Linkage Analysis Using High-Density SNP Panels
Author Information
Author(s): Murray Sarah Shaw, Joan E Bailey-Wilson, Laura Almasy, Mariza de Andrade, Julia Bailey, Heike Bickeböller, Heather J Cordell, E Warwick Daw, Lynn Goldin, Ellen L Goode, Courtney Gray-McGuire, Wayne Hening, Gail Jarvik, Brion S Maher, Nancy Mendell, Andrew D Paterson, John Rice, Glen Satten, Brian Suarez, Veronica Vieland, Marsha Wilcox, Heping Zhang, Andreas Ziegler, Jean W MacCluer
Primary Institution: Illumina, Inc.
Hypothesis
Does linkage disequilibrium (LD) between SNPs affect non-parametric multipoint linkage analysis?
Conclusion
The study suggests that LD between loci does not significantly affect the detection of linkage regions in a genome scan.
Supporting Evidence
- Genotype data from two high-density SNP panels were used for analysis.
- LD strength was evaluated using the expectation-maximization algorithm.
- Nine regions on six chromosomes were identified with significant linkage scores.
Takeaway
The study looked at how closely related genetic markers are and found that it doesn't really change the results when looking for genetic links to alcoholism.
Methodology
Genotype data from two SNP panels were analyzed for linkage disequilibrium and linkage analysis using nonparametric methods.
Potential Biases
LD may artificially inflate or deflate LOD scores in linkage analysis.
Limitations
The potential bias in LOD score due to underlying LD is largest in pedigrees without genotypes for founding individuals.
Participant Demographics
The majority of participants were White, non-Hispanic (n = 1074), followed by Black, non-Hispanic (n = 191).
Statistical Information
P-Value
p < 0.01
Statistical Significance
p < 0.01
Digital Object Identifier (DOI)
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