- Email: [email protected]
Development of a comprehensive next-generation targeted sequencing assay for detection of gene-fusions in solid tumors
abstracts
MSD. C. Saura: Advisory / Consultancy: AstraZeneca, Celgene, Daiichi Sankyo, Eisai, Roche, Genomic health, Novartis, Pfizer, Pierre Fabre, Puma, Synthon and Sanofi; Travel / Accommodation / Expenses: AstraZeneca, Celgene, Daiichi Sankyo, Eisai, Roche, Genomic health, Novartis, Pfizer, Pierre Fabre, Puma, Synthon and Sanofi. E. Elez: Honoraria (self): Hoffman La-Roche, Bristol Myers Squibb, Servier, Amgen, Merck Serono, Array, Sanofi; Advisory / Consultancy: Hoffman La-Roche, Bristol Myers Squibb, Servier, Amgen, Merck Serono, Array, Sanofi; Research grant / Funding (self): Hoffman La-Roche, Bristol Myers Squibb, Servier, Amgen, Merck Serono, Array, Sanofi; Honoraria (institution): Array, MSD, Abbvie, Amgen, GSK, AstraZeneca, Bristol Myers Squibb, Novartis, Boehringer, Ingelheim, Hoffman La-Roche.. E. Felip: Speaker Bureau / Expert testimony: AbbVie, AstraZeneca, Blueprint medicines, Boehringer Ingelheim, Bristol-Myers Squibb, Celgene, Eli Lilly, Guardant Health, Janssen, Medscape, Merck KGaA, Merck Sharp & Dohme, Novartis, Pfizer, Roche, Takeda, Touchtime.; Advisory / Consultancy: AbbVie, AstraZeneca, Blueprint medicines, Boehringer Ingelheim, Bristol-Myers Squibb, Celgene, Eli Lilly, Guardant Health, Janssen, Medscape, Merck KGaA, Merck Sharp & Dohme, Novartis, Pfizer, Roche, Takeda, Touchtime.; Research grant / Funding (institution): Fundaci on Merck Salud, Grant for Oncology Innovation EMD Serono. A. Oaknin: Advisory / Consultancy: Roche, AstraZeneca, PharmaMar, Clovis Oncology, Tesaro, Inmunogen and Genmab; Travel / Accommodation / Expenses: Roche, AstraZeneca, and PharmaMar. E. Mu~ noz-Couselo: Advisory / Consultancy: Amgen, Bristol-Myers Squibb, Merck, Sharp & Dohme, Novartis, Pierre Fabre, and Roche; Honoraria (self): Amgen, Bristol-Myers Squibb, Merck, Sharp & Dohme, Novartis, Pierre Fabre, Sanofi and Roche ; Leadership role, Clinical trial participation (principal investigator): Amgen, Bristol-Myers Squibb, GlaxoSmithKline, Merck, Sharp & Dohme, Novartis, Pierre Fabre, and Roche. T. Macarulla Mercade: Advisory / Consultancy: Shire Pharmaceuticals, Roche, Tesaro, Batxer, Sanofi, Celgene, QED Therapeutics, Genzyme Europe, Baxalta, Bayer, Incyte, Genzyme ; Travel / Accommodation / Expenses: from Merck, H3 Biomedicine, Bayer, Sanofi. M. Alsina Maqueda: Advisory / Consultancy: Servier, Lilly, BMS and MS. Honoraria for speaking issues from Servier, BMS, MSD, Lilly, Roche and Amge; Travel / Accommodation / Expenses: Servier, Roche, Amgen and Lilly. J. Carles: Advisory / Consultancy: Bayer / Johnson & Johnson / Bristol-Myers Squibb / Astellas Pharma / Pfizer / Sanofi / MSD Oncology / Roche/ AstraZe´neca; Speaker Bureau / Expert testimony: Bayer / Johnson & Johnson / Asofarma / Astellas Pharma; Research grant / Funding (institution): AB Science, Aragon Pharmaceuticals, Arog Pharmaceuticals, INC, Astellas Pharma., AstraZeneca AB, Aveo Pharmaceuticals INC, Bayer AG, Blueprint Medicines Corporation, BN Immunotherapeutics INC, Boehringer Ingelheim Espa~ na, S.A., Bristol-Myers Squibb Inter. R. Dienstmann: Advisory / Consultancy: Roche; Research grant / Funding (self): Merck. J. Tabernero: Advisory / Consultancy: Array Biopharma, AstraZeneca, Bayer, BeiGene, Boehringer Ingelheim, Chugai, Genentech, Inc., Genmab A/S, Halozyme, Imugene Limited, Inflection Biosciences Limited, Ipsen, Kura Oncology, Lilly, MSD, Menarini, Merck Serono, Merrimack, Merus, Molecular Part. E. Garralda: Advisory / Consultancy: F.Hoffmann-La Roche, Ellipses Pharma, Neomed Therapeutics1 Inc, Boehringer Ingelheim, Janssen Global Services, ; Speaker Bureau / Expert testimony: BristolMayers Squibb ; Travel / Accommodation / Expenses: Merck Sharp & Dohme, Glycotope, Menarini; Research grant / Funding (self), Scitron Project - VHIO Technology : Novartis; Research grant / Funding (institution), Clinical Trial Principal Investigator: Principia Biopharma Inc, Lilly, S.A, Novartis, Genentech, Loxo Oncologi Inc, F.Hoffmann-La Roche Ltd, Symphogen A/S, Merck, Sharp & Dohme de Espa~ na, S.A, Incyte Biosciences International, Pharma Mar, S.A.U, Kura Oncology Inc, Macrogenics Inc, Glycotope G; Leadership role: ESMO Women for Oncology - W4O. All other authors have declared no conflicts of interest.
1887P
Development of a comprehensive next-generation targeted sequencing assay for detection of gene-fusions in solid tumors
V.K. Mittal1, S.P. Myrand1, D. Cyanam1, P.D. Williams1, G.G. Bee2, A. Marcovitz3, R. Gottimukkala3, F. Hyland4, C. Allen5, E. Wong-Ho3, S. Sadis1, C. Van Loy2, J. Kilzer2, N. Khazanov1 1 Clinical Sequencing Division, Thermo Fisher Scientific, Ann Arbor, MI, USA, 2Clinical Sequencing Division, Thermo Fisher Scientific, Carlsbad, CA, USA, 3Clinical Sequencing Division, Thermo Fisher Scientific, South San Francisco, CA, USA, 4CSD, Thermo Fisher Scientific, San Francisco, USA, 5Field Applications, Thermo Fisher Scientific, Paisley, UK Background: Gene fusions caused by chromosomal rearrangements play an important role in oncogenesis, the progression of cancer and the selection of targeted therapies. Next-generation sequencing (NGS) using RNA enables sensitive, specific and precise detection of potentially clinically relevant gene fusions, especially when the fusion breakpoint is known. We have developed an NGS solution appropriate for FFPE tissues to detect fusion biomarkers in routine clinical research. Methods: Fusion content was selected based on prioritization of actionability, verified fusion isoforms reported in the literature and collaborations, as well as prevalence of solid tumor fusion driver genes. The assay was designed to use Ion AmpliSeq multiplex
v766 | Translational Research
PCR chemistry using manual or automated library preparation, automated templating on the Ion Chef, and sequencing on the Ion Torrent GeneStudioTM S5 sequencing platform. The analysis was supported by fully automated analysis software that performs sample QC, read-filtering, fusion calling and reporting. Streamlined access to decision support software was enabled by OncomineTM Reporter. Results: Over 1200 targeted isoforms from over 50 known fusion driver genes were incorporated into the assay that included prominent fusion drivers such as ALK, RET, ROS1, NTRK1/2/3 and FGFR1/2/3, and intragenic fusion events in MET, EGFR, BRAF and AR. The assay also reported non-targeted fusion events in relevant driver genes by using a novel statistically significant expression imbalance algorithm comparing 5’and 3’- end gene expression. A preliminary development study was performed using commercially available total RNA for a Tri-Fusion control and SeraseqTM Fusion RNA Mix v3 where all of the expected fusions were detected with 100% sensitivity and specificity. Results were also concordant when characterized FFPE tumor samples with known fusion targets were tested using the assay. Conclusions: A comprehensive NGS assay was developed to support clinical research in oncology for detecting relevant RNA structural alterations from solid tumor FFPEs. An update on assay performance will be presented. Legal entity responsible for the study: Thermo Fisher Scientific. Funding: Has not received any funding. Disclosure: V.K. Mittal: Shareholder / Stockholder / Stock options, Full / Part-time employment: Thermo Fisher Scientific. S.P. Myrand: Shareholder / Stockholder / Stock options, Full / Part-time employment: Thermo Fisher Scientific. D. Cyanam: Shareholder / Stockholder / Stock options, Full / Part-time employment: Thermo Fisher Scientific. P.D. Williams: Shareholder / Stockholder / Stock options, Full / Part-time employment: Thermo Fisher Scientific. G.G. Bee: Shareholder / Stockholder / Stock options, Full / Part-time employment: Thermo Fisher Scientific. A. Marcovitz: Shareholder / Stockholder / Stock options, Full / Part-time employment: Thermo Fisher Scientific. R. Gottimukkala: Shareholder / Stockholder / Stock options, Full / Part-time employment: Thermo Fisher Scientific. F. Hyland: Shareholder / Stockholder / Stock options, Full / Part-time employment: Thermo Fisher Scientific. C. Allen: Shareholder / Stockholder / Stock options, Full / Part-time employment: Thermo Fisher Scientific. E. Wong-Ho: Shareholder / Stockholder / Stock options, Full / Part-time employment: Thermo Fisher Scientific. S. Sadis: Shareholder / Stockholder / Stock options, Full / Part-time employment: Thermo Fisher Scientific. C. Van Loy: Shareholder / Stockholder / Stock options, Full / Part-time employment: Thermo Fisher Scientific. J. Kilzer: Shareholder / Stockholder / Stock options, Full / Part-time employment: Thermo Fisher Scientific. N. Khazanov: Shareholder / Stockholder / Stock options, Full / Part-time employment: Thermo Fisher Scientific.
1888P
Next-generation sequencing for better treatment strategy of cancer of unknown primary (CUP)
K.K. Lee1, M. Kim2, K-M. Kim3, S.T. Kim4, J. Lee4, S.J. Lee5 Hemato-Oncology, Dongsan Medical Center Kemyung University Hospital, Daegu, Republic of Korea, 2Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, Republic of Korea, 3Pathology, Samsung Medical Center, Seoul, Republic of Korea, 4Medicine, Samsung Medical Center, Seoul, Republic of Korea, 5Internal Medicine, EWHA Womans University Seoul Hospital, Seoul, Republic of Korea
1
Background: Cancer of unknown primary (CUP) consists of diverse histology types of cancer and have shown poor prognosis. In the era of precision medicine, next-generation sequencing (NGS) may contribute new therapeutic target which could improve treatment outcomes of CUP. Methods: Patients who were diagnosed with CUP and underwent NGS exam between August 2017 and August 2018 at Samsung medical center were included for the study. NGS data were analyzed, and medical records were reviewed retrospectively to evaluate clinical characteristics and response to various treatments. Results: A total of 21 patients with CUP who had NGS data were analyzed. The median age was 58 (range, 35-78 years). Male was dominant (57.1%) and most of the patients were ECOG 1 (90.5%). Among the patients, 14 (66.7%) were poorly differentiated carcinoma, 6 (28.6%) patients were adenocarcinoma, and one patient was squamous cell carcinoma. Most common metastatic site was lymph node (57.1%), followed by bone (38.1%), lung (19.0%), pleura (19.0%). Paclitaxel combined with carboplatin was most frequently used regimen for the first-line treatment (57.1%). Cisplatin-based chemotherapy was used second most (28.6%). One patient showed complete remission during the first-line treatment whereas 7 patients and 5 patients achieved the best response of partial response and stable disease, respectively. Median progression-free survival was 4 months (95% CI: 0.316-7.684), and median overall survival was not reached. Except four patients, 17 (81.0%) patients showed 25 gene alterations on the NGS results. TP53 mutation was observed most commonly (n ¼ 6, 25.6%), followed by ERBB2 alterations (n ¼ 3, mutations [n ¼ 2], amplification [n ¼ 1]), KRAS mutation (n ¼ 2), MET amplification (n ¼ 2), CDKN2A deletion (n ¼ 2), and MYC amplification (n ¼ 2). One patient harbored ERBB2 amplification was treated with trastuzumab combined with paclitaxel, and the patient demonstrated sustained partial response at 9 months, until the data cut-off date. Conclusions: Most of CUP patients had variety actionable gene alterations. Precision medicine based on molecular analysis with NGS will improve the prognosis of the patients with CUP. Legal entity responsible for the study: The authors. Funding: Has not received any funding. Disclosure: All authors have declared no conflicts of interest.
Volume 30 | Supplement 5 | October 2019
Downloaded from https://academic.oup.com/annonc/article-abstract/30/Supplement_5/mdz268.014/5576328 by guest on 24 October 2019
under ultrasound (60%), computed tomography (12%) guidance or non-guided (28%). Samples were formalin-fixed and paraffin embedded (FFPE, 48%), snap frozen (20%) or alternatively stabilized (32%) according to study protocol. Tumor content (TC) was determined in 1514 FFPE samples: 90% of them had tumor cells, 81% showed more than 10% TC and 59% more than 50% TC. No significant difference in TC was found between screening and on-treatment biopsies (p ¼ 0.12). Sample quality was negatively affected by biopsy site (<10% TC rates in non-visceral vs visceral were 26% vs 14%, respectively, p<.0001), method (non-guided vs guided, 37% vs 17%, p<.0001), and operator expertise (<50 vs > 50 biopsies x year, 31% vs 16.5%, p<.0001). In a multivariate logistic model, biopsy site and method were independent determinants of poor sample quality (<10% TC). Within the same biopsy procedure, inter-sample variability was low with 77% of samples showing between 0% to 30% difference in TC. Among 134 intra-trial sequential biopsies with available TC assessment, only 25% pairs were not suitable for performing downstream comparative analyses (<10% TC). Conclusions: Our experience provides important information to improve research biopsy effectiveness in a biomarker program linked to clinical trials. Legal entity responsible for the study: The authors. Funding: Has not received any funding. Disclosure: P.G. Nuciforo: Honoraria (self): Bayer; Honoraria (self): Novartis; Honoraria (self):
Annals of Oncology
MSD. C. Saura: Advisory / Consultancy: AstraZeneca, Celgene, Daiichi Sankyo, Eisai, Roche, Genomic health, Novartis, Pfizer, Pierre Fabre, Puma, Synthon and Sanofi; Travel / Accommodation / Expenses: AstraZeneca, Celgene, Daiichi Sankyo, Eisai, Roche, Genomic health, Novartis, Pfizer, Pierre Fabre, Puma, Synthon and Sanofi. E. Elez: Honoraria (self): Hoffman La-Roche, Bristol Myers Squibb, Servier, Amgen, Merck Serono, Array, Sanofi; Advisory / Consultancy: Hoffman La-Roche, Bristol Myers Squibb, Servier, Amgen, Merck Serono, Array, Sanofi; Research grant / Funding (self): Hoffman La-Roche, Bristol Myers Squibb, Servier, Amgen, Merck Serono, Array, Sanofi; Honoraria (institution): Array, MSD, Abbvie, Amgen, GSK, AstraZeneca, Bristol Myers Squibb, Novartis, Boehringer, Ingelheim, Hoffman La-Roche.. E. Felip: Speaker Bureau / Expert testimony: AbbVie, AstraZeneca, Blueprint medicines, Boehringer Ingelheim, Bristol-Myers Squibb, Celgene, Eli Lilly, Guardant Health, Janssen, Medscape, Merck KGaA, Merck Sharp & Dohme, Novartis, Pfizer, Roche, Takeda, Touchtime.; Advisory / Consultancy: AbbVie, AstraZeneca, Blueprint medicines, Boehringer Ingelheim, Bristol-Myers Squibb, Celgene, Eli Lilly, Guardant Health, Janssen, Medscape, Merck KGaA, Merck Sharp & Dohme, Novartis, Pfizer, Roche, Takeda, Touchtime.; Research grant / Funding (institution): Fundaci on Merck Salud, Grant for Oncology Innovation EMD Serono. A. Oaknin: Advisory / Consultancy: Roche, AstraZeneca, PharmaMar, Clovis Oncology, Tesaro, Inmunogen and Genmab; Travel / Accommodation / Expenses: Roche, AstraZeneca, and PharmaMar. E. Mu~ noz-Couselo: Advisory / Consultancy: Amgen, Bristol-Myers Squibb, Merck, Sharp & Dohme, Novartis, Pierre Fabre, and Roche; Honoraria (self): Amgen, Bristol-Myers Squibb, Merck, Sharp & Dohme, Novartis, Pierre Fabre, Sanofi and Roche ; Leadership role, Clinical trial participation (principal investigator): Amgen, Bristol-Myers Squibb, GlaxoSmithKline, Merck, Sharp & Dohme, Novartis, Pierre Fabre, and Roche. T. Macarulla Mercade: Advisory / Consultancy: Shire Pharmaceuticals, Roche, Tesaro, Batxer, Sanofi, Celgene, QED Therapeutics, Genzyme Europe, Baxalta, Bayer, Incyte, Genzyme ; Travel / Accommodation / Expenses: from Merck, H3 Biomedicine, Bayer, Sanofi. M. Alsina Maqueda: Advisory / Consultancy: Servier, Lilly, BMS and MS. Honoraria for speaking issues from Servier, BMS, MSD, Lilly, Roche and Amge; Travel / Accommodation / Expenses: Servier, Roche, Amgen and Lilly. J. Carles: Advisory / Consultancy: Bayer / Johnson & Johnson / Bristol-Myers Squibb / Astellas Pharma / Pfizer / Sanofi / MSD Oncology / Roche/ AstraZe´neca; Speaker Bureau / Expert testimony: Bayer / Johnson & Johnson / Asofarma / Astellas Pharma; Research grant / Funding (institution): AB Science, Aragon Pharmaceuticals, Arog Pharmaceuticals, INC, Astellas Pharma., AstraZeneca AB, Aveo Pharmaceuticals INC, Bayer AG, Blueprint Medicines Corporation, BN Immunotherapeutics INC, Boehringer Ingelheim Espa~ na, S.A., Bristol-Myers Squibb Inter. R. Dienstmann: Advisory / Consultancy: Roche; Research grant / Funding (self): Merck. J. Tabernero: Advisory / Consultancy: Array Biopharma, AstraZeneca, Bayer, BeiGene, Boehringer Ingelheim, Chugai, Genentech, Inc., Genmab A/S, Halozyme, Imugene Limited, Inflection Biosciences Limited, Ipsen, Kura Oncology, Lilly, MSD, Menarini, Merck Serono, Merrimack, Merus, Molecular Part. E. Garralda: Advisory / Consultancy: F.Hoffmann-La Roche, Ellipses Pharma, Neomed Therapeutics1 Inc, Boehringer Ingelheim, Janssen Global Services, ; Speaker Bureau / Expert testimony: BristolMayers Squibb ; Travel / Accommodation / Expenses: Merck Sharp & Dohme, Glycotope, Menarini; Research grant / Funding (self), Scitron Project - VHIO Technology : Novartis; Research grant / Funding (institution), Clinical Trial Principal Investigator: Principia Biopharma Inc, Lilly, S.A, Novartis, Genentech, Loxo Oncologi Inc, F.Hoffmann-La Roche Ltd, Symphogen A/S, Merck, Sharp & Dohme de Espa~ na, S.A, Incyte Biosciences International, Pharma Mar, S.A.U, Kura Oncology Inc, Macrogenics Inc, Glycotope G; Leadership role: ESMO Women for Oncology - W4O. All other authors have declared no conflicts of interest.
1887P
Development of a comprehensive next-generation targeted sequencing assay for detection of gene-fusions in solid tumors
V.K. Mittal1, S.P. Myrand1, D. Cyanam1, P.D. Williams1, G.G. Bee2, A. Marcovitz3, R. Gottimukkala3, F. Hyland4, C. Allen5, E. Wong-Ho3, S. Sadis1, C. Van Loy2, J. Kilzer2, N. Khazanov1 1 Clinical Sequencing Division, Thermo Fisher Scientific, Ann Arbor, MI, USA, 2Clinical Sequencing Division, Thermo Fisher Scientific, Carlsbad, CA, USA, 3Clinical Sequencing Division, Thermo Fisher Scientific, South San Francisco, CA, USA, 4CSD, Thermo Fisher Scientific, San Francisco, USA, 5Field Applications, Thermo Fisher Scientific, Paisley, UK Background: Gene fusions caused by chromosomal rearrangements play an important role in oncogenesis, the progression of cancer and the selection of targeted therapies. Next-generation sequencing (NGS) using RNA enables sensitive, specific and precise detection of potentially clinically relevant gene fusions, especially when the fusion breakpoint is known. We have developed an NGS solution appropriate for FFPE tissues to detect fusion biomarkers in routine clinical research. Methods: Fusion content was selected based on prioritization of actionability, verified fusion isoforms reported in the literature and collaborations, as well as prevalence of solid tumor fusion driver genes. The assay was designed to use Ion AmpliSeq multiplex
v766 | Translational Research
PCR chemistry using manual or automated library preparation, automated templating on the Ion Chef, and sequencing on the Ion Torrent GeneStudioTM S5 sequencing platform. The analysis was supported by fully automated analysis software that performs sample QC, read-filtering, fusion calling and reporting. Streamlined access to decision support software was enabled by OncomineTM Reporter. Results: Over 1200 targeted isoforms from over 50 known fusion driver genes were incorporated into the assay that included prominent fusion drivers such as ALK, RET, ROS1, NTRK1/2/3 and FGFR1/2/3, and intragenic fusion events in MET, EGFR, BRAF and AR. The assay also reported non-targeted fusion events in relevant driver genes by using a novel statistically significant expression imbalance algorithm comparing 5’and 3’- end gene expression. A preliminary development study was performed using commercially available total RNA for a Tri-Fusion control and SeraseqTM Fusion RNA Mix v3 where all of the expected fusions were detected with 100% sensitivity and specificity. Results were also concordant when characterized FFPE tumor samples with known fusion targets were tested using the assay. Conclusions: A comprehensive NGS assay was developed to support clinical research in oncology for detecting relevant RNA structural alterations from solid tumor FFPEs. An update on assay performance will be presented. Legal entity responsible for the study: Thermo Fisher Scientific. Funding: Has not received any funding. Disclosure: V.K. Mittal: Shareholder / Stockholder / Stock options, Full / Part-time employment: Thermo Fisher Scientific. S.P. Myrand: Shareholder / Stockholder / Stock options, Full / Part-time employment: Thermo Fisher Scientific. D. Cyanam: Shareholder / Stockholder / Stock options, Full / Part-time employment: Thermo Fisher Scientific. P.D. Williams: Shareholder / Stockholder / Stock options, Full / Part-time employment: Thermo Fisher Scientific. G.G. Bee: Shareholder / Stockholder / Stock options, Full / Part-time employment: Thermo Fisher Scientific. A. Marcovitz: Shareholder / Stockholder / Stock options, Full / Part-time employment: Thermo Fisher Scientific. R. Gottimukkala: Shareholder / Stockholder / Stock options, Full / Part-time employment: Thermo Fisher Scientific. F. Hyland: Shareholder / Stockholder / Stock options, Full / Part-time employment: Thermo Fisher Scientific. C. Allen: Shareholder / Stockholder / Stock options, Full / Part-time employment: Thermo Fisher Scientific. E. Wong-Ho: Shareholder / Stockholder / Stock options, Full / Part-time employment: Thermo Fisher Scientific. S. Sadis: Shareholder / Stockholder / Stock options, Full / Part-time employment: Thermo Fisher Scientific. C. Van Loy: Shareholder / Stockholder / Stock options, Full / Part-time employment: Thermo Fisher Scientific. J. Kilzer: Shareholder / Stockholder / Stock options, Full / Part-time employment: Thermo Fisher Scientific. N. Khazanov: Shareholder / Stockholder / Stock options, Full / Part-time employment: Thermo Fisher Scientific.
1888P
Next-generation sequencing for better treatment strategy of cancer of unknown primary (CUP)
K.K. Lee1, M. Kim2, K-M. Kim3, S.T. Kim4, J. Lee4, S.J. Lee5 Hemato-Oncology, Dongsan Medical Center Kemyung University Hospital, Daegu, Republic of Korea, 2Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, Republic of Korea, 3Pathology, Samsung Medical Center, Seoul, Republic of Korea, 4Medicine, Samsung Medical Center, Seoul, Republic of Korea, 5Internal Medicine, EWHA Womans University Seoul Hospital, Seoul, Republic of Korea
1
Background: Cancer of unknown primary (CUP) consists of diverse histology types of cancer and have shown poor prognosis. In the era of precision medicine, next-generation sequencing (NGS) may contribute new therapeutic target which could improve treatment outcomes of CUP. Methods: Patients who were diagnosed with CUP and underwent NGS exam between August 2017 and August 2018 at Samsung medical center were included for the study. NGS data were analyzed, and medical records were reviewed retrospectively to evaluate clinical characteristics and response to various treatments. Results: A total of 21 patients with CUP who had NGS data were analyzed. The median age was 58 (range, 35-78 years). Male was dominant (57.1%) and most of the patients were ECOG 1 (90.5%). Among the patients, 14 (66.7%) were poorly differentiated carcinoma, 6 (28.6%) patients were adenocarcinoma, and one patient was squamous cell carcinoma. Most common metastatic site was lymph node (57.1%), followed by bone (38.1%), lung (19.0%), pleura (19.0%). Paclitaxel combined with carboplatin was most frequently used regimen for the first-line treatment (57.1%). Cisplatin-based chemotherapy was used second most (28.6%). One patient showed complete remission during the first-line treatment whereas 7 patients and 5 patients achieved the best response of partial response and stable disease, respectively. Median progression-free survival was 4 months (95% CI: 0.316-7.684), and median overall survival was not reached. Except four patients, 17 (81.0%) patients showed 25 gene alterations on the NGS results. TP53 mutation was observed most commonly (n ¼ 6, 25.6%), followed by ERBB2 alterations (n ¼ 3, mutations [n ¼ 2], amplification [n ¼ 1]), KRAS mutation (n ¼ 2), MET amplification (n ¼ 2), CDKN2A deletion (n ¼ 2), and MYC amplification (n ¼ 2). One patient harbored ERBB2 amplification was treated with trastuzumab combined with paclitaxel, and the patient demonstrated sustained partial response at 9 months, until the data cut-off date. Conclusions: Most of CUP patients had variety actionable gene alterations. Precision medicine based on molecular analysis with NGS will improve the prognosis of the patients with CUP. Legal entity responsible for the study: The authors. Funding: Has not received any funding. Disclosure: All authors have declared no conflicts of interest.
Volume 30 | Supplement 5 | October 2019
Downloaded from https://academic.oup.com/annonc/article-abstract/30/Supplement_5/mdz268.014/5576328 by guest on 24 October 2019
under ultrasound (60%), computed tomography (12%) guidance or non-guided (28%). Samples were formalin-fixed and paraffin embedded (FFPE, 48%), snap frozen (20%) or alternatively stabilized (32%) according to study protocol. Tumor content (TC) was determined in 1514 FFPE samples: 90% of them had tumor cells, 81% showed more than 10% TC and 59% more than 50% TC. No significant difference in TC was found between screening and on-treatment biopsies (p ¼ 0.12). Sample quality was negatively affected by biopsy site (<10% TC rates in non-visceral vs visceral were 26% vs 14%, respectively, p<.0001), method (non-guided vs guided, 37% vs 17%, p<.0001), and operator expertise (<50 vs > 50 biopsies x year, 31% vs 16.5%, p<.0001). In a multivariate logistic model, biopsy site and method were independent determinants of poor sample quality (<10% TC). Within the same biopsy procedure, inter-sample variability was low with 77% of samples showing between 0% to 30% difference in TC. Among 134 intra-trial sequential biopsies with available TC assessment, only 25% pairs were not suitable for performing downstream comparative analyses (<10% TC). Conclusions: Our experience provides important information to improve research biopsy effectiveness in a biomarker program linked to clinical trials. Legal entity responsible for the study: The authors. Funding: Has not received any funding. Disclosure: P.G. Nuciforo: Honoraria (self): Bayer; Honoraria (self): Novartis; Honoraria (self):
Annals of Oncology