohol dependence: family-based association analysis in multiplex alcohol dependence families. | Hill SY et al. | — | 2015 | → |
| Multi-species data integration and gene ranking enrich significant results in an alcoholism genome-wide association study. | Zhao Z et al. | — | 2012 | → |
| Risk of nasopharyngeal carcinoma associated with polymorphic lactotransferrin haplotypes. | Zhou Y et al. | — | 2012 | → |
| The relationship of haplotype in lactotransferrin and its expression levels in Chinese Han ovarian cancer. | Cao L et al. | — | 2011 | → |
| Linkage analyses of cannabis dependence, craving, and withdrawal in the San Francisco family study. | Ehlers CL et al. | — | 2010 | → |
| A genomic imprinting test for ordinal traits in pedigree data. | Feng R et al. | — | 2008 | → |
| A Systematic single nucleotide polymorphism screen to fine-map alcohol dependence genes on chromosome 7 identifies association with a novel susceptibility gene ACN9. | Dick DM et al. | — | 2008 | → |
| Molecular genetics of alcohol dependence and related endophenotypes. | Strat YL et al. | — | 2008 | → |
| 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. | Suarez BK et al. | — | 2006 | → |
| Alcoholism and related traits: a summary of Group 13 contributions. | Rice JP et al. | — | 2005 | → |
| Multipoint identity-by-descent computations for single-point polymorphism and microsatellite maps. | Hinrichs AL et al. | — | 2005 | → |