Clinical Validation of Targeted Next Generation Sequencing for Colon and Lung Cancers
Recently, Next Generation Sequencing (NGS) has begun to supplant other technologies for gene mutation testing that is now required for targeted therapies. However, transfer of NGS technology to clinical daily practice requires validation. We validated the Ion Torrent AmpliSeq Colon and Lung cancer p...
Gespeichert in:
| Veröffentlicht in: | PloS one 2015-09, Vol.10 (9), p.e0138245-e0138245 |
|---|---|
| Hauptverfasser: | , , , , , , , , , , , |
| Format: | Artikel |
| Sprache: | eng |
| Schlagworte: | |
| Online-Zugang: | Volltext |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| container_end_page | e0138245 |
|---|---|
| container_issue | 9 |
| container_start_page | e0138245 |
| container_title | PloS one |
| container_volume | 10 |
| creator | D'Haene, Nicky Le Mercier, Marie De Nève, Nancy Blanchard, Oriane Delaunoy, Mélanie El Housni, Hakim Dessars, Barbara Heimann, Pierre Remmelink, Myriam Demetter, Pieter Tejpar, Sabine Salmon, Isabelle |
| description | Recently, Next Generation Sequencing (NGS) has begun to supplant other technologies for gene mutation testing that is now required for targeted therapies. However, transfer of NGS technology to clinical daily practice requires validation.
We validated the Ion Torrent AmpliSeq Colon and Lung cancer panel interrogating 1850 hotspots in 22 genes using the Ion Torrent Personal Genome Machine. First, we used commercial reference standards that carry mutations at defined allelic frequency (AF). Then, 51 colorectal adenocarcinomas (CRC) and 39 non small cell lung carcinomas (NSCLC) were retrospectively analyzed.
Sensitivity and accuracy for detecting variants at an AF >4% was 100% for commercial reference standards. Among the 90 cases, 89 (98.9%) were successfully sequenced. Among the 86 samples for which NGS and the reference test were both informative, 83 showed concordant results between NGS and the reference test; i.e. KRAS and BRAF for CRC and EGFR for NSCLC, with the 3 discordant cases each characterized by an AF |
| doi_str_mv | 10.1371/journal.pone.0138245 |
| format | Article |
| fullrecord | <record><control><sourceid>gale_plos_</sourceid><recordid>TN_cdi_plos_journals_1719284409</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><galeid>A428586995</galeid><doaj_id>oai_doaj_org_article_b17bb6a9aaa14d62b0cb8cefacd67156</doaj_id><sourcerecordid>A428586995</sourcerecordid><originalsourceid>FETCH-LOGICAL-c758t-647626a50877fb730e4e0933b240993a98bf3b29b67f44b9efec666b729af13a3</originalsourceid><addsrcrecordid>eNqNkl2P1CAUhhujcdfRf2C0iYnRixkLtFBuTDYTXSeZuIn7cUsOlHbYMDBCa_Tfy-x0N1OzF4YL4PCc98DhzbLXqFggwtCnWz8EB3ax804vCkRqXFZPslPECZ5TXJCnR-uT7EWMt0VRkZrS59kJpoTSqmKn2fXSGmcU2PwGrGmgN97lvs2vIHS6103-Xf_u83PtdDicXeqfg3bKuC5vfciX3qYguCZfDym0BKd0iC-zZy3YqF-N8yy7_vrlavltvr44Xy3P1nPFqrqf05JRTKEqasZayUihS11wQiQuC84J8Fq2acMlZW1ZSq5brSilkmEOLSJAZtnbg-7O-ijGjkSBGOK4LpNIIlYHovFwK3bBbCH8ER6MuAv40AkIvVFWC4mYlBQ4AKCyoVgWStZKt6AaylBFk9bnsdogt7pR2vUB7ER0euLMRnT-lygrytOfJYEPo0DwqYuxF1sTlbYWnPbD3b0xqxFO8Cx79w_6-OtGqoP0AONan-qqvag4K3Fd1ZTzKlGLR6g0Gr01KtmnNSk-Sfg4SUhMn2zQwRCjWF3--H_24mbKvj9iNxpsv4neDntjxSlYHkAVfIxBtw9NRoXYu_--G2LvfjG6P6W9Of6gh6R7u5O_5uv-2g</addsrcrecordid><sourcetype>Open Website</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>1719284409</pqid></control><display><type>article</type><title>Clinical Validation of Targeted Next Generation Sequencing for Colon and Lung Cancers</title><source>MEDLINE</source><source>DOAJ Directory of Open Access Journals</source><source>Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals</source><source>PubMed Central</source><source>Free Full-Text Journals in Chemistry</source><source>Public Library of Science (PLoS)</source><creator>D'Haene, Nicky ; Le Mercier, Marie ; De Nève, Nancy ; Blanchard, Oriane ; Delaunoy, Mélanie ; El Housni, Hakim ; Dessars, Barbara ; Heimann, Pierre ; Remmelink, Myriam ; Demetter, Pieter ; Tejpar, Sabine ; Salmon, Isabelle</creator><contributor>Scarpa, Aldo</contributor><creatorcontrib>D'Haene, Nicky ; Le Mercier, Marie ; De Nève, Nancy ; Blanchard, Oriane ; Delaunoy, Mélanie ; El Housni, Hakim ; Dessars, Barbara ; Heimann, Pierre ; Remmelink, Myriam ; Demetter, Pieter ; Tejpar, Sabine ; Salmon, Isabelle ; Scarpa, Aldo</creatorcontrib><description>Recently, Next Generation Sequencing (NGS) has begun to supplant other technologies for gene mutation testing that is now required for targeted therapies. However, transfer of NGS technology to clinical daily practice requires validation.
We validated the Ion Torrent AmpliSeq Colon and Lung cancer panel interrogating 1850 hotspots in 22 genes using the Ion Torrent Personal Genome Machine. First, we used commercial reference standards that carry mutations at defined allelic frequency (AF). Then, 51 colorectal adenocarcinomas (CRC) and 39 non small cell lung carcinomas (NSCLC) were retrospectively analyzed.
Sensitivity and accuracy for detecting variants at an AF >4% was 100% for commercial reference standards. Among the 90 cases, 89 (98.9%) were successfully sequenced. Among the 86 samples for which NGS and the reference test were both informative, 83 showed concordant results between NGS and the reference test; i.e. KRAS and BRAF for CRC and EGFR for NSCLC, with the 3 discordant cases each characterized by an AF <10%.
Overall, the AmpliSeq colon/lung cancer panel was specific and sensitive for mutation analysis of gene panels and can be incorporated into clinical daily practice.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0138245</identifier><identifier>PMID: 26366557</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Aerospace technology transfer ; Audio frequencies ; Cancer ; Carcinoma, Non-Small-Cell Lung - genetics ; Colon ; Colon cancer ; Colonic Neoplasms - genetics ; Colorectal cancer ; Deoxyribonucleic acid ; DNA ; DNA Mutational Analysis - methods ; DNA, Neoplasm - genetics ; Epidermal growth factor receptors ; Female ; Gene Frequency ; Gene mutation ; Gene sequencing ; Genes ; Genetics ; Genomes ; Genomics ; High-Throughput Nucleotide Sequencing - methods ; Humans ; Lung cancer ; Lung carcinoma ; Lung diseases ; Lung Neoplasms - genetics ; Male ; Mutation ; Neoplasm Proteins - genetics ; Non-small cell lung cancer ; Non-small cell lung carcinoma ; Pathology ; Point mutation ; Sensitivity analysis ; Sensitivity and Specificity ; Small cell lung carcinoma ; Technology application ; Technology transfer</subject><ispartof>PloS one, 2015-09, Vol.10 (9), p.e0138245-e0138245</ispartof><rights>COPYRIGHT 2015 Public Library of Science</rights><rights>2015 D’Haene et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2015 D’Haene et al 2015 D’Haene et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c758t-647626a50877fb730e4e0933b240993a98bf3b29b67f44b9efec666b729af13a3</citedby><cites>FETCH-LOGICAL-c758t-647626a50877fb730e4e0933b240993a98bf3b29b67f44b9efec666b729af13a3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4569137/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4569137/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,2096,2915,23847,27903,27904,53769,53771,79346,79347</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/26366557$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Scarpa, Aldo</contributor><creatorcontrib>D'Haene, Nicky</creatorcontrib><creatorcontrib>Le Mercier, Marie</creatorcontrib><creatorcontrib>De Nève, Nancy</creatorcontrib><creatorcontrib>Blanchard, Oriane</creatorcontrib><creatorcontrib>Delaunoy, Mélanie</creatorcontrib><creatorcontrib>El Housni, Hakim</creatorcontrib><creatorcontrib>Dessars, Barbara</creatorcontrib><creatorcontrib>Heimann, Pierre</creatorcontrib><creatorcontrib>Remmelink, Myriam</creatorcontrib><creatorcontrib>Demetter, Pieter</creatorcontrib><creatorcontrib>Tejpar, Sabine</creatorcontrib><creatorcontrib>Salmon, Isabelle</creatorcontrib><title>Clinical Validation of Targeted Next Generation Sequencing for Colon and Lung Cancers</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Recently, Next Generation Sequencing (NGS) has begun to supplant other technologies for gene mutation testing that is now required for targeted therapies. However, transfer of NGS technology to clinical daily practice requires validation.
We validated the Ion Torrent AmpliSeq Colon and Lung cancer panel interrogating 1850 hotspots in 22 genes using the Ion Torrent Personal Genome Machine. First, we used commercial reference standards that carry mutations at defined allelic frequency (AF). Then, 51 colorectal adenocarcinomas (CRC) and 39 non small cell lung carcinomas (NSCLC) were retrospectively analyzed.
Sensitivity and accuracy for detecting variants at an AF >4% was 100% for commercial reference standards. Among the 90 cases, 89 (98.9%) were successfully sequenced. Among the 86 samples for which NGS and the reference test were both informative, 83 showed concordant results between NGS and the reference test; i.e. KRAS and BRAF for CRC and EGFR for NSCLC, with the 3 discordant cases each characterized by an AF <10%.
Overall, the AmpliSeq colon/lung cancer panel was specific and sensitive for mutation analysis of gene panels and can be incorporated into clinical daily practice.</description><subject>Aerospace technology transfer</subject><subject>Audio frequencies</subject><subject>Cancer</subject><subject>Carcinoma, Non-Small-Cell Lung - genetics</subject><subject>Colon</subject><subject>Colon cancer</subject><subject>Colonic Neoplasms - genetics</subject><subject>Colorectal cancer</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA Mutational Analysis - methods</subject><subject>DNA, Neoplasm - genetics</subject><subject>Epidermal growth factor receptors</subject><subject>Female</subject><subject>Gene Frequency</subject><subject>Gene mutation</subject><subject>Gene sequencing</subject><subject>Genes</subject><subject>Genetics</subject><subject>Genomes</subject><subject>Genomics</subject><subject>High-Throughput Nucleotide Sequencing - methods</subject><subject>Humans</subject><subject>Lung cancer</subject><subject>Lung carcinoma</subject><subject>Lung diseases</subject><subject>Lung Neoplasms - genetics</subject><subject>Male</subject><subject>Mutation</subject><subject>Neoplasm Proteins - genetics</subject><subject>Non-small cell lung cancer</subject><subject>Non-small cell lung carcinoma</subject><subject>Pathology</subject><subject>Point mutation</subject><subject>Sensitivity analysis</subject><subject>Sensitivity and Specificity</subject><subject>Small cell lung carcinoma</subject><subject>Technology application</subject><subject>Technology transfer</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2015</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><sourceid>DOA</sourceid><recordid>eNqNkl2P1CAUhhujcdfRf2C0iYnRixkLtFBuTDYTXSeZuIn7cUsOlHbYMDBCa_Tfy-x0N1OzF4YL4PCc98DhzbLXqFggwtCnWz8EB3ax804vCkRqXFZPslPECZ5TXJCnR-uT7EWMt0VRkZrS59kJpoTSqmKn2fXSGmcU2PwGrGmgN97lvs2vIHS6103-Xf_u83PtdDicXeqfg3bKuC5vfciX3qYguCZfDym0BKd0iC-zZy3YqF-N8yy7_vrlavltvr44Xy3P1nPFqrqf05JRTKEqasZayUihS11wQiQuC84J8Fq2acMlZW1ZSq5brSilkmEOLSJAZtnbg-7O-ijGjkSBGOK4LpNIIlYHovFwK3bBbCH8ER6MuAv40AkIvVFWC4mYlBQ4AKCyoVgWStZKt6AaylBFk9bnsdogt7pR2vUB7ER0euLMRnT-lygrytOfJYEPo0DwqYuxF1sTlbYWnPbD3b0xqxFO8Cx79w_6-OtGqoP0AONan-qqvag4K3Fd1ZTzKlGLR6g0Gr01KtmnNSk-Sfg4SUhMn2zQwRCjWF3--H_24mbKvj9iNxpsv4neDntjxSlYHkAVfIxBtw9NRoXYu_--G2LvfjG6P6W9Of6gh6R7u5O_5uv-2g</recordid><startdate>20150914</startdate><enddate>20150914</enddate><creator>D'Haene, Nicky</creator><creator>Le Mercier, Marie</creator><creator>De Nève, Nancy</creator><creator>Blanchard, Oriane</creator><creator>Delaunoy, Mélanie</creator><creator>El Housni, Hakim</creator><creator>Dessars, Barbara</creator><creator>Heimann, Pierre</creator><creator>Remmelink, Myriam</creator><creator>Demetter, Pieter</creator><creator>Tejpar, Sabine</creator><creator>Salmon, Isabelle</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</general><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>IOV</scope><scope>ISR</scope><scope>3V.</scope><scope>7QG</scope><scope>7QL</scope><scope>7QO</scope><scope>7RV</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TG</scope><scope>7TM</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>KB.</scope><scope>KB0</scope><scope>KL.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>NAPCQ</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PDBOC</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope></search><sort><creationdate>20150914</creationdate><title>Clinical Validation of Targeted Next Generation Sequencing for Colon and Lung Cancers</title><author>D'Haene, Nicky ; Le Mercier, Marie ; De Nève, Nancy ; Blanchard, Oriane ; Delaunoy, Mélanie ; El Housni, Hakim ; Dessars, Barbara ; Heimann, Pierre ; Remmelink, Myriam ; Demetter, Pieter ; Tejpar, Sabine ; Salmon, Isabelle</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c758t-647626a50877fb730e4e0933b240993a98bf3b29b67f44b9efec666b729af13a3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2015</creationdate><topic>Aerospace technology transfer</topic><topic>Audio frequencies</topic><topic>Cancer</topic><topic>Carcinoma, Non-Small-Cell Lung - genetics</topic><topic>Colon</topic><topic>Colon cancer</topic><topic>Colonic Neoplasms - genetics</topic><topic>Colorectal cancer</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>DNA Mutational Analysis - methods</topic><topic>DNA, Neoplasm - genetics</topic><topic>Epidermal growth factor receptors</topic><topic>Female</topic><topic>Gene Frequency</topic><topic>Gene mutation</topic><topic>Gene sequencing</topic><topic>Genes</topic><topic>Genetics</topic><topic>Genomes</topic><topic>Genomics</topic><topic>High-Throughput Nucleotide Sequencing - methods</topic><topic>Humans</topic><topic>Lung cancer</topic><topic>Lung carcinoma</topic><topic>Lung diseases</topic><topic>Lung Neoplasms - genetics</topic><topic>Male</topic><topic>Mutation</topic><topic>Neoplasm Proteins - genetics</topic><topic>Non-small cell lung cancer</topic><topic>Non-small cell lung carcinoma</topic><topic>Pathology</topic><topic>Point mutation</topic><topic>Sensitivity analysis</topic><topic>Sensitivity and Specificity</topic><topic>Small cell lung carcinoma</topic><topic>Technology application</topic><topic>Technology transfer</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>D'Haene, Nicky</creatorcontrib><creatorcontrib>Le Mercier, Marie</creatorcontrib><creatorcontrib>De Nève, Nancy</creatorcontrib><creatorcontrib>Blanchard, Oriane</creatorcontrib><creatorcontrib>Delaunoy, Mélanie</creatorcontrib><creatorcontrib>El Housni, Hakim</creatorcontrib><creatorcontrib>Dessars, Barbara</creatorcontrib><creatorcontrib>Heimann, Pierre</creatorcontrib><creatorcontrib>Remmelink, Myriam</creatorcontrib><creatorcontrib>Demetter, Pieter</creatorcontrib><creatorcontrib>Tejpar, Sabine</creatorcontrib><creatorcontrib>Salmon, Isabelle</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Gale In Context: Opposing Viewpoints</collection><collection>Gale In Context: Science</collection><collection>ProQuest Central (Corporate)</collection><collection>Animal Behavior Abstracts</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Biotechnology Research Abstracts</collection><collection>Nursing & Allied Health Database</collection><collection>Ecology Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Immunology Abstracts</collection><collection>Meteorological & Geoastrophysical Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Agricultural Science Collection</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Public Health Database</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Technology Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>Materials Science & Engineering Collection</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest One Sustainability</collection><collection>ProQuest Central UK/Ireland</collection><collection>Advanced Technologies & Aerospace Collection</collection><collection>Agricultural & Environmental Science Collection</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Technology Collection</collection><collection>Natural Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Materials Science Collection</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Materials Science Database</collection><collection>Nursing & Allied Health Database (Alumni Edition)</collection><collection>Meteorological & Geoastrophysical Abstracts - Academic</collection><collection>ProQuest Engineering Collection</collection><collection>ProQuest Biological Science Collection</collection><collection>Agricultural Science Database</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biological Science Database</collection><collection>Engineering Database</collection><collection>Nursing & Allied Health Premium</collection><collection>Advanced Technologies & Aerospace Database</collection><collection>ProQuest Advanced Technologies & Aerospace Collection</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Environmental Science Database</collection><collection>Materials Science Collection</collection><collection>Publicly Available Content Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>Engineering Collection</collection><collection>Environmental Science Collection</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>D'Haene, Nicky</au><au>Le Mercier, Marie</au><au>De Nève, Nancy</au><au>Blanchard, Oriane</au><au>Delaunoy, Mélanie</au><au>El Housni, Hakim</au><au>Dessars, Barbara</au><au>Heimann, Pierre</au><au>Remmelink, Myriam</au><au>Demetter, Pieter</au><au>Tejpar, Sabine</au><au>Salmon, Isabelle</au><au>Scarpa, Aldo</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Clinical Validation of Targeted Next Generation Sequencing for Colon and Lung Cancers</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2015-09-14</date><risdate>2015</risdate><volume>10</volume><issue>9</issue><spage>e0138245</spage><epage>e0138245</epage><pages>e0138245-e0138245</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>Recently, Next Generation Sequencing (NGS) has begun to supplant other technologies for gene mutation testing that is now required for targeted therapies. However, transfer of NGS technology to clinical daily practice requires validation.
We validated the Ion Torrent AmpliSeq Colon and Lung cancer panel interrogating 1850 hotspots in 22 genes using the Ion Torrent Personal Genome Machine. First, we used commercial reference standards that carry mutations at defined allelic frequency (AF). Then, 51 colorectal adenocarcinomas (CRC) and 39 non small cell lung carcinomas (NSCLC) were retrospectively analyzed.
Sensitivity and accuracy for detecting variants at an AF >4% was 100% for commercial reference standards. Among the 90 cases, 89 (98.9%) were successfully sequenced. Among the 86 samples for which NGS and the reference test were both informative, 83 showed concordant results between NGS and the reference test; i.e. KRAS and BRAF for CRC and EGFR for NSCLC, with the 3 discordant cases each characterized by an AF <10%.
Overall, the AmpliSeq colon/lung cancer panel was specific and sensitive for mutation analysis of gene panels and can be incorporated into clinical daily practice.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>26366557</pmid><doi>10.1371/journal.pone.0138245</doi><tpages>e0138245</tpages><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1932-6203 |
| ispartof | PloS one, 2015-09, Vol.10 (9), p.e0138245-e0138245 |
| issn | 1932-6203 1932-6203 |
| language | eng |
| recordid | cdi_plos_journals_1719284409 |
| source | MEDLINE; DOAJ Directory of Open Access Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; PubMed Central; Free Full-Text Journals in Chemistry; Public Library of Science (PLoS) |
| subjects | Aerospace technology transfer Audio frequencies Cancer Carcinoma, Non-Small-Cell Lung - genetics Colon Colon cancer Colonic Neoplasms - genetics Colorectal cancer Deoxyribonucleic acid DNA DNA Mutational Analysis - methods DNA, Neoplasm - genetics Epidermal growth factor receptors Female Gene Frequency Gene mutation Gene sequencing Genes Genetics Genomes Genomics High-Throughput Nucleotide Sequencing - methods Humans Lung cancer Lung carcinoma Lung diseases Lung Neoplasms - genetics Male Mutation Neoplasm Proteins - genetics Non-small cell lung cancer Non-small cell lung carcinoma Pathology Point mutation Sensitivity analysis Sensitivity and Specificity Small cell lung carcinoma Technology application Technology transfer |
| title | Clinical Validation of Targeted Next Generation Sequencing for Colon and Lung Cancers |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-27T12%3A16%3A56IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Clinical%20Validation%20of%20Targeted%20Next%20Generation%20Sequencing%20for%20Colon%20and%20Lung%20Cancers&rft.jtitle=PloS%20one&rft.au=D'Haene,%20Nicky&rft.date=2015-09-14&rft.volume=10&rft.issue=9&rft.spage=e0138245&rft.epage=e0138245&rft.pages=e0138245-e0138245&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0138245&rft_dat=%3Cgale_plos_%3EA428586995%3C/gale_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=1719284409&rft_id=info:pmid/26366557&rft_galeid=A428586995&rft_doaj_id=oai_doaj_org_article_b17bb6a9aaa14d62b0cb8cefacd67156&rfr_iscdi=true |