Identifying SNPs Linked to Rheumatoid Arthritis on Chromosome 6
Author Information
Author(s): Lin Wan-Yu, Schaid Daniel J
Primary Institution: National Taiwan University
Hypothesis
Can joint modeling of linkage and association help identify SNPs responsible for the linkage signal of rheumatoid arthritis?
Conclusion
The study found that adding unrelated controls significantly increased the LOD scores for association tests in the presence of linkage.
Supporting Evidence
- The LOD score for association in the presence of linkage increased significantly with the addition of unrelated controls.
- Choosing a sufficient number of flanking markers is critical to distinguish between perfect and incomplete linkage disequilibrium.
- Results were consistent across 100 simulated replicates.
Takeaway
The researchers looked at how to find genes that cause rheumatoid arthritis by using data from families and unrelated people, and they discovered that including unrelated people helps find these genes better.
Methodology
The study used simulated rheumatoid arthritis data and analyzed it with the LAMP software, comparing results from affected sib pairs and unrelated controls.
Potential Biases
The computational intensity of the LAMP method may introduce bias in results.
Limitations
The assumption of linkage equilibrium between the candidate SNP and the flanking markers may not hold with high-density SNP data.
Participant Demographics
1500 families with one affected sib pair and 2000 unrelated controls.
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