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Bioinformatics Advance Access originally published online on August 27, 2004
Bioinformatics 2005 21(2):141-143; doi:10.1093/bioinformatics/bth492
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Bioinformatics vol. 21 issue 2 © Oxford University Press 2005; all rights reserved.

COMMENT ON ‘DISCREPANCIES IN dbSNP CONFIRMATIONS RATES AND ALLELE FREQUENCY DISTRIBUTIONS FROM VARYING GENOTYPING ERROR RATES AND PATTERNS’

Christopher S. Carlson *, Mark J. Reider , Deborah A. Nickerson , Michael A. Eberle and Leonid Kruglyak

Department of Genome Sciences, University of Washington 1705 NE Pacific, Seattle, WA 98109, USA
Division of Human Biology, Fred Hutchinson Cancer Research Center 1100 Fairview Avenue N, Seattle, WA 98109, USA
Leonid Kruglyak Howard Hughes Medical Institute Chevy Chase, MD, USA

* csc47@u.washington.edu

The first 150 words of the full text of this article appear below.

In their paper in Bioinformatics, Mitchell et al. (2004) constructed a model of single nucleotide polymorphism (SNP) genotyping errors in different studies, and based on this model concluded that our study (Carlson et al., 2003) missed 99% of heterozygous genotypes when the minor allele was present only in the heterozygous state. We show here that this oversimplified model strikingly fails to fit many descriptors of our data, such as nucleotide diversity and allele frequency distribution, and that the results of Mitchell et al. are based on an incorrect value of one of the two statistics that they used to describe our data.

Mitchell et al. stated that the best fit to our data was obtained with a model in which 99% of all heterozygous genotypes are wrongly called as homozygous for all SNPs with the minor allele observed only in the heterozygous state. . . . [Full Text of this Article]


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