Indel-correcting DNA barcodes for high-throughput sequencing.
Identifieur interne : 000881 ( PubMed/Checkpoint ); précédent : 000880; suivant : 000882Indel-correcting DNA barcodes for high-throughput sequencing.
Auteurs : John A. Hawkins [États-Unis] ; Stephen K. Jones [États-Unis] ; Ilya J. Finkelstein [États-Unis] ; William H. Press [États-Unis]Source :
- Proceedings of the National Academy of Sciences of the United States of America [ 1091-6490 ] ; 2018.
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Abstract
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 >106 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 >1015 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.
DOI: 10.1073/pnas.1802640115
PubMed: 29925596
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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. 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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><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">29925596</PMID><DateCompleted><Year>2018</Year><Month>09</Month><Day>04</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>14</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1091-6490</ISSN><JournalIssue CitedMedium="Internet"><Volume>115</Volume><Issue>27</Issue><PubDate><Year>2018</Year><Month>07</Month><Day>03</Day></PubDate></JournalIssue><Title>Proceedings of the National Academy of Sciences of the United States of America</Title><ISOAbbreviation>Proc. Natl. Acad. Sci. U.S.A.</ISOAbbreviation></Journal><ArticleTitle>Indel-correcting DNA barcodes for high-throughput sequencing.</ArticleTitle><Pagination><MedlinePgn>E6217-E6226</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1073/pnas.1802640115</ELocationID><Abstract><AbstractText>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.</AbstractText><CopyrightInformation>Copyright © 2018 the Author(s). Published by PNAS.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Hawkins</LastName><ForeName>John A</ForeName><Initials>JA</Initials><AffiliationInfo><Affiliation>Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, TX 78712.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Jones</LastName><ForeName>Stephen K</ForeName><Initials>SK</Initials><Suffix>Jr</Suffix><AffiliationInfo><Affiliation>Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Finkelstein</LastName><ForeName>Ilya J</ForeName><Initials>IJ</Initials><Identifier Source="ORCID">0000-0002-9371-2431</Identifier><AffiliationInfo><Affiliation>Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712; ifinkelstein@cm.utexas.edu wpress@cs.utexas.edu.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Press</LastName><ForeName>William H</ForeName><Initials>WH</Initials><AffiliationInfo><Affiliation>Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, TX 78712; ifinkelstein@cm.utexas.edu wpress@cs.utexas.edu.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>F32 AG053051</GrantID><Acronym>AG</Acronym><Agency>NIA NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>R01 GM120554</GrantID><Acronym>GM</Acronym><Agency>NIGMS NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>R01 GM124141</GrantID><Acronym>GM</Acronym><Agency>NIGMS NIH HHS</Agency><Country>United States</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D052061">Research Support, N.I.H., Extramural</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2018</Year><Month>06</Month><Day>20</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Proc Natl Acad Sci U S A</MedlineTA><NlmUniqueID>7505876</NlmUniqueID><ISSNLinking>0027-8424</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D001483" MajorTopicYN="Y">Base Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D058893" MajorTopicYN="Y">DNA Barcoding, Taxonomic</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D059014" MajorTopicYN="Y">High-Throughput Nucleotide Sequencing</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D054643" MajorTopicYN="Y">INDEL Mutation</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="Y">DNA barcodes</Keyword><Keyword MajorTopicYN="Y">error-correcting codes</Keyword><Keyword MajorTopicYN="Y">information storage</Keyword><Keyword MajorTopicYN="Y">massively parallel synthesis</Keyword></KeywordList><CoiStatement>The authors declare no conflict of interest.</CoiStatement></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2018</Year><Month>6</Month><Day>22</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2018</Year><Month>9</Month><Day>5</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2018</Year><Month>6</Month><Day>22</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">29925596</ArticleId><ArticleId IdType="pii">1802640115</ArticleId><ArticleId IdType="doi">10.1073/pnas.1802640115</ArticleId><ArticleId 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