Sequencing by hybridization: towards an automated sequencing of one million M13 clones arrayed on membranes.
Identifieur interne : 002952 ( PubMed/Corpus ); précédent : 002951; suivant : 002953Sequencing by hybridization: towards an automated sequencing of one million M13 clones arrayed on membranes.
Auteurs : R. Drmanac ; S. Drmanac ; I. Labat ; R. Crkvenjakov ; A. Vicentic ; A. GemmellSource :
- Electrophoresis [ 0173-0835 ] ; 1992.
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : DNA.
- genetics : Bacteriophage M13.
- Base Sequence, Cloning, Molecular, Membranes, Artificial, Molecular Sequence Data, Nucleic Acid Hybridization, Oligonucleotide Probes, Phosphorus Radioisotopes, Polymerase Chain Reaction, Robotics.
Abstract
An immediately applicable variant of the sequencing by hybridization (SBH) method is under development with the capacity to determine up to 100 million base pairs per year. The proposed method comprises six steps: (i) arraying genomic or cDNA M13 clones in 864-well plates (wells of 2 mm); (ii) preparation of DNA samples for spotting by growth of the M13 clones or by polymerase chain reaction (PCR) of the inserts using standard 96-well plates, or plates having as many as 864 correspondingly smaller wells; (iii) robotic spotting of 13,824 samples on an 8 x 12 cm nylon membrane, or correspondingly more, on up to 6 times larger filters, by offset printing with a 96 or 864 0.4 mm pin device; (iv) hybridization of dotted samples with 200-2000 32P-labeled probes comprising 16-256 10-mers having a common 8-mer, 7-mer, or 6-mer in the middle (20 probes per day, each hybridized with 250,000 dots); (v) scoring hybridization signals of 5 million sample-probe pairs per day using storage phosphor plates; and (vi) computing clone order and partial-to-complete DNA sequences using various heuristic algorithms. Genome sequencing based on a combination of this method and gel sequencing techniques may be significantly more economical than gel methods alone.
DOI: 10.1002/elps.11501301115
PubMed: 1451694
Links to Exploration step
pubmed:1451694Le document en format XML
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Vicentic</name></author><author><name sortKey="Gemmell, A" sort="Gemmell, A" uniqKey="Gemmell A" first="A" last="Gemmell">A. Gemmell</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="1992">1992</date><idno type="RBID">pubmed:1451694</idno><idno type="pmid">1451694</idno><idno type="doi">10.1002/elps.11501301115</idno><idno type="wicri:Area/PubMed/Corpus">002952</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">002952</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Sequencing by hybridization: towards an automated sequencing of one million M13 clones arrayed on membranes.</title><author><name sortKey="Drmanac, R" sort="Drmanac, R" uniqKey="Drmanac R" first="R" last="Drmanac">R. Drmanac</name><affiliation><nlm:affiliation>Biological and Medical Research Division, Argonne National Laboratory, IL 60439-4833.</nlm:affiliation></affiliation></author><author><name sortKey="Drmanac, S" sort="Drmanac, S" uniqKey="Drmanac S" first="S" last="Drmanac">S. Drmanac</name></author><author><name sortKey="Labat, I" sort="Labat, I" uniqKey="Labat I" first="I" last="Labat">I. Labat</name></author><author><name sortKey="Crkvenjakov, R" sort="Crkvenjakov, R" uniqKey="Crkvenjakov R" first="R" last="Crkvenjakov">R. Crkvenjakov</name></author><author><name sortKey="Vicentic, A" sort="Vicentic, A" uniqKey="Vicentic A" first="A" last="Vicentic">A. Vicentic</name></author><author><name sortKey="Gemmell, A" sort="Gemmell, A" uniqKey="Gemmell A" first="A" last="Gemmell">A. Gemmell</name></author></analytic><series><title level="j">Electrophoresis</title><idno type="ISSN">0173-0835</idno><imprint><date when="1992" type="published">1992</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Bacteriophage M13 (genetics)</term><term>Base Sequence</term><term>Cloning, Molecular</term><term>DNA (chemistry)</term><term>Membranes, Artificial</term><term>Molecular Sequence Data</term><term>Nucleic Acid Hybridization</term><term>Oligonucleotide Probes</term><term>Phosphorus Radioisotopes</term><term>Polymerase Chain Reaction</term><term>Robotics</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>DNA</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Bacteriophage M13</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Base Sequence</term><term>Cloning, Molecular</term><term>Membranes, Artificial</term><term>Molecular Sequence Data</term><term>Nucleic Acid Hybridization</term><term>Oligonucleotide Probes</term><term>Phosphorus Radioisotopes</term><term>Polymerase Chain Reaction</term><term>Robotics</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">An immediately applicable variant of the sequencing by hybridization (SBH) method is under development with the capacity to determine up to 100 million base pairs per year. The proposed method comprises six steps: (i) arraying genomic or cDNA M13 clones in 864-well plates (wells of 2 mm); (ii) preparation of DNA samples for spotting by growth of the M13 clones or by polymerase chain reaction (PCR) of the inserts using standard 96-well plates, or plates having as many as 864 correspondingly smaller wells; (iii) robotic spotting of 13,824 samples on an 8 x 12 cm nylon membrane, or correspondingly more, on up to 6 times larger filters, by offset printing with a 96 or 864 0.4 mm pin device; (iv) hybridization of dotted samples with 200-2000 32P-labeled probes comprising 16-256 10-mers having a common 8-mer, 7-mer, or 6-mer in the middle (20 probes per day, each hybridized with 250,000 dots); (v) scoring hybridization signals of 5 million sample-probe pairs per day using storage phosphor plates; and (vi) computing clone order and partial-to-complete DNA sequences using various heuristic algorithms. Genome sequencing based on a combination of this method and gel sequencing techniques may be significantly more economical than gel methods alone.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">1451694</PMID><DateCompleted><Year>1993</Year><Month>01</Month><Day>06</Day></DateCompleted><DateRevised><Year>2019</Year><Month>10</Month><Day>21</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Print">0173-0835</ISSN><JournalIssue CitedMedium="Print"><Volume>13</Volume><Issue>8</Issue><PubDate><Year>1992</Year><Month>Aug</Month></PubDate></JournalIssue><Title>Electrophoresis</Title><ISOAbbreviation>Electrophoresis</ISOAbbreviation></Journal><ArticleTitle>Sequencing by hybridization: towards an automated sequencing of one million M13 clones arrayed on membranes.</ArticleTitle><Pagination><MedlinePgn>566-73</MedlinePgn></Pagination><Abstract><AbstractText>An immediately applicable variant of the sequencing by hybridization (SBH) method is under development with the capacity to determine up to 100 million base pairs per year. The proposed method comprises six steps: (i) arraying genomic or cDNA M13 clones in 864-well plates (wells of 2 mm); (ii) preparation of DNA samples for spotting by growth of the M13 clones or by polymerase chain reaction (PCR) of the inserts using standard 96-well plates, or plates having as many as 864 correspondingly smaller wells; (iii) robotic spotting of 13,824 samples on an 8 x 12 cm nylon membrane, or correspondingly more, on up to 6 times larger filters, by offset printing with a 96 or 864 0.4 mm pin device; (iv) hybridization of dotted samples with 200-2000 32P-labeled probes comprising 16-256 10-mers having a common 8-mer, 7-mer, or 6-mer in the middle (20 probes per day, each hybridized with 250,000 dots); (v) scoring hybridization signals of 5 million sample-probe pairs per day using storage phosphor plates; and (vi) computing clone order and partial-to-complete DNA sequences using various heuristic algorithms. Genome sequencing based on a combination of this method and gel sequencing techniques may be significantly more economical than gel methods alone.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Drmanac</LastName><ForeName>R</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>Biological and Medical Research Division, Argonne National Laboratory, IL 60439-4833.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Drmanac</LastName><ForeName>S</ForeName><Initials>S</Initials></Author><Author ValidYN="Y"><LastName>Labat</LastName><ForeName>I</ForeName><Initials>I</Initials></Author><Author ValidYN="Y"><LastName>Crkvenjakov</LastName><ForeName>R</ForeName><Initials>R</Initials></Author><Author ValidYN="Y"><LastName>Vicentic</LastName><ForeName>A</ForeName><Initials>A</Initials></Author><Author ValidYN="Y"><LastName>Gemmell</LastName><ForeName>A</ForeName><Initials>A</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType><PublicationType UI="D013486">Research Support, U.S. Gov't, Non-P.H.S.</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>Germany</Country><MedlineTA>Electrophoresis</MedlineTA><NlmUniqueID>8204476</NlmUniqueID><ISSNLinking>0173-0835</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D008567">Membranes, Artificial</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D015345">Oligonucleotide Probes</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D010761">Phosphorus Radioisotopes</NameOfSubstance></Chemical><Chemical><RegistryNumber>9007-49-2</RegistryNumber><NameOfSubstance UI="D004247">DNA</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D017104" MajorTopicYN="N">Bacteriophage M13</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D001483" MajorTopicYN="N">Base Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D003001" MajorTopicYN="N">Cloning, Molecular</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D004247" MajorTopicYN="N">DNA</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D008567" MajorTopicYN="Y">Membranes, Artificial</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008969" MajorTopicYN="N">Molecular Sequence Data</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D009693" MajorTopicYN="N">Nucleic Acid Hybridization</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D015345" MajorTopicYN="N">Oligonucleotide Probes</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010761" MajorTopicYN="N">Phosphorus Radioisotopes</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016133" MajorTopicYN="N">Polymerase Chain Reaction</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012371" MajorTopicYN="N">Robotics</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>1992</Year><Month>8</Month><Day>1</Day></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>1992</Year><Month>8</Month><Day>1</Day><Hour>0</Hour><Minute>1</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>1992</Year><Month>8</Month><Day>1</Day><Hour>0</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">1451694</ArticleId><ArticleId IdType="doi">10.1002/elps.11501301115</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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