Nucleic Acids Research Advance Access originally published online on November 15, 2007
Nucleic Acids Research 2007 35(21):e148; doi:10.1093/nar/gkm918
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Nucleic Acids Research, 2007, Vol. 35, No. 21 e148
© 2007 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.
Methods Online |
A bioinformatic filter for improved base-call accuracy and polymorphism detection using the Affymetrix GeneChip® whole-genome resequencing platform
1Pathogen Functional Genomics Resource Center, The Institute for Genomic Research at the J. Craig Venter Institute, Rockville, MD 20850, USA and 2Affymetrix, Inc., Santa Clara, CA 95051, USA
*To whom correspondence should be addressed. Tel: +1 301 795 7539; Fax: +1 301 838 0208; Email: scottp{at}jcvi.org
Received August 13, 2007. Revised September 21, 2007. Accepted October 9, 2007.
DNA resequencing arrays enable rapid acquisition of high-quality sequence data. This technology represents a promising platform for rapid high-resolution genotyping of microorganisms. Traditional array-based resequencing methods have relied on the use of specific PCR-amplified fragments from the query samples as hybridization targets. While this specificity in the target DNA population reduces the potential for artifacts caused by cross-hybridization, the subsampling of the query genome limits the sequence coverage that can be obtained and therefore reduces the technique's resolution as a genotyping method. We have developed and validated an Affymetrix Inc. GeneChip® array-based, whole-genome resequencing platform for Francisella tularensis, the causative agent of tularemia. A set of bioinformatic filters that targeted systematic base-calling errors caused by cross-hybridization between the whole-genome sample and the array probes and by deletions in the sample DNA relative to the chip reference sequence were developed. Our approach eliminated 91% of the false-positive single-nucleotide polymorphism calls identified in the SCHU S4 query sample, at the cost of 10.7% of the true positives, yielding a total base-calling accuracy of 99.992%.
Present address: Andrew Sparks, Complete Genomics, 658 North Pastoria Avenue, Sunnyvale, CA 94085, USA