Small lung tumor biopsy samples are feasible for high quality targeted next generation sequencing
Next‐generation sequencing (NGS) has been implemented in clinical oncology to analyze multiple genes and to guide therapy. In patients with advanced lung cancer, small biopsies such as computed tomography‐guided needle biopsy (CTNB), endobronchial ultrasound‐guided transbronchial needle aspiration (...
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| Veröffentlicht in: | Cancer science 2019-08, Vol.110 (8), p.2652-2657 |
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| creator | Kage, Hidenori Kohsaka, Shinji Shinozaki‐Ushiku, Aya Hiraishi, Yoshihisa Sato, Jiro Nagayama, Kazuhiro Ushiku, Tetsuo Takai, Daiya Nakajima, Jun Miyagawa, Kiyoshi Aburatani, Hiroyuki Mano, Hiroyuki Nagase, Takahide |
| description | Next‐generation sequencing (NGS) has been implemented in clinical oncology to analyze multiple genes and to guide therapy. In patients with advanced lung cancer, small biopsies such as computed tomography‐guided needle biopsy (CTNB), endobronchial ultrasound‐guided transbronchial needle aspiration (EBUS‐TBNA) and transbronchial biopsy (TBB) are less invasive and are preferable to resection to make a pathological diagnosis. However, the quality of DNA/RNA and NGS from small lung tumor biopsy samples is unknown. Between April 2017 and March 2018, 107 consecutive samples were obtained from thoracic tumors or metastatic sites for targeted NGS analysis. Fifteen samples were obtained through CTNB, 11 through EBUS‐TBNA, 11 through TBB and 70 through surgical resection. All samples were formalin‐fixed and paraffin‐embedded. DNA and RNA quality was measured using the ddCq method and the percentage of RNA fragments above 200 nucleotides (DV200), respectively. Our custommade probes were designed to capture exon sequences of 464 cancer‐related genes and transcripts of 463 genes. DNA and RNA yield from the 3 biopsy methods were similar, and less than the yield obtained from resected samples. The quality of DNA and RNA was similar across all methods. Overall, 12 of 15 CTNB samples (80%), all 11 EBUS‐TBNA samples, and 9 of 11 TBB samples (82%) underwent successful NGS assays from DNA. NGS analysis from RNA was successful in all 12 CTNB samples, 9 of 11 EBUS‐TBNA samples (82%), and 8 of 11 TBB samples (73%). CTNB, EBUS‐TBNA and TBB mostly resulted in adequate DNA and RNA quality and enabled high‐quality targeted NGS analysis.
CT‐guided needle biospy, endobronchial ultrasound‐needle aspiration, and transbronchial biopsy mostly resulted in adequate DNA and RNA quality, which enalbled high‐quality targeted next generation sequencing (NGS) analysis. Our results indicate that small biopsies may be feasible for targeted NGS in general. |
| doi_str_mv | 10.1111/cas.14112 |
| format | Article |
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CT‐guided needle biospy, endobronchial ultrasound‐needle aspiration, and transbronchial biopsy mostly resulted in adequate DNA and RNA quality, which enalbled high‐quality targeted next generation sequencing (NGS) analysis. Our results indicate that small biopsies may be feasible for targeted NGS in general.</description><identifier>ISSN: 1347-9032</identifier><identifier>EISSN: 1349-7006</identifier><identifier>DOI: 10.1111/cas.14112</identifier><identifier>PMID: 31222846</identifier><language>eng</language><publisher>England: John Wiley & Sons, Inc</publisher><subject>Biopsy ; Biopsy - methods ; bronchoscopy ; Cancer therapies ; Computed tomography ; CT‐guided needle biopsy ; Deoxyribonucleic acid ; DNA ; DNA - genetics ; DNA probes ; High-Throughput Nucleotide Sequencing - methods ; Humans ; Invasiveness ; Lung cancer ; Lung Neoplasms - genetics ; Metastases ; Methods ; Mutation ; Next-generation sequencing ; Original ; Paraffin ; Quality control ; Ribonucleic acid ; RNA ; RNA - genetics ; targeted next generation sequencing ; Thoracic surgery ; Thorax ; Tumors ; Ultrasonic imaging ; Ultrasound ; Variance analysis</subject><ispartof>Cancer science, 2019-08, Vol.110 (8), p.2652-2657</ispartof><rights>2019 The Authors. published by John Wiley & Sons Australia, Ltd on behalf of Japanese Cancer Association.</rights><rights>2019 The Authors. Cancer Science published by John Wiley & Sons Australia, Ltd on behalf of Japanese Cancer Association.</rights><rights>2019. This work is published under http://creativecommons.org/licenses/by-nc/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c5332-3a10bac9f224ed4e528930ba3eb72b663514fd6ee33e8e5fab08d024bdb29e933</citedby><cites>FETCH-LOGICAL-c5332-3a10bac9f224ed4e528930ba3eb72b663514fd6ee33e8e5fab08d024bdb29e933</cites><orcidid>0000-0003-4645-0181 ; 0000-0001-8651-6136 ; 0000-0003-3658-4442</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6676108/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6676108/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,1411,11541,27901,27902,45550,45551,46027,46451,53766,53768</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/31222846$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Kage, Hidenori</creatorcontrib><creatorcontrib>Kohsaka, Shinji</creatorcontrib><creatorcontrib>Shinozaki‐Ushiku, Aya</creatorcontrib><creatorcontrib>Hiraishi, Yoshihisa</creatorcontrib><creatorcontrib>Sato, Jiro</creatorcontrib><creatorcontrib>Nagayama, Kazuhiro</creatorcontrib><creatorcontrib>Ushiku, Tetsuo</creatorcontrib><creatorcontrib>Takai, Daiya</creatorcontrib><creatorcontrib>Nakajima, Jun</creatorcontrib><creatorcontrib>Miyagawa, Kiyoshi</creatorcontrib><creatorcontrib>Aburatani, Hiroyuki</creatorcontrib><creatorcontrib>Mano, Hiroyuki</creatorcontrib><creatorcontrib>Nagase, Takahide</creatorcontrib><title>Small lung tumor biopsy samples are feasible for high quality targeted next generation sequencing</title><title>Cancer science</title><addtitle>Cancer Sci</addtitle><description>Next‐generation sequencing (NGS) has been implemented in clinical oncology to analyze multiple genes and to guide therapy. In patients with advanced lung cancer, small biopsies such as computed tomography‐guided needle biopsy (CTNB), endobronchial ultrasound‐guided transbronchial needle aspiration (EBUS‐TBNA) and transbronchial biopsy (TBB) are less invasive and are preferable to resection to make a pathological diagnosis. However, the quality of DNA/RNA and NGS from small lung tumor biopsy samples is unknown. Between April 2017 and March 2018, 107 consecutive samples were obtained from thoracic tumors or metastatic sites for targeted NGS analysis. Fifteen samples were obtained through CTNB, 11 through EBUS‐TBNA, 11 through TBB and 70 through surgical resection. All samples were formalin‐fixed and paraffin‐embedded. DNA and RNA quality was measured using the ddCq method and the percentage of RNA fragments above 200 nucleotides (DV200), respectively. Our custommade probes were designed to capture exon sequences of 464 cancer‐related genes and transcripts of 463 genes. DNA and RNA yield from the 3 biopsy methods were similar, and less than the yield obtained from resected samples. The quality of DNA and RNA was similar across all methods. Overall, 12 of 15 CTNB samples (80%), all 11 EBUS‐TBNA samples, and 9 of 11 TBB samples (82%) underwent successful NGS assays from DNA. NGS analysis from RNA was successful in all 12 CTNB samples, 9 of 11 EBUS‐TBNA samples (82%), and 8 of 11 TBB samples (73%). CTNB, EBUS‐TBNA and TBB mostly resulted in adequate DNA and RNA quality and enabled high‐quality targeted NGS analysis.
CT‐guided needle biospy, endobronchial ultrasound‐needle aspiration, and transbronchial biopsy mostly resulted in adequate DNA and RNA quality, which enalbled high‐quality targeted next generation sequencing (NGS) analysis. Our results indicate that small biopsies may be feasible for targeted NGS in general.</description><subject>Biopsy</subject><subject>Biopsy - methods</subject><subject>bronchoscopy</subject><subject>Cancer therapies</subject><subject>Computed tomography</subject><subject>CT‐guided needle biopsy</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA - genetics</subject><subject>DNA probes</subject><subject>High-Throughput Nucleotide Sequencing - methods</subject><subject>Humans</subject><subject>Invasiveness</subject><subject>Lung cancer</subject><subject>Lung Neoplasms - genetics</subject><subject>Metastases</subject><subject>Methods</subject><subject>Mutation</subject><subject>Next-generation sequencing</subject><subject>Original</subject><subject>Paraffin</subject><subject>Quality control</subject><subject>Ribonucleic acid</subject><subject>RNA</subject><subject>RNA - genetics</subject><subject>targeted next generation sequencing</subject><subject>Thoracic surgery</subject><subject>Thorax</subject><subject>Tumors</subject><subject>Ultrasonic imaging</subject><subject>Ultrasound</subject><subject>Variance analysis</subject><issn>1347-9032</issn><issn>1349-7006</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2019</creationdate><recordtype>article</recordtype><sourceid>24P</sourceid><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><recordid>eNp1kUtr3TAQhUVJaR7ton8gCLJJFk70smxtAuGStIVAF2nXQrLHvgqydCPZae-_j5qbhrbQ2cyg-Tic0UHoIyXntNRFZ_I5FZSyN-iAcqGqhhC59zw3lSKc7aPDnO8J4VIo8Q7tc8oYa4U8QOZuMt5jv4QRz8sUE7YubvIWZzNtPGRsEuABTHbWl6Hs125c44fFeDdv8WzSCDP0OMDPGY8QIJnZxYAzPCwQOhfG9-jtYHyGDy_9CH2_uf62-lzdfv30ZXV1W3U156zihhJrOjUwJqAXULNW8fLCwTbMSslrKoZeAnAOLdSDsaTtCRO2t0yB4vwIXe50N4udoO8gzMl4vUluMmmro3H6701waz3GRy1lIylpi8Dpi0CKxXye9eRyB96bAHHJuhirJVUNlwU9-Qe9j0sK5TzNRPnwRnGmCnW2o7oUc04wvJqhRP8KTpfg9HNwhT3-0_0r-TupAlzsgB_Ow_b_Snp1dbeTfALycqQQ</recordid><startdate>201908</startdate><enddate>201908</enddate><creator>Kage, Hidenori</creator><creator>Kohsaka, Shinji</creator><creator>Shinozaki‐Ushiku, Aya</creator><creator>Hiraishi, Yoshihisa</creator><creator>Sato, Jiro</creator><creator>Nagayama, Kazuhiro</creator><creator>Ushiku, Tetsuo</creator><creator>Takai, Daiya</creator><creator>Nakajima, Jun</creator><creator>Miyagawa, Kiyoshi</creator><creator>Aburatani, Hiroyuki</creator><creator>Mano, Hiroyuki</creator><creator>Nagase, Takahide</creator><general>John Wiley & Sons, Inc</general><general>John Wiley and Sons Inc</general><scope>24P</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>8FE</scope><scope>8FH</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>LK8</scope><scope>M7P</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0003-4645-0181</orcidid><orcidid>https://orcid.org/0000-0001-8651-6136</orcidid><orcidid>https://orcid.org/0000-0003-3658-4442</orcidid></search><sort><creationdate>201908</creationdate><title>Small lung tumor biopsy samples are feasible for high quality targeted next generation sequencing</title><author>Kage, Hidenori ; Kohsaka, Shinji ; Shinozaki‐Ushiku, Aya ; Hiraishi, Yoshihisa ; Sato, Jiro ; Nagayama, Kazuhiro ; Ushiku, Tetsuo ; Takai, Daiya ; Nakajima, Jun ; Miyagawa, Kiyoshi ; Aburatani, Hiroyuki ; Mano, Hiroyuki ; Nagase, Takahide</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c5332-3a10bac9f224ed4e528930ba3eb72b663514fd6ee33e8e5fab08d024bdb29e933</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2019</creationdate><topic>Biopsy</topic><topic>Biopsy - methods</topic><topic>bronchoscopy</topic><topic>Cancer therapies</topic><topic>Computed tomography</topic><topic>CT‐guided needle biopsy</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>DNA - genetics</topic><topic>DNA probes</topic><topic>High-Throughput Nucleotide Sequencing - methods</topic><topic>Humans</topic><topic>Invasiveness</topic><topic>Lung cancer</topic><topic>Lung Neoplasms - genetics</topic><topic>Metastases</topic><topic>Methods</topic><topic>Mutation</topic><topic>Next-generation sequencing</topic><topic>Original</topic><topic>Paraffin</topic><topic>Quality control</topic><topic>Ribonucleic acid</topic><topic>RNA</topic><topic>RNA - genetics</topic><topic>targeted next generation sequencing</topic><topic>Thoracic surgery</topic><topic>Thorax</topic><topic>Tumors</topic><topic>Ultrasonic imaging</topic><topic>Ultrasound</topic><topic>Variance analysis</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Kage, Hidenori</creatorcontrib><creatorcontrib>Kohsaka, Shinji</creatorcontrib><creatorcontrib>Shinozaki‐Ushiku, Aya</creatorcontrib><creatorcontrib>Hiraishi, Yoshihisa</creatorcontrib><creatorcontrib>Sato, Jiro</creatorcontrib><creatorcontrib>Nagayama, Kazuhiro</creatorcontrib><creatorcontrib>Ushiku, Tetsuo</creatorcontrib><creatorcontrib>Takai, Daiya</creatorcontrib><creatorcontrib>Nakajima, Jun</creatorcontrib><creatorcontrib>Miyagawa, Kiyoshi</creatorcontrib><creatorcontrib>Aburatani, Hiroyuki</creatorcontrib><creatorcontrib>Mano, Hiroyuki</creatorcontrib><creatorcontrib>Nagase, Takahide</creatorcontrib><collection>Wiley Online Library Open Access</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Biological Science Collection</collection><collection>Biological Science Database</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>ProQuest Central China</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Cancer science</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Kage, Hidenori</au><au>Kohsaka, Shinji</au><au>Shinozaki‐Ushiku, Aya</au><au>Hiraishi, Yoshihisa</au><au>Sato, Jiro</au><au>Nagayama, Kazuhiro</au><au>Ushiku, Tetsuo</au><au>Takai, Daiya</au><au>Nakajima, Jun</au><au>Miyagawa, Kiyoshi</au><au>Aburatani, Hiroyuki</au><au>Mano, Hiroyuki</au><au>Nagase, Takahide</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Small lung tumor biopsy samples are feasible for high quality targeted next generation sequencing</atitle><jtitle>Cancer science</jtitle><addtitle>Cancer Sci</addtitle><date>2019-08</date><risdate>2019</risdate><volume>110</volume><issue>8</issue><spage>2652</spage><epage>2657</epage><pages>2652-2657</pages><issn>1347-9032</issn><eissn>1349-7006</eissn><abstract>Next‐generation sequencing (NGS) has been implemented in clinical oncology to analyze multiple genes and to guide therapy. In patients with advanced lung cancer, small biopsies such as computed tomography‐guided needle biopsy (CTNB), endobronchial ultrasound‐guided transbronchial needle aspiration (EBUS‐TBNA) and transbronchial biopsy (TBB) are less invasive and are preferable to resection to make a pathological diagnosis. However, the quality of DNA/RNA and NGS from small lung tumor biopsy samples is unknown. Between April 2017 and March 2018, 107 consecutive samples were obtained from thoracic tumors or metastatic sites for targeted NGS analysis. Fifteen samples were obtained through CTNB, 11 through EBUS‐TBNA, 11 through TBB and 70 through surgical resection. All samples were formalin‐fixed and paraffin‐embedded. DNA and RNA quality was measured using the ddCq method and the percentage of RNA fragments above 200 nucleotides (DV200), respectively. Our custommade probes were designed to capture exon sequences of 464 cancer‐related genes and transcripts of 463 genes. DNA and RNA yield from the 3 biopsy methods were similar, and less than the yield obtained from resected samples. The quality of DNA and RNA was similar across all methods. Overall, 12 of 15 CTNB samples (80%), all 11 EBUS‐TBNA samples, and 9 of 11 TBB samples (82%) underwent successful NGS assays from DNA. NGS analysis from RNA was successful in all 12 CTNB samples, 9 of 11 EBUS‐TBNA samples (82%), and 8 of 11 TBB samples (73%). CTNB, EBUS‐TBNA and TBB mostly resulted in adequate DNA and RNA quality and enabled high‐quality targeted NGS analysis.
CT‐guided needle biospy, endobronchial ultrasound‐needle aspiration, and transbronchial biopsy mostly resulted in adequate DNA and RNA quality, which enalbled high‐quality targeted next generation sequencing (NGS) analysis. Our results indicate that small biopsies may be feasible for targeted NGS in general.</abstract><cop>England</cop><pub>John Wiley & Sons, Inc</pub><pmid>31222846</pmid><doi>10.1111/cas.14112</doi><tpages>6</tpages><orcidid>https://orcid.org/0000-0003-4645-0181</orcidid><orcidid>https://orcid.org/0000-0001-8651-6136</orcidid><orcidid>https://orcid.org/0000-0003-3658-4442</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | Biopsy Biopsy - methods bronchoscopy Cancer therapies Computed tomography CT‐guided needle biopsy Deoxyribonucleic acid DNA DNA - genetics DNA probes High-Throughput Nucleotide Sequencing - methods Humans Invasiveness Lung cancer Lung Neoplasms - genetics Metastases Methods Mutation Next-generation sequencing Original Paraffin Quality control Ribonucleic acid RNA RNA - genetics targeted next generation sequencing Thoracic surgery Thorax Tumors Ultrasonic imaging Ultrasound Variance analysis |
| title | Small lung tumor biopsy samples are feasible for high quality targeted next generation sequencing |
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