Indel-correcting DNA barcodes for high-throughput sequencing
Identifieur interne : 001E73 ( Ncbi/Merge ); précédent : 001E72; suivant : 001E74Indel-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.
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DOI: 10.1073/pnas.1802640115
PubMed: 29925596
PubMed Central: 6142223
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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. 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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" uniqKey="Lonnberg T">T Lönnberg</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zilionis, R" uniqKey="Zilionis R">R Zilionis</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Spies, N" uniqKey="Spies N">N Spies</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Eroshenko, N" uniqKey="Eroshenko N">N Eroshenko</name></author><author><name sortKey="Kosuri, S" uniqKey="Kosuri S">S Kosuri</name></author><author><name sortKey="Marblestone, Ah" uniqKey="Marblestone A">AH Marblestone</name></author><author><name sortKey="Conway, N" uniqKey="Conway N">N Conway</name></author><author><name sortKey="Church, Gm" uniqKey="Church G">GM Church</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Plesa, C" uniqKey="Plesa C">C Plesa</name></author><author><name sortKey="Sidore, Am" uniqKey="Sidore A">AM Sidore</name></author><author><name sortKey="Lubock, Nb" uniqKey="Lubock N">NB Lubock</name></author><author><name sortKey="Zhang, D" uniqKey="Zhang D">D Zhang</name></author><author><name sortKey="Kosuri, S" uniqKey="Kosuri S">S Kosuri</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Fan, R" uniqKey="Fan R">R Fan</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ma, C" uniqKey="Ma C">C Ma</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zimmermann, G" uniqKey="Zimmermann G">G Zimmermann</name></author><author><name sortKey="Neri, D" uniqKey="Neri D">D Neri</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Melkko, S" uniqKey="Melkko S">S Melkko</name></author><author><name sortKey="Scheuermann, J" uniqKey="Scheuermann J">J Scheuermann</name></author><author><name sortKey="Dumelin, Ce" uniqKey="Dumelin C">CE Dumelin</name></author><author><name sortKey="Neri, D" uniqKey="Neri D">D 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sortKey="Lyons, E" uniqKey="Lyons E">E Lyons</name></author><author><name sortKey="Sheridan, P" uniqKey="Sheridan P">P Sheridan</name></author><author><name sortKey="Tremmel, G" uniqKey="Tremmel G">G Tremmel</name></author><author><name sortKey="Miyano, S" uniqKey="Miyano S">S Miyano</name></author><author><name sortKey="Sugano, S" uniqKey="Sugano S">S Sugano</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Erlich, Y" uniqKey="Erlich Y">Y Erlich</name></author><author><name sortKey="Zielinski, D" uniqKey="Zielinski D">D Zielinski</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Levenshtein, Vi" uniqKey="Levenshtein V">VI Levenshtein</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Costea, Pi" uniqKey="Costea P">PI Costea</name></author><author><name sortKey="Lundeberg, J" uniqKey="Lundeberg J">J Lundeberg</name></author><author><name sortKey="Akan, P" uniqKey="Akan P">P 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uniqKey="Lu J">J Lu</name></author><author><name sortKey="Chang, S" uniqKey="Chang S">S Chang</name></author><author><name sortKey="Loparo, Jj" uniqKey="Loparo J">JJ Loparo</name></author><author><name sortKey="Xie, Xs" uniqKey="Xie X">XS Xie</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Markham, Nr" uniqKey="Markham N">NR Markham</name></author><author><name sortKey="Zuker, M" uniqKey="Zuker M">M Zuker</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Van Zanten, Aj" uniqKey="Van Zanten A">AJ van Zanten</name></author></analytic></biblStruct></listBibl></div1></back></TEI><double pmid="29925596"><pmc><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Indel-correcting DNA barcodes for high-throughput sequencing</title><author><name sortKey="Hawkins, John A" sort="Hawkins, John A" uniqKey="Hawkins J" first="John A." last="Hawkins">John A. 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. 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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></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" uniqKey="Lonnberg T">T Lönnberg</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zilionis, R" uniqKey="Zilionis R">R Zilionis</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Spies, N" uniqKey="Spies N">N Spies</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Eroshenko, N" uniqKey="Eroshenko N">N Eroshenko</name></author><author><name sortKey="Kosuri, S" uniqKey="Kosuri S">S Kosuri</name></author><author><name sortKey="Marblestone, Ah" uniqKey="Marblestone A">AH Marblestone</name></author><author><name sortKey="Conway, N" uniqKey="Conway N">N Conway</name></author><author><name sortKey="Church, Gm" uniqKey="Church G">GM Church</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Plesa, C" uniqKey="Plesa C">C Plesa</name></author><author><name sortKey="Sidore, Am" uniqKey="Sidore A">AM Sidore</name></author><author><name sortKey="Lubock, Nb" uniqKey="Lubock N">NB Lubock</name></author><author><name sortKey="Zhang, D" uniqKey="Zhang D">D Zhang</name></author><author><name sortKey="Kosuri, S" uniqKey="Kosuri S">S Kosuri</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Fan, R" uniqKey="Fan R">R Fan</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ma, C" uniqKey="Ma C">C Ma</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zimmermann, G" uniqKey="Zimmermann G">G Zimmermann</name></author><author><name sortKey="Neri, D" uniqKey="Neri D">D Neri</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Melkko, S" uniqKey="Melkko S">S Melkko</name></author><author><name sortKey="Scheuermann, J" uniqKey="Scheuermann J">J Scheuermann</name></author><author><name sortKey="Dumelin, Ce" uniqKey="Dumelin C">CE Dumelin</name></author><author><name sortKey="Neri, D" uniqKey="Neri D">D Neri</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kosuri, S" uniqKey="Kosuri S">S Kosuri</name></author><author><name sortKey="Church, Gm" uniqKey="Church G">GM Church</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Petrone, J" uniqKey="Petrone J">J Petrone</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Litovchick, A" uniqKey="Litovchick A">A Litovchick</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Peterson, Ww" uniqKey="Peterson W">WW Peterson</name></author><author><name sortKey="Weldon, Ej" uniqKey="Weldon E">EJ Weldon</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Macwilliams, Fj" uniqKey="Macwilliams F">FJ MacWilliams</name></author><author><name sortKey="Sloane, Nja" uniqKey="Sloane N">NJA Sloane</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lyons, E" uniqKey="Lyons E">E Lyons</name></author><author><name sortKey="Sheridan, P" uniqKey="Sheridan P">P Sheridan</name></author><author><name sortKey="Tremmel, G" uniqKey="Tremmel G">G Tremmel</name></author><author><name sortKey="Miyano, S" uniqKey="Miyano S">S Miyano</name></author><author><name sortKey="Sugano, S" uniqKey="Sugano S">S Sugano</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Erlich, Y" uniqKey="Erlich Y">Y Erlich</name></author><author><name sortKey="Zielinski, D" uniqKey="Zielinski D">D Zielinski</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Levenshtein, Vi" uniqKey="Levenshtein V">VI Levenshtein</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Costea, Pi" uniqKey="Costea P">PI Costea</name></author><author><name sortKey="Lundeberg, J" uniqKey="Lundeberg J">J Lundeberg</name></author><author><name sortKey="Akan, P" uniqKey="Akan P">P Akan</name></author><author><name sortKey="Tag, Gd" uniqKey="Tag G">GD Tag</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Houghten, Sk" uniqKey="Houghten S">SK Houghten</name></author><author><name sortKey="Ashlock, D" uniqKey="Ashlock D">D Ashlock</name></author><author><name sortKey="Lenarz, J" uniqKey="Lenarz J">J Lenarz</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Quail, Ma" uniqKey="Quail M">MA Quail</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hamming, Rw" uniqKey="Hamming R">RW Hamming</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Buschmann, T" uniqKey="Buschmann T">T Buschmann</name></author><author><name sortKey="Bystrykh, Lv" uniqKey="Bystrykh L">LV Bystrykh</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lee, Df" uniqKey="Lee D">DF Lee</name></author><author><name sortKey="Lu, J" uniqKey="Lu J">J Lu</name></author><author><name sortKey="Chang, S" uniqKey="Chang S">S Chang</name></author><author><name sortKey="Loparo, Jj" uniqKey="Loparo J">JJ Loparo</name></author><author><name sortKey="Xie, Xs" uniqKey="Xie X">XS Xie</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Markham, Nr" uniqKey="Markham N">NR Markham</name></author><author><name sortKey="Zuker, M" uniqKey="Zuker M">M Zuker</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Van Zanten, Aj" uniqKey="Van Zanten A">AJ van Zanten</name></author></analytic></biblStruct></listBibl></div1></back></TEI></pmc><pubmed><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Indel-correcting DNA barcodes for high-throughput sequencing.</title><author><name sortKey="Hawkins, John A" sort="Hawkins, John A" uniqKey="Hawkins J" first="John A" last="Hawkins">John A. Hawkins</name><affiliation wicri:level="2"><nlm:affiliation>Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, TX 78712.</nlm:affiliation><country xml:lang="fr">États-Unis</country><placeName><region type="state">Texas</region></placeName><wicri:cityArea>Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin</wicri:cityArea></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 wicri:level="2"><nlm:affiliation>Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712.</nlm:affiliation><country xml:lang="fr">États-Unis</country><placeName><region type="state">Texas</region></placeName><wicri:cityArea>Department of Molecular Biosciences, The University of Texas at Austin, Austin</wicri:cityArea></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 wicri:level="4"><nlm:affiliation>Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712; ifinkelstein@cm.utexas.edu wpress@cs.utexas.edu.</nlm:affiliation><country wicri:rule="url">États-Unis</country><wicri:regionArea>Department of Molecular Biosciences, The University of Texas at Austin, Austin</wicri:regionArea><orgName type="university">Université du Texas à Austin</orgName><placeName><settlement type="city">Austin (Texas)</settlement><region type="state">Texas</region></placeName></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 wicri:level="4"><nlm:affiliation>Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, TX 78712; ifinkelstein@cm.utexas.edu wpress@cs.utexas.edu.</nlm:affiliation><country wicri:rule="url">États-Unis</country><wicri:regionArea>Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin</wicri:regionArea><orgName type="university">Université du Texas à Austin</orgName><placeName><settlement type="city">Austin (Texas)</settlement><region type="state">Texas</region></placeName></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2018">2018</date><idno type="RBID">pubmed:29925596</idno><idno type="pmid">29925596</idno><idno type="doi">10.1073/pnas.1802640115</idno><idno type="wicri:Area/PubMed/Corpus">000860</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000860</idno><idno type="wicri:Area/PubMed/Curation">000860</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">000860</idno><idno type="wicri:Area/PubMed/Checkpoint">000881</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">000881</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Indel-correcting DNA barcodes for high-throughput sequencing.</title><author><name sortKey="Hawkins, John A" sort="Hawkins, John A" uniqKey="Hawkins J" first="John A" last="Hawkins">John A. Hawkins</name><affiliation wicri:level="2"><nlm:affiliation>Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, TX 78712.</nlm:affiliation><country xml:lang="fr">États-Unis</country><placeName><region type="state">Texas</region></placeName><wicri:cityArea>Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin</wicri:cityArea></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 wicri:level="2"><nlm:affiliation>Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712.</nlm:affiliation><country xml:lang="fr">États-Unis</country><placeName><region type="state">Texas</region></placeName><wicri:cityArea>Department of Molecular Biosciences, The University of Texas at Austin, Austin</wicri:cityArea></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 wicri:level="4"><nlm:affiliation>Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712; ifinkelstein@cm.utexas.edu wpress@cs.utexas.edu.</nlm:affiliation><country wicri:rule="url">États-Unis</country><wicri:regionArea>Department of Molecular Biosciences, The University of Texas at Austin, Austin</wicri:regionArea><orgName type="university">Université du Texas à Austin</orgName><placeName><settlement type="city">Austin (Texas)</settlement><region type="state">Texas</region></placeName></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 wicri:level="4"><nlm:affiliation>Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, TX 78712; ifinkelstein@cm.utexas.edu wpress@cs.utexas.edu.</nlm:affiliation><country wicri:rule="url">États-Unis</country><wicri:regionArea>Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin</wicri:regionArea><orgName type="university">Université du Texas à Austin</orgName><placeName><settlement type="city">Austin (Texas)</settlement><region type="state">Texas</region></placeName></affiliation></author></analytic><series><title level="j">Proceedings of the National Academy of Sciences of the United States of America</title><idno type="eISSN">1091-6490</idno><imprint><date when="2018" type="published">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">Many large-scale, high-throughput experiments use DNA barcodes, short DNA sequences prepended to DNA libraries, for identification of individuals in pooled biomolecule populations. However, DNA synthesis and sequencing errors confound the correct interpretation of observed barcodes and can lead to significant data loss or spurious results. Widely used error-correcting codes borrowed from computer science (e.g., Hamming, Levenshtein codes) do not properly account for insertions and deletions (indels) in DNA barcodes, even though deletions are the most common type of synthesis error. Here, we present and experimentally validate filled/truncated right end edit (FREE) barcodes, which correct substitution, insertion, and deletion errors, even when these errors alter the barcode length. FREE barcodes are designed with experimental considerations in mind, including balanced guanine-cytosine (GC) content, minimal homopolymer runs, and reduced internal hairpin propensity. We generate and include lists of barcodes with different lengths and error correction levels that may be useful in diverse high-throughput applications, including >10<sup>6</sup> single-error-correcting 16-mers that strike a balance between decoding accuracy, barcode length, and library size. Moreover, concatenating two or more FREE codes into a single barcode increases the available barcode space combinatorially, generating lists with >10<sup>15</sup> error-correcting barcodes. The included software for creating barcode libraries and decoding sequenced barcodes is efficient and designed to be user-friendly for the general biology community.</div></front></TEI></pubmed></double></record>Pour manipuler ce document sous Unix (Dilib)
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