A bioinformatic filter for improved base-call accuracy and polymorphism detection using the Affymetrix GeneChip® whole-genome resequencing platform
Identifieur interne : 003841 ( Main/Exploration ); précédent : 003840; suivant : 003842A bioinformatic filter for improved base-call accuracy and polymorphism detection using the Affymetrix GeneChip® whole-genome resequencing platform
Auteurs : Gagan A. Pandya [États-Unis] ; Michael H. Holmes [États-Unis] ; Sirisha Sunkara [États-Unis] ; Andrew Sparks [États-Unis] ; Yun Bai [États-Unis] ; Kathleen Verratti [États-Unis] ; Kelly Saeed [États-Unis] ; Pratap Venepally [États-Unis] ; Behnam Jarrahi [États-Unis] ; Robert D. Fleischmann [États-Unis] ; Scott N. Peterson [États-Unis]Source :
- Nucleic Acids Research [ 0305-1048 ] ; 2007.
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%.
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DOI: 10.1093/nar/gkm918
Affiliations:
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Craig Venter Institute, Rockville, MD 20850, USA and Affymetrix, Inc., Santa Clara, CA 95051</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation><affiliation></affiliation><affiliation></affiliation></author></analytic><monogr></monogr><series><title level="j" type="main">Nucleic Acids Research</title><idno type="ISSN">0305-1048</idno><idno type="eISSN">1362-4962</idno><imprint><publisher>Oxford University Press</publisher><date type="published">2007</date><date type="e-published">2007</date><biblScope unit="vol">35</biblScope><biblScope unit="issue">21</biblScope><biblScope unit="page" from="e148">e148</biblScope><biblScope unit="page" to="e148">e148</biblScope></imprint><idno type="ISSN">0305-1048</idno></series></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">0305-1048</idno></seriesStmt></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="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%.</div></front></TEI><affiliations><list><country><li>États-Unis</li></country><region><li>Californie</li></region></list><tree><country name="États-Unis"><region name="Californie"><name sortKey="Pandya, Gagan A" sort="Pandya, Gagan A" uniqKey="Pandya G" first="Gagan A." last="Pandya">Gagan A. Pandya</name></region><name sortKey="Bai, Yun" sort="Bai, Yun" uniqKey="Bai Y" first="Yun" last="Bai">Yun Bai</name><name sortKey="Fleischmann, Robert D" sort="Fleischmann, Robert D" uniqKey="Fleischmann R" first="Robert D." last="Fleischmann">Robert D. Fleischmann</name><name sortKey="Holmes, Michael H" sort="Holmes, Michael H" uniqKey="Holmes M" first="Michael H." last="Holmes">Michael H. Holmes</name><name sortKey="Jarrahi, Behnam" sort="Jarrahi, Behnam" uniqKey="Jarrahi B" first="Behnam" last="Jarrahi">Behnam Jarrahi</name><name sortKey="Peterson, Scott N" sort="Peterson, Scott N" uniqKey="Peterson S" first="Scott N." last="Peterson">Scott N. Peterson</name><name sortKey="Saeed, Kelly" sort="Saeed, Kelly" uniqKey="Saeed K" first="Kelly" last="Saeed">Kelly Saeed</name><name sortKey="Sparks, Andrew" sort="Sparks, Andrew" uniqKey="Sparks A" first="Andrew" last="Sparks">Andrew Sparks</name><name sortKey="Sunkara, Sirisha" sort="Sunkara, Sirisha" uniqKey="Sunkara S" first="Sirisha" last="Sunkara">Sirisha Sunkara</name><name sortKey="Venepally, Pratap" sort="Venepally, Pratap" uniqKey="Venepally P" first="Pratap" last="Venepally">Pratap Venepally</name><name sortKey="Verratti, Kathleen" sort="Verratti, Kathleen" uniqKey="Verratti K" first="Kathleen" last="Verratti">Kathleen Verratti</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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