|
Deep Blue at the University of Michigan >
All Collections >
Interdisciplinary and Peer-Reviewed >
|
Please use this persistent URL to cite or link to this item:
|
| Title: | A coalescent simulation of marker selection strategy for candidate gene association studies Please cite this article as follows: Cole SM, Long JC. 2007. A Coalescent Simulation of Marker Selection Strategy for Candidate Gene Association Studies. Am J Med Genet Part B 147B:86–93. |
| Authors: | Cole, Suzanne M.
Long, Jeffrey C. |
| Issue Date: | 5-Jan-2008 |
| Publisher: | Wiley Subscription Services, Inc., A Wiley Company |
| Citation: | Cole, Suzanne M.; Long, Jeffrey C. (2008). "A coalescent simulation of marker selection strategy for candidate gene association studies Please cite this article as follows: Cole SM, Long JC. 2007. A Coalescent Simulation of Marker Selection Strategy for Candidate Gene Association Studies. Am J Med Genet Part B 147B:86–93. ." American Journal of Medical Genetics Part B: Neuropsychiatric Genetics 147B(1): 86-93. <http://hdl.handle.net/2027.42/57544> |
| Abstract: | Recent efforts have focused on the challenges of finding alleles that contribute to health-related phenotypes in genome-wide association studies. However, in candidate gene studies, where the genomic region of interest is small and recombination is limited, factors that affect the ability to detect disease-susceptibility alleles remain poorly understood. In particular, it is unclear how varying the number of markers on a haplotype, the type of marker (e.g., single nucleotide polymorphism (SNP), short tandem repeat (STR)), including the causative site ( cs ) as a genetic marker, or population demographics influences the power to detect a candidate gene. We evaluated the power of association tests using coalescent-modeled computer simulations. Results show that an effective number of markers on a haplotype is dependent on whether the cs is included as a marker. When the analyses include the cs , highest power is achieved with a single-marker association test. However, when the cs is excluded from analyses, the addition of more nonfunctional SNPs on the haplotype increases power to a certain point under most scenarios. We find a rapidly expanding population always has lower power compared to a population of constant size; although utilizing markers with a frequency of at least 5% improves the chance of detecting an association. Comparing the mutational properties of a nonfunctional SNP versus an STR, multi-allelic STRs provide more or comparable power than a bi-allelic SNP unless SNP frequencies are constrained to 10% or more. Similarly, including an STR with SNPs on a haplotype improves power unless SNP frequencies are 5% or more. © 2007 Wiley-Liss, Inc. |
| URI: | http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=retrieve&db
=pubmed&list_uids=17722024&dopt=citation |
| ISSN: | 1552-4841
1552-485X |
| DOI: | 10.1002/ajmg.b.30564 |
| PMID: | 17722024 |
| Appears in Collections: | Environmental Health Sciences, Department of (SPH)
Interdisciplinary and Peer-Reviewed
|
Files in This Item:
| File |
Description |
Size | Format | |
|---|
| 30564_ftp.pdf | | 552Kb | Adobe PDF | View/Open |
|
Deep Blue encourages the fair use of copyrighted material, and you are free to link to content here without asking for permission. Consult the document(s) and/or contact the copyright holder for additional rights questions and requests.
|
