Clinical Trial Assay Research Articles

Analytical and Clinical Validation of the Oncomine Dx Target Test to Assess HER2 Mutation Status in Tumor Tissue Samples From Patients With Non–Small Cell Lung Cancer Treated With Trastuzumab Deruxtecan in the DESTINY-Lung01 and DESTINY-Lung02 Studies

Context.— Trastuzumab deruxtecan (T-DXd), a human epidermal growth factor receptor 2 (HER2)–targeted therapy, has demonstrated durable anticancer activity in patients with advanced, metastatic HER2 (also known as ERBB2)–mutant (HER2m) non–small cell lung cancer (NSCLC) who have limited treatment options and poor prognosis. Objective.— To analytically validate and assess the clinical utility of the Oncomine Dx Target (ODxT) Test as a companion diagnostic to identify patients with HER2m NSCLC. Design.— Tumor samples from patients in DESTINY-Lung01 and DESTINY-Lung02 were retrospectively analyzed alongside commercially procured samples using the ODxT test and compared to the assays used for screening in these clinical trials. Results.— Positive percent agreement (PPA) and negative percent agreement (NPA) between the ODxT Test and TruSight Tumor 170 assay when testing DESTINY-Lung01 and commercially procured samples met prespecified thresholds (PPA and NPA ≥90%) for analytical accuracy (100% and 99.1%). The ODxT Test results were highly concordant with clinical trial assays (CTAs) used in DESTINY-Lung01 (PPA and NPA, 98.0% and 100%) and DESTINY-Lung02 (PPA and NPA, 96.7% and 100%) to identify activating HER2 mutations in tumor samples. Confirmed objective response rates were similar between patients with HER2m tumors identified by the ODxT Test and by CTAs in DESTINY-Lung01 (58.3% and 54.9%) and DESTINY-Lung02 (53.6% and 53.8%). Response duration was 12.0 and 9.3 months for patients identified by the ODxT Test and CTAs, respectively, in DESTINY-Lung01. Conclusions.— The ODxT Test detected HER2 mutations in NSCLC with high analytical and clinical accuracy and identified HER2m populations with response rates similar to populations identified by CTAs, supporting clinical utility of the ODxT Test to inform treatment decisions for HER2m NSCLC.

Abstract 1030: Concordance between the DESTINY-Breast04 clinical trial assay (4B5[CDx]) and other HER2 IHC assays for HER2-low breast cancer in real-world practice: First phase of a large-scale, multicenter global ring study

Abstract Background: DESTINY-Breast04 (DB-04) showed that trastuzumab deruxtecan improves survival vs chemotherapy in patients with human epidermal growth factor receptor 2 (HER2)-low (immunohistochemistry [IHC] 1+ or IHC 2+ with in situ hybridization negative) metastatic breast cancer (BC). The VENTANA 4B5(CDx) IHC assay, now approved in the United States (US) as a companion diagnostic, was used as the clinical trial assay (CTA) in DB-04. Real-world differentiation of HER2-low vs HER2 IHC 0 BC with non-CTAs is difficult. This is the first phase of a study assessing agreement between CTA and non-CTA scores. Methods: 50 clinical BC samples with HER2 IHC scores of 0, 1+, 2+, and 3+ were sent to laboratories in Europe, Canada, and the US for HER2 IHC testing per ASCO/CAP 2018 guidelines. After routine protocol scoring, pathologists were trained and rescored the samples 2 weeks later. Post training scores were compared with reference CTA scores determined by a central laboratory and a panel of experts. The primary endpoint was positive percentage agreement (PPA) and negative percentage agreement (NPA) between CTA and non-CTA scores, assessed after training, considering HER2-low as positive and HER2 IHC 0 as negative. Results: A total of 3449 post training non-CTA scores were available for analysis. PPA for HER2-low vs HER2 IHC 0 was 87.5% and NPA was 61.9%, with Cohen κ of 0.51 (Table). HER2-low vs HER2 IHC 0 agreement between CTA and non-CTA varied across subgroups. PPA >95% was shown with 4B5 Laboratory Developed Tests (LDTs) and HercepTest (Omnis), NPA of 80% with Leica, and overall agreement >80% with HercepTest (Link48), 4B5 LDTs, and German, French, and Italian laboratories. Conclusions: The degree of concordance between the CTA and non-CTAs varied among assay types and laboratory locations. A low NPA for some non-CTAs suggests the need for further assay optimization for HER2 IHC 0 evaluation. Post training non-CTA results HER2-low vs HER2 IHC 0 BC Post training scores PPA (95% CI), % NPA (95% CI), % Overall percentage agreement (95% CI), % Cohen κ (95% CI) Overall non-CTA test results (N = 3449) 87.5 (86.0-89.0) 61.9 (58.9-64.9) 78.7 (77.1-80.1) 0.51 (0.48-0.54) Non-CTA subgroups HercepTest (Omnis) (n = 467) 95.5 (92.3-97.7) 36.9 (28.9-45.4) 75.2 (70.8-79.4) 0.37 (0.28-0.46) HercepTest (Link48) (n = 790) 88.5 (85.2-91.2) 64.3 (57.8-70.4) 80.3 (77.2-83.2) 0.55 (0.48-0.61) Leica (n = 96) 59.3 (45.0-72.4) 80.0 (61.4-92.3) 66.7 (55.5-76.6) 0.35 (0.17-0.53) Non-4B5 LDTs (n = 1609) 83.8 (81.2-86.1) 67.8 (63.5-72.0) 78.2 (75.9-80.3) 0.52 (0.47-0.57) 4B5 LDTs (n = 487) 96.0 (93.0-98.0) 58.8 (50.4-66.8) 83.0 (79.1-86.4) 0.59 (0.51-0.68) Country subgroups Germany (n = 340) 93.1 (88.5-96.3) 64.4 (54.2-73.6) 83.1 (78.3-87.2) 0.61 (0.51-0.70) France (n = 342) 95.4 (91.5-97.9) 64.4 (54.4-73.6) 84.7 (80.1-88.6) 0.64 (0.55-0.73) Italy (n = 395) 89.9 (85.2-93.5) 72.5 (63.6-80.3) 83.9 (79.6-87.6) 0.64 (0.55-0.72) Spain (n = 567) 83.0 (78.4-86.9) 64.2 (56.6-71.3) 76.3 (72.3-80.0) 0.48 (0.40-0.56) US/Canada (n = 1029) 86.6 (83.6-89.2) 61.8 (56.1-67.3) 78.2 (75.4-80.8) 0.50 (0.44-0.56) Europe, other (n = 776) 85.0 (81.3-88.2) 52.8 (46.2-59.3) 73.8 (70.3-77.1) 0.40 (0.32-0.47) Citation Format: Hans-Ulrich Schildhaus, Sunil Badve, Corrado D’Arrigo, Gelareh Farshid, Annette Lebeau, Vicente Peg, Fréderique Penault-Llorca, Josef Rueschoff, Wentao Yang, Neil Atkey, Jessica Baumann, Elisabeth Beyerlein, Amy Hanlon Newell, Alexander Penner, Akira Moh, Guiseppe Viale. Concordance between the DESTINY-Breast04 clinical trial assay (4B5[CDx]) and other HER2 IHC assays for HER2-low breast cancer in real-world practice: First phase of a large-scale, multicenter global ring study [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1030.

Abstract 7627: First NGS-based companion diagnostic to aid in selecting non-small cell lung cancer patients with ERBB2 (HER2) activating mutations for treatment with trastuzumab deruxtecan

Abstract Introduction The ERBB2 companion diagnostic program aims to expand the intended use of the Oncomine ™ Dx Target Test (ODxTT) to determine ERBB2 single nucleotide variants (SNVs) in exons 8, 17, 18, 19, 20, 21 and 22 and exon 20 insertions from formalin-fixed, paraffin-embedded (FFPE) tumor samples in non-small cell lung cancer (NSCLC) patients who may benefit from targeted drug therapy. Methods The ODxTT is a qualitative in vitro diagnostic test that uses targeted high throughput, parallel-sequencing technology to detect SNVs, deletions, insertions, and CNVs in genes from DNA and fusions from RNA isolated from FFPE tissue samples using the Ion PGM ™ Dx System. Analytical validation (AV) studies interrogated ODxTT’s ability to detect ERBB2 mutations. The clinical validation (CV) study involved a method comparison/concordance analysis of ERBB2 mutations between the ODxTT and the TruSight Tumor 170 (TST170) assay, as well as a series of clinical trial assays (CTAs). The CV study was conducted using clinical specimens from 91 patients enrolled in Destiny-Lung01 and 121 stage-matched commercially procured samples. The aim was to evaluate positive percent agreement (PPA), negative percent agreement (NPA) and overall percent agreement (OPA) for CTAs and TST170 assay. Results A total of 91 ERBB2 subjects were included in the full analysis of the Destiny-Lung01 clinical trial. 49 samples had valid ODxTT results available and 42 samples were unevaluable which included 13 unknowns and 29 test not performed. The 49 patient samples that were evaluable were used to assess the clinical efficacy based on ODxTT results. In the series of 121 samples that were used to assess clinical efficacy in the CV study, 109 had evaluable ODxTT results. The PPA, NPA and OPA of ODxTT to the CTAs when excluding unknowns were 98%, 100% and 99.4%, respectively, and based off the Clopper-Pearson method for binomial distribution a 95% lower bound confidence interval (CI) were 89.6%, 96.6% and 96.5%, respectively. There was one discordant sample with a negative ODxTT and a positive CTA result (false negative). The PPA, NPA and OPA of ODxTT to TST170 assay were 100%, 99.1% and 99.3% respectively with a 95% lower bound CI of 90.8%, 95.0% and 96.3%, respectively. There was one discordant sample with a negative TST170 and a positive ODxTT result (false positive). Conclusion AV and CV studies successfully verified and validated the ODxTT for the detection of ERBB2 mutations in NSCLC FFPE samples. The 6 AV studies met the necessary product requirements and acceptance criteria to detect clinical samples with ERBB2 mutations. Additionally, the CV study clinical accuracy and clinical efficacy results demonstrated the safety and effectiveness of the use of the ODxTT in FFPE samples as an aid to identify NSCLC patients eligible for treatment with the Daiichi Sankyo lung cancer therapeutic T-DXd. Citation Format: Thomas Ha. First NGS-based companion diagnostic to aid in selecting non-small cell lung cancer patients with ERBB2 (HER2) activating mutations for treatment with trastuzumab deruxtecan [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7627.

Quantum-First (Q-F): Clinical Bridging Study for FMS-like Tyrosine Kinase 3-Internal Tandem Duplication ( FLT3-ITD) Companion Diagnostic Development

Background Q-F (NCT02668653) showed that the highly potent, selective, type 2 FLT3 inhibitor quizartinib (Q) + standard chemotherapy ± transplantation, followed by Q monotherapy for ≥36 cycles, reduced the relative risk of death by 22.4% vs placebo (P) in newly diagnosed (nd) FLT3-ITD+ AML, with HR of 0.776 and P value of 0.0324 (PMID: 37116523). In Q-F, FLT3-ITD mutation status was determined using a FLT3-ITD mutation detection clinical trial assay (CTA) validated under design control by Navigate BioPharma Services, Inc. We describe the results of the bridging study, aimed to show agreement between the CTA & the LeukoStrat CDx FLT3 Mutation Assay (CDx, by Invivoscribe) in FLT3-ITD+ pt selection and to determine if Q efficacy (overall survival [OS]) was maintained in nd FLT3-ITD+ AML pts from Q-F, if pts had been selected using the CDx. Methods In both CTA & CDx, DNA, extracted from bone marrow (n=884 each) or peripheral blood (n=139 each), was amplified via PCR and amplicons were detected via capillary electrophoresis. A sample was considered CTA+ if the variant allele frequency ( FLT3-ITD/total FLT3) was ≥3% and CDx+ if the signal ratio (SR; FLT3-ITD/ FLT3 WT) was ≥0.05. The agreement between CTA & CDx was based on evaluating CTA+ & CTA− samples with the CDx assay. A primary analysis included the CDx detected (CDx+ & CDx−) and the CDx invalid results. A secondary analysis used CDx+ and CDx− results only. To establish agreement between CDx & CTA, positive % agreement (PPA) and negative % agreement (NPA) were determined using CTA results as reference for the agreement analysis set (AAS). Concordance was established if the lower bounds of the 95% CIs for both PPA & NPA exceeded 90% for the analysis that included the invalid CDx results. Median OS in the subgroups was calculated based on Kaplan-Meier estimates. Stratified Cox proportional hazards regression model was used to estimate HRs, 95% CI, and P value. Results Full analysis set (N=3468) included all Q-F screened CTA+ pts (n=863), all screened CTA− pts (n=2556), and pts with unknown CTA status not eligible for randomization due to other criteria (n=49). Of these, 1032 pts formed the primary analysis set (PAS), including all pts randomized in Q-F with samples available for CDx testing (N=513: Q, n=254; P, n=259) and a randomly selected subset of CTA− pts (n=519). The ascertainment rate was 95.2% (513/539), as 26 of the 539 pts randomized in Q-F were excluded from the bridging study. Within the PAS, 3 samples were not tested by CDx due to insufficient volume/DNA amount. The AAS (N=1029: CTA+, n=513; CTA−, n=516) included pts in the PAS with valid CTA results and tested with CDx. In the AAS, 6 samples (3 CTA+, 3 CTA−) did not yield valid CDx results, resulting in 1023 CDx-evaluable total pts (CTA+, n=510; CTA−, n=513). Among 510 CTA+ samples, 483 were CDx+. Among 513 CTA− samples, 513 were CDx−. Therefore, 996 samples yielded concordant results, 27 samples yielded discordant results, and 6 samples did not yield a valid CDx result for comparison. Point estimates of PPA & NPA were 94.2% & 99.4%, respectively, with invalid CDx results included in the calculation, and 94.7% & 100%, respectively, without invalid CDx results. The lower bounds of the 95% CIs were all above the corresponding acceptance criterion of 90% for PPA & NPA (Table 1). In Q-F, the prevalence of CTA+ was 24.9% among screened pts (863/3468), whereas in the bridging study, 49.9% (510/1023) of pts were CTA+: this enrichment in CTA+ pts could lead to a biased estimate of the agreement between CDx & CTA when using CDx as reference. The positive predictive value (PPV) and negative predictive value (NPV) of the CDx adjusted for this enrichment ± invalid CDx results, showed that the lower bounds of the 95% CIs were all >95% (Table 1). The efficacy OS analysis in the intent-to-treat (ITT) CDx+ population (ITT CDx+=CTA+ & CDx+; N=483: Q, n=242; P, n=241) demonstrated a clinically relevant OS improvement with Q (median OS of 29.4 months) vs P (median OS of 14.8 months), resulting in 14.6 months prolongation of median OS, with an HR of 0.794 (95% CI 0.621-1.014), corresponding to a 20.6% reduction in relative risk of death (Figure 1). Conclusions This study showed 1) agreement between CDx & CTA in identifying nd FLT3-ITD+ AML pts and 2) that OS benefit provided by Q in the ITT CDx+ population is comparable with the OS benefit in the ITT population of Q-F. The LeukoStrat CDx FLT3 Mutation Assay aids in assessing AML pts for Q therapy.

Mobocertinib efficacy in patients with NSCLC and EGFR exon 20 insertion mutations (ex20ins) identified by next-generation sequencing (NGS) of circulating tumor DNA (ctDNA).

9082 Background: EGFR ex20ins are distinct targetable driver mutations present in ~2% of all NSCLC. While most EGFR TKIs have limited effectiveness, mobocertinib is the first oral therapy approved for this unmet need. EGFR ex20ins are heterogeneous ( > 60 variants), and PCR testing detects a limited number of variants, leading to undetected disease in ~50% of cases, whereas NGS can identify all such mutations. Testing plasma ctDNA is a noninvasive approach for detection of genomic variants, such as EGFR ex20ins. Methods: In the mobocertinib phase 1/2 study (NCT02716116), patients were enrolled based on EGFR ex20ins detected by various local tissue or liquid clinical trial assays (CTAs). Baseline plasma samples were collected and processed to extract cell-free DNA and were evaluated for EGFR ex20ins status using FoundationOne Liquid CDX (F1LCDX), an NGS-based plasma ctDNA test. Concordance between F1LCDX and the CTAs was demonstrated by testing patient samples from the phase 1/2 trial and paired tissue and plasma samples from commercially acquired and stage-matched patients with NSCLC (N = 305). Efficacy analyses by assay method were performed in EGFR ex20ins–positive platinum-pretreated patients (PPP; n = 114 [FDA approved population]; data cutoff: 1 Nov 2021) in the phase 1/2 trial. Results: Concordance between F1LCDX and CTAs was demonstrated with samples from the CTA-positive (n = 159) and CTA-negative populations (n = 87) tested by F1LCDX where tissue and plasma were assessable; the point estimate of positive percentage agreement (95% CI) was 68.6% (61.0–75.3), and the point estimate of negative percentage agreement was 100% (95.8–100). F1LCDX detected 34 individual EGFR ex20ins variant types. In the response evaluable population, patients who tested EGFR ex20ins positive by F1LCDX (n = 55) demonstrated confirmed ORR (34.5%) and disease control rate (74.5%), which was comparable to those observed among all PPP in the phase 1/2 trial (confirmed ORR: 28%; confirmed disease control rate: 78%). Conclusions: Mobocertinib has shown efficacy in PPP with EGFR ex20ins NSCLC. F1LCDX effectively identified patients with EGFR ex20ins who may benefit from mobocertinib, providing an additional noninvasive diagnostic option to guide treatment. Clinical trial information: NCT02716116 .

Pre- and post-treatment blood-based genomic landscape of patients with ROS1 or NTRK fusion-positive solid tumours treated with entrectinib.

Genomic tumour profiling informs targeted treatment options. Entrectinib is a tyrosine kinase inhibitor with efficacy in NTRK fusion‐positive (‐fp) solid tumours and ROS1‐fp non‐small cell lung cancer. FoundationOne® Liquid CDx (F1L CDx), a non‐invasive in vitro next‐generation sequencing (NGS)‐based diagnostic, detects genomic alterations in plasma circulating tumour DNA (ctDNA). We evaluated the clinical validity of F1L CDx as an aid in identifying patients with NTRK‐fp or ROS1‐fp tumours and assessed the genomic landscape pre‐ and post‐entrectinib treatment. Among evaluable pre‐treatment clinical samples (N = 85), positive percentage agreements between F1L CDx and clinical trial assays (CTAs) were 47.4% (NTRK fusions) and 64.5% (ROS1 fusions); positive predictive value was 100% for both. The objective response rate for CTA+ F1L CDx+ patients was 72.2% in both cohorts. The median duration of response significantly differed between F1L CDx+ and F1L CDx− samples in ROS1‐fp (5.6 vs. 17.3 months) but not NTRK‐fp (9.2 vs. 12.9 months) patients. Fifteen acquired resistance mutations were detected. We conclude that F1L CDx is a clinically valid complement to tissue‐based testing to identify patients who may benefit from entrectinib and those with acquired resistance mutations associated with disease progression.

The Challenge to the Pathologist of PD-L1 Expression in Tumor Cells of Non-Small-Cell Lung Cancer-An Overview.

In recent years, the treatment of non-small-cell lung cancer (NSCLC) has been fundamentally changed by immunotherapy where the immune system is reactivated using anti-programmed cell death protein 1/programmed death ligand 1 (PD1/PD-L1) checkpoint inhibition. With this, the immunohistological detection of PD-L1 has become one of the most important predictive biomarkers, leading pathologists to play a central role in the immuno-oncological therapy decisions. This has brought them the challenge of requiring the knowledge of relevant checkpoint inhibitors (CI), different PD-L1 scores and cut-offs as well as the choice of the right tissues and controls. Their involvement is also required in the careful validation of both clinical trial assays (CTAs) and laboratory developed tests (LDTs), in addition to the internal and external quality assessment and the interpretation and scoring of the staining based on specialist training. After the training of tumor proportion score (TPS) scoring in NSCLC, pathologists show a high level of concordance, with some variation between different cut-offs. Since not all patients benefit from immunotherapy, further research is needed to validate new predictive markers and optimize existing ones. In this context, these studies focus on a combination of PD-L1 and molecular signatures.

A Companion Diagnostic With Significant Clinical Impact in Treatment of Breast and Gastric Cancer.

The development of trastuzumab (Herceptin®) was one of the most significant cancer drug development projects of the 20th century. Not only was it a scientific and medical achievement but it also paved the way for the drug-diagnostic codevelopment model, where a predictive biomarker assay is developed in parallel to the drug. One of the challenges in the development of trastuzumab was to select the right patient population likely to respond and here, it was critical to have access to an accurate, robust and reliable assay for detection of HER2 overexpression in tumors. In the clinical development of trastuzumab, a clinical trial assay (CTA), developed by Genentech, was used for selection of HER2 positive patients. However, during the phase III trial with trastuzumab, a new optimized IHC assay, HercepTest™ was designed and developed by Dako. In the final stage of its development, a comparative study with the CTA was conducted in order to show concordance between the two assays. In September 1998, the Food and Drug Administration (FDA) simultaneously granted approval to trastuzumab and HercepTest™. The assay has been used for patient selection in a number of significant breast cancer clinical trials such as the HERA, CLEOPATRA, EMILIA and more. In these trials, HercepTest™ demonstrated its clinical utility in the neoadjuvant, adjuvant, and metastatic setting as well as in relation to different types of HER2 targeted therapies. Likewise, the assay was used for selection of HER2 positive gastric cancer patients in the important ToGA trail. HercepTest™ was the first companion diagnostic ever approved by the FDA, and more than 20 years of use has documented its clinical impact.

Abstract LB056: Accurate detection of MET exon 14 skipping using a liquid biopsy assay in NSCLC patients in the GEOMETRY mono-1 study

Abstract IntroductionCapmatinib, a highly selective and potent MET inhibitor, was approved for patients with advanced METex14 NSCLC in the US and Japan in 2020, with the FoundationOne® CDx (F1CDx; a next-generation sequencing assay using DNA isolated from FFPE tumor tissue), based on results of the ongoing phase 2 GEOMETRY mono-1 study (NCT02414139). Previously, the F1CDx demonstrated 99% concordance with the METex14 RT-PCR clinical trial assay (CTA) used in the GEOMETRY mono-1 study. Here, we report findings of METex14 detection using the an NGS-based liquid biopsy assay (LDx), which detects MET single nucleotide variants and indels that lead to METex14 in circulating tumor (ct)DNA. MethodsDuring the GEOMETRY mono-1 study, patients were screened for METex14 status using a METex14 RT-PCR CTA on FFPE tissue. Clinical validation of the LDx was performed using plasma samples from patients enrolled in the GEOMETRY mono-1 study, which include METex14-positive samples from Cohort (C)4 (pretreated) and C5b (treatment-naïve), in addition to METex14-negative samples from C1b, C2, and C3, and samples from commercial sources. Concordance of the CTA and LDx were evaluated by positive percent agreement (PPA) and negative percent agreement (NPA). Clinical utility of the LDx in identifying METex14 positive patients for treatment with capmatinib was evaluated by comparing overall response rate (ORR) by BIRC in METex14 positive patients by the CTA and LDx. ResultsOf the 97 patients with METex14 NSCLC in C4 (n=69) and C5b (n=28), 88 patients had plasma volume ≥2.5 mL and cell free DNA ≥20 ng (minimum input). Of the 88 CTA METex14 positive patients, 57 were LDx positive, 26 were LDx negative; 5 had invalid sequencing results. Review of the 26 CTA discordant (METex14-negative) cases on LDx identified 3 with an alternate MET alteration, while the vast majority had evidence of low ctDNA levels. Of the 97 CTA METex14-negative patients who met minimum input requirements, 88 were LDx negative and 9 had invalid sequencing results; the LDx identified no CTA METex14-negative patient as positive. The PPA and NPA for these were 68.7% (95% CI: 57.6%, 78.4%) and 100% (95% CI: 95.9%, 100%), respectively. A post-hoc analysis comparing LDx with F1CDx in patients with METex14 showed similar results. For patients identified as METex14-positive by the LDx, the ORR (95% CI) by BIRC was determined as 48.8% (32.9–64.9%; n=20/41) for C4, and 81.3% (54.4–96.0%; n=13/16) for C5b; corresponding ORRs for patients identified as METex14-positive by the CTA were 40.6% (28.9-53.1%; n=28/69) for C4 and 67.9% (47.6-84.1%; n=19/28) for C5b.ConclusionsCurrent findings from the GEOMETRY mono-1 study support the feasibility and clinical utility of identifying advanced NSCLC patients with METex14 in ctDNA using LDx. For patients identified as METex14-negative by LDx, further testing should be performed on tissue samples, as a negative liquid biopsy result does not preclude a positive result by tissue biopsy. Citation Format: Rebecca S. Heist, Edward B. Garon, Daniel S. Tan, Harry J. Groen, Takashi Seto, Egbert F. Smit, Mike Zou, Yiqun Yang, Ying Li, Andrea Chassot Agostinho, Juergen Wolf. Accurate detection of MET exon 14 skipping using a liquid biopsy assay in NSCLC patients in the GEOMETRY mono-1 study [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr LB056.

Capmatinib efficacy in patients with NSCLC identified as METex14 using an NGS-based liquid biopsy assay: Results from the GEOMETRY mono-1 study.

9111 Background: Capmatinib, a highly selective and potent MET inhibitor, was approved for patients (pts) with advanced MET exon 14 skipping mutation (METex14) NSCLC in the US and Japan, with the FoundationOne CDx (tissue NGS assay), based on results of the ongoing GEOMETRY mono-1 study (NCT02414139). Here, we report efficacy findings in pts from GEOMETRY mono-1, who were identified as METex14 using a next-generation sequencing (NGS)-based liquid biopsy test (LDx), which detects METex14 in circulating tumor (ct)DNA. Methods: During the GEOMETRY mono-1 study, pts were screened for METex14 status using a METex14 RT-PCR clinical trial assay (CTA) on FFPE tissue. Clinical validation of the LDx was performed using plasma samples from pts enrolled in the GEOMETRY mono-1 study, which include METex14-positive samples from Cohort (C)4 (pretreated) and C5b (treatment-naïve), in addition to METex14-negative samples from C1b, C2, and C3, and 21 tissue-matched NSCLC plasma samples from commercial sources to supplement the total number of METex14 deletion negative patients. Concordance of the CTA and LDx were evaluated by positive percent agreement (PPA) and negative percent agreement (NPA). This retrospective analysis reports overall response rate (ORR), duration of response (DOR), and progression-free survival (PFS), all by BIRC, and overall survival (OS) in pts identified as METex14 by the LDx (data cutoff: Sep 18, 2020). Results: Of the 97 pts with METex14 NSCLC in C4 (n = 69) and C5b (n = 28), 88 pts had plasma volume ≥2.5 mL and cell free DNA ≥20 ng (minimum input); of these 57 were LDx positive (C4, n = 41; C5b, n = 16), 26 were negative; 5 had invalid sequencing results. Of the 97 CTA METex14-negative patients who met minimum input requirements, 88 were LDx negative and 9 had invalid sequencing results; none of the CTA METex14-negative pts (N = 97) were reported as positive by the LDx. The PPA and NPA for these were 68.7% (95% CI: 57.6%, 78.4%) and 100% (95% CI: 95.9%, 100%), respectively, when excluding LDx invalid results. In pts identified as METex14 positive by LDx, the ORR (95% CI) was 81.3% (54.4‒96.0; n = 16) in C5b and 48.8% (32.9‒64.9; n = 41) in C4; median DOR (95% CI) was 20.3 (4.2, NE; n = 13) months in C5b and 9.8 (4.2‒19.5; n = 20) months in C4; median PFS (95% CI) was 12.4 (4.5‒NE; n = 16) months in C5b and 5.4 (4.0‒6.6; n = 41) months in C4; median OS was 17.9 (9.8‒NE; n = 16) months in C5b and 13.6 (6.6‒23.3; n = 41) months in C4. Clinical findings in those identified as METex14 positive by LDx were comparable with those identified by the CTA. Conclusions: Current findings from the GEOMETRY mono-1 study support the activity of capmatinib in advanced NSCLC pts with METex14 identified using LDx. For pts identified as METex14-negative by the LDx, further testing should be performed on tissue samples, as a negative LDx result does not preclude a positive result by tissue biopsy. Clinical trial information: NCT02414139.

Abstract PS5-06: Prospective testing for PIK3CA/AKT1/PTEN alterations in tumor tissue from 1440 patients with advanced hormone receptor-positive HER2-negative breast cancer (HR+/HER2- BC) or triple-negative breast cancer (TNBC) screened for the IPATunity130 randomized phase 3 trial

Abstract Background The PI3K/AKT signaling pathway plays a significant role in both HR+ BC and TNBC. IPATunity130 is a double-blind, placebo-controlled, randomized phase 3 trial of ipatasertib in combination with paclitaxel in patients with PI3K/AKT1/PTEN-altered HR+ or TNBC. A next-generation sequencing (NGS)-based assay from Foundation Medicine Inc. (FMI) was used to select patients prospectively for enrollment in this trial.Patients and methods An investigational clinical trial assay (CTA) of a composite 3-gene biomarker signature [Kim, Lancet Oncol 2017] based on the FoundationOne® CDx assay was used to identify patients with PI3K/AKT pathway-activated tumors as eligible for enrollment in IPATunity130 (NCT03337724). Qualifying alterations for the 3-gene signature (referred to as ‘biomarker-positive’) comprised activating mutations in PIK3CA and/or AKT1, and/or loss of function (LOF) alterations in PTEN represented by homozygous or heterozygous deletions, dominant-negative mutations, or inactivating mutations under loss of heterozygosity. Study sites were required to submit formalin-fixed paraffin-embedded archival or fresh biopsy tissue derived from primary or metastatic tumors for patient screening. IPATunity130 includes three independent cohorts: Cohort A (biomarker-positive TNBC); Cohort B (biomarker-positive HR+/HER2– BC); and Cohort C (biomarker-negative TNBC). Results In total, 1736 patients were screened, from whom 1690 samples were tested by FMI. Of these, 1475 (87%) produced a valid NGS result. The remaining 215 (13%) failed quality control for reasons including insufficient tissue, DNA yield, lab error, and computational failure. Alteration status for PIK3CA and/or AKT1 and/or PTEN was positive in 703 (49%) of 1440 CTA-evaluable samples. In the HR+/HER2– cohort, the breakdown of CTA-positive samples was 301/356 (85%) PIK3CA/AKT1 mutations and 86/356 (24%) PTEN LOF alterations. In TNBC, 183/347 (53%) had PIK3CA/AKT1 mutations and 193/347 (56%) had PTEN LOF alterations. CTA results according to baseline characteristics are shown overall and by subtype below. The most common mutations detected outside the 3-gene biomarker signature in the screened population were in the TP53, BRCA1, RB1, BRCA2, and NF1 genes in the TNBC cohort and the TP53, GATA3, CDH1, MAP3K1, and ESR1 genes in the HR+/HER2– cohort. In the HR+/HER2– cohort, 30 (14%) of 213 metastatic tumors had ESR1 mutations compared with 10/414 (2%) primary tumors. Tumor BRCA1 mutations were more common in patients aged ≤50 years whereas MAP3K1 mutations were more common in those aged >50 years.Conclusions IPATunity130 is the first reported pivotal trial to utilize the 3-gene biomarker CTA in HR+/HER2– BC and TNBC to screen for patients with PI3K/AKT pathway-activated tumors. The 3-gene biomarker CTA detected alterations in 49% of screened patients, with a higher prevalence of PIK3CA/AKT1/PTEN alterations in HR+/HER2– BC than TNBC. Additional analyses are planned to assess correlations between clinical outcomes and tumor characteristics. SubgroupPIK3CA/AKT1/PTEN alteration, n/N (%)OverallHR+/HER2–TNBCAll patient samples703/1440 (49)356/647 (55)347/793 (44)Age, years≤50219/475 (46)99/195 (51)120/280 (43)>50484/965 (50)257/452 (57)227/513 (44)Sample sourcePrimary456/941 (48)232/414 (56)224/527 (43)Metastatic222/448 (50)112/213 (53)110/235 (47)Geographic regionNorth America60/102 (59)33/49 (67)27/53 (51)Asia-Pacific172/330 (52)81/145 (56)91/185 (49)Europe301/633 (48)171/310 (55)130/323 (40)Rest of world170/375 (45)71/143 (50)99/232 (43) Citation Format: Heidi Savage, Wendy Lin, Mafalda Oliveira, Carlos Barrios, Joyce O’Shaughnessy, Nicholas Turner, Rebecca Dent, Steven J Isakoff, Shigehira Saji, Qinshu Lian, Denise Bradley, Sarah-Jayne Reilly, Heather Hinton, Matthew J Wongchenko, Aruna Mani, Sung-Bae Kim. Prospective testing for PIK3CA/AKT1/PTEN alterations in tumor tissue from 1440 patients with advanced hormone receptor-positive HER2-negative breast cancer (HR+/HER2- BC) or triple-negative breast cancer (TNBC) screened for the IPATunity130 randomized phase 3 trial [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS5-06.

Selection of RARA-Positive Newly Diagnosed Unfit AML Patients with Elevated RARA Gene Expression Enriches for Features Associated with Primary Resistance to Venetoclax and Clinical Response to SY-1425, a Potent and Selective RARα Agonist, Plus Azacitidine

Selection of RARA-Positive Newly Diagnosed Unfit AML Patients with Elevated RARA Gene Expression Enriches for Features Associated with Primary Resistance to Venetoclax and Clinical Response to SY-1425, a Potent and Selective RARα Agonist, Plus Azacitidine

1193P Clinical validity of FoundationOne liquid CDx (F1L CDx) assay as an aid in selecting patients for treatment with entrectinib

F1L CDx is a next generation sequencing-based in vitro diagnostic for detecting genetic alterations in circulating cell-free DNA. We studied concordance between gene rearrangement status (NTRK and ROS1 fusion and non-fusion rearrangements) determined by F1L CDx and clinical trial assays (CTAs), and clinical efficacy of the TRK/ROS1 kinase inhibitor, entrectinib, in patients (pts) with NTRK rearrangement-positive (rp) or ROS1 rp tumours according to F1L CDx (FL1 CDx+). A total of 107 frozen pre-treatment plasma samples were obtained from pts with NTRK-rp solid tumours (n=49) and ROS1-rp NSCLC (n=37), according to CTAs, enrolled in the entrectinib phase II STARTRK-2 trial (NCT02568267), and pts with NTRK/ROS1 rearrangement-negative (rn) non-NSCLC tumours (n=21; external vendor). Positive and negative percentage agreements (PPA; NPA) between F1L CDx and CTA results were calculated. Positive and negative predictive values (PPV; NPV) were computed after adjustment for fusion prevalence (NTRK, 0.32%; ROS1, 1%). Clinical efficacy in F1L CDx+ cohorts was calculated by clinical bridging and compared with primary efficacy populations from pivotal entrectinib clinical trials. A total of 98 samples were evaluable by F1L CDx, of which 85 were included in primary analyses (NTRK-rp, 38; ROS1-rp, 31; NTRK/ROS1-rn, 16). Clinical efficacy of entrectinib according to CTA and F1L CDx results are presented (Table). Clinical bridging from CTAs to F1L CDx estimated the objective response rate (ORR) as 72.2% (95% CI 50.0–88.9) in both the F1L CDx NTRK-rp and ROS1-rp cohorts; greater than the CTA+ NTRK-rp subset and similar to the CTA+ ROS1-rp subset (Table). Observed PPA (Table) likely reflects comparison vs multiple tissue DNA/RNA based CTAs and is in line with plasma vs tissue PPA of FDA-approved plasma CDx. We show the clinical validity of using F1L CDx to identify pts with NTRK-rp tumours and ROS1-rp NSCLC who may benefit from entrectinib treatment.Table: 1193PNTRK-rpROS1-rpORR, % (95% CI) in primary efficacy population subsetsCTA+†57.4 (43.2–70.8), n=5478.4 (64.8–88.7), n=51*CTA+ FL1 CDx+72.2 (46.5–90.3), n=1872.2 (46.5–90.3), n=18CTA+ F1L CDx-55.0 (31.5–76.9), n=2072.7 (39.0–94.0), n=11CTA+ F1L CDx unknown43.8 (19.8–70.1), n=1686.4 (65.1–97.1), n=22Performance, % (95% CI); n/NPPA F1L CDx vs CTA47.4 (31.0–64.2); 18/3864.5 (45.4–80.8); 20/31NPA F1L CDx vs CTA100 (92.5–100.0); 47/47100 (93.4–100); 54/54PPV F1L CDx‡100 (82.4–100.0)100 (83.9–100)NPV F1L CDx§99.8 (98.8–99.9)99.6 (99.4–99.8)*2 ROS1-rp pts removed per FDA request†ORR in ALKA/STARTRK-1/STARTRK-2 integrated analysis‡95% CI Wilson score method§95% CI 5000 bootstraps Open table in a new tab

Abstract 5427: Genomic prevalence analysis in TNBC patients in the Phase 2 VIOLETTE study

Abstract Introduction: Triple-negative breast cancer (TNBC) accounts for ~15-20% of all breast carcinomas. VIOLETTE is a global, multicentre, open-label, randomized phase 2b study (NCT03330847), recruiting patients with metastatic TNBC to 2 treatment arms: olaparib and olaparib + ceralasertib (ATR inhibitor AZD6738). Patients are prospectively tested for mutations in genes involved in homologous recombination repair (HRR) by tumor DNA sequencing for stratification into BRCA mutated (BRCAm), non-BRCA HRR mutated (HRRm), and HRR wild-type (HRRwt) strata in each treatment arm. Patients can also be recruited as a result of a local test and tumor sample for those patients is analysed retrospectively. Methods: Sequencing of VIOLETTE tumor samples (prospective and retrospective) (n=518; DCO Sep 2019) using the FoundationOneCDx Clinical trial assay (CTA) test (Foundation Medicine [FMI]) was conducted to detect deleterious/suspected deleterious alterations, classified using AstraZeneca rules. Mutational zygosity and germline vs somatic status were assessed by a Somatic/ Germline/ Zygosity (SGZ) algorithm at FMI (Sun et al., 2018) and genome-wide LOH (loss of heterozygosity - gLOH) scores were generated. Results: The most prevalent alterations were in TP53 (86%) and MYC (25%). Alterations in main cancer signaling pathways included the HRR pathway (23%: BRCA1, BRCA2, ATM, RAD51B, RAD51C, RAD54L, RAD51D, BRIP1, FANCL, PALB2, BARD1, CHEK1, CHEK2, CDK12, PPP2R2A), the PI3K pathway (39%; (PIK3CA - 17.8%; PTEN - 20.1%; AKT1 - 5%)), cell cycle (37%: RB1, CDKN2A, CCNE1, CCND1) and RTK/RAS (22%: NF1, KRAS, FGFR1, FGF19/FGF3/FGF4). Preclinical and clinical data suggest that alterations in HRR pathway genes are associated with sensitivity to PARP inhibitors including olaparib. The most prevalent HRR gene alterations were BRCA1 (9.5%) and BRCA2 (3%) and non-BRCAm HRRm prevalence was 11%. Out of 96 patients with reported zygosity, 81% (44/54) of BRCAm and 64% (27/42) of non-BRCAm HRRm tumors had biallelic inactivation. Consistent with gLOH being a measure of HRR deficiency, gLOH scores were significantly higher in BRCAm patients compared to HRRwt patients (mean BRCAm 28, mean HRRwt 19, P=2.1E-08). Interestingly, we observed a significant mutual exclusivity between alterations in the HRR pathway and activating PIK3CA variants (P=0.01), suggesting distinct disease segments within TNBC. Conclusions: The genomic prevalence of breast cancer related alterations in VIOLETTE is as expected for TNBC, excepting HRRm, which was lower than anticipated from the TCGA dataset (23% VIOLETTE vs 35% TCGA). This may reflect the specific eligibility criteria for VIOLETTE. This is the largest dataset of genomic prevalence in TNBC reported, providing a deeper understanding of the prevalence of potentially actionable alterations to guide clinical development of targeted therapies. Citation Format: Joshua Armenia, Zhongwu Lai, Andrew Tutt, Emma Dean, Bienvenu Loembe, Hannah McGarvey, Sarah Edgington, J Carl Barrett, Andrew J. Pierce, Elizabeth A. Harrington, Natalia Lukashchuk. Genomic prevalence analysis in TNBC patients in the Phase 2 VIOLETTE study [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5427.

Identifying fibroblast growth factor receptor genetic alterations using RNA-based assays in patients with metastatic or locally advanced, surgically unresectable, urothelial carcinoma who may benefit from erdafitinib treatment.

Erdafitinib, a pan‐fibroblast growth factor receptor (FGFR) inhibitor received accelerated approval from the US Food and Drug Administration (FDA) for locally advanced or metastatic urothelial carcinoma (mUC) in adult patients with specific FGFR3/2 genetic alterations who progressed during or after ≥1 line of prior platinum‐containing chemotherapy (PCC), including within 12 months of neoadjuvant or adjuvant PCC. Concordance between the clinical trial assay (CTA) used in a phase 2 study and QIAGEN's therascreen® FGFR kit (a two‐step, multiplex, real‐time, RT‐PCR assay), the FDA‐approved companion diagnostic (CDx) with erdafitinib, was evaluated in this bridging study. Study samples included 100 CTA‐confirmed FGFR‐positive samples from 100 erdafitinib‐treated mUC patients, plus 200 CTA‐confirmed FGFR‐negative samples from the phase 2 study. The primary objective was met if the lower bound of 95% CI of objective response rate (ORR) in CDx‐confirmed patients with FGFR alterations was >25%. Demographics were similar between the bridging study and CTA‐screened patients. In total, 292 of 300 samples (97.3%) with valid CDx results showed high analytical concordance versus CTA (percent agreement [95% CI]: positive percent agreement, 87.2 [79.0; 92.5]; negative percent agreement, 97.0 [93.5; 98.6]; overall percent agreement, 93.8 [90.5; 96.1]). Investigator‐assessed ORR in the 81 CDx‐identified, erdafitinib‐treated patients who tested positive for both assays was 45.7% (95% CI: 35.3%; 56.5%) versus 40.4% (95% CI: 30.7%; 50.1%) for CTA and met the criteria for primary objective. High ORR and clinical concordance to CTA suggest that QIAGEN's CDx can reliably select mUC patients who would potentially benefit from erdafitinib treatment.

Statistical evaluation of drug efficacy for bridging study in companion diagnostic test trials

ABSTRACTPersonalized medicine is an area of growing attention in medical research and practice. A market-ready companion diagnostic test (CDx) is used in personalized medicine for identifying the best treatment for an individual patient. Unfortunately, development of CDx may lag behind the development of the drug, and consequently we use a clinical trial assay (CTA) to enroll patients into the drug pivotal clinical trial instead. Thus, when CDx becomes available, a bridging study will be required to assess the drug efficacy in the CDx intended use (CDx IU) population. Due to missingness of the CDx results that could be associated with randomization, one challenge we face in a bridging study is covariate imbalance between treatment arms for the subpopulation with both positive CDx and CTA. In this paper, we evaluate the performance of two methods in bridging studies under a causal inference framework. Particularly, we aim to use the propensity score method with doubly robust estimation and optimal matching to address the challenge. We extend under a current framework on drug efficacy estimation in the CDx IU population, using data from both the bridging study and the CTA drug pivotal clinical trial. Both approaches are discussed in the context of a randomized bridging study, and a targeted design clinical trial with simulations, followed by analyzing simulated data that mimic a real ongoing clinic trial.

Abstract CT104: Efficacy of pembrolizumab (MK-3475) and relationship with PD-L1 expression in patients with non-small cell lung cancer: Findings from KEYNOTE-001)

Abstract Background: Preliminary KEYNOTE-001 data showed that the PD-1 inhibitor pembro has manageable safety and antitumor activity in previously treated and treatment-naive advanced non-small cell lung cancer (NSCLC). In a training set of 182 pts, 129 of whom had measurable disease and tumor evaluable by an IHC clinical trial assay (CTA) for PD-L1 expression, ORR was higher in pts with membranous PD-L1 expression in ≥50% of tumor cells (proportion score [PS] ≥50%) vs PS <50%. We aimed to verify the relationship between PD-L1 expression and ORR in an independent validation set of NSCLC pts enrolled in KEYNOTE-001 and to assess the impact of PD-L1 expression in the combined training and validation sets. Methods: Advanced or metastatic NSCLC pts received pembro 2 mg/kg Q3W, 10 mg/kg Q3W, or 10 mg/kg Q2W. Response was assessed every 9 wk. Treatment decisions were managed per investigator-assessed irRC. Efficacy evaluation was per centrally assessed RECIST v1.1. PD-L1 expression was determined by the CTA. Before analysis, ORR and PD-L1 data from the validation set were merged in pts with measurable disease and CTA-evaluable tumors. Duration of response (DOR), PFS, and OS were assessed in all treated pts from the training and validation sets with CTA-evaluable tumors. Results: In all 495 pts from the training and validation sets, irrespective of PD-L1 expression, ORR was 19.4%, median DOR was 12.4 mo, median PFS was 3.7 mo, and median OS was 12.0 mo. 9% experienced grade 3-5 treatment-related AEs; 4% discontinued due to a treatment-related AE. There was 1 treatment-related death (pneumonitis). Of the 313 pts in the validation set, ORR in the 204 pts evaluable by the CTA was 45.2% in those with PS ≥50% (Table). The relationship between ORR and PD-L1 expression was observed in previously treated and treatment-naive pts (Table). In the 356 pts evaluable by the CTA in the total population, PFS and OS were longer in pts with PS ≥50% (Table). Median OS was not reached in pts with PS ≥50%, regardless of prior treatment. Median (range) DOR was similar in pts with PS ≥50% (12.4 mo [2+ to 22.8+]), 1-49% (10.3 mo [1.4+ to 10.3]), and <1% (NR [0.9+ to 10.8+]). Conclusion: Pembro provides durable antitumor efficacy and safety in pts with treatment-naive and previously treated NSCLC. These data validate that membranous PD-L1 expression in ≥50% of tumor cells identifies pts with advanced NSCLC who are particularly likely to obtain clinical benefit from pembro. Proportion Score (PS)≥50%1-49%<1%ORR in evaluable pts in the validation set,% (95% CI)Totaln = 73n = 103n = 2845.2 (33.5-57.3)16.5 (9.9-25.1)10.7 (2.3-28.2)Previously treatedn = 57n = 77n = 2243.9 (30.7-57.6)15.6 (8.3-25.6)9.1 (1.1-29.2)Treatment naiven = 16n = 26n = 650.0 (24.7-75.3)19.2 (6.6-39.4)16.7 (0.4-64.1)Survival in evaluable pts in the total population, mo, median (95% CI)PFSTotaln = 119n = 161n = 766.3 (2.9-12.5)3.3 (2.1-4.1)2.3 (2.1-4.0)Previously treatedn = 99n = 127n = 686.1 (2.1-12.5)2.3 (2.1-3.4)2.2 (2.0-4.1)Treatment naiven = 20n = 34n = 812.5 (2.4-12.5)4.3 (3.1-6.4)3.5 (2.1-4.2)OS [NR, not reached.]Totaln = 119n = 161n = 76NR (13.7-NR)8.8 (6.8-12.4)8.8 (5.5-12.0)Previously treatedn = 99n = 127n = 68NR (9.3-NR)7.3 (5.8-12.1)8.6 (5.5-12.0)Treatment naiven = 20n = 34n = 8NR (NR-NR)16.2 (8.6-16.2)10.4 (3.4-NR) Citation Format: Edward B. Garon, Naiyer Rizvi, Rina Hui, Natasha B. Leighl, Ani S. Balmanoukian, Joseph P. Eder, Amita Patnaik, Charu Aggarwal, Matthew A. Gubens, Leora Horn, Enric Carcereny, Myung-Ju Ahn, Enriqueta Felip, Jong-Seok Lee, Jin Zhang, Reshma A. Rangwala, Gregory M. Lubiniecki, Charlotte M. Roach, Kenneth Emancipator, Leena Gandhi. Efficacy of pembrolizumab (MK-3475) and relationship with PD-L1 expression in patients with non-small cell lung cancer: Findings from KEYNOTE-001). [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr CT104. doi:10.1158/1538-7445.AM2015-CT104

Statistical Consideration and Challenges in Bridging Study of Personalized Medicine

Applications of personalized medicine are becoming increasingly prominent. A well-characterized market-ready companion diagnostic assay (CDx) is often desired for patient enrollment in device-drug pivotal clinical trial(s) so that Food and Drug Administration can ensure that appropriate clinical and analytical validation studies are planned and carried out for CDx. However, such a requirement may be difficult or impractical to accomplish. A clinical trial assay (CTA) instead of CDx may be used for patient enrollment in the clinical trial. A concordance study (or bridging study) will be required to assess the agreement between CDx and CTA in order to bridge the clinical data (e.g. overall survival) from CTA to CDx and to evaluate the drug efficacy in CDx intended use population. In this article, we will discuss statistical challenges in study design and data analysis for bridging study. Particularly, we aimed to provide statistical methods on how to estimate the drug efficacy in CDx intended use population using results from bridging study and CTA-drug pivotal clinical trial.

Determination of HER2 Gene Amplification by Fluorescence In situ Hybridization and Concordance with the Clinical Trials Immunohistochemical Assay in Women with Metastatic Breast Cancer Evaluated for Treatment with Trastuzumab

To evaluate the concordance between HER2 gene amplification, determined by fluorescence in situ hybridization (FISH), and HER2 protein overexpression assessed by an immunohistochemical (IHC) assay. The IHC protocol used was a research assay, known as the Clinical Trial Assay (CTA), developed to select women with metastatic breast cancer (MBC) for three pivotal clinical trials of trastuzumab therapy. A direct-labeled, dual-probe FISH assay was used to determine HER2 amplification in 623 fixed breast cancer tissue specimens. These specimens had been stored as paraffin-embedded sections for 25 years. All specimens had been analyzed for HER2 protein expression by the CTA. To assess the reproducibility of FISH results in archived material, we evaluated a separate group of 617 breast cancer tissue specimens at two different laboratories. Informative FISH results were available for 529 (85%) of the 623 specimens. Overall concordance between FISH and IHC results was 82% (95% CI; 7885%). Assay agreement between FISH results and specimens with immunostaining scores of 0, 1+, and 3+ were 97, 93 and 89%, respectively. However, only 24% of specimens with 2+ immunostaining scores had HER2 amplification by FISH; there was assay disagreement in 76% of specimens in this IHC subgroup. Interlaboratory FISH concordance was 92% (95% CI; 8994%), indicating very good assay reproducibility in these archived specimens. HER2 status determined by CTA-IHC and FISH are significantly correlated; however, differences between these two assays can a ect patient selection for trastuzumab therapy.