BOCS: DNA k-mer content and scoring for rapid genetic biomarker identification at low coverage.
Identifieur interne : 000687 ( Main/Exploration ); précédent : 000686; suivant : 000688BOCS: DNA k-mer content and scoring for rapid genetic biomarker identification at low coverage.
Auteurs : Lee E. Korshoj [États-Unis] ; Prashant Nagpal [États-Unis]Source :
- Computers in biology and medicine [ 1879-0534 ] ; 2019.
Abstract
A single, inexpensive diagnostic test capable of rapidly identifying a wide range of genetic biomarkers would prove invaluable in precision medicine. Previous work has demonstrated the potential for high-throughput, label-free detection of A-G-C-T content in DNA k-mers, providing an alternative to single-letter sequencing while also having inherent lossy data compression and massively parallel data acquisition. Here, we apply a new bioinformatics algorithm - block optical content scoring (BOCS) - capable of using the high-throughput content k-mers for rapid, broad-spectrum identification of genetic biomarkers. BOCS uses content-based sequence alignment for probabilistic mapping of k-mer contents to gene sequences within a biomarker database, resulting in a probability ranking of genes on a content score. Simulations of the BOCS algorithm reveal high accuracy for identification of single antibiotic resistance genes, even in the presence of significant sequencing errors (100% accuracy for no sequencing errors, and >90% accuracy for sequencing errors at 20%), and at well below full coverage of the genes. Simulations for detecting multiple resistance genes within a methicillin-resistant Staphylococcus aureus (MRSA) strain showed 100% accuracy at an average gene coverage of merely 0.515, when the k-mer lengths were variable and with 4% sequencing error within the k-mer blocks. Extension of BOCS to cancer and other genetic diseases met or exceeded the results for resistance genes. Combined with a high-throughput content-based sequencing technique, the BOCS algorithm potentiates a test capable of rapid diagnosis and profiling of genetic biomarkers ranging from antibiotic resistance to cancer and other genetic diseases.
DOI: 10.1016/j.compbiomed.2019.05.022
PubMed: 31173943
Affiliations:
Links toward previous steps (curation, corpus...)
- to stream PubMed, to step Corpus: 000509
- to stream PubMed, to step Curation: 000509
- to stream PubMed, to step Checkpoint: 000660
- to stream Ncbi, to step Merge: 002248
- to stream Ncbi, to step Curation: 002248
- to stream Ncbi, to step Checkpoint: 002248
- to stream Main, to step Merge: 000690
- to stream Main, to step Curation: 000687
Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">BOCS: DNA k-mer content and scoring for rapid genetic biomarker identification at low coverage.</title>
<author><name sortKey="Korshoj, Lee E" sort="Korshoj, Lee E" uniqKey="Korshoj L" first="Lee E" last="Korshoj">Lee E. Korshoj</name>
<affiliation wicri:level="1"><nlm:affiliation>Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, 80303, USA; Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder, CO, 80303, USA.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, 80303, USA; Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder, CO, 80303</wicri:regionArea>
<wicri:noRegion>80303</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Nagpal, Prashant" sort="Nagpal, Prashant" uniqKey="Nagpal P" first="Prashant" last="Nagpal">Prashant Nagpal</name>
<affiliation wicri:level="1"><nlm:affiliation>Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, 80303, USA; Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder, CO, 80303, USA; Materials Science and Engineering, University of Colorado Boulder, Boulder, CO, 80303, USA. Electronic address: pnagpal@colorado.edu.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, 80303, USA; Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder, CO, 80303, USA; Materials Science and Engineering, University of Colorado Boulder, Boulder, CO, 80303</wicri:regionArea>
<wicri:noRegion>80303</wicri:noRegion>
</affiliation>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PubMed</idno>
<date when="2019">2019</date>
<idno type="RBID">pubmed:31173943</idno>
<idno type="pmid">31173943</idno>
<idno type="doi">10.1016/j.compbiomed.2019.05.022</idno>
<idno type="wicri:Area/PubMed/Corpus">000509</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000509</idno>
<idno type="wicri:Area/PubMed/Curation">000509</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">000509</idno>
<idno type="wicri:Area/PubMed/Checkpoint">000660</idno>
<idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">000660</idno>
<idno type="wicri:Area/Ncbi/Merge">002248</idno>
<idno type="wicri:Area/Ncbi/Curation">002248</idno>
<idno type="wicri:Area/Ncbi/Checkpoint">002248</idno>
<idno type="wicri:Area/Main/Merge">000690</idno>
<idno type="wicri:Area/Main/Curation">000687</idno>
<idno type="wicri:Area/Main/Exploration">000687</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en">BOCS: DNA k-mer content and scoring for rapid genetic biomarker identification at low coverage.</title>
<author><name sortKey="Korshoj, Lee E" sort="Korshoj, Lee E" uniqKey="Korshoj L" first="Lee E" last="Korshoj">Lee E. Korshoj</name>
<affiliation wicri:level="1"><nlm:affiliation>Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, 80303, USA; Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder, CO, 80303, USA.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, 80303, USA; Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder, CO, 80303</wicri:regionArea>
<wicri:noRegion>80303</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Nagpal, Prashant" sort="Nagpal, Prashant" uniqKey="Nagpal P" first="Prashant" last="Nagpal">Prashant Nagpal</name>
<affiliation wicri:level="1"><nlm:affiliation>Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, 80303, USA; Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder, CO, 80303, USA; Materials Science and Engineering, University of Colorado Boulder, Boulder, CO, 80303, USA. Electronic address: pnagpal@colorado.edu.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, 80303, USA; Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder, CO, 80303, USA; Materials Science and Engineering, University of Colorado Boulder, Boulder, CO, 80303</wicri:regionArea>
<wicri:noRegion>80303</wicri:noRegion>
</affiliation>
</author>
</analytic>
<series><title level="j">Computers in biology and medicine</title>
<idno type="eISSN">1879-0534</idno>
<imprint><date when="2019" type="published">2019</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass></textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en">A single, inexpensive diagnostic test capable of rapidly identifying a wide range of genetic biomarkers would prove invaluable in precision medicine. Previous work has demonstrated the potential for high-throughput, label-free detection of A-G-C-T content in DNA k-mers, providing an alternative to single-letter sequencing while also having inherent lossy data compression and massively parallel data acquisition. Here, we apply a new bioinformatics algorithm - block optical content scoring (BOCS) - capable of using the high-throughput content k-mers for rapid, broad-spectrum identification of genetic biomarkers. BOCS uses content-based sequence alignment for probabilistic mapping of k-mer contents to gene sequences within a biomarker database, resulting in a probability ranking of genes on a content score. Simulations of the BOCS algorithm reveal high accuracy for identification of single antibiotic resistance genes, even in the presence of significant sequencing errors (100% accuracy for no sequencing errors, and >90% accuracy for sequencing errors at 20%), and at well below full coverage of the genes. Simulations for detecting multiple resistance genes within a methicillin-resistant Staphylococcus aureus (MRSA) strain showed 100% accuracy at an average gene coverage of merely 0.515, when the k-mer lengths were variable and with 4% sequencing error within the k-mer blocks. Extension of BOCS to cancer and other genetic diseases met or exceeded the results for resistance genes. Combined with a high-throughput content-based sequencing technique, the BOCS algorithm potentiates a test capable of rapid diagnosis and profiling of genetic biomarkers ranging from antibiotic resistance to cancer and other genetic diseases.</div>
</front>
</TEI>
<affiliations><list><country><li>États-Unis</li>
</country>
</list>
<tree><country name="États-Unis"><noRegion><name sortKey="Korshoj, Lee E" sort="Korshoj, Lee E" uniqKey="Korshoj L" first="Lee E" last="Korshoj">Lee E. Korshoj</name>
</noRegion>
<name sortKey="Nagpal, Prashant" sort="Nagpal, Prashant" uniqKey="Nagpal P" first="Prashant" last="Nagpal">Prashant Nagpal</name>
</country>
</tree>
</affiliations>
</record>
Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/MersV1/Data/Main/Exploration
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000687 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 000687 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien |wiki= Sante |area= MersV1 |flux= Main |étape= Exploration |type= RBID |clé= pubmed:31173943 |texte= BOCS: DNA k-mer content and scoring for rapid genetic biomarker identification at low coverage. }}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:31173943" \ | HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \ | NlmPubMed2Wicri -a MersV1
![]() | This area was generated with Dilib version V0.6.33. | ![]() |