- Email: [email protected]
Prospective testing of circulating tumour DNA in metastatic breast cancer facilitates clinical trial enrollment and precision oncology
abstracts Therapeutics. J. Snider: Full / Part-time employment: Flatiron Health; Shareholder / Stockholder / Stock options: Roche. E. Castellanos: Full / Part-time employment: Flatiron Health. S. Nanda: Full / Part-time employment: Bayer. V. Fisher: Full / Part-time employment: Foundation Medicine. J. Zong: Full / Part-time employment: Bayer. K. Keating: Full / Part-time employment: Bayer. M. Fellous: Full / Part-time employment: Bayer.
103P
Prospective comparative study of next-generation sequencing on fine needle aspirations versus core needle biopsies in cancer patients included in SHIVA02 trial
Background: High throughput molecular screening of solid tumours using core needle biopsies (CNB) allows the identification of actionable molecular alterations. Several reports revealed that success rate of genomic analyses based on CNB is around 70% with failures being mostly related to low proportion of tumour cells. Although several studies have demonstrated the utility of small biopsy specimens for molecular testing, there remains debate as to the sensitivity of CNB to detect actionable alterations compared to the less invasive fine needle aspiration (FNA). We aim to prospectively evaluate the ability of FNA to detect molecular alterations identified on CNB in cancer patients (pts) included in SHIVA02 trial. Methods: In-house targeted sequencing amplicon based panel (Illumina TSCA 99.3 Kb, 1,504 amplicons covering 87 genes) was used to identify pathogenic variants and gene copy number alterations (CNVs) in both CNB and FNA for pts enrolled in the SHIVA02 trial (NCT03084757). Results: CNB and FNA specimen from 39 pts enrolled in the SHIVA02 trial were assessed. Main tumour locations were breast (17pts, 44%), pancreatic (4pts, 10%), and colorectal cancers (3pts, 8%). 91 somatic variants were identified in both specimens with a good correlation of variants’ allelic ratios (r: 0.772). CNV profiles of CNB and FNA were concordant. When taking into account molecular alterations validated during the molecular biology board, 88 alterations (55 variants and 35 CNVs) were reported among which 69 alterations (78%) where concordant between CNB and FNA. Among the 50 actionable alterations, only 12 (3 variants and 9 CNVs) (24%) were discordant between FNA and CNB. Main discordances were related to homozygous deletions and amplifications but false negative results were not related to FNA samples alone (5 CNVs in favour of FNA versus 4 in favour of CNB). Conclusions: Comparative analyses of molecular alterations in CNB compared to FNA showed high concordance in terms of variants as well as CNVs identified. FNA could therefore be easily used in routine diagnostics workflow and clinical trials for tumour molecular screening with the advantage of being minimally invasive. Clinical trial identification: NCT03084757 SHIVA02; Trial release date: April 1, 2017. Legal entity responsible for the study: Institut Curie. Funding: MSD Avenir Fundation. Disclosure: C. Le Tourneau: Advisory / Consultancy: MSD, BMS, Merck Serono, AstraZeneca, Novartis, Roche, Nanobiotix. All other authors have declared no conflicts of interest.
104P
First national external quality assessment for the interpretation of somatic variants: Assessment of 25 variants in colorectal, lung, ovarian cancers and melanoma in France
E. Rouleau1, K. Leroy2, K. Dufraing3, A. Harle´4, L. Lacroix5, K. Vanwelden6, M.G. Denis7, A. Lamy8, E. Dequeker3 1 Tumor Genetics, Gustave Roussy - Cancer Campus, Villejuif, France, 2Service de Genetique et Biologie Moleculaire, Hoˆpital Cochin, Paris, France, 3Quality, University Hospitals Leuven - Campus Gasthuisberg, Leuven, Belgium, 4Service de Biopathologie, Institut de Cance´rologie de Lorraine - Alexis Vautrin, Vandoeuvre Les Nancy, France, 5 AMMICA, INSERM US23/CNRS UMS3655, Institut Gustave Roussy, Villejuif, France, 6 Biomedical Quality Assurance Research Unit, KU Leuven, Leuven, Belgium, 7 Biochemistry, Nantes University Hospital, Nantes, France, 8Pathology, Hop. Charles Nicolle, Rouen, France Background: The interpretation of testing results in molecular pathology is an essential phase. It is difficult to assesss this in external quality assessment on real samples. Here we propose a national measure of the concordance in the variant interpretation between laboratories participating in the national French quality control program Gen&tiss. Methods: Laboratories were asked to interpret 5 variants each for melanoma, lung and colorectal cancers and 10 for ovarian cancer. These variants in KRAS, NRAS, BRAF, PIK3CA, PTEN, AKT1, TP53, EGFR, RAC1, KIT, BRCA1 and BRCA2 were not classical hotspots of mutation and 15 of these were annotated in OncoKB. A maximum of 25 variants was assessed per laboratories. Nine possible interpretations were proposed: from neutral to oncogenic and from no therapeutic impact to targeted by a drug. For each variant, a consensus score was determined based on public database as OncoKb
v30 | Biomarkers
and validated by 4 molecular experts with literature review. Three scores were possible: right answer (2 points), acceptable answer without clinical impact (1 point), wrong answer with clinical impact (0 points). Results: 60 laboratories participated to the program for variant interpretation. The average scores on 10 were 5.9 for colorectal (N ¼ 52), 7.0 for lung (N ¼ 49), 6.0 for melanoma (N ¼ 49) and 7.0 for ovarian cancer (N ¼ 25). For BRCA genes in ovarian cancer, there was a pilot project in 2017, in which 5 identical variants were proposed to interpretation. 18 laboratories participated both in 2017 and 2018: 50% performed better, 28% performed worse, 17% had similar results. Conclusions: As test results have will have a direct impact on patient management, ensuring a correct interpretation becomes more and more important. This EQA could help to validate the interpretation process used in the laboratories (SOP and databases) and could be extend to the individual expertise.The average score is acceptable, yet improvable and it really depends on the variants proposed. International consensus guidelines equivalent to the ACMG classification of constitutional variants would be helpful to improve reproducibility and inter-laboratory homogeneity. Legal entity responsible for the study: Gen&tiss - GFCO and AFAQAP. Funding: AstraZeneca. Disclosure: All authors have declared no conflicts of interest.
105P
Prospective testing of circulating tumour DNA in metastatic breast cancer facilitates clinical trial enrollment and precision oncology
A.Z. Bujak, C.-F. Weng, M.-J. Silva, M. Yeung, L. Lo, S. Ftouni, C. Litchfield, A. Ko, K. Kuykhoven, C. van Geelen, S. Chandrashekar, M.A. Dawson, S. Loi, S.Q. Wong, S.-J. Dawson Cancer Research, Peter MacCallum Cancer Center, Melbourne, Australia, Background: The increasing availability of targeted agents for treatment of metastatic breast cancer (mBC) necessitates accurate and timely molecular characterisation of disease. As a minimally invasive test, circulating tumour DNA (ctDNA) is well positioned to overcome many of the limitations associated with traditional tumor biopsies. Here, we established a program to assess the feasibility of routine prospective ctDNA testing for the clinical management of mBC patients. Methods: Detection of somatic mutations from patient plasma was performed using a multiplexed droplet digital PCR (ddPCR) approach to identify hotspot mutations in PIK3CA, ESR1, ERBB2 and AKT1. In parallel, a subset of samples were also analysed via next generation sequencing (targeted amplicon (TA) sequencing and low-coverage whole-genome sequencing). Results were discussed at a multidisciplinary breast cancer meeting prior to therapy selection. Results: 234 mBC patients were enrolled on this study, with a median age at diagnosis of 54 years (28-80) and a median of 2 lines of prior therapy. The average turnaround time for ctDNA testing using ddPCR was 9 days (1-49). Using ddPCR, 80/234 (34.2%) patients had 1 mutation identified, with 52/234 (22.2%) patients having an alteration in PIK3CA, 35/234 (15.0%) in ESR1, 9/234 (3.8%) in AKT1 and 2/234 (0.9%) in ERBB2. TA sequencing performed in the first 159 patients, identified actionable mutations (classified using the OncoKB database) in 63 patients (39.6%) and showed that a mean variant allele fraction of > 5% was significantly associated with inferior overall survival (Hazard ratio: 1.8; 95% Confidence interval: 1.1-3.1; p < 0.02). Of 97/234 patients where an actionable alteration was identified, the result influenced clinical management in 41 (42.3%), including 18 who were enrolled in a clinical trial. In one patient initially diagnosed with ERþ/HER2- disease, a HER2 gene amplification was identified through ctDNA analysis leading to the initiation of HER2-targeted treatment and a near complete metabolic response to treatment. Conclusions: Prospective ctDNA testing of mBC patients is a practical and feasible approach to guide clinical trial enrolment and patient management. Legal entity responsible for the study: The authors. Funding: National Health and Medical Research Council Australia. Disclosure: S.Q. Wong: Travel / Accommodation / Expenses: Bio-Rad Laboratories. S. Dawson: Research grant / Funding (self): Genentech. All other authors have declared no conflicts of interest.
106P
Elevated driver mutational burden or number of perturbed pathways and poor response to abiraterone or enzalutamide in metastatic castration-resistant prostate cancer
B. De Laere1, A. Crippa1, C. Ghysel2, P. Ost3, P. Rajan4, M. Eklund1, L. Dirix5, H. Gro¨nberg1, J. Lindberg1 1 Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden, 2 Department of Urology, AZ Sint-Jan Brugge-Oostende AV, Brugge, Belgium, 3 Department of Radiation Oncology, Ghent University Hospital, Ghent, Belgium, 4 Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK, 5Department of Oncology & Center for Oncological Research, GZA Hospitals Sint-Augustinus & University of Antwerp, Antwerp, Belgium Background: Metastatic castration-resistant prostate cancer (mCRPC) is a heterogeneous disease with rare driver gene alteration combinations in most men, requiring large sample sizes for stratified evaluations. We therefore hypothesized that the number of
Volume 30 | Supplement 5 | October 2019
Downloaded from https://academic.oup.com/annonc/article-abstract/30/Supplement_5/mdz239.016/5577297 by guest on 27 October 2019
J. Masliah-Planchon1, M. Kamal2, E. Borcoman2, E. Girard3, P. Gestraud3, G. Bataillon4, A. Vincent-Salomon4, C. Lecerf2, C. Callens1, S. Antonio1, C. Franck1, O. Mariani4, I. Bieche1, C. Le Tourneau2, V. Servois5 1 Department of Genetics, Institut Curie, Paris, France, 2Department of Drug Development and Innovation, Institut Curie, Paris, France, 3INSERM U900 Research Unit, Institut Curie, Saint-Cloud, France, 4Department of Pathology, Institut Curie, Paris, France, 5Department of Radiology, Institut Curie, Paris, France
Annals of Oncology
103P
Prospective comparative study of next-generation sequencing on fine needle aspirations versus core needle biopsies in cancer patients included in SHIVA02 trial
Background: High throughput molecular screening of solid tumours using core needle biopsies (CNB) allows the identification of actionable molecular alterations. Several reports revealed that success rate of genomic analyses based on CNB is around 70% with failures being mostly related to low proportion of tumour cells. Although several studies have demonstrated the utility of small biopsy specimens for molecular testing, there remains debate as to the sensitivity of CNB to detect actionable alterations compared to the less invasive fine needle aspiration (FNA). We aim to prospectively evaluate the ability of FNA to detect molecular alterations identified on CNB in cancer patients (pts) included in SHIVA02 trial. Methods: In-house targeted sequencing amplicon based panel (Illumina TSCA 99.3 Kb, 1,504 amplicons covering 87 genes) was used to identify pathogenic variants and gene copy number alterations (CNVs) in both CNB and FNA for pts enrolled in the SHIVA02 trial (NCT03084757). Results: CNB and FNA specimen from 39 pts enrolled in the SHIVA02 trial were assessed. Main tumour locations were breast (17pts, 44%), pancreatic (4pts, 10%), and colorectal cancers (3pts, 8%). 91 somatic variants were identified in both specimens with a good correlation of variants’ allelic ratios (r: 0.772). CNV profiles of CNB and FNA were concordant. When taking into account molecular alterations validated during the molecular biology board, 88 alterations (55 variants and 35 CNVs) were reported among which 69 alterations (78%) where concordant between CNB and FNA. Among the 50 actionable alterations, only 12 (3 variants and 9 CNVs) (24%) were discordant between FNA and CNB. Main discordances were related to homozygous deletions and amplifications but false negative results were not related to FNA samples alone (5 CNVs in favour of FNA versus 4 in favour of CNB). Conclusions: Comparative analyses of molecular alterations in CNB compared to FNA showed high concordance in terms of variants as well as CNVs identified. FNA could therefore be easily used in routine diagnostics workflow and clinical trials for tumour molecular screening with the advantage of being minimally invasive. Clinical trial identification: NCT03084757 SHIVA02; Trial release date: April 1, 2017. Legal entity responsible for the study: Institut Curie. Funding: MSD Avenir Fundation. Disclosure: C. Le Tourneau: Advisory / Consultancy: MSD, BMS, Merck Serono, AstraZeneca, Novartis, Roche, Nanobiotix. All other authors have declared no conflicts of interest.
104P
First national external quality assessment for the interpretation of somatic variants: Assessment of 25 variants in colorectal, lung, ovarian cancers and melanoma in France
E. Rouleau1, K. Leroy2, K. Dufraing3, A. Harle´4, L. Lacroix5, K. Vanwelden6, M.G. Denis7, A. Lamy8, E. Dequeker3 1 Tumor Genetics, Gustave Roussy - Cancer Campus, Villejuif, France, 2Service de Genetique et Biologie Moleculaire, Hoˆpital Cochin, Paris, France, 3Quality, University Hospitals Leuven - Campus Gasthuisberg, Leuven, Belgium, 4Service de Biopathologie, Institut de Cance´rologie de Lorraine - Alexis Vautrin, Vandoeuvre Les Nancy, France, 5 AMMICA, INSERM US23/CNRS UMS3655, Institut Gustave Roussy, Villejuif, France, 6 Biomedical Quality Assurance Research Unit, KU Leuven, Leuven, Belgium, 7 Biochemistry, Nantes University Hospital, Nantes, France, 8Pathology, Hop. Charles Nicolle, Rouen, France Background: The interpretation of testing results in molecular pathology is an essential phase. It is difficult to assesss this in external quality assessment on real samples. Here we propose a national measure of the concordance in the variant interpretation between laboratories participating in the national French quality control program Gen&tiss. Methods: Laboratories were asked to interpret 5 variants each for melanoma, lung and colorectal cancers and 10 for ovarian cancer. These variants in KRAS, NRAS, BRAF, PIK3CA, PTEN, AKT1, TP53, EGFR, RAC1, KIT, BRCA1 and BRCA2 were not classical hotspots of mutation and 15 of these were annotated in OncoKB. A maximum of 25 variants was assessed per laboratories. Nine possible interpretations were proposed: from neutral to oncogenic and from no therapeutic impact to targeted by a drug. For each variant, a consensus score was determined based on public database as OncoKb
v30 | Biomarkers
and validated by 4 molecular experts with literature review. Three scores were possible: right answer (2 points), acceptable answer without clinical impact (1 point), wrong answer with clinical impact (0 points). Results: 60 laboratories participated to the program for variant interpretation. The average scores on 10 were 5.9 for colorectal (N ¼ 52), 7.0 for lung (N ¼ 49), 6.0 for melanoma (N ¼ 49) and 7.0 for ovarian cancer (N ¼ 25). For BRCA genes in ovarian cancer, there was a pilot project in 2017, in which 5 identical variants were proposed to interpretation. 18 laboratories participated both in 2017 and 2018: 50% performed better, 28% performed worse, 17% had similar results. Conclusions: As test results have will have a direct impact on patient management, ensuring a correct interpretation becomes more and more important. This EQA could help to validate the interpretation process used in the laboratories (SOP and databases) and could be extend to the individual expertise.The average score is acceptable, yet improvable and it really depends on the variants proposed. International consensus guidelines equivalent to the ACMG classification of constitutional variants would be helpful to improve reproducibility and inter-laboratory homogeneity. Legal entity responsible for the study: Gen&tiss - GFCO and AFAQAP. Funding: AstraZeneca. Disclosure: All authors have declared no conflicts of interest.
105P
Prospective testing of circulating tumour DNA in metastatic breast cancer facilitates clinical trial enrollment and precision oncology
A.Z. Bujak, C.-F. Weng, M.-J. Silva, M. Yeung, L. Lo, S. Ftouni, C. Litchfield, A. Ko, K. Kuykhoven, C. van Geelen, S. Chandrashekar, M.A. Dawson, S. Loi, S.Q. Wong, S.-J. Dawson Cancer Research, Peter MacCallum Cancer Center, Melbourne, Australia, Background: The increasing availability of targeted agents for treatment of metastatic breast cancer (mBC) necessitates accurate and timely molecular characterisation of disease. As a minimally invasive test, circulating tumour DNA (ctDNA) is well positioned to overcome many of the limitations associated with traditional tumor biopsies. Here, we established a program to assess the feasibility of routine prospective ctDNA testing for the clinical management of mBC patients. Methods: Detection of somatic mutations from patient plasma was performed using a multiplexed droplet digital PCR (ddPCR) approach to identify hotspot mutations in PIK3CA, ESR1, ERBB2 and AKT1. In parallel, a subset of samples were also analysed via next generation sequencing (targeted amplicon (TA) sequencing and low-coverage whole-genome sequencing). Results were discussed at a multidisciplinary breast cancer meeting prior to therapy selection. Results: 234 mBC patients were enrolled on this study, with a median age at diagnosis of 54 years (28-80) and a median of 2 lines of prior therapy. The average turnaround time for ctDNA testing using ddPCR was 9 days (1-49). Using ddPCR, 80/234 (34.2%) patients had 1 mutation identified, with 52/234 (22.2%) patients having an alteration in PIK3CA, 35/234 (15.0%) in ESR1, 9/234 (3.8%) in AKT1 and 2/234 (0.9%) in ERBB2. TA sequencing performed in the first 159 patients, identified actionable mutations (classified using the OncoKB database) in 63 patients (39.6%) and showed that a mean variant allele fraction of > 5% was significantly associated with inferior overall survival (Hazard ratio: 1.8; 95% Confidence interval: 1.1-3.1; p < 0.02). Of 97/234 patients where an actionable alteration was identified, the result influenced clinical management in 41 (42.3%), including 18 who were enrolled in a clinical trial. In one patient initially diagnosed with ERþ/HER2- disease, a HER2 gene amplification was identified through ctDNA analysis leading to the initiation of HER2-targeted treatment and a near complete metabolic response to treatment. Conclusions: Prospective ctDNA testing of mBC patients is a practical and feasible approach to guide clinical trial enrolment and patient management. Legal entity responsible for the study: The authors. Funding: National Health and Medical Research Council Australia. Disclosure: S.Q. Wong: Travel / Accommodation / Expenses: Bio-Rad Laboratories. S. Dawson: Research grant / Funding (self): Genentech. All other authors have declared no conflicts of interest.
106P
Elevated driver mutational burden or number of perturbed pathways and poor response to abiraterone or enzalutamide in metastatic castration-resistant prostate cancer
B. De Laere1, A. Crippa1, C. Ghysel2, P. Ost3, P. Rajan4, M. Eklund1, L. Dirix5, H. Gro¨nberg1, J. Lindberg1 1 Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden, 2 Department of Urology, AZ Sint-Jan Brugge-Oostende AV, Brugge, Belgium, 3 Department of Radiation Oncology, Ghent University Hospital, Ghent, Belgium, 4 Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK, 5Department of Oncology & Center for Oncological Research, GZA Hospitals Sint-Augustinus & University of Antwerp, Antwerp, Belgium Background: Metastatic castration-resistant prostate cancer (mCRPC) is a heterogeneous disease with rare driver gene alteration combinations in most men, requiring large sample sizes for stratified evaluations. We therefore hypothesized that the number of
Volume 30 | Supplement 5 | October 2019
Downloaded from https://academic.oup.com/annonc/article-abstract/30/Supplement_5/mdz239.016/5577297 by guest on 27 October 2019
J. Masliah-Planchon1, M. Kamal2, E. Borcoman2, E. Girard3, P. Gestraud3, G. Bataillon4, A. Vincent-Salomon4, C. Lecerf2, C. Callens1, S. Antonio1, C. Franck1, O. Mariani4, I. Bieche1, C. Le Tourneau2, V. Servois5 1 Department of Genetics, Institut Curie, Paris, France, 2Department of Drug Development and Innovation, Institut Curie, Paris, France, 3INSERM U900 Research Unit, Institut Curie, Saint-Cloud, France, 4Department of Pathology, Institut Curie, Paris, France, 5Department of Radiology, Institut Curie, Paris, France
Annals of Oncology