High-throughput sequencing: a failure mode analysis.
Identifieur interne : 004024 ( Main/Exploration ); précédent : 004023; suivant : 004025High-throughput sequencing: a failure mode analysis.
Auteurs : George S. Yang [Canada] ; Jeffery M. Stott ; Duane Smailus ; Sarah A. Barber ; Miruna Balasundaram ; Marco A. Marra ; Robert A. HoltSource :
- BMC genomics [ 1471-2164 ] ; 2005.
Descripteurs français
- KwdFr :
- Amorces ADN (MeSH), Analyse de profil d'expression de gènes (MeSH), Analyse de séquence d'ADN (méthodes), Analyse de séquence d'ADN (économie), Automatisation (MeSH), Banque de gènes (MeSH), Biologie informatique (méthodes), Biotechnologie (instrumentation), Biotechnologie (méthodes), Biotechnologie (économie), Cartographie chromosomique (MeSH), Logiciel (MeSH), Modèles statistiques (MeSH), Plasmides (métabolisme), Populus (métabolisme), Étiquettes de séquences exprimées (MeSH).
- MESH :
- métabolisme : Plasmides, Populus.
- méthodes : Analyse de séquence d'ADN, Biologie informatique, Biotechnologie.
- économie : Analyse de séquence d'ADN, Biotechnologie.
- Amorces ADN, Analyse de profil d'expression de gènes, Automatisation, Banque de gènes, Cartographie chromosomique, Logiciel, Modèles statistiques, Étiquettes de séquences exprimées.
English descriptors
- KwdEn :
- Automation (MeSH), Biotechnology (economics), Biotechnology (instrumentation), Biotechnology (methods), Chromosome Mapping (MeSH), Computational Biology (methods), DNA Primers (MeSH), Expressed Sequence Tags (MeSH), Gene Expression Profiling (MeSH), Gene Library (MeSH), Models, Statistical (MeSH), Plasmids (metabolism), Populus (metabolism), Sequence Analysis, DNA (economics), Sequence Analysis, DNA (methods), Software (MeSH).
- MESH :
- chemical : DNA Primers.
- economics : Biotechnology, Sequence Analysis, DNA.
- instrumentation : Biotechnology.
- metabolism : Plasmids, Populus.
- methods : Biotechnology, Computational Biology, Sequence Analysis, DNA.
- Automation, Chromosome Mapping, Expressed Sequence Tags, Gene Expression Profiling, Gene Library, Models, Statistical, Software.
Abstract
BACKGROUND
Basic manufacturing principles are becoming increasingly important in high-throughput sequencing facilities where there is a constant drive to increase quality, increase efficiency, and decrease operating costs. While high-throughput centres report failure rates typically on the order of 10%, the causes of sporadic sequencing failures are seldom analyzed in detail and have not, in the past, been formally reported.
RESULTS
Here we report the results of a failure mode analysis of our production sequencing facility based on detailed evaluation of 9,216 ESTs generated from two cDNA libraries. Two categories of failures are described; process-related failures (failures due to equipment or sample handling) and template-related failures (failures that are revealed by close inspection of electropherograms and are likely due to properties of the template DNA sequence itself).
CONCLUSIONS
Preventative action based on a detailed understanding of failure modes is likely to improve the performance of other production sequencing pipelines.
DOI: 10.1186/1471-2164-6-2
PubMed: 15631628
PubMed Central: PMC546001
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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Stott</name></author><author><name sortKey="Smailus, Duane" sort="Smailus, Duane" uniqKey="Smailus D" first="Duane" last="Smailus">Duane Smailus</name></author><author><name sortKey="Barber, Sarah A" sort="Barber, Sarah A" uniqKey="Barber S" first="Sarah A" last="Barber">Sarah A. Barber</name></author><author><name sortKey="Balasundaram, Miruna" sort="Balasundaram, Miruna" uniqKey="Balasundaram M" first="Miruna" last="Balasundaram">Miruna Balasundaram</name></author><author><name sortKey="Marra, Marco A" sort="Marra, Marco A" uniqKey="Marra M" first="Marco A" last="Marra">Marco A. Marra</name></author><author><name sortKey="Holt, Robert A" sort="Holt, Robert A" uniqKey="Holt R" first="Robert A" last="Holt">Robert A. Holt</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2005">2005</date><idno type="RBID">pubmed:15631628</idno><idno type="pmid">15631628</idno><idno type="doi">10.1186/1471-2164-6-2</idno><idno type="pmc">PMC546001</idno><idno type="wicri:Area/Main/Corpus">004143</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">004143</idno><idno type="wicri:Area/Main/Curation">004143</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">004143</idno><idno type="wicri:Area/Main/Exploration">004143</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">High-throughput sequencing: a failure mode analysis.</title><author><name sortKey="Yang, George S" sort="Yang, George S" uniqKey="Yang G" first="George S" last="Yang">George S. Yang</name><affiliation wicri:level="1"><nlm:affiliation>Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Centre, Suite 100, 570 West 7th Avenue, Vancouver, BC, Canada. gyang@bcgsc.ca</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Centre, Suite 100, 570 West 7th Avenue, Vancouver, BC</wicri:regionArea><wicri:noRegion>BC</wicri:noRegion></affiliation></author><author><name sortKey="Stott, Jeffery M" sort="Stott, Jeffery M" uniqKey="Stott J" first="Jeffery M" last="Stott">Jeffery M. Stott</name></author><author><name sortKey="Smailus, Duane" sort="Smailus, Duane" uniqKey="Smailus D" first="Duane" last="Smailus">Duane Smailus</name></author><author><name sortKey="Barber, Sarah A" sort="Barber, Sarah A" uniqKey="Barber S" first="Sarah A" last="Barber">Sarah A. Barber</name></author><author><name sortKey="Balasundaram, Miruna" sort="Balasundaram, Miruna" uniqKey="Balasundaram M" first="Miruna" last="Balasundaram">Miruna Balasundaram</name></author><author><name sortKey="Marra, Marco A" sort="Marra, Marco A" uniqKey="Marra M" first="Marco A" last="Marra">Marco A. Marra</name></author><author><name sortKey="Holt, Robert A" sort="Holt, Robert A" uniqKey="Holt R" first="Robert A" last="Holt">Robert A. Holt</name></author></analytic><series><title level="j">BMC genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2005" type="published">2005</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Automation (MeSH)</term><term>Biotechnology (economics)</term><term>Biotechnology (instrumentation)</term><term>Biotechnology (methods)</term><term>Chromosome Mapping (MeSH)</term><term>Computational Biology (methods)</term><term>DNA Primers (MeSH)</term><term>Expressed Sequence Tags (MeSH)</term><term>Gene Expression Profiling (MeSH)</term><term>Gene Library (MeSH)</term><term>Models, Statistical (MeSH)</term><term>Plasmids (metabolism)</term><term>Populus (metabolism)</term><term>Sequence Analysis, DNA (economics)</term><term>Sequence Analysis, DNA (methods)</term><term>Software (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Amorces ADN (MeSH)</term><term>Analyse de profil d'expression de gènes (MeSH)</term><term>Analyse de séquence d'ADN (méthodes)</term><term>Analyse de séquence d'ADN (économie)</term><term>Automatisation (MeSH)</term><term>Banque de gènes (MeSH)</term><term>Biologie informatique (méthodes)</term><term>Biotechnologie (instrumentation)</term><term>Biotechnologie (méthodes)</term><term>Biotechnologie (économie)</term><term>Cartographie chromosomique (MeSH)</term><term>Logiciel (MeSH)</term><term>Modèles statistiques (MeSH)</term><term>Plasmides (métabolisme)</term><term>Populus (métabolisme)</term><term>Étiquettes de séquences exprimées (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" xml:lang="en"><term>DNA Primers</term></keywords><keywords scheme="MESH" qualifier="economics" xml:lang="en"><term>Biotechnology</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" qualifier="instrumentation" xml:lang="en"><term>Biotechnology</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Plasmids</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Biotechnology</term><term>Computational Biology</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Plasmides</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="méthodes" xml:lang="fr"><term>Analyse de séquence d'ADN</term><term>Biologie informatique</term><term>Biotechnologie</term></keywords><keywords scheme="MESH" qualifier="économie" xml:lang="fr"><term>Analyse de séquence d'ADN</term><term>Biotechnologie</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Automation</term><term>Chromosome Mapping</term><term>Expressed Sequence Tags</term><term>Gene Expression Profiling</term><term>Gene Library</term><term>Models, Statistical</term><term>Software</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Amorces ADN</term><term>Analyse de profil d'expression de gènes</term><term>Automatisation</term><term>Banque de gènes</term><term>Cartographie chromosomique</term><term>Logiciel</term><term>Modèles statistiques</term><term>Étiquettes de séquences exprimées</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><b>BACKGROUND</b></p><p>Basic manufacturing principles are becoming increasingly important in high-throughput sequencing facilities where there is a constant drive to increase quality, increase efficiency, and decrease operating costs. While high-throughput centres report failure rates typically on the order of 10%, the causes of sporadic sequencing failures are seldom analyzed in detail and have not, in the past, been formally reported.</p></div><div type="abstract" xml:lang="en"><p><b>RESULTS</b></p><p>Here we report the results of a failure mode analysis of our production sequencing facility based on detailed evaluation of 9,216 ESTs generated from two cDNA libraries. Two categories of failures are described; process-related failures (failures due to equipment or sample handling) and template-related failures (failures that are revealed by close inspection of electropherograms and are likely due to properties of the template DNA sequence itself).</p></div><div type="abstract" xml:lang="en"><p><b>CONCLUSIONS</b></p><p>Preventative action based on a detailed understanding of failure modes is likely to improve the performance of other production sequencing pipelines.</p></div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">15631628</PMID><DateCompleted><Year>2006</Year><Month>05</Month><Day>01</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2164</ISSN><JournalIssue CitedMedium="Internet"><Volume>6</Volume><PubDate><Year>2005</Year><Month>Jan</Month><Day>04</Day></PubDate></JournalIssue><Title>BMC genomics</Title><ISOAbbreviation>BMC Genomics</ISOAbbreviation></Journal><ArticleTitle>High-throughput sequencing: a failure mode analysis.</ArticleTitle><Pagination><MedlinePgn>2</MedlinePgn></Pagination><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">Basic manufacturing principles are becoming increasingly important in high-throughput sequencing facilities where there is a constant drive to increase quality, increase efficiency, and decrease operating costs. While high-throughput centres report failure rates typically on the order of 10%, the causes of sporadic sequencing failures are seldom analyzed in detail and have not, in the past, been formally reported.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">Here we report the results of a failure mode analysis of our production sequencing facility based on detailed evaluation of 9,216 ESTs generated from two cDNA libraries. 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ValidYN="Y"><LastName>Smailus</LastName><ForeName>Duane</ForeName><Initials>D</Initials></Author><Author ValidYN="Y"><LastName>Barber</LastName><ForeName>Sarah A</ForeName><Initials>SA</Initials></Author><Author ValidYN="Y"><LastName>Balasundaram</LastName><ForeName>Miruna</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Marra</LastName><ForeName>Marco A</ForeName><Initials>MA</Initials></Author><Author ValidYN="Y"><LastName>Holt</LastName><ForeName>Robert A</ForeName><Initials>RA</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2005</Year><Month>01</Month><Day>04</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>BMC 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IdType="pubmed">15631628</ArticleId><ArticleId IdType="pii">1471-2164-6-2</ArticleId><ArticleId IdType="doi">10.1186/1471-2164-6-2</ArticleId><ArticleId IdType="pmc">PMC546001</ArticleId></ArticleIdList><ReferenceList><Reference><Citation>Genome Res. 2001 Jul;11(7):1269-74</Citation><ArticleIdList><ArticleId IdType="pubmed">11435410</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Res. 1998 Mar;8(3):186-94</Citation><ArticleIdList><ArticleId IdType="pubmed">9521922</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 1991 Dec 11;19(23):6481-3</Citation><ArticleIdList><ArticleId IdType="pubmed">1754386</ArticleId></ArticleIdList></Reference></ReferenceList></PubmedData></pubmed><affiliations><list><country><li>Canada</li></country></list><tree><noCountry><name sortKey="Balasundaram, Miruna" sort="Balasundaram, Miruna" uniqKey="Balasundaram M" first="Miruna" last="Balasundaram">Miruna Balasundaram</name><name sortKey="Barber, Sarah A" sort="Barber, Sarah A" uniqKey="Barber S" first="Sarah A" last="Barber">Sarah A. Barber</name><name sortKey="Holt, Robert A" sort="Holt, Robert A" uniqKey="Holt R" first="Robert A" last="Holt">Robert A. Holt</name><name sortKey="Marra, Marco A" sort="Marra, Marco A" uniqKey="Marra M" first="Marco A" last="Marra">Marco A. Marra</name><name sortKey="Smailus, Duane" sort="Smailus, Duane" uniqKey="Smailus D" first="Duane" last="Smailus">Duane Smailus</name><name sortKey="Stott, Jeffery M" sort="Stott, Jeffery M" uniqKey="Stott J" first="Jeffery M" last="Stott">Jeffery M. Stott</name></noCountry><country name="Canada"><noRegion><name sortKey="Yang, George S" sort="Yang, George S" uniqKey="Yang G" first="George S" last="Yang">George S. Yang</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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