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dc:abstract "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%." ;
dc:creator "['Pandya, Gagan A.', 'Holmes, Michael H.', 'Sunkara, Sirisha', 'Sparks, Andrew', 'Bai, Yun', 'Verratti, Kathleen', 'Saeed, Kelly', 'Venepally, Pratap', 'Jarrahi, Behnam', 'Fleischmann, Robert D.', 'Peterson, Scott N.']" ;
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dc:issued "2007-01-01"^^xsd:date ;
dc:license "CC BY-NC" ;
dc:title "A bioinformatic filter for improved base-call accuracy and polymorphism detection using the Affymetrix GeneChip® whole-genome resequencing platform" ;
sso:has_full_text "True" ;
sso:journal "Nucleic Acids Res" ;
sso:sha "63c64ba93501a9ec60ab113b55c23d5bc602a13c" ;
sso:source_x "PMC" .