Comparison of Nanostring nCounter® Data on FFPE Colon Cancer Samples and Affymetrix Microarray Data on Matched Frozen Tissues
The prognosis of colorectal cancer (CRC) stage II and III patients remains a challenge due to the difficulties of finding robust biomarkers suitable for testing clinical samples. The majority of published gene signatures of CRC have been generated on fresh frozen colorectal tissues. Because collecti...
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| Veröffentlicht in: | PloS one 2016-05, Vol.11 (5), p.e0153784-e0153784 |
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| creator | Chen, Xi Deane, Natasha G Lewis, Keeli B Li, Jiang Zhu, Jing Washington, M Kay Beauchamp, R Daniel |
| description | The prognosis of colorectal cancer (CRC) stage II and III patients remains a challenge due to the difficulties of finding robust biomarkers suitable for testing clinical samples. The majority of published gene signatures of CRC have been generated on fresh frozen colorectal tissues. Because collection of frozen tissue is not practical for routine surgical pathology practice, a clinical test that improves prognostic capabilities beyond standard pathological staging of colon cancer will need to be designed for formalin-fixed paraffin-embedded (FFPE) tissues. The NanoString nCounter® platform is a gene expression analysis tool developed for use with FFPE-derived samples. We designed a custom nCounter® codeset based on elements from multiple published fresh frozen tissue microarray-based prognostic gene signatures for colon cancer, and we used this platform to systematically compare gene expression data from FFPE with matched microarray array data from frozen tissues. Our results show moderate correlation of gene expression between two platforms and discovery of a small subset of genes as candidate biomarkers for colon cancer prognosis that are detectable and quantifiable in FFPE tissue sections. |
| doi_str_mv | 10.1371/journal.pone.0153784 |
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The majority of published gene signatures of CRC have been generated on fresh frozen colorectal tissues. Because collection of frozen tissue is not practical for routine surgical pathology practice, a clinical test that improves prognostic capabilities beyond standard pathological staging of colon cancer will need to be designed for formalin-fixed paraffin-embedded (FFPE) tissues. The NanoString nCounter® platform is a gene expression analysis tool developed for use with FFPE-derived samples. We designed a custom nCounter® codeset based on elements from multiple published fresh frozen tissue microarray-based prognostic gene signatures for colon cancer, and we used this platform to systematically compare gene expression data from FFPE with matched microarray array data from frozen tissues. Our results show moderate correlation of gene expression between two platforms and discovery of a small subset of genes as candidate biomarkers for colon cancer prognosis that are detectable and quantifiable in FFPE tissue sections.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0153784</identifier><identifier>PMID: 27176004</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Bayesian analysis ; Biology ; Biology and Life Sciences ; Biomarkers ; Cancer ; Chemotherapy ; Colon ; Colon cancer ; Colonic Neoplasms - genetics ; Colorectal cancer ; Colorectal carcinoma ; DNA microarrays ; Formaldehyde ; Frozen Sections ; Gene expression ; Gene Expression Regulation, Neoplastic ; Humans ; Medical prognosis ; Medical research ; Medicine and Health Sciences ; Metastasis ; Oligonucleotide Array Sequence Analysis - methods ; Oncology ; Paraffin ; Paraffin Embedding - methods ; Pathology ; Patients ; Prognosis ; Research and Analysis Methods ; RNA, Neoplasm - isolation & purification ; Signatures ; Surgery ; Surgical instruments ; Survival Analysis ; Tissue Fixation - methods ; Tissues ; Tumors</subject><ispartof>PloS one, 2016-05, Vol.11 (5), p.e0153784-e0153784</ispartof><rights>2016 Chen 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>2016 Chen et al 2016 Chen et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c592t-a9c2ba66a56d7d8a21b69f104fb8488a31e2dd2a3dc44f185d38107bffb5d6c03</citedby><cites>FETCH-LOGICAL-c592t-a9c2ba66a56d7d8a21b69f104fb8488a31e2dd2a3dc44f185d38107bffb5d6c03</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/PMC4866771/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4866771/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,2096,2915,23845,27901,27902,53766,53768,79343,79344</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/27176004$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Chen, Xi</creatorcontrib><creatorcontrib>Deane, Natasha G</creatorcontrib><creatorcontrib>Lewis, Keeli B</creatorcontrib><creatorcontrib>Li, Jiang</creatorcontrib><creatorcontrib>Zhu, Jing</creatorcontrib><creatorcontrib>Washington, M Kay</creatorcontrib><creatorcontrib>Beauchamp, R Daniel</creatorcontrib><title>Comparison of Nanostring nCounter® Data on FFPE Colon Cancer Samples and Affymetrix Microarray Data on Matched Frozen Tissues</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>The prognosis of colorectal cancer (CRC) stage II and III patients remains a challenge due to the difficulties of finding robust biomarkers suitable for testing clinical samples. The majority of published gene signatures of CRC have been generated on fresh frozen colorectal tissues. Because collection of frozen tissue is not practical for routine surgical pathology practice, a clinical test that improves prognostic capabilities beyond standard pathological staging of colon cancer will need to be designed for formalin-fixed paraffin-embedded (FFPE) tissues. The NanoString nCounter® platform is a gene expression analysis tool developed for use with FFPE-derived samples. We designed a custom nCounter® codeset based on elements from multiple published fresh frozen tissue microarray-based prognostic gene signatures for colon cancer, and we used this platform to systematically compare gene expression data from FFPE with matched microarray array data from frozen tissues. Our results show moderate correlation of gene expression between two platforms and discovery of a small subset of genes as candidate biomarkers for colon cancer prognosis that are detectable and quantifiable in FFPE tissue sections.</description><subject>Bayesian analysis</subject><subject>Biology</subject><subject>Biology and Life Sciences</subject><subject>Biomarkers</subject><subject>Cancer</subject><subject>Chemotherapy</subject><subject>Colon</subject><subject>Colon cancer</subject><subject>Colonic Neoplasms - genetics</subject><subject>Colorectal cancer</subject><subject>Colorectal carcinoma</subject><subject>DNA microarrays</subject><subject>Formaldehyde</subject><subject>Frozen Sections</subject><subject>Gene expression</subject><subject>Gene Expression Regulation, Neoplastic</subject><subject>Humans</subject><subject>Medical prognosis</subject><subject>Medical research</subject><subject>Medicine and Health Sciences</subject><subject>Metastasis</subject><subject>Oligonucleotide Array Sequence Analysis - methods</subject><subject>Oncology</subject><subject>Paraffin</subject><subject>Paraffin Embedding - methods</subject><subject>Pathology</subject><subject>Patients</subject><subject>Prognosis</subject><subject>Research and Analysis Methods</subject><subject>RNA, Neoplasm - isolation & purification</subject><subject>Signatures</subject><subject>Surgery</subject><subject>Surgical instruments</subject><subject>Survival Analysis</subject><subject>Tissue Fixation - methods</subject><subject>Tissues</subject><subject>Tumors</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2016</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><sourceid>DOA</sourceid><recordid>eNptUstu1DAUjRCIlsIfILDEhs0MduzEzgapCh2o1AISZW3d-DHNKLGDnSCGBZ_ER_BleDrpqEWsfGWfc3zuvSfLnhO8JJSTNxs_BQfdcvDOLDEpKBfsQXZMKpovyhzTh3fqo-xJjBuMCyrK8nF2lHPCS4zZcfar9v0AoY3eIW_RR3A-jqF1a-RqP7nRhD-_0TsYASXAavX5DNW-S2UNTpmAvkA_dCYicBqdWrvtTSL_QJetCh5CgO2BewmjujYarYL_aRy6amOcTHyaPbLQRfNsPk-yr6uzq_rD4uLT-_P69GKhiiofF1CpvIGyhKLUXAvISVNWlmBmG8GEAEpMrnUOVCvGLBGFpoJg3ljbFLpUmJ5kL_e6Q-ejnEcXJeFCcEJEyRPifI_QHjZyCG0PYSs9tPLmwoe1hDC2qjOScZ4GWDHW5IRxKBpFsKA0ObCkqsAmrbfzb1PTG62MGwN090Tvv7j2Wq79d8nSejgnSeD1LBD8tzSmUfZtVKbrwBk_3fiuWMVysfP96h_o_7tje1TaS4zB2IMZguUuTrcsuYuTnOOUaC_uNnIg3eaH_gWz9coh</recordid><startdate>20160513</startdate><enddate>20160513</enddate><creator>Chen, Xi</creator><creator>Deane, Natasha G</creator><creator>Lewis, Keeli B</creator><creator>Li, Jiang</creator><creator>Zhu, Jing</creator><creator>Washington, M Kay</creator><creator>Beauchamp, R Daniel</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>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>PRINS</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope></search><sort><creationdate>20160513</creationdate><title>Comparison of Nanostring nCounter® Data on FFPE Colon Cancer Samples and Affymetrix Microarray Data on Matched Frozen Tissues</title><author>Chen, Xi ; Deane, Natasha G ; Lewis, Keeli B ; Li, Jiang ; Zhu, Jing ; Washington, M Kay ; Beauchamp, R Daniel</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c592t-a9c2ba66a56d7d8a21b69f104fb8488a31e2dd2a3dc44f185d38107bffb5d6c03</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2016</creationdate><topic>Bayesian analysis</topic><topic>Biology</topic><topic>Biology and Life Sciences</topic><topic>Biomarkers</topic><topic>Cancer</topic><topic>Chemotherapy</topic><topic>Colon</topic><topic>Colon cancer</topic><topic>Colonic Neoplasms - 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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>Chen, Xi</au><au>Deane, Natasha G</au><au>Lewis, Keeli B</au><au>Li, Jiang</au><au>Zhu, Jing</au><au>Washington, M Kay</au><au>Beauchamp, R Daniel</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Comparison of Nanostring nCounter® Data on FFPE Colon Cancer Samples and Affymetrix Microarray Data on Matched Frozen Tissues</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2016-05-13</date><risdate>2016</risdate><volume>11</volume><issue>5</issue><spage>e0153784</spage><epage>e0153784</epage><pages>e0153784-e0153784</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>The prognosis of colorectal cancer (CRC) stage II and III patients remains a challenge due to the difficulties of finding robust biomarkers suitable for testing clinical samples. The majority of published gene signatures of CRC have been generated on fresh frozen colorectal tissues. Because collection of frozen tissue is not practical for routine surgical pathology practice, a clinical test that improves prognostic capabilities beyond standard pathological staging of colon cancer will need to be designed for formalin-fixed paraffin-embedded (FFPE) tissues. The NanoString nCounter® platform is a gene expression analysis tool developed for use with FFPE-derived samples. We designed a custom nCounter® codeset based on elements from multiple published fresh frozen tissue microarray-based prognostic gene signatures for colon cancer, and we used this platform to systematically compare gene expression data from FFPE with matched microarray array data from frozen tissues. Our results show moderate correlation of gene expression between two platforms and discovery of a small subset of genes as candidate biomarkers for colon cancer prognosis that are detectable and quantifiable in FFPE tissue sections.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>27176004</pmid><doi>10.1371/journal.pone.0153784</doi><oa>free_for_read</oa></addata></record> |
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| subjects | Bayesian analysis Biology Biology and Life Sciences Biomarkers Cancer Chemotherapy Colon Colon cancer Colonic Neoplasms - genetics Colorectal cancer Colorectal carcinoma DNA microarrays Formaldehyde Frozen Sections Gene expression Gene Expression Regulation, Neoplastic Humans Medical prognosis Medical research Medicine and Health Sciences Metastasis Oligonucleotide Array Sequence Analysis - methods Oncology Paraffin Paraffin Embedding - methods Pathology Patients Prognosis Research and Analysis Methods RNA, Neoplasm - isolation & purification Signatures Surgery Surgical instruments Survival Analysis Tissue Fixation - methods Tissues Tumors |
| title | Comparison of Nanostring nCounter® Data on FFPE Colon Cancer Samples and Affymetrix Microarray Data on Matched Frozen Tissues |
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