Clinical Validation of Companion Diagnostics for the Selection of Patients with Non–Small Cell Lung Cancer Tumors Harboring Epidermal Growth Factor Receptor Exon 20 Insertion Mutations for Treatment with Amivantamab

Amivantamab, an epidermal growth factor receptor (EGFR)–c-Met bispecific antibody, targets activating/resistance EGFR mutations and MET mutations/amplifications. In the ongoing CHRYSALIS study (ClinicalTrials.gov Identifier: NCT02609776), amivantamab demonstrated antitumor activity in patients with non–small cell lung cancer harboring EGFR exon 20 insertion mutations (ex20ins) that progressed on or after platinum-based chemotherapy, a population in which amivantamab use has been approved by the US Food and Drug Administration. This bridging study clinically validated two novel candidate companion diagnostics (CDx) for use in detecting EGFR ex20ins in plasma and tumor tissue, Guardant360 CDx and Oncomine Dx Target Test (ODxT), respectively. From the 81 patients in the CHRYSALIS efficacy population, 78 plasma and 51 tissue samples were tested. Guardant360 CDx identified 62 positive (16 negative), and ODxT identified 39 positive (3 negative), samples with EGFR ex20ins. Baseline demographic and clinical characteristics were similar between the CHRYSALIS-, Guardant360 CDx–, and ODxT–identified populations. Agreement with local PCR/next-generation sequencing tests used for enrollment into CHRYSALIS demonstrated high adjusted negative (99.6% and 99.9%) and positive (100% for both) predictive values with the Guardant360 CDx and ODxT tests, respectively. Overall response rates were comparable between the CHRYSALIS, Guardant360 CDx, and ODxT populations. Both the plasma- and tissue-based diagnostic tests provided accurate, comprehensive, and complementary approaches to identifying patients with EGFR ex20ins who could benefit from amivantamab therapy. Amivantamab, an epidermal growth factor receptor (EGFR)–c-Met bispecific antibody, targets activating/resistance EGFR mutations and MET mutations/amplifications. In the ongoing CHRYSALIS study (ClinicalTrials.gov Identifier: NCT02609776), amivantamab demonstrated antitumor activity in patients with non–small cell lung cancer harboring EGFR exon 20 insertion mutations (ex20ins) that progressed on or after platinum-based chemotherapy, a population in which amivantamab use has been approved by the US Food and Drug Administration. This bridging study clinically validated two novel candidate companion diagnostics (CDx) for use in detecting EGFR ex20ins in plasma and tumor tissue, Guardant360 CDx and Oncomine Dx Target Test (ODxT), respectively. From the 81 patients in the CHRYSALIS efficacy population, 78 plasma and 51 tissue samples were tested. Guardant360 CDx identified 62 positive (16 negative), and ODxT identified 39 positive (3 negative), samples with EGFR ex20ins. Baseline demographic and clinical characteristics were similar between the CHRYSALIS-, Guardant360 CDx–, and ODxT–identified populations. Agreement with local PCR/next-generation sequencing tests used for enrollment into CHRYSALIS demonstrated high adjusted negative (99.6% and 99.9%) and positive (100% for both) predictive values with the Guardant360 CDx and ODxT tests, respectively. Overall response rates were comparable between the CHRYSALIS, Guardant360 CDx, and ODxT populations. Both the plasma- and tissue-based diagnostic tests provided accurate, comprehensive, and complementary approaches to identifying patients with EGFR ex20ins who could benefit from amivantamab therapy. Mutations of the epidermal growth factor receptor gene (EGFR) are among the most frequent genetic alterations in non–small cell lung cancer (NSCLC). The targeting of EGFR-activating mutations with EGFR tyrosine kinase inhibitors (TKIs) has dramatically improved clinical outcomes and survival in some patients.1Ramalingam S.S. Vansteenkiste J. Planchard D. Cho B.C. Gray J.E. Ohe Y. Zhou C. Reungwetwattana T. Cheng Y. Chewaskulyong B. Shah R. 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Amivantamab is a fully human EGFR–c-Met bispecific antibody that targets activating and resistance EGFR mutations as well as MET mutations and amplifications. In the ongoing phase 1 CHRYSALIS study (Study of Amivantamab, a Human Bispecific EGFR and c-Met Antibody, in Participants with Advanced Non–Small Cell Lung Cancer; https://clinicaltrials.gov identifier NCT02609776, last accessed January 19, 2022), amivantamab demonstrated clinically meaningful efficacy in patients with EGFR ex20ins.17Cho B.C. Lee J.-S. Han J.-Y. Cho E.K. Haura E. Lee K.H. Bauml J. Sanborn R.E. Curtis M. Attiyeh E. Haddish-Berhane N. Bae K. Knoblauch R. Sherman L. Lorenzi M.V. Park K. JNJ-61186372 (JNJ-372), an EGFR-cMET bispecific antibody, in advanced non-small cell lung cancer (NSCLC): an update on phase 1 results.Ann Oncol. 2018; 29: mdy292.118Abstract Full Text Full Text PDF Google Scholar, 18Haura E.B. Cho B.C. Lee J.S. Han J.-Y. Lee K.H. Sanborn R.E. Govindan R. Cho E.K. Kim S.-W. Reckamp K.L. Sabari J.K. 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Amivantamab (JNJ-61186372), an anti-EGFR-MET bispecific antibody, in patients with EGFR exon 20 insertion (exon20ins)-mutated non-small cell lung cancer (NSCLC).J Clin Oncol. 2020; 38: 9512Crossref Google Scholar, 21Sabari J.K. Shu C.A. Park K. Leighl N. Mitchell P. Kim S. Lee J. Kim D. Viteri S. Spira A. Han J. Trigo J. Lee C.K. Lee K.H. Girard N. Yang T. Goto K. Sanborn R.E. Yang J.C. Xie J. Roshak A. Thayu M. Knoblauch R.E. Cho B.C. OA04.04 amivantamab in post-platinum EGFR exon 20 insertion mutant non-small cell lung cancer.J Thorac Oncol. 2021; 16: S108-S109Abstract Full Text Full Text PDF Google Scholar Based on the early data from that study, the use of amivantamab for the treatment of patients with EGFR ex20ins NSCLC that progressed on or after platinum-based chemotherapy was approved by the US Food and Drug Administration and was given the Breakthrough Therapy designation in China. The availability of accurate companion diagnostics (CDx) ensures that patients with genomic profiles most likely to benefit are identified to receive treatment. To date, the US Food and Drug Administration has approved the use of several CDx tools with their paired therapeutics for the treatment of patients with lung cancers, highlighting the usefulness and value of this approach in guiding treatment decisions (https://www.fda.gov/medical-devices/vitro-diagnostics/list-cleared-or-approved-companion-diagnostic-devices-vitro-and-imaging-tools, last accessed January 19, 2022). In the CHRYSALIS study of amivantamab, patients with EGFR ex20ins were enrolled based on local PCR or next-generation sequencing (NGS) testing (and centrally confirmed) of circulating tumor DNA or tissue. The present bridging study compared the efficacy outcomes with amivantamab in patients with EGFR ex20ins identified using local PCR/NGS tests in the CHRYSALIS study and in those who would have been identified using the Guardant360 CDx liquid biopsy test (Guardant Health, Inc., Redwood City, CA) or the Oncomine Dx Target Test (ODxT) tumor biopsy test (Thermo Fisher Scientific, Waltham, MA). The ongoing phase 1 CHRYSALIS study is evaluating the safety and efficacy of amivantamab in patients with advanced NSCLC and includes a subgroup of patients who harbor EGFR ex20ins (https://clinicaltrials.gov identifier NCT02609776, last accessed January 19, 2022). Patients with EGFR ex20ins were enrolled based on local PCR/NGS testing (and centrally confirmed) of circulating tumor DNA or tissue. Local PCR/NGS testing was required to be designed according to strict quality standards, outfitted with enhanced controls, and subsequently validated under Clinical Laboratory Improvement Amendments or local health authority guidelines. This bridging study was focused on the pivotal efficacy population from CHRYSALIS, which included the first 81 patients enrolled with EGFR ex20ins NSCLC, after progression on platinum-based chemotherapy, who were treated at the recommended phase 2 dose (RP2D) and who had at least three scheduled disease assessments or who had discontinued, progressed, or died by the June 8, 2020, data cutoff date.21Sabari J.K. Shu C.A. Park K. Leighl N. Mitchell P. Kim S. Lee J. Kim D. Viteri S. Spira A. Han J. Trigo J. Lee C.K. Lee K.H. Girard N. Yang T. Goto K. Sanborn R.E. Yang J.C. Xie J. Roshak A. Thayu M. Knoblauch R.E. Cho B.C. OA04.04 amivantamab in post-platinum EGFR exon 20 insertion mutant non-small cell lung cancer.J Thorac Oncol. 2021; 16: S108-S109Abstract Full Text Full Text PDF Google Scholar The primary objective of this bridging study was to compare the efficacy outcomes in patients who would have been identified by the Guardant360 CDx or ODxT test to those observed in the efficacy population from the CHRYSALIS study. The primary end point was the overall response rate [ORR; defined as partial response or better, per RECIST22Eisenhauer E.A. Therasse P. Bogaerts J. Schwartz L.H. Sargent D. Ford R. Dancey J. Arbuck S. Gwyther S. Mooney M. Rubinstein L. Shankar L. Dodd L. Kaplan R. Lacombe D. Verweij J. New response evaluation criteria in solid tumours: revised RECIST guideline (version 1.1).Eur J Cancer. 2009; 45: 228-247Abstract Full Text Full Text PDF PubMed Scopus (20167) Google Scholar (Response Evaluation Criteria in Solid Tumours) guideline version 1.1], as assessed by blinded independent central review; duration of response (DOR) was a secondary end point of the study. Banked plasma and tumor samples from patients in the CHRYSALIS efficacy population were used for CDx testing; additional samples from patients with EGFR ex20ins mutations who were not included in the efficacy population were also tested. Additional samples tested by assays representative of the local PCR/NGS tests used in the CHRYSALIS study were acquired to estimate the performance of each CDx when samples were expected to be negative for EGFR ex20ins (the number of samples analyzed is described in Guardant360 CDx and Oncomine Dx Target Test). Plasma samples were sourced from patients who did not meet the criteria for eligibility in the CHRYSALIS study (screen fails from the non–EGFR ex20ins cohorts of CHRYSALIS), as were previously generated samples from patients enrolled in the NILE (Noninvasive versus Invasive Lung Evaluation) study (https://clinicaltrials.gov identifier NCT03615443, last accessed January 19, 2022). NSCLC tissue samples were commercially sourced (BioChain, Newark, CA, and Bio-Options, Brea, CA). The bridging study protocol was approved by the relevant Institutional Review Board. Written informed consent was obtained from patients who were enrolled in the CHRYSALIS study. Guardant360 CDx is a qualitative NGS-based in vitro diagnostic device that uses targeted high-throughput hybridization–based capture technology for the detection of EGFR ex20ins utilizing circulating tumor DNA from the plasma of peripheral whole blood. The developer of Guardant360 CDx defines EGFR ex20ins as any in-frame insertion occurring between codons 763 and 773 of the EGFR gene (hg19 chr7:55248992–55249021). For the evaluation of negative data, data from patients who did not meet eligibility requirements from the other non–EGFR ex20ins cohorts of the CHRYSALIS study (n = 83), as well as previously generated clinical sample data from the NILE study (n = 88), were used. Four samples from the screen fails (from the non-EGFR ex20ins cohorts of CHRYSALIS) and three from the NILE study were positive for EGFR ex20ins by local PCR/NGS tests. An additional 19 patients with EGFR ex20ins from the CHRYSALIS study were included in the concordance analysis but not in the primary efficacy analysis (as they did not have sufficient post-baseline disease assessments). Testing using Guardant360 CDx was performed according to the standard operating procedures of the Guardant Health clinical laboratory.23Odegaard J.I. Vincent J.J. Mortimer S. Vowles J.V. Ulrich B.C. Banks K.C. Fairclough S.R. Zill O.A. Sikora M. Mokhtari R. Abdueva D. Nagy R.J. Lee C.E. Kiedrowski L.A. Paweletz C.P. Eltoukhy H. Lanman R.B. Chudova D.I. Talasaz A. Validation of a plasma-based comprehensive cancer genotyping assay utilizing orthogonal tissue- and plasma-based methodologies.Clin Cancer Res. 2018; 24: 3539-3549Crossref PubMed Scopus (268) Google Scholar ODxT is a qualitative in vitro diagnostic test that uses targeted high-throughput, parallel-sequencing technology to detect EGFR ex20ins from DNA isolated from formalin-fixed, paraffin-embedded tumor samples using the Ion PGM Dx System (Thermo Fisher Scientific). A hematoxylin and eosin–stained slide of each clinical sample was evaluated by a board-certified pathologist to determine the section surface area and estimated tumor content or tumor content within the region of interest; if the percentage of tumor cells among total viable cells (viable cells excluded necrotic cells) was <20%, the samples were macrodissected. Samples that met the ODxT Test requirements for tumor content and slide number were tested. Amplicon libraries were prepared from the extracted DNA samples, barcode-adapted, and pooled into an emulsion PCR–based reaction to generate the templated beads used for sequencing. Signal processing and subsequent base calling occurred in real time during the sequencing procedure, and the base calls were assembled into reads that were mapped to a reference sequence by the system software. Based on sample and run performance, quality-control metrics, and software algorithm parameters, variant calls were generated for each EGFR ex20ins target region on the ODxT Test panel. For the evaluation of negative data, 103 commercially sourced NSCLC samples that were identified as negative by NGS or PCR testing were evaluated. An additional 18 patients with EGFR ex20ins from the CHRYSALIS study were included in the concordance analysis but not in the primary efficacy analysis (as they did not have sufficient post-baseline disease assessments). Testing was performed at Covance Central Laboratory Services, Inc. (Indianapolis, IN) using the ODxT according to the manufacturer’s protocols (Thermo Fisher Scientific). The t-test and the χ2 test were used to compare baseline demographic and disease characteristics between populations. The observed ORR and its two-sided exact 95% CI are presented in patients with advanced NSCLC (metastases within 12 months from last platinum-based chemotherapy treatment) treated at the RP2D and whose disease progressed on or after platinum-based chemotherapy and who were positive by the CDx tests for EGFR ex20ins. Confirmation of investigator-assessed ORR was performed through blinded independent central review. The Kaplan-Meier method was used to descriptively summarize the DOR in responders in the CDx-positive populations. Median DOR and the corresponding 95% CI are provided. Investigator-assessed DOR was confirmed through blinded independent central review. Positive and negative percent agreement values were calculated using the local PCR/NGS test as the reference assay. Two-sided score CIs are reported for each agreement measure. Positive and negative predictive values with each CDx were calculated by adjustment of the observed positive and negative predictive values to an EGFR ex20ins prevalence of 1.8%.12Riess J.W. Gandara D.R. Frampton G.M. Madison R. Peled N. Bufill J.A. Dy G.K. Ou S.I. Stephens P.J. McPherson J.D. Lara Jr., P.N. Burich R.A. Ross J.S. Miller V.A. Ali S.M. Mack P.C. Schrock A.B. Diverse EGFR exon 20 insertions and co-occurring molecular alterations identified by comprehensive genomic profiling of NSCLC.J Thorac Oncol. 2018; 13: 1560-1568Abstract Full Text Full Text PDF PubMed Scopus (142) Google Scholar CIs of the adjusted positive and negative predictive value estimates were determined using bootstrap, except where the point estimate was 100%, in which case the score CI was used. The efficacy population from the CHRYSALIS study comprised the first 81 patients with EGFR ex20ins who were treated at the RP2D and whose disease had progressed on or after platinum-based chemotherapy. Plasma and tissue samples available from these patients were tested using the Guardant360 and ODxT tests. Of the 81 patients, 3 did not have plasma samples available for Guardant360 testing, and among the 78 patients who were tested, 62 were identified as EGFR ex20ins positive and 16 as ex20ins negative (Figure 1). On ODxT testing, 35 samples were either not available or failed pathology review. Of the 46 tumor tissue samples that were tested with ODxT, 39 were EGFR ex20ins positive, 3 were ex20ins negative, and 4 had invalid results (Figure 1). The demographic and baseline characteristics were not statistically significantly different between the groups with EGFR ex20ins identified by local PCR/NGS, Guardant360, or ODxT (Table 1). Across all three identified EGFR ex20ins–positive populations, the median age was 62 years, a higher percentage of women was observed, and approximately half of the patients were Asian.Table 1Demographic and Baseline Disease CharacteristicsCharacteristicLocal PCR/NGS tests (N = 81)Guardant360 CDx (N = 62)ODxT (N = 39)Age, median (range), years62 (42 to 84)62 (42 to 84)62 (45 to 79)Sex, n (%) Male33 (40.7)22 (35.5)18 (46.2) Female48 (59.3)40 (64.5)21 (53.8)Race, n (%) Asian40 (49.4)34 (54.8)20 (51.3) Black2 (2.5)1 (1.6)0 White30 (37.0)21 (33.9)15 (38.5) Unknown/not reported9 (11.1)6 (9.7)4 (10.3)Local test type, n (%) NGS38 (46.9)27 (43.5)18 (46.1)Blood4 (4.9)3 (4.8)2 (5.1)Tissue34 (42.0)24 (38.7)16 (41.0) PCR31 (38.3)24 (38.7)14 (35.9)Blood1 (1.2)1 (1.6)1 (2.6)Tissue30 (37.0)23 (37.1)13 (33.3) Other8 (9.9)8 (12.9)4 (10.3) Unknown4 (4.9)3 (4.8)3 (7.7)History of smoking, n (%)38 (46.9)25 (40.3)19 (48.7)Previous lines of therapy, median (range)2.0 (1 to 7)2.0 (1 to 7)2.0 (1 to 5)CDx, companion diagnostics; NGS, next-generation sequencing; ODxT, Oncomine Dx Target Test. Open table in a new tab CDx, companion diagnostics; NGS, next-generation sequencing; ODxT, Oncomine Dx Target Test. For evaluation of the agreement between the results from the local PCR/NGS and the CDx tests, the positive and negative percent agreement values were calculated using samples with a valid CDx result from multiple populations: the CHRYSALIS efficacy population, patients with EGFR ex20ins who were not part of the efficacy population, screen-failed patients, samples from the NILE study, and commercially sourced samples. With both assays, a high positive percent agreement was achieved (Guardant360, 80.8% [95% CI, 72.2%–87.2%]; ODxT, 94.1% [95% CI, 92.6%–100%]) and no false positives were observed with either assay (Tables 2 and 3). Without a false-positive result, the point estimate for negative percent agreement was 100%. Based on the agreement analyses and adjusting for an EGFR ex20ins prevalence of 1.8%,12Riess J.W. Gandara D.R. Frampton G.M. Madison R. Peled N. Bufill J.A. Dy G.K. Ou S.I. Stephens P.J. McPherson J.D. Lara Jr., P.N. Burich R.A. Ross J.S. Miller V.A. Ali S.M. Mack P.C. Schrock A.B. Diverse EGFR exon 20 insertions and co-occurring molecular alterations identified by comprehensive genomic profiling of NSCLC.J Thorac Oncol. 2018; 13: 1560-1568Abstract Full Text Full Text PDF PubMed Scopus (142) Google Scholar the adjusted negative predictive value with Guardant360 was 99.6% (95% CI, 99.5%–99.8%), and the adjusted positive predictive value was 100% (95% CI, 95.6%–100%). A similar high degree of agreement was observed with ODxT, with an adjusted positive predictive value of 100% (95% CI, 92.6%–100%) and a negative predictive value of 99.9% (95% CI, 99.8%–100%). Despite the low prevalence of EGFR ex20ins, there was a 100% probability that a positive assay result by either ODxT or Guardant360 was truly positive by a local PCR/NGS test, given that no false positives for EGFR ex20ins were observed with either test.Table 2Agreement between Local PCR/NGS Testing and Guardant360 CDx Assay Results of Plasma Samples, Excluding Invalid Guardant360 CDx Assay ResultsGuardant360 CDx assay resultLocal PCR/NGS testingPositiveNegativeTotalPositive84084Negative20164184Total104164268PPA, % (95% CI)80.8 (72.2–87.2)NPA, % (95% CI)100 (97.7–100)OPA, % (95% CI)92.5 (88.8–95.1)CDx, companion diagnostics; NGS, next-generation sequencing; NPA, negative percent agreement; OPA, overall percent agreement; PPA, positive percent agreement. Open table in a new tab Table 3Agreement between Local PCR/NGS Testing and ODxT Results of Tissue Samples, Excluding Invalid ODxT ResultsODxT resultLocal PCR/NGS testingPositiveNegativeTotalPositive48048Negative36164Total5161112PPA, % (95% CI)94.1 (92.6 to 100.0)NPA, % (95% CI)100 (87.1 to 98.4)OPA, % (95% CI)97.3 (92.4 to 99.1)NGS, next-generation sequencing; NPA, negative percent agreement; ODxT, Oncomine Dx Target Test; OPA, overall percent agreement; PPA, positive percent agreement. Open table in a new tab CDx, companion diagnostics; NGS, next-generation sequencing; NPA, negative percent agreement; OPA, overall percent agreement; PPA, positive percent agreement. NGS, next-generation sequencing; NPA, negative percent agreement; ODxT, Oncomine Dx Target Test; OPA, overall percent agreement; PPA, positive percent agreement. The primary objective of the bridging study was to clinically validate the CDx tests by demonstrating comparable efficacy between the group that would have been identified using CDx and the group identified using local PCR/NGS tests from the CHRYSALIS study. The ORRs of 39% in the Guardant360-identified group and 46% in the ODxT-identified g