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Human Molecular Genetics Advance Access published online on April 27, 2006
Human Molecular Genetics, doi:10.1093/hmg/ddl115
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© 2006 The Author(s). This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Received January 23, 2006
Revised April 25, 2006
Accepted April 25, 2006

Article

Direct detection of null alleles in SNP genotyping data

Christopher S. Carlson 1, Joshua D. Smith 1, Ian B. Stanaway 1, Mark J. Rieder 1, and Deborah A. Nickerson 1 *

1 Department of Genome Sciences, University of Washington, 1705 NE Pacific St., Seattle, WA 98195-7730

* To whom correspondence should be addressed.
Deborah A. Nickerson, E-mail: debnick{at}u.washington.edu


  Abstract

Pinpointing genetic associations in the human genome relies heavily on the accuracy of the underlying genotype data. Null alleles can generate significant inaccuracies in genotype data, and can negatively affect the statistical power of a study. Existing quality control (QC) tests, including tests of Hardy-Weinberg equilibrium, are not sensitive enough to detect the presence of even moderately frequent null alleles in the data. We show that direct analysis of raw data from a quantitative genotyping platform can detect up to 75% of null alleles, even at frequencies below the sensitivity of more traditional methods. Detecting unexpected null alleles not only has benefits in QC of genotype data, but may also be valuable in detecting rare, functional null alleles that would otherwise be missed.


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