Indel-correcting DNA barcodes for high-throughput sequencing
Identifieur interne : 000560 ( Pmc/Checkpoint ); précédent : 000559; suivant : 000561Indel-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.
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. 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" 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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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<front><journal-meta><journal-id journal-id-type="nlm-ta">Proc Natl Acad Sci U S A</journal-id><journal-id journal-id-type="iso-abbrev">Proc. Natl. Acad. Sci. U.S.A</journal-id><journal-id journal-id-type="hwp">pnas</journal-id><journal-id journal-id-type="pmc">pnas</journal-id><journal-id journal-id-type="publisher-id">PNAS</journal-id><journal-title-group><journal-title>Proceedings of the National Academy of Sciences of the United States of America</journal-title></journal-title-group><issn pub-type="ppub">0027-8424</issn><issn pub-type="epub">1091-6490</issn><publisher><publisher-name>National Academy of Sciences</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">29925596</article-id><article-id pub-id-type="pmc">6142223</article-id><article-id pub-id-type="publisher-id">201802640</article-id><article-id pub-id-type="doi">10.1073/pnas.1802640115</article-id><article-categories><subj-group subj-group-type="heading"><subject>PNAS Plus</subject></subj-group><subj-group subj-group-type="heading"><subject>Biological Sciences</subject><subj-group><subject>Cell Biology</subject></subj-group></subj-group><subj-group subj-group-type="heading"><subject>Physical Sciences</subject><subj-group><subject>Biophysics and Computational Biology</subject></subj-group></subj-group><series-title>PNAS Plus</series-title></article-categories><title-group><article-title>Indel-correcting DNA barcodes for high-throughput sequencing</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Hawkins</surname><given-names>John A.</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref><xref ref-type="aff" rid="aff2"><sup>b</sup></xref><xref ref-type="aff" rid="aff3"><sup>c</sup></xref></contrib><contrib contrib-type="author"><name><surname>Jones</surname><given-names>Stephen K.</given-names><suffix>Jr.</suffix></name><xref ref-type="aff" rid="aff2"><sup>b</sup></xref><xref ref-type="aff" rid="aff3"><sup>c</sup></xref></contrib><contrib contrib-type="author"><contrib-id contrib-id-type="orcid" authenticated="false">http://orcid.org/0000-0002-9371-2431</contrib-id><name><surname>Finkelstein</surname><given-names>Ilya J.</given-names></name><xref ref-type="aff" rid="aff2"><sup>b</sup></xref><xref ref-type="aff" rid="aff3"><sup>c</sup></xref><xref ref-type="aff" rid="aff4"><sup>d</sup></xref><xref ref-type="corresp" rid="cor1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Press</surname><given-names>William H.</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref><xref ref-type="aff" rid="aff3"><sup>c</sup></xref><xref ref-type="aff" rid="aff5"><sup>e</sup></xref><xref ref-type="corresp" rid="cor1"><sup>1</sup></xref></contrib><aff id="aff1"><sup>a</sup>Institute for Computational Engineering and Sciences,<institution>The University of Texas at Austin</institution>, Austin,<addr-line>TX</addr-line> 78712;</aff><aff id="aff2"><sup>b</sup>Department of Molecular Biosciences,<institution>The University of Texas at Austin</institution>, Austin,<addr-line>TX</addr-line> 78712;</aff><aff id="aff3"><sup>c</sup>Institute for Cellular and Molecular Biology,<institution>The University of Texas at Austin</institution>, Austin,<addr-line>TX</addr-line> 78712;</aff><aff id="aff4"><sup>d</sup>Center for Systems and Synthetic Biology,<institution>The University of Texas at Austin</institution>, Austin,<addr-line>TX</addr-line> 78712;</aff><aff id="aff5"><sup>e</sup>Department of Integrative Biology,<institution>The University of Texas at Austin</institution>, Austin,<addr-line>TX</addr-line> 78712</aff></contrib-group><author-notes><corresp id="cor1"><sup>1</sup>To whom correspondence may be addressed. Email: <email>ifinkelstein@cm.utexas.edu</email> or <email>wpress@cs.utexas.edu</email>.</corresp><fn fn-type="edited-by"><p>Contributed by William H. Press, May 25, 2018 (sent for review February 13, 2018; reviewed by Curtis G. Callan Jr., Olga G. Troyanskaya, and Jonathan S. Weissman)</p></fn><fn fn-type="con"><p>Author contributions: J.A.H., I.J.F., and W.H.P. designed research; J.A.H. and S.K.J. performed research; J.A.H. analyzed data; and J.A.H., S.K.J., I.J.F., and W.H.P. wrote the paper.</p></fn><fn fn-type="con"><p>Reviewers: C.G.C., Princeton University; O.G.T., Princeton University; and J.S.W., University of California, San Francisco.</p></fn></author-notes><pub-date pub-type="ppub"><day>3</day><month>7</month><year>2018</year></pub-date><pub-date pub-type="epub"><day>20</day><month>6</month><year>2018</year></pub-date><pub-date pub-type="pmc-release"><day>20</day><month>6</month><year>2018</year></pub-date><pmc-comment> PMC Release delay is 0 months and 0 days and was based on the
<volume>115</volume><issue>27</issue><fpage>E6217</fpage><lpage>E6226</lpage><permissions><copyright-statement>Copyright © 2018 the Author(s). Published by PNAS.</copyright-statement><copyright-year>2018</copyright-year><license license-type="open-access" xlink:href="https://creativecommons.org/licenses/by-nc-nd/4.0/"><ali:license_ref specific-use="vor"></ali:license_ref><license-p>This open access article is distributed under <ext-link ext-link-type="uri" xlink:href="https://creativecommons.org/licenses/by-nc-nd/4.0/">Creative Commons Attribution-NonCommercial-NoDerivatives License 4.0 (CC BY-NC-ND)</ext-link>.</license-p></license></permissions><self-uri xlink:title="pdf" xlink:href="pnas.201802640.pdf"></self-uri><abstract abstract-type="executive-summary"><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></abstract><abstract><p>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.</p></abstract><kwd-group><kwd>DNA barcodes</kwd><kwd>error-correcting codes</kwd><kwd>information storage</kwd><kwd>massively parallel synthesis</kwd></kwd-group><funding-group><award-group id="gs1"><funding-source id="sp1">Welch Foundation<named-content content-type="funder-id">100000928</named-content></funding-source><award-id rid="sp1">F-1808</award-id><principal-award-recipient>Ilya J Finkelstein</principal-award-recipient></award-group><award-group id="gs2"><funding-source id="sp2">HHS | National Institutes of Health (NIH)<named-content content-type="funder-id">100000002</named-content></funding-source><award-id rid="sp2">GM120554 and GM124141</award-id><principal-award-recipient>Stephen K Jones</principal-award-recipient><principal-award-recipient>Ilya J Finkelstein</principal-award-recipient></award-group><award-group id="gs3"><funding-source id="sp3">HHS | National Institutes of Health (NIH)<named-content content-type="funder-id">100000002</named-content></funding-source><award-id rid="sp3">AG053051</award-id><principal-award-recipient>Stephen K Jones</principal-award-recipient><principal-award-recipient>Ilya J Finkelstein</principal-award-recipient></award-group></funding-group><counts><page-count count="10"></page-count></counts></article-meta></front></pmc><affiliations><list></list><tree><noCountry><name sortKey="Finkelstein, Ilya J" sort="Finkelstein, Ilya J" uniqKey="Finkelstein I" first="Ilya J." last="Finkelstein">Ilya J. 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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HfdIndexSelect -h $EXPLOR_AREA/Data/Pmc/Checkpoint/RBID.i -Sk "pubmed:29925596" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Pmc/Checkpoint/biblio.hfd \
| NlmPubMed2Wicri -a MersV1
| This area was generated with Dilib version V0.6.33. |  |