Indel-correcting DNA barcodes for high-throughput sequencing
Identifieur interne : 000938 ( Main/Exploration ); précédent : 000937; suivant : 000939Indel-correcting DNA barcodes for high-throughput sequencing
Auteurs : John A. Hawkins ; Stephen K. Jones ; Ilya J. Finkelstein ; William H. PressSource :
- Proceedings of the National Academy of Sciences of the United States of America [ 0027-8424 ] ; 2018.
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Abstract
Modern high-throughput biological assays study pooled populations of individual members by labeling each member with a unique DNA sequence called a “barcode.” DNA barcodes are frequently corrupted by DNA synthesis and sequencing errors, leading to significant data loss and incorrect data interpretation. Here, we describe an error correction strategy to improve the efficiency and statistical power of DNA barcodes. Our strategy accurately handles insertions and deletions (indels) in DNA barcodes, the most common type of error encountered during DNA synthesis and sequencing, resulting in order-of-magnitude increases in accuracy, efficiency, and signal-to-noise ratio. The accompanying software package makes deployment of these barcodes straightforward for the broader experimental scientist community.
Url:
DOI: 10.1073/pnas.1802640115
PubMed: 29925596
PubMed Central: 6142223
Affiliations:
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Hawkins</name><affiliation><nlm:aff id="aff1">Institute for Computational Engineering and Sciences,<institution>The University of Texas at Austin</institution>, Austin,<addr-line>TX</addr-line> 78712;</nlm:aff></affiliation><affiliation><nlm:aff id="aff2">Department of Molecular Biosciences,<institution>The University of Texas at Austin</institution>, Austin,<addr-line>TX</addr-line> 78712;</nlm:aff></affiliation><affiliation><nlm:aff id="aff3">Institute for Cellular and Molecular Biology,<institution>The University of Texas at Austin</institution>, Austin,<addr-line>TX</addr-line> 78712;</nlm:aff></affiliation></author><author><name sortKey="Jones, Stephen K" sort="Jones, Stephen K" uniqKey="Jones S" first="Stephen K." last="Jones">Stephen K. 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Hawkins</name><affiliation><nlm:aff id="aff1">Institute for Computational Engineering and Sciences,<institution>The University of Texas at Austin</institution>, Austin,<addr-line>TX</addr-line> 78712;</nlm:aff></affiliation><affiliation><nlm:aff id="aff2">Department of Molecular Biosciences,<institution>The University of Texas at Austin</institution>, Austin,<addr-line>TX</addr-line> 78712;</nlm:aff></affiliation><affiliation><nlm:aff id="aff3">Institute for Cellular and Molecular Biology,<institution>The University of Texas at Austin</institution>, Austin,<addr-line>TX</addr-line> 78712;</nlm:aff></affiliation></author><author><name sortKey="Jones, Stephen K" sort="Jones, Stephen K" uniqKey="Jones S" first="Stephen K." last="Jones">Stephen K. Jones</name><affiliation><nlm:aff id="aff2">Department of Molecular Biosciences,<institution>The University of Texas at Austin</institution>, Austin,<addr-line>TX</addr-line> 78712;</nlm:aff></affiliation><affiliation><nlm:aff id="aff3">Institute for Cellular and Molecular Biology,<institution>The University of Texas at Austin</institution>, Austin,<addr-line>TX</addr-line> 78712;</nlm:aff></affiliation></author><author><name sortKey="Finkelstein, Ilya J" sort="Finkelstein, Ilya J" uniqKey="Finkelstein I" first="Ilya J." last="Finkelstein">Ilya J. Finkelstein</name><affiliation><nlm:aff id="aff2">Department of Molecular Biosciences,<institution>The University of Texas at Austin</institution>, Austin,<addr-line>TX</addr-line> 78712;</nlm:aff></affiliation><affiliation><nlm:aff id="aff3">Institute for Cellular and Molecular Biology,<institution>The University of Texas at Austin</institution>, Austin,<addr-line>TX</addr-line> 78712;</nlm:aff></affiliation><affiliation><nlm:aff id="aff4">Center for Systems and Synthetic Biology,<institution>The University of Texas at Austin</institution>, Austin,<addr-line>TX</addr-line> 78712;</nlm:aff></affiliation></author><author><name sortKey="Press, William H" sort="Press, William H" uniqKey="Press W" first="William H." last="Press">William H. Press</name><affiliation><nlm:aff id="aff1">Institute for Computational Engineering and Sciences,<institution>The University of Texas at Austin</institution>, Austin,<addr-line>TX</addr-line> 78712;</nlm:aff></affiliation><affiliation><nlm:aff id="aff3">Institute for Cellular and Molecular Biology,<institution>The University of Texas at Austin</institution>, Austin,<addr-line>TX</addr-line> 78712;</nlm:aff></affiliation><affiliation><nlm:aff id="aff5">Department of Integrative Biology,<institution>The University of Texas at Austin</institution>, Austin,<addr-line>TX</addr-line> 78712</nlm:aff></affiliation></author></analytic><series><title level="j">Proceedings of the National Academy of Sciences of the United States of America</title><idno type="ISSN">0027-8424</idno><idno type="eISSN">1091-6490</idno><imprint><date when="2018">2018</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Base Sequence</term><term>DNA Barcoding, Taxonomic</term><term>High-Throughput Nucleotide Sequencing</term><term>INDEL Mutation</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Codage à barres de l'ADN pour la taxonomie</term><term>Mutation de type INDEL</term><term>Séquence nucléotidique</term><term>Séquençage nucléotidique à haut débit</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Base Sequence</term><term>DNA Barcoding, Taxonomic</term><term>High-Throughput Nucleotide Sequencing</term><term>INDEL Mutation</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Codage à barres de l'ADN pour la taxonomie</term><term>Mutation de type INDEL</term><term>Séquence nucléotidique</term><term>Séquençage nucléotidique à haut débit</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><title>Significance</title><p>Modern high-throughput biological assays study pooled populations of individual members by labeling each member with a unique DNA sequence called a “barcode.” DNA barcodes are frequently corrupted by DNA synthesis and sequencing errors, leading to significant data loss and incorrect data interpretation. Here, we describe an error correction strategy to improve the efficiency and statistical power of DNA barcodes. Our strategy accurately handles insertions and deletions (indels) in DNA barcodes, the most common type of error encountered during DNA synthesis and sequencing, resulting in order-of-magnitude increases in accuracy, efficiency, and signal-to-noise ratio. The accompanying software package makes deployment of these barcodes straightforward for the broader experimental scientist community.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Klein, Am" uniqKey="Klein A">AM Klein</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Macosko, Ez" uniqKey="Macosko E">EZ Macosko</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zheng, Gxy" uniqKey="Zheng G">GXY Zheng</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kitzman, Jo" uniqKey="Kitzman J">JO Kitzman</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Haque, A" uniqKey="Haque A">A Haque</name></author><author><name sortKey="Engel, J" uniqKey="Engel J">J Engel</name></author><author><name sortKey="Teichmann, Sa" uniqKey="Teichmann S">SA Teichmann</name></author><author><name sortKey="Lonnberg, T" 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Finkelstein</name><name sortKey="Hawkins, John A" sort="Hawkins, John A" uniqKey="Hawkins J" first="John A." last="Hawkins">John A. Hawkins</name><name sortKey="Jones, Stephen K" sort="Jones, Stephen K" uniqKey="Jones S" first="Stephen K." last="Jones">Stephen K. Jones</name><name sortKey="Press, William H" sort="Press, William H" uniqKey="Press W" first="William H." last="Press">William H. Press</name></noCountry></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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