Diagnostic yield of NanoString nCounter FusionPlex profiling in soft tissue tumors
Diagnostic histopathology of soft tissue tumors can be troublesome as many entities are quite rare and have overlapping morphologic features. Many soft tissue tumors harbor tumor‐defining gene translocations, which may provide an important ancillary tool for tumor diagnosis. The NanoString nCounter...
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| Veröffentlicht in: | Genes chromosomes & cancer 2020-05, Vol.59 (5), p.318-324 |
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| creator | Song, Wangzhao Platteel, Inge Suurmeijer, Albert J. H. Kempen, Léon C. |
| description | Diagnostic histopathology of soft tissue tumors can be troublesome as many entities are quite rare and have overlapping morphologic features. Many soft tissue tumors harbor tumor‐defining gene translocations, which may provide an important ancillary tool for tumor diagnosis. The NanoString nCounter platform enables multiplex detection of pre‐defined gene fusion transcripts in formalin‐fixed and paraffin‐embedded tissue. A cohort of 104 soft tissue tumors representing 20 different histological types was analyzed for the expression of 174 unique gene fusion transcripts. A tumor‐defining gene fusion transcript was detected in 60 cases (58%). Sensitivity and specificity of the NanoString assay calculated against the result of an alternative molecular method were 85% and 100%, respectively. Highest diagnostic coverage was obtained for Ewing sarcoma, synovial sarcoma, myxoid liposarcoma, alveolar rhabdomyosarcoma, and desmoplastic small round cell tumor. For these tumor types, the NanoString assay is a rapid, cost‐effective, sensitive, and specific ancillary screening tool for molecular diagnosis. For other sarcomas, additional molecular testing may be required when a translocation transcript is not identified with the current 174 gene fusion panel. |
| doi_str_mv | 10.1002/gcc.22834 |
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H. ; Kempen, Léon C.</creator><creatorcontrib>Song, Wangzhao ; Platteel, Inge ; Suurmeijer, Albert J. H. ; Kempen, Léon C.</creatorcontrib><description>Diagnostic histopathology of soft tissue tumors can be troublesome as many entities are quite rare and have overlapping morphologic features. Many soft tissue tumors harbor tumor‐defining gene translocations, which may provide an important ancillary tool for tumor diagnosis. The NanoString nCounter platform enables multiplex detection of pre‐defined gene fusion transcripts in formalin‐fixed and paraffin‐embedded tissue. A cohort of 104 soft tissue tumors representing 20 different histological types was analyzed for the expression of 174 unique gene fusion transcripts. A tumor‐defining gene fusion transcript was detected in 60 cases (58%). Sensitivity and specificity of the NanoString assay calculated against the result of an alternative molecular method were 85% and 100%, respectively. Highest diagnostic coverage was obtained for Ewing sarcoma, synovial sarcoma, myxoid liposarcoma, alveolar rhabdomyosarcoma, and desmoplastic small round cell tumor. For these tumor types, the NanoString assay is a rapid, cost‐effective, sensitive, and specific ancillary screening tool for molecular diagnosis. For other sarcomas, additional molecular testing may be required when a translocation transcript is not identified with the current 174 gene fusion panel.</description><identifier>ISSN: 1045-2257</identifier><identifier>EISSN: 1098-2264</identifier><identifier>DOI: 10.1002/gcc.22834</identifier><identifier>PMID: 31965673</identifier><language>eng</language><publisher>Hoboken, USA: John Wiley & Sons, Inc</publisher><subject>Alveoli ; Biomarkers, Tumor - genetics ; Cohort Studies ; Diagnosis ; Ewing's sarcoma ; fusion genes ; Gene fusion ; Gene Rearrangement ; Humans ; Liposarcoma ; molecular pathology ; NanoString ; Oncogene Proteins, Fusion - genetics ; Paraffin ; Paraffin Embedding - methods ; Rhabdomyosarcoma ; sarcoma ; Soft Tissue Neoplasms - classification ; Soft Tissue Neoplasms - diagnosis ; Soft Tissue Neoplasms - genetics ; soft tissue tumor ; Synovial sarcoma ; Transcription ; Translocation ; Translocation, Genetic ; Tumors</subject><ispartof>Genes chromosomes & cancer, 2020-05, Vol.59 (5), p.318-324</ispartof><rights>2020 The Authors. published by Wiley Periodicals, Inc.</rights><rights>2020 The Authors. Genes, Chromosomes & Cancer published by Wiley Periodicals, Inc.</rights><rights>2020 Wiley Periodicals, Inc.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c4434-1a99d14127195c68e7c9dc210fe0c98998c271274a983c710ef85c36229b5bc53</citedby><cites>FETCH-LOGICAL-c4434-1a99d14127195c68e7c9dc210fe0c98998c271274a983c710ef85c36229b5bc53</cites><orcidid>0000-0002-7935-6493</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1002%2Fgcc.22834$$EPDF$$P50$$Gwiley$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1002%2Fgcc.22834$$EHTML$$P50$$Gwiley$$Hfree_for_read</linktohtml><link.rule.ids>230,314,780,784,885,1416,27915,27916,45565,45566</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/31965673$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Song, Wangzhao</creatorcontrib><creatorcontrib>Platteel, Inge</creatorcontrib><creatorcontrib>Suurmeijer, Albert J. H.</creatorcontrib><creatorcontrib>Kempen, Léon C.</creatorcontrib><title>Diagnostic yield of NanoString nCounter FusionPlex profiling in soft tissue tumors</title><title>Genes chromosomes & cancer</title><addtitle>Genes Chromosomes Cancer</addtitle><description>Diagnostic histopathology of soft tissue tumors can be troublesome as many entities are quite rare and have overlapping morphologic features. Many soft tissue tumors harbor tumor‐defining gene translocations, which may provide an important ancillary tool for tumor diagnosis. The NanoString nCounter platform enables multiplex detection of pre‐defined gene fusion transcripts in formalin‐fixed and paraffin‐embedded tissue. A cohort of 104 soft tissue tumors representing 20 different histological types was analyzed for the expression of 174 unique gene fusion transcripts. A tumor‐defining gene fusion transcript was detected in 60 cases (58%). Sensitivity and specificity of the NanoString assay calculated against the result of an alternative molecular method were 85% and 100%, respectively. Highest diagnostic coverage was obtained for Ewing sarcoma, synovial sarcoma, myxoid liposarcoma, alveolar rhabdomyosarcoma, and desmoplastic small round cell tumor. For these tumor types, the NanoString assay is a rapid, cost‐effective, sensitive, and specific ancillary screening tool for molecular diagnosis. For other sarcomas, additional molecular testing may be required when a translocation transcript is not identified with the current 174 gene fusion panel.</description><subject>Alveoli</subject><subject>Biomarkers, Tumor - genetics</subject><subject>Cohort Studies</subject><subject>Diagnosis</subject><subject>Ewing's sarcoma</subject><subject>fusion genes</subject><subject>Gene fusion</subject><subject>Gene Rearrangement</subject><subject>Humans</subject><subject>Liposarcoma</subject><subject>molecular pathology</subject><subject>NanoString</subject><subject>Oncogene Proteins, Fusion - genetics</subject><subject>Paraffin</subject><subject>Paraffin Embedding - methods</subject><subject>Rhabdomyosarcoma</subject><subject>sarcoma</subject><subject>Soft Tissue Neoplasms - classification</subject><subject>Soft Tissue Neoplasms - diagnosis</subject><subject>Soft Tissue Neoplasms - genetics</subject><subject>soft tissue tumor</subject><subject>Synovial sarcoma</subject><subject>Transcription</subject><subject>Translocation</subject><subject>Translocation, Genetic</subject><subject>Tumors</subject><issn>1045-2257</issn><issn>1098-2264</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2020</creationdate><recordtype>article</recordtype><sourceid>24P</sourceid><sourceid>WIN</sourceid><sourceid>EIF</sourceid><recordid>eNp1kF1LwzAUhoMobk4v_AMS8MqLbvlq09wIUt0URMWP69Clac3okpm06v69nZtDL7w6B96H5xxeAI4xGmKEyKhSakhIStkO6GMk0oiQhO2udhZ3e8x74CCEGUIooSLeBz2KRRInnPbB46XJK-tCYxRcGl0X0JXwLrfuqfHGVtBmrrWN9nDcBuPsQ60_4cK70tSr1FgYXNnAxoTQati0c-fDIdgr8zroo80cgJfx1XN2Hd3eT26yi9tIMUZZhHMhCsww4VjEKkk1V6JQBKNSIyVSIVLVRYSzXKRUcYx0mcaKJoSIaTxVMR2A87V30U7nulDaNj6v5cKbee6X0uVG_k2seZWVe5cccYHRSnC6EXj31urQyJlrve1-loQmgrCUd6cH4GxNKe9C8LrcXsBIruqXXf3yu_6OPfn90pb86bsDRmvgw9R6-b9JTrJsrfwCcTiPVA</recordid><startdate>202005</startdate><enddate>202005</enddate><creator>Song, Wangzhao</creator><creator>Platteel, Inge</creator><creator>Suurmeijer, Albert J. H.</creator><creator>Kempen, Léon C.</creator><general>John Wiley & Sons, Inc</general><general>Wiley Subscription Services, Inc</general><scope>24P</scope><scope>WIN</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>7QP</scope><scope>7TM</scope><scope>7TO</scope><scope>8FD</scope><scope>FR3</scope><scope>H94</scope><scope>K9.</scope><scope>P64</scope><scope>RC3</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0002-7935-6493</orcidid></search><sort><creationdate>202005</creationdate><title>Diagnostic yield of NanoString nCounter FusionPlex profiling in soft tissue tumors</title><author>Song, Wangzhao ; Platteel, Inge ; Suurmeijer, Albert J. H. ; Kempen, Léon C.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c4434-1a99d14127195c68e7c9dc210fe0c98998c271274a983c710ef85c36229b5bc53</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2020</creationdate><topic>Alveoli</topic><topic>Biomarkers, Tumor - genetics</topic><topic>Cohort Studies</topic><topic>Diagnosis</topic><topic>Ewing's sarcoma</topic><topic>fusion genes</topic><topic>Gene fusion</topic><topic>Gene Rearrangement</topic><topic>Humans</topic><topic>Liposarcoma</topic><topic>molecular pathology</topic><topic>NanoString</topic><topic>Oncogene Proteins, Fusion - genetics</topic><topic>Paraffin</topic><topic>Paraffin Embedding - methods</topic><topic>Rhabdomyosarcoma</topic><topic>sarcoma</topic><topic>Soft Tissue Neoplasms - classification</topic><topic>Soft Tissue Neoplasms - diagnosis</topic><topic>Soft Tissue Neoplasms - genetics</topic><topic>soft tissue tumor</topic><topic>Synovial sarcoma</topic><topic>Transcription</topic><topic>Translocation</topic><topic>Translocation, Genetic</topic><topic>Tumors</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Song, Wangzhao</creatorcontrib><creatorcontrib>Platteel, Inge</creatorcontrib><creatorcontrib>Suurmeijer, Albert J. H.</creatorcontrib><creatorcontrib>Kempen, Léon C.</creatorcontrib><collection>Wiley Online Library Open Access</collection><collection>Wiley Online Library Free Content</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Calcium & Calcified Tissue Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Oncogenes and Growth Factors Abstracts</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Genes chromosomes & cancer</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Song, Wangzhao</au><au>Platteel, Inge</au><au>Suurmeijer, Albert J. H.</au><au>Kempen, Léon C.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Diagnostic yield of NanoString nCounter FusionPlex profiling in soft tissue tumors</atitle><jtitle>Genes chromosomes & cancer</jtitle><addtitle>Genes Chromosomes Cancer</addtitle><date>2020-05</date><risdate>2020</risdate><volume>59</volume><issue>5</issue><spage>318</spage><epage>324</epage><pages>318-324</pages><issn>1045-2257</issn><eissn>1098-2264</eissn><abstract>Diagnostic histopathology of soft tissue tumors can be troublesome as many entities are quite rare and have overlapping morphologic features. Many soft tissue tumors harbor tumor‐defining gene translocations, which may provide an important ancillary tool for tumor diagnosis. The NanoString nCounter platform enables multiplex detection of pre‐defined gene fusion transcripts in formalin‐fixed and paraffin‐embedded tissue. A cohort of 104 soft tissue tumors representing 20 different histological types was analyzed for the expression of 174 unique gene fusion transcripts. A tumor‐defining gene fusion transcript was detected in 60 cases (58%). Sensitivity and specificity of the NanoString assay calculated against the result of an alternative molecular method were 85% and 100%, respectively. Highest diagnostic coverage was obtained for Ewing sarcoma, synovial sarcoma, myxoid liposarcoma, alveolar rhabdomyosarcoma, and desmoplastic small round cell tumor. For these tumor types, the NanoString assay is a rapid, cost‐effective, sensitive, and specific ancillary screening tool for molecular diagnosis. 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| subjects | Alveoli Biomarkers, Tumor - genetics Cohort Studies Diagnosis Ewing's sarcoma fusion genes Gene fusion Gene Rearrangement Humans Liposarcoma molecular pathology NanoString Oncogene Proteins, Fusion - genetics Paraffin Paraffin Embedding - methods Rhabdomyosarcoma sarcoma Soft Tissue Neoplasms - classification Soft Tissue Neoplasms - diagnosis Soft Tissue Neoplasms - genetics soft tissue tumor Synovial sarcoma Transcription Translocation Translocation, Genetic Tumors |
| title | Diagnostic yield of NanoString nCounter FusionPlex profiling in soft tissue tumors |
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