publication . Article . Other literature type . 2009

The effect of minor allele frequency on the likelihood of obtaining false positives

Tabangin, Meredith E; Woo, Jessica G; Martin, Lisa J;
Open Access English
  • Published: 01 Dec 2009 Journal: BMC Proceedings, volume 3, issue Suppl 7, page S41 (issn: 1753-6561, Copyright policy)
  • Publisher: Springer Nature
Abstract
<p>Abstract</p> <p>Determining the most promising single-nucleotide polymorphisms (SNPs) presents a challenge in genome-wide association studies, when hundreds of thousands of association tests are conducted. The power to detect genetic effects is dependent on minor allele frequency (MAF), and genome-wide association studies SNP arrays include SNPs with a wide distribution of MAFs. Therefore, it is critical to understand MAF's effect on the false positive rate.</p> <p>Data from the Framingham Heart Study simulated data (Problem 3, with answers) was used to examine the effects of varying MAFs on the likelihood of false positives. Replication set 1 was used to gen...
Subjects
free text keywords: General Biochemistry, Genetics and Molecular Biology, General Medicine, SNP, Genetic association, Bioinformatics, Text mining, business.industry, business, Minor allele frequency, Medicine, Single-nucleotide polymorphism, False positive rate, False positive paradox, Genetics, Association tests, R, Science, Q, Proceedings
Related Organizations
Funded by
NIH| Genetic Analysis of Common Diseases: An Evaluation
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01GM031575-22
  • Funding stream: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES

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