Multigene amplification and massively parallel sequencing for cancer mutation discovery
We have developed a procedure for massively parallel resequencing of multiple human genes by combining a highly multiplexed and target-specific amplification process with a high-throughput parallel sequencing technology. The amplification process is based on oligonucleotide constructs, called select...
Gespeichert in:
| Veröffentlicht in: | Proceedings of the National Academy of Sciences - PNAS 2007-05, Vol.104 (22), p.9387-9392 |
|---|---|
| Hauptverfasser: | , , , , , , , , , |
| Format: | Artikel |
| Sprache: | eng |
| Schlagworte: | |
| Online-Zugang: | Volltext |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| container_end_page | 9392 |
|---|---|
| container_issue | 22 |
| container_start_page | 9387 |
| container_title | Proceedings of the National Academy of Sciences - PNAS |
| container_volume | 104 |
| creator | Dahl, Fredrik Stenberg, Johan Fredriksson, Simon Welch, Katrina Zhang, Michael Nilsson, Mats Bicknell, David Bodmer, Walter F Davis, Ronald W Ji, Hanlee |
| description | We have developed a procedure for massively parallel resequencing of multiple human genes by combining a highly multiplexed and target-specific amplification process with a high-throughput parallel sequencing technology. The amplification process is based on oligonucleotide constructs, called selectors, that guide the circularization of specific DNA target regions. Subsequently, the circularized target sequences are amplified in multiplex and analyzed by using a highly parallel sequencing-by-synthesis technology. As a proof-of-concept study, we demonstrate parallel resequencing of 10 cancer genes covering 177 exons with average sequence coverage per sample of 93%. Seven cancer cell lines and one normal genomic DNA sample were studied with multiple mutations and polymorphisms identified among the 10 genes. Mutations and polymorphisms in the TP53 gene were confirmed by traditional sequencing. |
| doi_str_mv | 10.1073/pnas.0702165104 |
| format | Article |
| fullrecord | <record><control><sourceid>jstor_proqu</sourceid><recordid>TN_cdi_proquest_journals_201412032</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><jstor_id>25427863</jstor_id><sourcerecordid>25427863</sourcerecordid><originalsourceid>FETCH-LOGICAL-c655t-4be73c9c6ff02bfab69f9a3ea34ffa1fe3214ffa49ff855135a6542578b63fe03</originalsourceid><addsrcrecordid>eNqFkktv1DAUhSMEokNhzQqIWCAWpL1-JxukqjylIhZQWFpOxh48cuxgJ9POv8dhRh3KAhaWLfk7x_dc36J4jOAEgSCng1fpBARgxBkCeqdYIGhQxWkDd4sFABZVTTE9Kh6ktAaAhtVwvzhCgiHBab0ovn-a3GhX2utS9YOzxnZqtMGXyi_LXqVkN9pty0FF5Zx2ZdI_J-0761elCbHslO90LPtp3KmWNnVho-P2YXHPKJf0o_1-XFy-e_v1_EN18fn9x_Ozi6rjjI0VbbUgXdNxYwC3RrW8MY0iWhFqjEJGE4zmE22MqRlDhCnOKGaibjkxGshx8Wrnm670MLVyiLZXcSuDsvKN_XYmQ1zJaZIIEBCe8dc7PLO9XnbajznYLdXtG29_yFXYSFQLxDjJBi_2BjHkTqRR9jmydk55HaYkBTCOKGX_BVHDa9HguaTnf4HrMEWfmyYxIIowEJyh0x3UxZBS1OamZARyngQ5T4I8TEJWPP0z6YHff30Gnu2BWXmwoxJj2ZBaZOLlvwlpJudGfT1m9MkOXacxxBsW578S9e-27R8zKki1ijbJyy85HgEQ9bzIL9s43LI</addsrcrecordid><sourcetype>Open Access Repository</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>201412032</pqid></control><display><type>article</type><title>Multigene amplification and massively parallel sequencing for cancer mutation discovery</title><source>MEDLINE</source><source>Jstor Complete Legacy</source><source>PubMed Central</source><source>Alma/SFX Local Collection</source><source>Free Full-Text Journals in Chemistry</source><creator>Dahl, Fredrik ; Stenberg, Johan ; Fredriksson, Simon ; Welch, Katrina ; Zhang, Michael ; Nilsson, Mats ; Bicknell, David ; Bodmer, Walter F ; Davis, Ronald W ; Ji, Hanlee</creator><creatorcontrib>Dahl, Fredrik ; Stenberg, Johan ; Fredriksson, Simon ; Welch, Katrina ; Zhang, Michael ; Nilsson, Mats ; Bicknell, David ; Bodmer, Walter F ; Davis, Ronald W ; Ji, Hanlee</creatorcontrib><description>We have developed a procedure for massively parallel resequencing of multiple human genes by combining a highly multiplexed and target-specific amplification process with a high-throughput parallel sequencing technology. The amplification process is based on oligonucleotide constructs, called selectors, that guide the circularization of specific DNA target regions. Subsequently, the circularized target sequences are amplified in multiplex and analyzed by using a highly parallel sequencing-by-synthesis technology. As a proof-of-concept study, we demonstrate parallel resequencing of 10 cancer genes covering 177 exons with average sequence coverage per sample of 93%. Seven cancer cell lines and one normal genomic DNA sample were studied with multiple mutations and polymorphisms identified among the 10 genes. Mutations and polymorphisms in the TP53 gene were confirmed by traditional sequencing.</description><identifier>ISSN: 0027-8424</identifier><identifier>ISSN: 1091-6490</identifier><identifier>EISSN: 1091-6490</identifier><identifier>DOI: 10.1073/pnas.0702165104</identifier><identifier>PMID: 17517648</identifier><language>eng</language><publisher>United States: National Academy of Sciences</publisher><subject>Base Sequence ; Biological Sciences ; Cancer ; cancer analysis ; Cell Line, Tumor ; Cell lines ; Colorectal cancer ; Deoxyribonucleic acid ; DNA ; DNA probes ; Exons ; Gene amplification ; Genes ; Genes, Neoplasm - genetics ; Genetic mutation ; Genetic Testing - methods ; Genomics ; high-throughput sequencing ; Humans ; MEDICIN ; MEDICINE ; Molecular Sequence Data ; multiplex amplification ; Mutation ; Mutation - genetics ; Neoplasms - genetics ; Nucleic Acid Amplification Techniques - methods ; Oligonucleotide probes ; Oligonucleotides ; Polymorphism ; Sequencing ; Tumor Suppressor Protein p53 - genetics</subject><ispartof>Proceedings of the National Academy of Sciences - PNAS, 2007-05, Vol.104 (22), p.9387-9392</ispartof><rights>Copyright 2007 The National Academy of Sciences of the United States of America</rights><rights>Copyright National Academy of Sciences May 29, 2007</rights><rights>2007 by The National Academy of Sciences of the USA 2007</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c655t-4be73c9c6ff02bfab69f9a3ea34ffa1fe3214ffa49ff855135a6542578b63fe03</citedby><cites>FETCH-LOGICAL-c655t-4be73c9c6ff02bfab69f9a3ea34ffa1fe3214ffa49ff855135a6542578b63fe03</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Uhttp://www.pnas.org/content/104/22.cover.gif</thumbnail><linktopdf>$$Uhttps://www.jstor.org/stable/pdf/25427863$$EPDF$$P50$$Gjstor$$H</linktopdf><linktohtml>$$Uhttps://www.jstor.org/stable/25427863$$EHTML$$P50$$Gjstor$$H</linktohtml><link.rule.ids>230,314,727,780,784,803,885,27915,27916,53782,53784,58008,58241</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/17517648$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-101036$$DView record from Swedish Publication Index$$Hfree_for_read</backlink></links><search><creatorcontrib>Dahl, Fredrik</creatorcontrib><creatorcontrib>Stenberg, Johan</creatorcontrib><creatorcontrib>Fredriksson, Simon</creatorcontrib><creatorcontrib>Welch, Katrina</creatorcontrib><creatorcontrib>Zhang, Michael</creatorcontrib><creatorcontrib>Nilsson, Mats</creatorcontrib><creatorcontrib>Bicknell, David</creatorcontrib><creatorcontrib>Bodmer, Walter F</creatorcontrib><creatorcontrib>Davis, Ronald W</creatorcontrib><creatorcontrib>Ji, Hanlee</creatorcontrib><title>Multigene amplification and massively parallel sequencing for cancer mutation discovery</title><title>Proceedings of the National Academy of Sciences - PNAS</title><addtitle>Proc Natl Acad Sci U S A</addtitle><description>We have developed a procedure for massively parallel resequencing of multiple human genes by combining a highly multiplexed and target-specific amplification process with a high-throughput parallel sequencing technology. The amplification process is based on oligonucleotide constructs, called selectors, that guide the circularization of specific DNA target regions. Subsequently, the circularized target sequences are amplified in multiplex and analyzed by using a highly parallel sequencing-by-synthesis technology. As a proof-of-concept study, we demonstrate parallel resequencing of 10 cancer genes covering 177 exons with average sequence coverage per sample of 93%. Seven cancer cell lines and one normal genomic DNA sample were studied with multiple mutations and polymorphisms identified among the 10 genes. Mutations and polymorphisms in the TP53 gene were confirmed by traditional sequencing.</description><subject>Base Sequence</subject><subject>Biological Sciences</subject><subject>Cancer</subject><subject>cancer analysis</subject><subject>Cell Line, Tumor</subject><subject>Cell lines</subject><subject>Colorectal cancer</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA probes</subject><subject>Exons</subject><subject>Gene amplification</subject><subject>Genes</subject><subject>Genes, Neoplasm - genetics</subject><subject>Genetic mutation</subject><subject>Genetic Testing - methods</subject><subject>Genomics</subject><subject>high-throughput sequencing</subject><subject>Humans</subject><subject>MEDICIN</subject><subject>MEDICINE</subject><subject>Molecular Sequence Data</subject><subject>multiplex amplification</subject><subject>Mutation</subject><subject>Mutation - genetics</subject><subject>Neoplasms - genetics</subject><subject>Nucleic Acid Amplification Techniques - methods</subject><subject>Oligonucleotide probes</subject><subject>Oligonucleotides</subject><subject>Polymorphism</subject><subject>Sequencing</subject><subject>Tumor Suppressor Protein p53 - genetics</subject><issn>0027-8424</issn><issn>1091-6490</issn><issn>1091-6490</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2007</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkktv1DAUhSMEokNhzQqIWCAWpL1-JxukqjylIhZQWFpOxh48cuxgJ9POv8dhRh3KAhaWLfk7x_dc36J4jOAEgSCng1fpBARgxBkCeqdYIGhQxWkDd4sFABZVTTE9Kh6ktAaAhtVwvzhCgiHBab0ovn-a3GhX2utS9YOzxnZqtMGXyi_LXqVkN9pty0FF5Zx2ZdI_J-0761elCbHslO90LPtp3KmWNnVho-P2YXHPKJf0o_1-XFy-e_v1_EN18fn9x_Ozi6rjjI0VbbUgXdNxYwC3RrW8MY0iWhFqjEJGE4zmE22MqRlDhCnOKGaibjkxGshx8Wrnm670MLVyiLZXcSuDsvKN_XYmQ1zJaZIIEBCe8dc7PLO9XnbajznYLdXtG29_yFXYSFQLxDjJBi_2BjHkTqRR9jmydk55HaYkBTCOKGX_BVHDa9HguaTnf4HrMEWfmyYxIIowEJyh0x3UxZBS1OamZARyngQ5T4I8TEJWPP0z6YHff30Gnu2BWXmwoxJj2ZBaZOLlvwlpJudGfT1m9MkOXacxxBsW578S9e-27R8zKki1ijbJyy85HgEQ9bzIL9s43LI</recordid><startdate>20070529</startdate><enddate>20070529</enddate><creator>Dahl, Fredrik</creator><creator>Stenberg, Johan</creator><creator>Fredriksson, Simon</creator><creator>Welch, Katrina</creator><creator>Zhang, Michael</creator><creator>Nilsson, Mats</creator><creator>Bicknell, David</creator><creator>Bodmer, Walter F</creator><creator>Davis, Ronald W</creator><creator>Ji, Hanlee</creator><general>National Academy of Sciences</general><general>National Acad Sciences</general><scope>FBQ</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QG</scope><scope>7QL</scope><scope>7QP</scope><scope>7QR</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TK</scope><scope>7TM</scope><scope>7TO</scope><scope>7U9</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>H94</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7QO</scope><scope>7X8</scope><scope>5PM</scope><scope>ADTPV</scope><scope>AOWAS</scope><scope>DF2</scope></search><sort><creationdate>20070529</creationdate><title>Multigene amplification and massively parallel sequencing for cancer mutation discovery</title><author>Dahl, Fredrik ; Stenberg, Johan ; Fredriksson, Simon ; Welch, Katrina ; Zhang, Michael ; Nilsson, Mats ; Bicknell, David ; Bodmer, Walter F ; Davis, Ronald W ; Ji, Hanlee</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c655t-4be73c9c6ff02bfab69f9a3ea34ffa1fe3214ffa49ff855135a6542578b63fe03</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2007</creationdate><topic>Base Sequence</topic><topic>Biological Sciences</topic><topic>Cancer</topic><topic>cancer analysis</topic><topic>Cell Line, Tumor</topic><topic>Cell lines</topic><topic>Colorectal cancer</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>DNA probes</topic><topic>Exons</topic><topic>Gene amplification</topic><topic>Genes</topic><topic>Genes, Neoplasm - genetics</topic><topic>Genetic mutation</topic><topic>Genetic Testing - methods</topic><topic>Genomics</topic><topic>high-throughput sequencing</topic><topic>Humans</topic><topic>MEDICIN</topic><topic>MEDICINE</topic><topic>Molecular Sequence Data</topic><topic>multiplex amplification</topic><topic>Mutation</topic><topic>Mutation - genetics</topic><topic>Neoplasms - genetics</topic><topic>Nucleic Acid Amplification Techniques - methods</topic><topic>Oligonucleotide probes</topic><topic>Oligonucleotides</topic><topic>Polymorphism</topic><topic>Sequencing</topic><topic>Tumor Suppressor Protein p53 - genetics</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Dahl, Fredrik</creatorcontrib><creatorcontrib>Stenberg, Johan</creatorcontrib><creatorcontrib>Fredriksson, Simon</creatorcontrib><creatorcontrib>Welch, Katrina</creatorcontrib><creatorcontrib>Zhang, Michael</creatorcontrib><creatorcontrib>Nilsson, Mats</creatorcontrib><creatorcontrib>Bicknell, David</creatorcontrib><creatorcontrib>Bodmer, Walter F</creatorcontrib><creatorcontrib>Davis, Ronald W</creatorcontrib><creatorcontrib>Ji, Hanlee</creatorcontrib><collection>AGRIS</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Animal Behavior Abstracts</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Calcium & Calcified Tissue Abstracts</collection><collection>Chemoreception Abstracts</collection><collection>Ecology Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Immunology Abstracts</collection><collection>Neurosciences Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Oncogenes and Growth Factors Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>Biotechnology Research Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>SwePub</collection><collection>SwePub Articles</collection><collection>SWEPUB Uppsala universitet</collection><jtitle>Proceedings of the National Academy of Sciences - PNAS</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Dahl, Fredrik</au><au>Stenberg, Johan</au><au>Fredriksson, Simon</au><au>Welch, Katrina</au><au>Zhang, Michael</au><au>Nilsson, Mats</au><au>Bicknell, David</au><au>Bodmer, Walter F</au><au>Davis, Ronald W</au><au>Ji, Hanlee</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Multigene amplification and massively parallel sequencing for cancer mutation discovery</atitle><jtitle>Proceedings of the National Academy of Sciences - PNAS</jtitle><addtitle>Proc Natl Acad Sci U S A</addtitle><date>2007-05-29</date><risdate>2007</risdate><volume>104</volume><issue>22</issue><spage>9387</spage><epage>9392</epage><pages>9387-9392</pages><issn>0027-8424</issn><issn>1091-6490</issn><eissn>1091-6490</eissn><abstract>We have developed a procedure for massively parallel resequencing of multiple human genes by combining a highly multiplexed and target-specific amplification process with a high-throughput parallel sequencing technology. The amplification process is based on oligonucleotide constructs, called selectors, that guide the circularization of specific DNA target regions. Subsequently, the circularized target sequences are amplified in multiplex and analyzed by using a highly parallel sequencing-by-synthesis technology. As a proof-of-concept study, we demonstrate parallel resequencing of 10 cancer genes covering 177 exons with average sequence coverage per sample of 93%. Seven cancer cell lines and one normal genomic DNA sample were studied with multiple mutations and polymorphisms identified among the 10 genes. Mutations and polymorphisms in the TP53 gene were confirmed by traditional sequencing.</abstract><cop>United States</cop><pub>National Academy of Sciences</pub><pmid>17517648</pmid><doi>10.1073/pnas.0702165104</doi><tpages>6</tpages><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 0027-8424 |
| ispartof | Proceedings of the National Academy of Sciences - PNAS, 2007-05, Vol.104 (22), p.9387-9392 |
| issn | 0027-8424 1091-6490 1091-6490 |
| language | eng |
| recordid | cdi_proquest_journals_201412032 |
| source | MEDLINE; Jstor Complete Legacy; PubMed Central; Alma/SFX Local Collection; Free Full-Text Journals in Chemistry |
| subjects | Base Sequence Biological Sciences Cancer cancer analysis Cell Line, Tumor Cell lines Colorectal cancer Deoxyribonucleic acid DNA DNA probes Exons Gene amplification Genes Genes, Neoplasm - genetics Genetic mutation Genetic Testing - methods Genomics high-throughput sequencing Humans MEDICIN MEDICINE Molecular Sequence Data multiplex amplification Mutation Mutation - genetics Neoplasms - genetics Nucleic Acid Amplification Techniques - methods Oligonucleotide probes Oligonucleotides Polymorphism Sequencing Tumor Suppressor Protein p53 - genetics |
| title | Multigene amplification and massively parallel sequencing for cancer mutation discovery |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-15T03%3A30%3A58IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-jstor_proqu&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Multigene%20amplification%20and%20massively%20parallel%20sequencing%20for%20cancer%20mutation%20discovery&rft.jtitle=Proceedings%20of%20the%20National%20Academy%20of%20Sciences%20-%20PNAS&rft.au=Dahl,%20Fredrik&rft.date=2007-05-29&rft.volume=104&rft.issue=22&rft.spage=9387&rft.epage=9392&rft.pages=9387-9392&rft.issn=0027-8424&rft.eissn=1091-6490&rft_id=info:doi/10.1073/pnas.0702165104&rft_dat=%3Cjstor_proqu%3E25427863%3C/jstor_proqu%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=201412032&rft_id=info:pmid/17517648&rft_jstor_id=25427863&rfr_iscdi=true |