Diagnosis of pancreatic lesions collected by endoscopic ultrasound-guided fine-needle aspiration using next-generation sequencing
Endoscopic ultrasound-guided fine-needle aspiration (EUF-FNA) has improved the diagnosis of pancreatic lesions. Next-generation sequencing (NGS) facilitates the production of millions of sequences concurrently. Therefore, in the current study, to improve the detectability of oncogenic mutations in p...
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| Veröffentlicht in: | Oncology letters 2016-11, Vol.12 (5), p.3875-3881 |
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| creator | Kameta, Eri Sugimori, Kazuya Kaneko, Takashi Ishii, Tomohiro Miwa, Haruo Sato, Takeshi Ishii, Yasuaki Sue, Soichiro Sasaki, Tomohiko Yamashita, Yuki Shibata, Wataru Matsumoto, Naomichi Maeda, Shin |
| description | Endoscopic ultrasound-guided fine-needle aspiration (EUF-FNA) has improved the diagnosis of pancreatic lesions. Next-generation sequencing (NGS) facilitates the production of millions of sequences concurrently. Therefore, in the current study, to improve the detectability of oncogenic mutations in pancreatic lesions, an NGS system was used to diagnose EUS-FNA samples. A total of 38 patients with clinically diagnosed EUS-FNA specimens were analyzed; 27 patients had pancreatic ductal adenocarcinoma (PDAC) and 11 had non-PDAC lesions. DNA samples were isolated and sequenced by NGS using an Ion Personal Genome Machine system. The Cancer Hotspot Panel v2, which includes 50 cancer-related genes and 2,790 COSMIC mutations, was used. A >2% mutation frequency was defined as positive. KRAS mutations were detected in 26 of 27 PDAC aspirates (96%) and 0 of 11 non-PDAC lesions (0%). The G12, G13, and Q61 KRAS mutations were found in 25, 0, and 1 of the 27 PDAC samples, respectively. Mutations were confirmed by TaqMan® polymerase chain reaction analysis. TP53 mutations were detected in 12 of 27 PDAC aspirates (44%). SMAD4 was observed in 3 PDAC lesions and cyclin-dependent kinase inhibitor 2A in 4 PDAC lesions. Therefore, the current study was successfully able to develop an NGS assay with high clinical sensitivity for EUS-FNA samples. |
| doi_str_mv | 10.3892/ol.2016.5168 |
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Next-generation sequencing (NGS) facilitates the production of millions of sequences concurrently. Therefore, in the current study, to improve the detectability of oncogenic mutations in pancreatic lesions, an NGS system was used to diagnose EUS-FNA samples. A total of 38 patients with clinically diagnosed EUS-FNA specimens were analyzed; 27 patients had pancreatic ductal adenocarcinoma (PDAC) and 11 had non-PDAC lesions. DNA samples were isolated and sequenced by NGS using an Ion Personal Genome Machine system. The Cancer Hotspot Panel v2, which includes 50 cancer-related genes and 2,790 COSMIC mutations, was used. A >2% mutation frequency was defined as positive. KRAS mutations were detected in 26 of 27 PDAC aspirates (96%) and 0 of 11 non-PDAC lesions (0%). The G12, G13, and Q61 KRAS mutations were found in 25, 0, and 1 of the 27 PDAC samples, respectively. Mutations were confirmed by TaqMan® polymerase chain reaction analysis. TP53 mutations were detected in 12 of 27 PDAC aspirates (44%). SMAD4 was observed in 3 PDAC lesions and cyclin-dependent kinase inhibitor 2A in 4 PDAC lesions. Therefore, the current study was successfully able to develop an NGS assay with high clinical sensitivity for EUS-FNA samples.</description><identifier>ISSN: 1792-1074</identifier><identifier>EISSN: 1792-1082</identifier><identifier>DOI: 10.3892/ol.2016.5168</identifier><identifier>PMID: 27895743</identifier><language>eng</language><publisher>Greece: D.A. Spandidos</publisher><subject>Antigens ; Cyclin-dependent kinases ; Deoxyribonucleic acid ; Diagnosis ; DNA ; endoscopic ultrasound-guided fine-needle aspiration ; Endoscopy ; Genes ; Genomes ; Kinases ; KRAS ; Medical diagnosis ; Metastasis ; Methods ; Mutation ; Needle biopsy ; next-generation sequencing ; Oncology ; Pancreatic cancer ; pancreatic ductal adenocarcinoma ; Patient outcomes ; Proteins ; Software ; Studies ; TP53 ; Tumors ; Ultrasonic imaging</subject><ispartof>Oncology letters, 2016-11, Vol.12 (5), p.3875-3881</ispartof><rights>Copyright: © Kameta et al.</rights><rights>COPYRIGHT 2016 Spandidos Publications</rights><rights>Copyright Spandidos Publications UK Ltd. 2016</rights><rights>Copyright: © Kameta et al. 2016</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c605t-6beede9d8dab377790cb793a53849c2e7be20879104c6231febc5b33b3aecb203</citedby><cites>FETCH-LOGICAL-c605t-6beede9d8dab377790cb793a53849c2e7be20879104c6231febc5b33b3aecb203</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/PMC5104195/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5104195/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,885,5570,27923,27924,53790,53792</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/27895743$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Kameta, Eri</creatorcontrib><creatorcontrib>Sugimori, Kazuya</creatorcontrib><creatorcontrib>Kaneko, Takashi</creatorcontrib><creatorcontrib>Ishii, Tomohiro</creatorcontrib><creatorcontrib>Miwa, Haruo</creatorcontrib><creatorcontrib>Sato, Takeshi</creatorcontrib><creatorcontrib>Ishii, Yasuaki</creatorcontrib><creatorcontrib>Sue, Soichiro</creatorcontrib><creatorcontrib>Sasaki, Tomohiko</creatorcontrib><creatorcontrib>Yamashita, Yuki</creatorcontrib><creatorcontrib>Shibata, Wataru</creatorcontrib><creatorcontrib>Matsumoto, Naomichi</creatorcontrib><creatorcontrib>Maeda, Shin</creatorcontrib><title>Diagnosis of pancreatic lesions collected by endoscopic ultrasound-guided fine-needle aspiration using next-generation sequencing</title><title>Oncology letters</title><addtitle>Oncol Lett</addtitle><description>Endoscopic ultrasound-guided fine-needle aspiration (EUF-FNA) has improved the diagnosis of pancreatic lesions. Next-generation sequencing (NGS) facilitates the production of millions of sequences concurrently. Therefore, in the current study, to improve the detectability of oncogenic mutations in pancreatic lesions, an NGS system was used to diagnose EUS-FNA samples. A total of 38 patients with clinically diagnosed EUS-FNA specimens were analyzed; 27 patients had pancreatic ductal adenocarcinoma (PDAC) and 11 had non-PDAC lesions. DNA samples were isolated and sequenced by NGS using an Ion Personal Genome Machine system. The Cancer Hotspot Panel v2, which includes 50 cancer-related genes and 2,790 COSMIC mutations, was used. A >2% mutation frequency was defined as positive. KRAS mutations were detected in 26 of 27 PDAC aspirates (96%) and 0 of 11 non-PDAC lesions (0%). The G12, G13, and Q61 KRAS mutations were found in 25, 0, and 1 of the 27 PDAC samples, respectively. Mutations were confirmed by TaqMan® polymerase chain reaction analysis. TP53 mutations were detected in 12 of 27 PDAC aspirates (44%). SMAD4 was observed in 3 PDAC lesions and cyclin-dependent kinase inhibitor 2A in 4 PDAC lesions. Therefore, the current study was successfully able to develop an NGS assay with high clinical sensitivity for EUS-FNA samples.</description><subject>Antigens</subject><subject>Cyclin-dependent kinases</subject><subject>Deoxyribonucleic acid</subject><subject>Diagnosis</subject><subject>DNA</subject><subject>endoscopic ultrasound-guided fine-needle aspiration</subject><subject>Endoscopy</subject><subject>Genes</subject><subject>Genomes</subject><subject>Kinases</subject><subject>KRAS</subject><subject>Medical diagnosis</subject><subject>Metastasis</subject><subject>Methods</subject><subject>Mutation</subject><subject>Needle biopsy</subject><subject>next-generation sequencing</subject><subject>Oncology</subject><subject>Pancreatic cancer</subject><subject>pancreatic ductal adenocarcinoma</subject><subject>Patient outcomes</subject><subject>Proteins</subject><subject>Software</subject><subject>Studies</subject><subject>TP53</subject><subject>Tumors</subject><subject>Ultrasonic imaging</subject><issn>1792-1074</issn><issn>1792-1082</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2016</creationdate><recordtype>article</recordtype><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><recordid>eNptksuLFDEQxhtR3GXdm2dpUMSDPebRncdFWNYnDOxFzyGP6p4smWTsdIt79D837YzjjpgcEqp-9VVSfFX1FKMVFZK8SWFFEGarDjPxoDrHXJIGI0EeHu-8Pasuc75FZXUMC8EeV2eEC9nxlp5XP995PcSUfa5TX-90tCPoyds6QPYp5tqmEMBO4GpzV0N0Kdu0K_k5TKPOaY6uGWbvSr73EZoI4ALUOu_8WHRSrOfs41BH-DE1A0Q4RDN8myHaknpSPep1yHB5OC-qrx_ef7n-1KxvPn6-vlo3lqFuapgpyiCdcNpQzrlE1nBJdUdFKy0BboAgwSVGrWWE4h6M7QylhmqwhiB6Ub3d6-5mswVnIZYPBLUb_VaPdyppr04z0W_UkL6rrkhi2RWBVweBMZXH50ltfbYQgo6Q5qywaFuGOJK8oM__QW_TPMbyPYUlJYxRIehfatABlI99Kn3tIqquWk6poEwsbVf_ocp2sPU2Reh9iZ8UvLxXsAEdpk1OYV7mnk_B13vQjinnEfrjMDBSi71UCmqxl1rsVfBn9wd4hP-YqQAv9kAuPnK-WOXI3KwbVPZvnV9_TdiY</recordid><startdate>20161101</startdate><enddate>20161101</enddate><creator>Kameta, Eri</creator><creator>Sugimori, Kazuya</creator><creator>Kaneko, Takashi</creator><creator>Ishii, Tomohiro</creator><creator>Miwa, Haruo</creator><creator>Sato, Takeshi</creator><creator>Ishii, Yasuaki</creator><creator>Sue, Soichiro</creator><creator>Sasaki, Tomohiko</creator><creator>Yamashita, Yuki</creator><creator>Shibata, Wataru</creator><creator>Matsumoto, Naomichi</creator><creator>Maeda, Shin</creator><general>D.A. Spandidos</general><general>Spandidos Publications</general><general>Spandidos Publications UK Ltd</general><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7X7</scope><scope>7XB</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AN0</scope><scope>BENPR</scope><scope>CCPQU</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>K9.</scope><scope>M0S</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20161101</creationdate><title>Diagnosis of pancreatic lesions collected by endoscopic ultrasound-guided fine-needle aspiration using next-generation sequencing</title><author>Kameta, Eri ; Sugimori, Kazuya ; Kaneko, Takashi ; Ishii, Tomohiro ; Miwa, Haruo ; Sato, Takeshi ; Ishii, Yasuaki ; Sue, Soichiro ; Sasaki, Tomohiko ; Yamashita, Yuki ; Shibata, Wataru ; Matsumoto, Naomichi ; Maeda, Shin</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c605t-6beede9d8dab377790cb793a53849c2e7be20879104c6231febc5b33b3aecb203</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2016</creationdate><topic>Antigens</topic><topic>Cyclin-dependent kinases</topic><topic>Deoxyribonucleic acid</topic><topic>Diagnosis</topic><topic>DNA</topic><topic>endoscopic ultrasound-guided fine-needle aspiration</topic><topic>Endoscopy</topic><topic>Genes</topic><topic>Genomes</topic><topic>Kinases</topic><topic>KRAS</topic><topic>Medical diagnosis</topic><topic>Metastasis</topic><topic>Methods</topic><topic>Mutation</topic><topic>Needle biopsy</topic><topic>next-generation sequencing</topic><topic>Oncology</topic><topic>Pancreatic cancer</topic><topic>pancreatic ductal adenocarcinoma</topic><topic>Patient outcomes</topic><topic>Proteins</topic><topic>Software</topic><topic>Studies</topic><topic>TP53</topic><topic>Tumors</topic><topic>Ultrasonic imaging</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Kameta, Eri</creatorcontrib><creatorcontrib>Sugimori, Kazuya</creatorcontrib><creatorcontrib>Kaneko, Takashi</creatorcontrib><creatorcontrib>Ishii, Tomohiro</creatorcontrib><creatorcontrib>Miwa, Haruo</creatorcontrib><creatorcontrib>Sato, Takeshi</creatorcontrib><creatorcontrib>Ishii, Yasuaki</creatorcontrib><creatorcontrib>Sue, Soichiro</creatorcontrib><creatorcontrib>Sasaki, Tomohiko</creatorcontrib><creatorcontrib>Yamashita, Yuki</creatorcontrib><creatorcontrib>Shibata, Wataru</creatorcontrib><creatorcontrib>Matsumoto, Naomichi</creatorcontrib><creatorcontrib>Maeda, Shin</creatorcontrib><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>British Nursing Database</collection><collection>ProQuest Central</collection><collection>ProQuest One Community College</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Oncology letters</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Kameta, Eri</au><au>Sugimori, Kazuya</au><au>Kaneko, Takashi</au><au>Ishii, Tomohiro</au><au>Miwa, Haruo</au><au>Sato, Takeshi</au><au>Ishii, Yasuaki</au><au>Sue, Soichiro</au><au>Sasaki, Tomohiko</au><au>Yamashita, Yuki</au><au>Shibata, Wataru</au><au>Matsumoto, Naomichi</au><au>Maeda, Shin</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Diagnosis of pancreatic lesions collected by endoscopic ultrasound-guided fine-needle aspiration using next-generation sequencing</atitle><jtitle>Oncology letters</jtitle><addtitle>Oncol Lett</addtitle><date>2016-11-01</date><risdate>2016</risdate><volume>12</volume><issue>5</issue><spage>3875</spage><epage>3881</epage><pages>3875-3881</pages><issn>1792-1074</issn><eissn>1792-1082</eissn><abstract>Endoscopic ultrasound-guided fine-needle aspiration (EUF-FNA) has improved the diagnosis of pancreatic lesions. Next-generation sequencing (NGS) facilitates the production of millions of sequences concurrently. Therefore, in the current study, to improve the detectability of oncogenic mutations in pancreatic lesions, an NGS system was used to diagnose EUS-FNA samples. A total of 38 patients with clinically diagnosed EUS-FNA specimens were analyzed; 27 patients had pancreatic ductal adenocarcinoma (PDAC) and 11 had non-PDAC lesions. DNA samples were isolated and sequenced by NGS using an Ion Personal Genome Machine system. The Cancer Hotspot Panel v2, which includes 50 cancer-related genes and 2,790 COSMIC mutations, was used. A >2% mutation frequency was defined as positive. KRAS mutations were detected in 26 of 27 PDAC aspirates (96%) and 0 of 11 non-PDAC lesions (0%). The G12, G13, and Q61 KRAS mutations were found in 25, 0, and 1 of the 27 PDAC samples, respectively. Mutations were confirmed by TaqMan® polymerase chain reaction analysis. TP53 mutations were detected in 12 of 27 PDAC aspirates (44%). SMAD4 was observed in 3 PDAC lesions and cyclin-dependent kinase inhibitor 2A in 4 PDAC lesions. Therefore, the current study was successfully able to develop an NGS assay with high clinical sensitivity for EUS-FNA samples.</abstract><cop>Greece</cop><pub>D.A. Spandidos</pub><pmid>27895743</pmid><doi>10.3892/ol.2016.5168</doi><tpages>7</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Antigens Cyclin-dependent kinases Deoxyribonucleic acid Diagnosis DNA endoscopic ultrasound-guided fine-needle aspiration Endoscopy Genes Genomes Kinases KRAS Medical diagnosis Metastasis Methods Mutation Needle biopsy next-generation sequencing Oncology Pancreatic cancer pancreatic ductal adenocarcinoma Patient outcomes Proteins Software Studies TP53 Tumors Ultrasonic imaging |
| title | Diagnosis of pancreatic lesions collected by endoscopic ultrasound-guided fine-needle aspiration using next-generation sequencing |
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