Multiplatform comparison of molecular oncology tests performed on cytology specimens and formalin‐fixed, paraffin‐embedded tissue
BACKGROUND Molecular oncology testing is important for patient management, and requests for the molecular analysis of cytology specimens are increasingly being made. Formalin‐fixed, paraffin‐embedded (FFPE) cell blocks of such specimens have been routinely used for molecular diagnosis. However, the...
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| Veröffentlicht in: | Cancer cytopathology 2015-01, Vol.123 (1), p.30-39 |
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| creator | Gailey, Michael P. Stence, Aaron A. Jensen, Chris S. Ma, Deqin |
| description | BACKGROUND
Molecular oncology testing is important for patient management, and requests for the molecular analysis of cytology specimens are increasingly being made. Formalin‐fixed, paraffin‐embedded (FFPE) cell blocks of such specimens have been routinely used for molecular diagnosis. However, the inability to assess cellularity before cell block preparation is a pitfall of their use. In this study, various cytologic preparations were tested with several molecular test platforms, and the results were compared with paired FFPE tissue.
METHODS
Seventy‐seven cytology cases, including fine‐needle aspiration smears, touch preparations, and SurePath thin‐layer preparations, were selected from the archives. Areas of interest were removed from the slide with a matrix capture solution. DNA extracted from the cells was evaluated by mutation analysis for BRAF, epidermal growth factor receptor (EGFR), RAS, and a 50‐gene panel with various testing platforms (single‐nucleotide primer extension assay, Sanger sequencing, and next‐generation sequencing). Thirty‐eight tumors with available FFPE tissue were tested in parallel.
RESULTS
The average DNA concentration was 299 ng/µL for the cytology specimens and 171 ng/µg for the paired FFPE tissue. Point mutations and large deletions were detected in BRAF, KRAS, NRAS, HRAS, and EGFR genes. In comparison with FFPE tissue, 5‐ to 8‐fold less input DNA was needed when cytology preparations were used. The concordance between cytology specimens and FFPE tissue was 100%.
CONCLUSIONS
Cytologic preparations were found to be a reliable source for molecular oncology testing. DNA derived from cytology specimens performed well on multiple platforms, and 100% concordance was observed between cytology specimens and FFPE tissue. Cancer (Cancer Cytopathol) 2015;123:30–9. © 2014 American Cancer Society.
Cytology specimens are a cost‐effective, reliable source for molecular oncology testing and may save patients from additional procedures when adequate material is available. |
| doi_str_mv | 10.1002/cncy.21476 |
| format | Article |
| fullrecord | <record><control><sourceid>proquest_cross</sourceid><recordid>TN_cdi_proquest_miscellaneous_1652436911</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>3556907921</sourcerecordid><originalsourceid>FETCH-LOGICAL-c4236-4c05d6a8ae6f1de65ccd526dfd46d12788b185a2562ee2b9975c22648d8abc0c3</originalsourceid><addsrcrecordid>eNp90UFP3iAcBnCyaKZzXvYBDIkXY_a6QoHyHs0b3ZbodpmJnhoKfwyGlgpttLddvPsZ_STjtc6DB08Q-PEEeBD6QoojUhT0m-70dEQJq8QHtE2WJVsIUcqN1zm93EKfUropCiIrSj6iLcqJFKwqt9HD-egH13s12BBbrEPbq-hS6HCwuA0e9OhVxKHTwYfrCQ-QhoR7iGsOJm9gPQ3zXupBuxa6hFVn8Boo77qnv4_W3YP5inOysvZ5BdoGjMnnB5fSCJ_RplU-we7LuIMuTk_-rH4szn5__7k6PltoRkuxYLrgRiipQFhiQHCtDafCWMOEIbSSsiGSK8oFBaDNcllxTalg0kjV6EKXO-hgzu1juB3zU-rWJQ3eqw7CmGoiOGWlWBKS6f4behPG2OXbZcU4JVSWVVaHs9IxpBTB1n10rYpTTYp6XU69Lqd-LifjvZfIscl_90r_t5EBmcGd8zC9E1Wvfq2u5tB_KFefFw</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>1645212837</pqid></control><display><type>article</type><title>Multiplatform comparison of molecular oncology tests performed on cytology specimens and formalin‐fixed, paraffin‐embedded tissue</title><source>MEDLINE</source><source>Wiley Online Library Journals Frontfile Complete</source><source>Wiley Online Library Free Content</source><source>EZB-FREE-00999 freely available EZB journals</source><creator>Gailey, Michael P. ; Stence, Aaron A. ; Jensen, Chris S. ; Ma, Deqin</creator><creatorcontrib>Gailey, Michael P. ; Stence, Aaron A. ; Jensen, Chris S. ; Ma, Deqin</creatorcontrib><description>BACKGROUND
Molecular oncology testing is important for patient management, and requests for the molecular analysis of cytology specimens are increasingly being made. Formalin‐fixed, paraffin‐embedded (FFPE) cell blocks of such specimens have been routinely used for molecular diagnosis. However, the inability to assess cellularity before cell block preparation is a pitfall of their use. In this study, various cytologic preparations were tested with several molecular test platforms, and the results were compared with paired FFPE tissue.
METHODS
Seventy‐seven cytology cases, including fine‐needle aspiration smears, touch preparations, and SurePath thin‐layer preparations, were selected from the archives. Areas of interest were removed from the slide with a matrix capture solution. DNA extracted from the cells was evaluated by mutation analysis for BRAF, epidermal growth factor receptor (EGFR), RAS, and a 50‐gene panel with various testing platforms (single‐nucleotide primer extension assay, Sanger sequencing, and next‐generation sequencing). Thirty‐eight tumors with available FFPE tissue were tested in parallel.
RESULTS
The average DNA concentration was 299 ng/µL for the cytology specimens and 171 ng/µg for the paired FFPE tissue. Point mutations and large deletions were detected in BRAF, KRAS, NRAS, HRAS, and EGFR genes. In comparison with FFPE tissue, 5‐ to 8‐fold less input DNA was needed when cytology preparations were used. The concordance between cytology specimens and FFPE tissue was 100%.
CONCLUSIONS
Cytologic preparations were found to be a reliable source for molecular oncology testing. DNA derived from cytology specimens performed well on multiple platforms, and 100% concordance was observed between cytology specimens and FFPE tissue. Cancer (Cancer Cytopathol) 2015;123:30–9. © 2014 American Cancer Society.
Cytology specimens are a cost‐effective, reliable source for molecular oncology testing and may save patients from additional procedures when adequate material is available.</description><identifier>ISSN: 1934-662X</identifier><identifier>EISSN: 1934-6638</identifier><identifier>DOI: 10.1002/cncy.21476</identifier><identifier>PMID: 25186473</identifier><identifier>CODEN: CANCAR</identifier><language>eng</language><publisher>United States: Wiley Subscription Services, Inc</publisher><subject>Cytodiagnosis ; DNA extraction ; fine‐needle aspirate ; GTP Phosphohydrolases - genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Membrane Proteins - genetics ; Microsatellite Instability ; molecular oncology test ; Mutation ; Neoplasms - diagnosis ; Neoplasms - genetics ; Neoplasms - pathology ; next‐generation sequencing ; Paraffin Embedding ; Proto-Oncogene Proteins - genetics ; Proto-Oncogene Proteins B-raf - genetics ; Proto-Oncogene Proteins p21(ras) ; ras Proteins - genetics ; Receptor, Epidermal Growth Factor - genetics ; Sanger sequencing ; single‐nucleotide primer extension assay</subject><ispartof>Cancer cytopathology, 2015-01, Vol.123 (1), p.30-39</ispartof><rights>2015 American Cancer Society</rights><rights>2015 American Cancer Society.</rights><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c4236-4c05d6a8ae6f1de65ccd526dfd46d12788b185a2562ee2b9975c22648d8abc0c3</citedby><cites>FETCH-LOGICAL-c4236-4c05d6a8ae6f1de65ccd526dfd46d12788b185a2562ee2b9975c22648d8abc0c3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1002%2Fcncy.21476$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1002%2Fcncy.21476$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>314,776,780,1411,1427,27901,27902,45550,45551,46384,46808</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/25186473$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Gailey, Michael P.</creatorcontrib><creatorcontrib>Stence, Aaron A.</creatorcontrib><creatorcontrib>Jensen, Chris S.</creatorcontrib><creatorcontrib>Ma, Deqin</creatorcontrib><title>Multiplatform comparison of molecular oncology tests performed on cytology specimens and formalin‐fixed, paraffin‐embedded tissue</title><title>Cancer cytopathology</title><addtitle>Cancer Cytopathol</addtitle><description>BACKGROUND
Molecular oncology testing is important for patient management, and requests for the molecular analysis of cytology specimens are increasingly being made. Formalin‐fixed, paraffin‐embedded (FFPE) cell blocks of such specimens have been routinely used for molecular diagnosis. However, the inability to assess cellularity before cell block preparation is a pitfall of their use. In this study, various cytologic preparations were tested with several molecular test platforms, and the results were compared with paired FFPE tissue.
METHODS
Seventy‐seven cytology cases, including fine‐needle aspiration smears, touch preparations, and SurePath thin‐layer preparations, were selected from the archives. Areas of interest were removed from the slide with a matrix capture solution. DNA extracted from the cells was evaluated by mutation analysis for BRAF, epidermal growth factor receptor (EGFR), RAS, and a 50‐gene panel with various testing platforms (single‐nucleotide primer extension assay, Sanger sequencing, and next‐generation sequencing). Thirty‐eight tumors with available FFPE tissue were tested in parallel.
RESULTS
The average DNA concentration was 299 ng/µL for the cytology specimens and 171 ng/µg for the paired FFPE tissue. Point mutations and large deletions were detected in BRAF, KRAS, NRAS, HRAS, and EGFR genes. In comparison with FFPE tissue, 5‐ to 8‐fold less input DNA was needed when cytology preparations were used. The concordance between cytology specimens and FFPE tissue was 100%.
CONCLUSIONS
Cytologic preparations were found to be a reliable source for molecular oncology testing. DNA derived from cytology specimens performed well on multiple platforms, and 100% concordance was observed between cytology specimens and FFPE tissue. Cancer (Cancer Cytopathol) 2015;123:30–9. © 2014 American Cancer Society.
Cytology specimens are a cost‐effective, reliable source for molecular oncology testing and may save patients from additional procedures when adequate material is available.</description><subject>Cytodiagnosis</subject><subject>DNA extraction</subject><subject>fine‐needle aspirate</subject><subject>GTP Phosphohydrolases - genetics</subject><subject>High-Throughput Nucleotide Sequencing</subject><subject>Humans</subject><subject>Membrane Proteins - genetics</subject><subject>Microsatellite Instability</subject><subject>molecular oncology test</subject><subject>Mutation</subject><subject>Neoplasms - diagnosis</subject><subject>Neoplasms - genetics</subject><subject>Neoplasms - pathology</subject><subject>next‐generation sequencing</subject><subject>Paraffin Embedding</subject><subject>Proto-Oncogene Proteins - genetics</subject><subject>Proto-Oncogene Proteins B-raf - genetics</subject><subject>Proto-Oncogene Proteins p21(ras)</subject><subject>ras Proteins - genetics</subject><subject>Receptor, Epidermal Growth Factor - genetics</subject><subject>Sanger sequencing</subject><subject>single‐nucleotide primer extension assay</subject><issn>1934-662X</issn><issn>1934-6638</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2015</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp90UFP3iAcBnCyaKZzXvYBDIkXY_a6QoHyHs0b3ZbodpmJnhoKfwyGlgpttLddvPsZ_STjtc6DB08Q-PEEeBD6QoojUhT0m-70dEQJq8QHtE2WJVsIUcqN1zm93EKfUropCiIrSj6iLcqJFKwqt9HD-egH13s12BBbrEPbq-hS6HCwuA0e9OhVxKHTwYfrCQ-QhoR7iGsOJm9gPQ3zXupBuxa6hFVn8Boo77qnv4_W3YP5inOysvZ5BdoGjMnnB5fSCJ_RplU-we7LuIMuTk_-rH4szn5__7k6PltoRkuxYLrgRiipQFhiQHCtDafCWMOEIbSSsiGSK8oFBaDNcllxTalg0kjV6EKXO-hgzu1juB3zU-rWJQ3eqw7CmGoiOGWlWBKS6f4behPG2OXbZcU4JVSWVVaHs9IxpBTB1n10rYpTTYp6XU69Lqd-LifjvZfIscl_90r_t5EBmcGd8zC9E1Wvfq2u5tB_KFefFw</recordid><startdate>201501</startdate><enddate>201501</enddate><creator>Gailey, Michael P.</creator><creator>Stence, Aaron A.</creator><creator>Jensen, Chris S.</creator><creator>Ma, Deqin</creator><general>Wiley Subscription Services, Inc</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>K9.</scope><scope>7X8</scope></search><sort><creationdate>201501</creationdate><title>Multiplatform comparison of molecular oncology tests performed on cytology specimens and formalin‐fixed, paraffin‐embedded tissue</title><author>Gailey, Michael P. ; Stence, Aaron A. ; Jensen, Chris S. ; Ma, Deqin</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c4236-4c05d6a8ae6f1de65ccd526dfd46d12788b185a2562ee2b9975c22648d8abc0c3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2015</creationdate><topic>Cytodiagnosis</topic><topic>DNA extraction</topic><topic>fine‐needle aspirate</topic><topic>GTP Phosphohydrolases - genetics</topic><topic>High-Throughput Nucleotide Sequencing</topic><topic>Humans</topic><topic>Membrane Proteins - genetics</topic><topic>Microsatellite Instability</topic><topic>molecular oncology test</topic><topic>Mutation</topic><topic>Neoplasms - diagnosis</topic><topic>Neoplasms - genetics</topic><topic>Neoplasms - pathology</topic><topic>next‐generation sequencing</topic><topic>Paraffin Embedding</topic><topic>Proto-Oncogene Proteins - genetics</topic><topic>Proto-Oncogene Proteins B-raf - genetics</topic><topic>Proto-Oncogene Proteins p21(ras)</topic><topic>ras Proteins - genetics</topic><topic>Receptor, Epidermal Growth Factor - genetics</topic><topic>Sanger sequencing</topic><topic>single‐nucleotide primer extension assay</topic><toplevel>online_resources</toplevel><creatorcontrib>Gailey, Michael P.</creatorcontrib><creatorcontrib>Stence, Aaron A.</creatorcontrib><creatorcontrib>Jensen, Chris S.</creatorcontrib><creatorcontrib>Ma, Deqin</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>MEDLINE - Academic</collection><jtitle>Cancer cytopathology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Gailey, Michael P.</au><au>Stence, Aaron A.</au><au>Jensen, Chris S.</au><au>Ma, Deqin</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Multiplatform comparison of molecular oncology tests performed on cytology specimens and formalin‐fixed, paraffin‐embedded tissue</atitle><jtitle>Cancer cytopathology</jtitle><addtitle>Cancer Cytopathol</addtitle><date>2015-01</date><risdate>2015</risdate><volume>123</volume><issue>1</issue><spage>30</spage><epage>39</epage><pages>30-39</pages><issn>1934-662X</issn><eissn>1934-6638</eissn><coden>CANCAR</coden><abstract>BACKGROUND
Molecular oncology testing is important for patient management, and requests for the molecular analysis of cytology specimens are increasingly being made. Formalin‐fixed, paraffin‐embedded (FFPE) cell blocks of such specimens have been routinely used for molecular diagnosis. However, the inability to assess cellularity before cell block preparation is a pitfall of their use. In this study, various cytologic preparations were tested with several molecular test platforms, and the results were compared with paired FFPE tissue.
METHODS
Seventy‐seven cytology cases, including fine‐needle aspiration smears, touch preparations, and SurePath thin‐layer preparations, were selected from the archives. Areas of interest were removed from the slide with a matrix capture solution. DNA extracted from the cells was evaluated by mutation analysis for BRAF, epidermal growth factor receptor (EGFR), RAS, and a 50‐gene panel with various testing platforms (single‐nucleotide primer extension assay, Sanger sequencing, and next‐generation sequencing). Thirty‐eight tumors with available FFPE tissue were tested in parallel.
RESULTS
The average DNA concentration was 299 ng/µL for the cytology specimens and 171 ng/µg for the paired FFPE tissue. Point mutations and large deletions were detected in BRAF, KRAS, NRAS, HRAS, and EGFR genes. In comparison with FFPE tissue, 5‐ to 8‐fold less input DNA was needed when cytology preparations were used. The concordance between cytology specimens and FFPE tissue was 100%.
CONCLUSIONS
Cytologic preparations were found to be a reliable source for molecular oncology testing. DNA derived from cytology specimens performed well on multiple platforms, and 100% concordance was observed between cytology specimens and FFPE tissue. Cancer (Cancer Cytopathol) 2015;123:30–9. © 2014 American Cancer Society.
Cytology specimens are a cost‐effective, reliable source for molecular oncology testing and may save patients from additional procedures when adequate material is available.</abstract><cop>United States</cop><pub>Wiley Subscription Services, Inc</pub><pmid>25186473</pmid><doi>10.1002/cncy.21476</doi><tpages>11</tpages></addata></record> |
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| source | MEDLINE; Wiley Online Library Journals Frontfile Complete; Wiley Online Library Free Content; EZB-FREE-00999 freely available EZB journals |
| subjects | Cytodiagnosis DNA extraction fine‐needle aspirate GTP Phosphohydrolases - genetics High-Throughput Nucleotide Sequencing Humans Membrane Proteins - genetics Microsatellite Instability molecular oncology test Mutation Neoplasms - diagnosis Neoplasms - genetics Neoplasms - pathology next‐generation sequencing Paraffin Embedding Proto-Oncogene Proteins - genetics Proto-Oncogene Proteins B-raf - genetics Proto-Oncogene Proteins p21(ras) ras Proteins - genetics Receptor, Epidermal Growth Factor - genetics Sanger sequencing single‐nucleotide primer extension assay |
| title | Multiplatform comparison of molecular oncology tests performed on cytology specimens and formalin‐fixed, paraffin‐embedded tissue |
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