ctDNA Samples Research Articles

Perioperative ctDNA-Based MRD Detection in NSCLC-Letter.

We read with great interest the article by Xia and colleagues reporting circulating tumor DNA (ctDNA) as biomarker for early detection of molecular residual disease (MRD) and predictor for relapse after surgery in patients with non–small cell lung cancer in a prospective multicenter cohort named LUNGCA-1 (1).LUNGCA-1 was designed to predict prognosis by perioperative ctDNA detection, including preoperative, 3 days postoperative and 1 month postoperative ctDNA. The number of patients in prognosis analysis is 330 (Fig. 1), whereas Supplementary Table S5 shows only 329 patients with at least one postoperative ctDNA sample. In LUNGCA-1, some patients tested postoperative ctDNA before or without adjuvant therapies, while others tested postoperative ctDNA after adjuvant therapies. We questioned the trial design because the authors mixed different aims: MRD detection at a specific postoperative timepoint for recurrence prediction; MRD detection at both preadjuvant/postadjuvant therapies timepoints for evaluation of the outcome of adjuvant therapies. The authors could separate different aims into different trials or do statistics separately in preadjuvant/postadjuvant groups.The authors defined “MRD positive” for patients with detectable ctDNA at 3 days and/or 1 month postoperatively. We noticed that 5 of 26 patients with MRD positive (19.2%) had ctDNA positive only in the detection at postoperative 3 days and their ctDNA detection was negative before and 1 month after surgery. Therefore, we consider the issue of timepoint setting for postoperative blood collection. Diehl and colleagues reported that ctDNA increased after surgery, most likely due to release of ctDNA from damaged tissue (2). Thus, it may be more reasonable to collect blood at a later timepoint after surgery from 10 days to 16 weeks (3). As reported by Chaudhuri and colleagues (4) and Moding and colleagues (5), blood sample should be collected within 4 months for ctDNA detection after surgery or completing radiation and chemotherapy. In this article, the cell-free DNA concentration at 3 days after surgery is also significantly higher than before and 1 month after surgery (Supplementary Table S1), suggesting a more reasonable manner to collect blood for a longer period after surgery. Also, whether the 5 patients with ctDNA positive for only 3 days after surgery relapsed or not was not mentioned.Chaudhuri and colleagues (4) reported that concentration of ctDNA should be correlated with stage and tumor volume, which the authors did not mention. Furthermore, how to determine ctDNA status is positive or negative needs to be clarified. In addition, the criteria for judging the patient's disease relapse were not mentioned in the text or Supplementary Materials and Methods.See the Response, p. 1156No disclosures were disclosed.We thank the grant from the Fundamental Research Funds for the Central Universities in China (4206-413100049).

Next-generation sequencing (NGS) profiling of matched tumor and circulating tumor DNA (ctDNA) in head and neck squamous cell carcinoma (HNSCC)

ObjectivesThe aim of this pilot study was to evaluate the presence of somatic mutations in matched tumor and circulating DNA (ctDNA) samples from patients with primary head and neck squamous cell carcinoma (HNSCC) and assess the association of changes in ctDNA levels with survival. Materials and methodsOur study included 62 patients with stage I-IVB HNSCC treated with surgery or radical chemoradiotherapy with curative intent. Plasma samples were obtained at baseline, at the end of treatment (EOT), and at disease progression. Tumor DNA was extracted from plasma (ctDNA) and tumor tissue (tDNA). The Safe Sequencing System was used assess the presence of pathogenic variants in four genes (TP53, CDKN2A, HRAS and PI3KCA) in both ctDNA and tDNA. ResultsForty-five patients had available tissue and plasma samples. Concordance of genotyping results between tDNA and ctDNA at baseline was 53.3%. TP53 mutations were most commonly identified at baseline in both ctDNA (32.6%) and tDNA (40%). The presence of mutations in this restricted set of 4 genes in tissue samples at baseline was associated with decreased overall survival (OS) [median 58.3 months for patients with mutations vs. 89 months for patients without mutations, p < 0.013]. Similarly, patients presenting with mutations in ctDNA had shorter OS [median 53.8 vs. 78.6 months, p < 0.037]. CtDNA clearance at EOT did not show any association with PFS or OS. ConclusionsLiquid biopsy enables real-time molecular characterization of HNSCC and might predict survival. Larger studies are needed to validate the utility of ctDNA as a biomarker in HNSCC.

Lesion Shedding Model: unraveling site-specific contributions to ctDNA.

Sampling circulating tumor DNA (ctDNA) using liquid biopsies offers clinically important benefits for monitoring cancer progression. A single ctDNA sample represents a mixture of shed tumor DNA from all known and unknown lesions within a patient. Although shedding levels have been suggested to hold the key to identifying targetable lesions and uncovering treatment resistance mechanisms, the amount of DNA shed by any one specific lesion is still not well characterized. We designed the Lesion Shedding Model (LSM) to order lesions from the strongest to the poorest shedding for a given patient. By characterizing the lesion-specific ctDNA shedding levels, we can better understand the mechanisms of shedding and more accurately interpret ctDNA assays to improve their clinical impact. We verified the accuracy of the LSM under controlled conditions using a simulation approach as well as testing the model on three cancer patients. The LSM obtained an accurate partial order of the lesions according to their assigned shedding levels in simulations and its accuracy in identifying the top shedding lesion was not significantly impacted by number of lesions. Applying LSM to three cancer patients, we found that indeed there were lesions that consistently shed more than others into the patients' blood. In two of the patients, the top shedding lesion was one of the only clinically progressing lesions at the time of biopsy suggesting a connection between high ctDNA shedding and clinical progression. The LSM provides a much needed framework with which to understand ctDNA shedding and to accelerate discovery of ctDNA biomarkers. The LSM source code has been available in the IBM BioMedSciAI Github (https://github.com/BiomedSciAI/Geno4SD).

Abstract P4-02-04: Serial monitoring of circulating tumor cells and circulating tumor DNA in metastatic lobular breast cancer identifies intra-tumor heterogeneity and precision and immuno-oncology biomarkers of therapeutic importance

Abstract Clinical decisions on precision and immuno-oncology therapies are based on predictive biomarkers commonly obtained from a single metastatic biopsy or archived primary tumor tissue. Circulating genomic biomarkers offer a minimally invasive approach to monitor intra-patient tumor heterogeneity and detect in real-time the clinically-relevant evolving clonal architecture. Although currently underutilized, we hypothesize that single-cell DNA next generation sequencing (scNGS) of circulating tumor cells (CTC) is a particularly well-suited method to complement biomarker information obtained from tissue and cell-free circulating tumor DNA (ctDNA). In this study we analyzed 113 individual CTC, 21 ctDNA, and 15 white blood cells (WBC) samples, from 15 CTC-positive lobular breast cancer patients, four of whom had CTC available at both metastatic baseline and after progression on a variety of therapies chosen at their physician’s discretion. Clinical NGS data from 15 tumor tissue biopsies obtained using a ~1700-gene DNA panel and whole transcriptome sequencing were available for comparison. CTC were enriched with the CellSearch® system and isolated as single cells with the DEPArray™ system. Whole genome amplified CTC and WBC, as well as ctDNA underwent scNGS with the Oncomine Comprehensive Assay covering ~500 genes and 1.1Mb of genomic space to detect mutations, copy number alterations, tumor mutation burden (TMB) and microsatellite instability (MSI). 99.1% of single cells and 95.2% of ctDNA samples were informative, with a mean sequencing depth of 664x. Using our previously developed, CTC-based precision medicine reporting platform, MI-CTCSeq, CTC in 9 of 15 patients (60%) had mutations that were actionable by FDA-approved targeted therapies including in the oncogenes PIK3CA and FGFR2 and HER2. 3 of these 9 patients (33%) harbored actionable alterations not shared between all 3 analyte types (tissue, CTC and ctDNA). These included 3 actionable mutations found in CTC and ctDNA only, 1 in tissue and ctDNA only, and 1 in ctDNA only. However, 2 of those ctDNA mutations were identified near the limit of detection and with a priori knowledge of their presence from tissue or CTC. Further, 1 patient with plentiful CTC had no detectable ctDNA and one patient’s tissue biopsy was inadequate for sequencing while both liquid biopsy analytes were abundant. 13 patients (87%) displayed intra-patient, inter-CTC genomic heterogeneity of putative driver mutations. 1 of 4 (25%) patients with CTC available in &amp;gt;1 timepoint displayed fluctuations in their CTC subclonal makeup between timepoints. Data from this patient’s 2 tissue biopsies, 3 ctDNA samples, and 27 individual CTC over 4 timepoints combined to reveal in unprecedented detail inter-metastatic lesion and inter-CTC heterogeneity and tumor evolution in response to endocrine and immunotherapy selective pressures. ScNGS of CTC helped provide an additional level of detail not appreciated by sequencing of the other two analyte types. In another patient, CTC were composed of 2 subclones which were indistinguishable by ctDNA, 1 of which appears to have not been sampled by the tissue biopsy. Using a novel method, we enabled detection of single-cell CTC TMB and MSI. CTC TMB scores (dichotomized as above/below 10 mutations/Mb) were 100% concordant with those measured in the corresponding tissue biopsies. Further, in a novel observation, we detected intra patient, inter-CTC heterogeneity of TMB and MSI, which has potential implications for immunotherapy response and development of resistance. Taken together, these data support the non-invasive biomarker interrogation and monitoring by liquid biopsy that incorporates CTC scNGS and complements tissue in informing precision and immuno-oncology approaches. This may have important implications for appropriate treatment selection and identification of therapeutic resistance mechanisms. Citation Format: Andi Cani, Emily Dolce, Alissa Turnbull, Kevin Hu, Chia-Jen Liu, Elizabeth Darga, Dan Robinson, Yi-Mi Wu, Dafydd G. Thomas, Costanza Paoletti, Scott Tomlins, James Rae, Aaron Udager, Arul Chinnaiyan, Erin F. Cobain, Daniel F. Hayes. Serial monitoring of circulating tumor cells and circulating tumor DNA in metastatic lobular breast cancer identifies intra-tumor heterogeneity and precision and immuno-oncology biomarkers of therapeutic importance [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P4-02-04.

Abstract P2-23-08: Concordance of Targeted Sequencing from Circulating Tumor DNA and Paired Tumor Tissue

Abstract Purpose: In this study, we evaluated the concordance of targeted sequencing results between paired ctDNA and tumor samples from early breast cancers scheduled for curative surgery with or without adjuvant therapy. If high concordance was observed, pre-operative ctDNA testing could serve as a non-invasive surrogate for variants meant to be revealed after definite surgery. On the other hand, poor concordance may hamper wide clinical absorption of liquid biopsy early breast cancer. Materials and Methods: The study VGH-TAYLOR: Comprehensive precision medicine research on the heterogeneity of Taiwanese breast cancer patients, consisted of three years enrollment and approximately four years follow-up after enrollment. Individual subject was assigned into Group 1 [planned to received surgery as first-line treatment and followed by adjuvant therapy, Group 2 [planned to receive neoadjuvant therapy as the first-line treatment and followed by surgery], and Group 3 [diagnosed with de novo and treatment naïve stage IV breast cancer, or stage IV breast cancer with recurrence beyond three years after surgery]. Molecular profiling and potential biomarkers were determined using Oncomine Comprehensive Assay v3 from FFPE tissues and Oncomine Breast cfDNA Assay v2 from plasma. Oncomine Comprehensive Assay is a targeted sequencing of NGS experiments were performed with TMO comprehensive using FFPE tissues, included 161 cancer-releant genes and types of mutation detected such as frameshift, missense, synonymous, SNV, Indel, and CNV. Oncomine Breast cfDNA Assay detects breast-derived cfDNA including hotspot genes: AKT1, EGFR, ERBB2, ERBB3, ESR1, FBXW7, KRAS, PIK3CA, SF3B1, TP53 (~152 hotspots), CNVs: CCND1, ERBB2, FGFR1, and full length TP53 (~80% coverage). Common genes interrogated by both ctDNA and TMO assay were identified, and concordance between paired targeted sequencing results from the same individuals were reported. Results: We reported the mutational landscape of initial 612 patients interrogated with the Oncomine Breast cfDNA assay; 239 out of 612 patients reported at least one mutation (39%). Among 246 patients assayed for both ctDNA and tumor tissue, cfDNA assay detected 73 (29.6%) and TMO comprehensive assay detected 201 (81.7%) breast cancers with at least one variant (c2 test, p=0.001). Sixty-seven (25.6%) were tested positive for both liquid and tissue assays, while cfDNA and TMO comprehensive assay detected additional 10 (4%) and 138 (56%) cases, which were not identified by the other platform. Table 1 details the distributions of called variants among common targeted genes. Conclusion: In current study, we evaluated the concordance of called variants between targeted sequencing from ctDNA and tumor tissue among an early breast cancer cohort in Taiwan. Only one-quarter of patients were positive for both cfDNA and TMO comprehensive assays from the same subject, indicating assay-specific sensitivity inevitably resulting in diagnostic discrepancy. Another plausible explanation came from the early stage nature of interrogated patients, which may inherit fewer ctDNA spillage from tumor and compromise detectability from liquid biopsy. The most prevalent mutant genes from both platforms were TP53 (68.3%) and KRAS (53.5%), both were well-known drivers in cancers. From breast cancer actionability, PIK3CA (39.4%) mutation is a biomarker for the FDA-approved PI3Ka inhibitor such as alpelisib, AKT1 (45.9%) mutation for agents such as capivasertib (AZD5363) and ipatasertib, and ERBB2 mutation for tyrosine kinase inhibitor such as neratinib. Our study showed that tumor should be the preferred source for targeted sequencing, and additional 4% of variants wound be revealed from liquid biopsy. Table 1. Distributions of variants from common targeted genes (n=6) from cfDNA and TMO comprehensive assay. Citation Format: Chi-Cheng Huang, Ling-Ming Tseng. Concordance of Targeted Sequencing from Circulating Tumor DNA and Paired Tumor Tissue [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P2-23-08.

Abstract P4-09-12: Baseline and End-of-Treatment Biomarkers in Patients With PIK3CA-Mutated, Hormone Receptor-Positive, Human Epidermal Growth Factor Receptor 2-Negative Advanced Breast Cancer From BYLieve Study Cohorts A and B

Abstract Introduction: Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (PIK3CA) is mutated in ~40% of patients (pts) with hormone receptor-positive (HR+), human epidermal growth factor receptor 2-negative (HER2−) advanced breast cancer (ABC). PIK3CA mutations are associated with resistance to endocrine therapy (ET) and worse overall survival. Alpelisib (ALP), an α-selective PI3K inhibitor and degrader, is indicated in combination with fulvestrant (FUL) for pts with PIK3CA-mutated (mut) HR+, HER2− ABC following progression on/after ET-based treatments. In the Phase 2, open-label, 3-cohort, noncomparative BYLieve study, clinical benefit of ALP in combination with ET was observed in the post-cyclin-dependent kinase 4/6 inhibitor (CDK4/6i) setting in pts with PIK3CA-mut, HR+, HER2− ABC. Here we report the results of a biomarker analysis using paired baseline (Cycle 1 Day 1) and end-of-treatment (EOT) circulating tumor DNA (ctDNA) samples from pts in BYLieve Cohorts A and B. Methods: In the BYLieve study, pts with PIK3CA-mut, HR+, HER2− ABC had CDK4/6i + aromatase inhibitor (Cohort A; N=127) or CDK4/6i + FUL (Cohort B; N=126) as treatment immediately prior to receiving ALP + FUL and ALP + letrozole, respectively. In this biomarker analysis, gene alterations were detected in ctDNA at baseline and EOT using next-generation sequencing (PanCancer V2 panel). Pts included in this interim analysis had confirmed PIK3CA mutations and matched baseline/EOT samples with enough sequencing coverage and ctDNA fraction to detect mutations at both time points. ctDNA fractions, tumor mutation burden (TMB) distributions, genomic landscapes, gain/loss of PIK3CA and estrogen receptor 1 (ESR1), chromosome 8/11 amplification profiles, and alterations in PI3K pathway and potential CDK4/6i resistance markers were assessed across time points. Sample sizes were small; results should thus be interpreted with caution. Results: Forty-three pts were included in the Cohort A biomarker population and 40 pts were included in Cohort B. ctDNA fraction was numerically higher at EOT compared with baseline in both cohorts; further analyses will be presented. In Cohort A, no significant differences were observed in TMB at EOT compared with baseline (P=0.21). In Cohort B, TMB was higher at EOT compared with baseline (P=0.053). Chromosome 8/11 amplifications were consistent between baseline and EOT for both cohorts. Small variations were observed in ESR1/PIK3CA mutations between baseline and EOT on both cohorts (Table). The status of potential CDK4/6i resistance markers was relatively unchanged at EOT (Table). Loss-of-function mutations in PTEN, a known PI3K inhibitor resistance marker, increased from 9% at baseline to 14% at EOT in Cohort A and from 12% at baseline to 22% at EOT in Cohort B. Conclusions: Between baseline and EOT, only small variations in gene alterations in PIK3CA-mutated HR+, HER2– ABC were observed in the post-CDK4/6i setting. As the disease progressed, increases in loss-of-function mutations in PTEN at EOT in both Cohorts A and B suggested loss of PTEN in PI3K pathway may drive resistance to ALP. Early intervention with ALP, when the tumor is particularly driven by PIK3CA oncogenic mutations and before it develops more genomic complexity, may potentially provide better clinical outcomes. Table. Gene Alteration Gain/Loss at Baseline/EOT Across Cohorts A and B Citation Format: Dejan Juric, Nicholas Turner, Sherene Loi, Fabrice Andre, Stephen K. Chia, Komal Jhaveri, Patrick Neven, Rebecca Dent, Eva Ciruelos, Mukta Joshi, Estelle Roux, Heather Patino, Murat Akdere, Hope Rugo. Baseline and End-of-Treatment Biomarkers in Patients With PIK3CA-Mutated, Hormone Receptor-Positive, Human Epidermal Growth Factor Receptor 2-Negative Advanced Breast Cancer From BYLieve Study Cohorts A and B [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P4-09-12.

Abstract P1-13-07: Investigating NF1 Mutations in Circulating Tumor DNA of Patients with Hormone-receptor Positive (HR+) Breast Tumors Resistant to CDK4/6 Inhibition (CDK4/6i): A Retrospective Clinical Analysis

Abstract Background: CDK4/6 inhibitors (CDK4/6i) are standard of care for the management of HR+/HER2- metastatic breast cancer (MBC). Genomic alterations that drive resistance to CDK4/6i are diverse, and while the molecular landscape is heterogeneous, several mechanisms of CDK4/6i resistance converge on the RAS/MAPK and PI3K/AKT/mTOR signaling pathways. NF1 downregulates RAS and dampens cellular proliferation. Laboratory-based models demonstrate that loss of NF1 is associated with resistance to endocrine therapy (ET), and emergence of NF1 mutations (NF1m) are correlated with progressive disease (PD) in circulating tumor DNA (ctDNA). While NF1m may diminish CDK4/6i susceptibility, a clear relationship has not been elucidated. The primary objective of this study was to characterize patient (pt) response to CDK4/6i in NF1m HR+/HER2- MBC. Methods: We identified 47 pts with NF1m via a database with one or more ctDNA samples sequenced at variable time-points as part of routine care for MBC. NF1m were categorized as pathogenic (p)NF1m or variants of uncertain significance (VUS) based on their associated Guardant report. We identified 27 pts with HR+/HER2- MBC and NF1m that received at least 1 line of CDK4/6i in the metastatic setting. Intrinsic resistance was defined as PD &amp;lt; 6 months on a CDK4/6i regimen, and acquired resistance was defined as PD &amp;gt;6 months. Pts with intrinsic resistance or acquired resistance and NF1m detected post-PD were categorized as having a resistance phenotype potentially driven by NF1m. Pts with NF1m detected prior to therapy and &amp;gt;6 months clinical response on a CDK4/6i were categorized as having NF1m tumors sensitive to CDK4/6i. Results: The NF1m cohort (n = 27) had 9 pts with pNF1m, while 18 pts expressed VUS. The median age at MBC diagnosis was 54 years, and 67% had visceral metastasis at ctDNA collection. Pts received a median of 1 prior line (range: 0 - 6) of ET or chemotherapy in the metastatic setting before CDK4/6i. Amongst pts with pathogenic variants (n = 9), we found 3 pts with pNF1m were intrinsically resistant to CDK4/6i. Acquired resistance was seen in 1 pt with pNF1m detected post-PD, and 2 pts had evidence of both acquired and subsequent intrinsic resistance to a later line of CDK4/6i. Overall, 67% (6/9) of pNF1m pts demonstrated a CDK4/6i resistance phenotype; mutant allele fraction (AF) ranged from 0.2% - 29.9%, and the mean maximum allele fraction (MAF) was 6.0%. Pre- and post-treatment samples were available on 3 pts with pNF1m, and 1 of these pts had an AF rise from 2.7% to 12.3% when comparing ctDNA pre- and post-CDK4/6i. ctDNA from 4 of 6 resistant tumors harbored other putative drivers including alterations in FGFR, KRAS, PTEN, and RB. We identified 2 counter-examples of pNF1m tumors sensitive to CDK4/6i. These pts expressed relatively low NF1m AF, ranging 0.1% - 0.5% with a mean MAF 0.3%. Another pNF1m pt had intrinsic resistance to initial CDK4/6i but was sensitive to later-line CDK4/6i. In the subgroup of pts with VUS-NF1m (n = 18), a more mixed picture of resistance and sensitivity was seen. 8 pts had intrinsic or acquired resistance, 8 pts had NF1m tumors sensitive to CDK4/6i, and 1 pt had evidence of both; 61% (n = 11) of pts expressed alterations in other resistance mediating genes. 1 pt stopped therapy due to toxicity rather than PD. Conclusions: Our work demonstrates that tumor expression of pNF1m may be associated with CDK4/6i resistance in pts with HR+/HER2- MBC, and allele fraction could be predictive of drug susceptibility. Tumors harboring VUS had varied sensitivity, suggesting that some of these mutations may not be pathogenic, and counter-examples of pNF1m MBC benefiting from CDK4/6i plus ET highlight the complexities in predicting drug response based on single gene alteration. Future effort is warranted to explore the potential impact of NF1 on CDK4/6i resistance, as well as the potential role for therapies targeting the MAPK pathway in this patient population. Citation Format: Maxwell R. Lloyd, Lianne Ryan, Arielle J. Medford, Jennifer C. Keenan, Laura M. Spring, Neelima Vidula, Beverly Moy, Dejan Juric, Leif Ellisen, Aditya Bardia, Seth A. Wander. Investigating NF1 Mutations in Circulating Tumor DNA of Patients with Hormone-receptor Positive (HR+) Breast Tumors Resistant to CDK4/6 Inhibition (CDK4/6i): A Retrospective Clinical Analysis [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P1-13-07.

Abstract PD13-04: PD13-04 Exploratory subgroup and biomarker analyses of acelERA Breast Cancer: Phase II study of giredestrant (GDC-9545) vs physician’s choice of endocrine therapy for previously treated, estrogen receptor+, HER2– advanced breast cancer

Abstract BACKGROUND Endocrine therapy (ET) is the mainstay for management of estrogen receptor (ER)+ advanced breast cancer (aBC). Giredestrant is a highly potent, nonsteroidal, oral selective ER antagonist and degrader (SERD) that achieves robust ER occupancy. The Phase II randomized, open-label acelERA BC study (NCT04576455) evaluated giredestrant vs physician’s choice of ET (PCET) in the second- or third-line ER+, HER2– aBC setting. While the study did not reach statistical significance for its primary endpoint of investigator-assessed progression-free survival (INV-PFS), the giredestrant arm demonstrated a numerical improvement vs the PCET arm, with a hazard ratio of 0.81 (95% confidence interval: 0.60, 1.10), and encouraging results for key secondary efficacy endpoints (clinical benefit rate [CBR]: 32% vs 21%, respectively; objective response rate [ORR]: 13% vs 7%, respectively). We report exploratory subgroup analyses of these efficacy endpoints by prior treatments and by baseline circulating tumor (ct)DNA biomarkers. METHODS Patients were post- and pre- or peri-menopausal women, or men, with ER+, HER2– aBC who had progressed after 1–2 lines of systemic therapy in the advanced setting (≤1 targeted agent; ≤1 chemotherapy regimen; prior fulvestrant allowed). Randomization was 1:1 to giredestrant (30 mg oral daily) or PCET between fulvestrant or an aromatase inhibitor (AI), stratified by disease site (visceral vs non-visceral), prior CDK4/6 inhibitor, and prior fulvestrant. Biomarkers were assessed in baseline ctDNA isolated from plasma using the FoundationOne Liquid CDx or PredicineCARE assays. ESR1 mutations were defined as short variants with known or likely impact on ER protein function. RESULTS Among the 303 patients enrolled, prior aBC therapies included CDK4/6 inhibitors (42%), fulvestrant (19%), and chemotherapy (32%). Overall, most baseline characteristics were balanced across arms in subgroups. Efficacy in key subgroups by prior treatment and in ESR1-mutated tumors is shown in the table. Efficacy by PCET (75% received fulvestrant; 25%, an AI) and by type of ESR1 mutation will be presented. Clinical benefit (INV-PFS, CBR, ORR) was most prominently observed with giredestrant in patients with ESR1-mutated tumors. In the baseline ctDNA-evaluable population (232/303 patients; 77%), ESR1 and PIK3CA were the most prevalent mutations overall (39% and 36%, respectively). The most common ESR1 mutations were D538G, Y537S, Y537N, and E380Q; 54% of baseline ctDNA samples classified as ESR1-mutated had multiple ESR1 mutations detected (range of 2–7 mutations), demonstrating clonal heterogeneity. Clinical benefit was also observed with giredestrant in patients expressing different ESR1 mutations. Updated data will be presented. CONCLUSIONS Exploratory subgroup analyses showed favorable outcomes with giredestrant in terms of INV-PFS, CBR, and ORR across most key subgroups. The benefit was more pronounced in a) patients with ESR1-mutated tumors and b) patients who received prior fulvestrant (the majority of AI-treated patients in the PCET arm). Overall, these data support continued investigation of giredestrant to advance and improve treatment outcomes in hormone receptor+ BC. Table 1: Exploratory subgroup analyses Citation Format: Elgene Lim, Marianna Chavez, Aditya Bardia, Joo Hyuk Sohn, Heather M. Moore, Mahesh Shivhare, Jorge Martinalbo, Laura Roncoroni, Pablo D. Perez-Moreno, Miguel Martín. PD13-04 Exploratory subgroup and biomarker analyses of acelERA Breast Cancer: Phase II study of giredestrant (GDC-9545) vs physician’s choice of endocrine therapy for previously treated, estrogen receptor+, HER2– advanced breast cancer [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr PD13-04.

Evaluation of ctDNA in patients with CRPC with pathogenic germline mutations in BRCA2.

253 Background: Approximately 3-5% of advanced prostate cancer patients have pathogenic BRCA2 mutations in germline tests. In this study, we examine the relationship between pathogenic germline BRCA2 mutation and somatic changes in ctDNA. Methods: Germline screenings were performed by Invitae multi-cancer gene panel which includes 50-84 genes. ctDNA alterations were detected by Guardant 360 assays which report somatic changes in 70-83 genes. All ctDNA samples were collected in post-abiraterone and/or enzalutamide (in CRPC patients). Any pathogenic/likely pathogenic somatic alterations in the ctDNAs with more than 0.1% of allelic fraction were included in this cohort. The type of mutation detected in ctDNA was also assessed (truncating, point, etc.). Statistical significance for comparison is calculated with Fischer Exact Probablity Test and Chi-Square Test. Results: A total of 11 patients had germline BRCA2 pathogenic mutations and ctDNA assays; 267 patients had no germline DNA pathogenic alterations and ctDNA assays. Compared to germline normal patients, the germline BRCA2 mutations were less likely to have AR alterations on ctDNA (OR=0.2133, 95% C.I. [0.087, 0.525], p-value = 0.0003). BRCA2 germline positive patients were also more likely to have a mutated BRCA1, BRCA2, and TP53 ctDNA (OR=7.899, 95% C.I. [1.2745, 48.9548], p=0.055), (OR=7.899, 95% C.I. [1.7529, 16.059], p=0.008), and (OR=6.442, 95% C.I. [2.449, 16.946], p=0.00001), respectively. All other ctDNA assessed genes were mutated at a similar frequency between germline BRCA2 mutated and “normal” germline patients. BRCA2 germline mutations patients are less likely to have copy number alterations (CNVs) (OR=0.3992, 95% C.I. [0.2168, 0.7352], p=0.0031) and more likely to have frameshift mutations (OR=2.3182, 95% C.I. [1.169, 4.5972], p=0.0183). Conclusions: The ctDNA testing in this CRPC population (after abiraterone and/or enzalutamide) was less likely to find AR alterations and more likely to find pathogenic mutations for BRCA1, BRCA2, and TP53 in BRCA2 germline positive patients. In addition, BRCA2 germline positive CRPC patients were more likely to have frameshift mutations and less likely to have CNVs than those with an intact germline. Characterizing the mutational landscape in BRCA2 germline mutated patients may help to better define underlying disease biology. Those with BRCA mutated germline may be less likely to have AR driven tumors. More study is needed to better understand patients with underlying DNA repair defects.

Evaluation of the aggressive variant prostate cancer molecular profile (AVPCm) in CLIA environments.

250 Background: 20-30% of prostate cancers respond poorly to androgen receptor (AR)-directed therapies and have an atypical, virulent course. The aggressive variant prostate cancers ( AVPC) encompass virulent androgen indifferent tumors and are characterized by combined defects in ≥ 2/3 of TP53, RB1, and PTEN (AVPC-m). Post-hoc analysis in a phase I/II trial indicated a benefit of carboplatin+cabazitaxel in men with AVPCm+ metastatic castrate resistant prostate cancer (mCRPC). We assess the feasibility of detecting the AVPCm in CLIA-certified environments. Methods: Men with progression of mCRPC undergoing biopsies for standard molecular profiling at MD Anderson Cancer Center (MDACC) were eligible. TP53, RB1, and PTEN expression was assessed by immunohistochemistry (IHC) and read by 2 pathologists independently. Next generation sequencing of solid tumor DNA (stDNA) and circulating tumor DNA (ctDNA) was performed on the MDACC Molecular Diagnostics Laboratory and the University of Washington OncoPlex ctDNA platforms respectively . Results: Of 64 eligible patients, 49 (77%), 37 (58%), and 54 (84%) had results reported for IHC, stDNA, and ctDNA respectively. Concordance of IHC reads between pathologists was variable: Kappa 0.78, 0.67, and 0.91 for TP53, RB1, and PTEN respectively. 36 (66.7%) ctDNA samples had low tumor content, such that false negatives could not be excluded. AVPC-m was detected in 14 (29%) of patients by IHC per the original reading pathologist, 2 (5%) by stDNA NGS, and 7 (39%) by ctDNA NGS. Median turnaround times for IHC, stDNA and ctDNA were 12 (2-35), 28 (12-56) and 16 (11-56) days respectively. Conclusions: We show the operational characteristics of the AVPCm detection using CLIA certified assays. IHC detected a greater proportion of patients with AVPCm+ tumors than stDNA, likely due, partly, to the challenges of copy number loss detection. ctDNA detected the greatest proportion of AVPCm+ tumors but was not evaluable in two thirds of patients. These data serve to inform the design of clinical trials using AVPCm as a criterion for patient selection or stratification. [Table: see text]

Real-world assessment of AR-LBD mutations in metastatic castration-resistant prostate cancer.

204 Background: Treatment of men with metastatic castration-resistant prostate cancer (mCRPC) using drugs targeting the AR pathway is hampered by development of resistance including activating AR ligand-binding domain (LBD) point mutations. AR LBD mutations are found in approximately 10-20% of patients (pts) with mCRPC progressing on AR pathway inhibition (ARPi) therapy and may be associated with AR activation by alternative steroid hormones. We utilized the Guardant INFORM real-world database to explore the detection rate and clinical features associated with AR-LBD mutations in men with mCRPC. Methods: This observational study was conducted in a nationally representative clinical-genomic database of 200,000+ advanced cancer pts undergoing comprehensive ctDNA analysis (Guardant360, Redwood City, CA) between 2014 and 2021, with associated clinical information from administrative claims. ctDNA samples of men with mCRPC were assessed for presence or absence of an activating AR-LBD mutation. The incidence of co-occurring genetic alterations was also investigated. Clinical outcomes were studied for matched cohorts comparing pts following first line (1L) or second line (2L) mCRPC therapy with or without AR-LBD mutations. Results: Of 15,705 prostate cancer pts included in the database, 8420 (53.6%) had mCRPC at the time of sample collection. 4122 (49.0%) of these mCRPC pts had prior treatment with an ARPi, of which 854 (21%) had an AR-LBD mutation. AR-LBD mutation prevalence was 15% in mCRPC pts untreated with an ARPi, 23% in those after 1 line, and 24% in those after 2 lines of ARPi treatment. AR L702H and T878A/S showed the greatest increase in prevalence post abiraterone, whereas AR L702H, T878S and F877L had the greatest increase in prevalence post enzalutamide. Prevalence of AR L702H and H875Y doubled (from 8.8% to 17.5%) for pts that received chemotherapy post ARPi, while AR F877L incidence declined by half (3.5% to 1.7%). Compared to pts without AR-LBD mutations, AR-LBD+ mCRPC pts were enriched for co-alterations in APC, CTNNB1, PTEN, BRCA2, and ARID1A. Rates of TP53 and RB1 alterations were comparable in the AR-LBD+ and ARLBD- cohorts. Matched mCRPC pts had similar time-to-treatment-discontinuation (TTD) and time-to-next-treatment (TTNT) between AR-LBD+ and AR-LBD- mCRPC pts in the 1L and 2L settings; however, AR-LBD+ pts exhibited worse overall survival from 1L mCRPC therapy (50.1 vs 60.7 months, log-rank P=0.013). Conclusions: In this large database, the overall detection rate of activating AR-LBD mutations in men with mCRPC undergoing ctDNA analysis was 21%, and increased with prior use of 2nd generation ARPi (abiraterone and enzalutamide). Men with AR-LBD mutations were more likely to harbor other alterations relevant to tumor progression. These findings inform on the ctDNA prevalence and impact of AR-LBD mutations in a real-world dataset of mCRPC.

Prognostic value of genomic mutations in metastatic prostate cancer

Metastatic prostate cancer (mPC) has a poor prognosis, and new treatment strategies are currently being offered for patients in clinical practice, but mPC is still incurable. A considerable proportion of patients with mPC harbor homologous recombination repair (HRR) mutations, which may be more sensitive to poly (ADP-ribose) polymerase inhibitors (PARPis). We retrospectively included genomic and clinical data from 147 patients with mPC from a single clinical center, with a total of 102 circulating tumor DNA (ctDNA) samples and 60 tissue samples. The frequency of genomic mutations was analyzed and compared with that in Western cohorts. Cox analysis was used to assess progression-free survival (PFS) and prognostic factors related to prostate-specific antigen (PSA) after standard systemic therapy for mPC. The most frequently mutated gene in the HRR pathway was CDK12 (18.3%), followed by ATM (13.7%) and BRCA2 (13.0%). The remaining common ones were TP53 (31.3%), PTEN (12.2%), and PIK3CA (11.5%). The frequency of BRCA2 mutation was close to that of the SU2C-PCF cohort (13.3%), but the frequency of CDK12, ATM, and PIK3CA mutations was significantly higher than that in the SU2C-PCF cohort: 4.7%, 7.3%, and 5.3%, respectively. CDK12 mutation were less responsive to androgen receptor signaling inhibitors (ARSIs), docetaxel, and PARPi. BRCA2 mutation helps predict PARPi efficacy. Additionally, androgen receptor (AR)–amplified patients do not respond well to ARSIs, and PTEN mutation are associated with poorer docetaxel response. These findings support the genetic profiling of patients with mPC after diagnosis to guide treatment stratification to customize personalized treatment.

Bintrafusp alfa plus paclitaxel for advanced gastric cancer as a second-line treatment: An open label, single-arm, phase Ib/II study.

374 Background: Anti-PD-1 monotherapy did not improve overall survival compared with paclitaxel in second-line treatment for advanced gastric cancer (AGC) in KEYNOTE-061 trial. Recent studies suggest that inhibition of transforming growth factor beta (TGF-β) signaling reverses immunosuppressive tumor microenvironment into improved responses to cancer immunotherapy. Especially, genomically stable subtype of AGC showed the increased level of TGF-β pathway. Here, we report the results of phase Ib/II trial of bintrafusp alfa (M7824), a first-in-class bifunctional fusion protein composed of the extracellular domain of TGF-βRII fused to a human IgG1 mAb blocking PD-L1, in combination with paclitaxel as a 2nd line treatment for AGC. Methods: This investigator-initiated, single-arm, open-label, phase Ib/II study enrolled HER2-negative, histologically confirmed AGC patients with evaluable disease who failed prior palliative 1st line treatment. Prior immune checkpoint inhibitor was not allowed. Phase 1b was planned to enroll 3 to 12 patients in a 3+3 design (bintrafusp alfa 1200mg on days 1 and 15 plus paclitaxel 80 mg/m2 (level 1) or 70 mg/m2 (level -1) on days 1, 8 and 15) every 28 days). The primary endpoints were to determine recommended phase II dose (RP2D) for phase Ib, and progression-free survival (PFS) at 6 months for phase II. Secondary endpoints included PFS, OS, ORR, DCR, and safety. Exploratory endpoints included immune-related biomarker changes from serial liquid biopsies (NCT04835896). Results: In phase 1b, dose limiting toxicities were not observed, and the RP2D was determined as dose level 1. During phase II, enrollment was stopped after 30 patients were recruited, following negative readouts from bintrafusp alfa trials in other indications. With a median follow-up duration of 10.9 months (95% CI 9.5–12.6), 7 patients remained on treatment (treatment duration range: 1.0 to 15.1 months) as of September, 2022. Median PFS was 3.8 months (95% CI, 2.6-7.8) and PFS rate at 6 months was 36.7% (95% CI, 20.1-53.4). Median OS was 9.6 months (95% CI, 4.1-not reached). In patients with measurable lesions (n=25), ORR was 28% (PR, n=7) and DCR was 68%. No patient was EBV-related. Patients with MSI-H (n=3; mPFS, 7.8 months; mOS, not reached) or PD-L1-positive (CPS≥1) (n=9; mPFS, 7.8 months; mOS, not reached) showed durable efficacy. Treatment-related AEs (≥G3) occurred in 23 pts (76.7%), including anemia (G3, n=12, 40%) and neutropenia (G3, n=9, 30%). Immune-related AE included urticaria (G3, n=2, 6.7%; G2, n=4, 13.3%), rash (G3, n=1, 3.3%), and pneumonitis (G3, n=1, 3.3%). Conclusions: Combination of bintrafusp alfa and paclitaxel was feasible with modest efficacy as 2nd line treatment for AGC. There was subset of patients with durable responses. Analyses of targeted next-generation sequencing from serial ctDNA sampling are ongoing. Clinical trial information: NCT04835896 .

Circulating tumor DNA–based genomic landscape of KRAS wild-type pancreatic adenocarcinoma.

747 Background: Pancreatic ductal adenocarcinoma (PDAC) is the third leading cause of cancer deaths. KRAS is a primary oncogenic driver in the majority of PDAC patients. KRAS wild-type (wt) PDAC (~10%) is a molecularly heterogeneous subgroup that may harbor alternate drivers and targetable alterations. In this study, we sought to characterize the circulating tumor DNA (ctDNA) landscape of alterations in PDAC patients harboring KRAS mutations ( KRAS mut) compared to KRAS wt. Methods: We analyzed ctDNA samples from 2000 patients ( N= 1000 each for KRAS mut and KRAS wt) collected prospectively between 2019-2022 using a 74-83 gene next generation sequencing panel (Guardant360). KRAS mutation not detected was used as a proxy for KRAS wt. To limit bias from low tumor shed, samples were excluded if they did not have maximum variant allele fraction (VAF) &gt; 0.34% and if the only maximum VAF &gt; 0.34% was within putative germline range (40-60%). Statistical analyses were performed using Fisher’s exact test or t-test. Results: No significant gender differences were noted between KRAS wt and KRAS mut patients. Median age was 72yo in KRAS wt and 69yo in KRAS mut patients. Overall, KRAS wt patients had higher frequency of alterations in ATM, BRAF, ERBB2, FGFR2, JAK3, MET and NOTCH1 compared to KRAS mut (all p &lt; 0.05). Meanwhile, KRAS wt patients had lower frequency of alterations in CDKN2A, SMAD4, CDK6, ARID1A, and TP53 compared to KRAS mut (all p &lt; 0.05). The most frequently mutated gene in KRAS wt PDAC was TP53 (46%), followed by ATM (26%) and EGFR (11%). The most common currently targetable alterations identified in KRAS wt patients were ATM (26%), BRCA1/2 (12%), EGFR (11%; 70% mutations, 30% amplifications), FGFR1/2 (9%), BRAF (8%; 91% mutations, 9% amplifications), PIK3CA (7%), MET (7%; 80% mutations, 20% amplifications) and ERBB2 (5.8%; 79% mutations, 21% amplifications) among others. Median tumor mutational burden for KRAS wt patients was higher than KRAS mut (10.0 vs. 7.77 mut/Mb, p = 0.035). There were no significant differences in rates of MSI-H between KRAS wt and KRAS mut patients (1.9% vs. 1.3%, p = 0.37). KRAS wt patients harbored higher number of oncogenic gene fusions compared to KRAS mut (1.6% vs 0.2%, p = 0.0013). The most common fusion partners among KRAS wt patients included FGFR2 (0.4%), BRAF (0.4%), ALK (0.2%), NTRK (0.2%), RET (0.2%), FGFR3 (0.1%) and EGFR (0.1%). Potential germline variants (pathogenic/likely pathogenic) were detected in both KRAS wt and mut patients, most commonly in the DNA-damage repair genes, including ATM (3.5%), BRCA2 (1.8%) and BRCA1 (0.6%). Conclusions: Targetable alterations and oncogenic rearrangements are enriched in KRAS wt PDAC compared to KRAS mut. These analyses provide additional therapeutic options and may improve outcomes for KRAS wt patients, warranting blood-based ctDNA genomic profiling in PDAC, especially when a tissue biopsy is not feasible or sufficient for comprehensive genomic profiling.

APOLLO: A randomized phase II double-blind study of olaparib versus placebo following curative intent therapy in patients with resected pancreatic cancer and a pathogenic BRCA1, BRCA2 or PALB2 mutation—ECOG-ACRIN EA2192.

TPS763 Background: A meaningful subset of PDAC is characterized by a homologous recombination deficiency (HRD). The most well-defined patients within this group are those with pathogenic variants in BRCA1, BRCA2 and PALB2. In the metastatic setting, PARP inhibitor maintenance provides a progression-free survival benefit after a period of platinum based chemotherapy1,2, but the role of PARP inhibitors in the curative intent setting is undefined. The OlympiA study established one year of olaparib as the standard of care for patients with BRCA-related, early stage breast cancer who completed all other curative-intent treatment3. Therefore, we have designed a randomized, phase II double-blind study of one year of olaparib vs placebo in patients with pancreatic cancer and a germline or somatic variant in BRCA or PALB2 who have completed all curative intent therapy. Methods: We have enrolled and treated 23 of 152 planned patients on study NCT 04858334/EA2192. Eligibility criteria include: a pathogenic germline or somatic variant in BRCA1, BRCA2 or PALB2 as determined by local laboratory (central review required); completion of curative-intent resection and ≥ three months of multi-agent chemotherapy; no evidence of recurrent disease. At enrollment, patients must be within 12 weeks of their last anti-cancer intervention. Patients are randomized 2:1 to receive oral olaparib 300 mg twice daily or placebo for 12 28-day cycles. The primary endpoint is relapse-free survival. Overall survival is a secondary endpoint. Tumor tissue, fecal material (for microbiome analysis) and serial ctDNA samples are being collected. 1.Golan T, Locker GY, Kindler HL: N Engl J Med 381:1492-1493, 2019. 2. Reiss KA, Mick R, O'Hara MH, et al: J Clin Oncol 39:2497-2505, 2021. 3. Tutt ANJ, Garber JE, Geyer CE, Jr.: N Engl J Med 385:1440, 2021. Clinical trial information: NCT04858334 .

Utility of circulating tumor DNA (ctDNA) in the management of appendiceal adenocarcinoma (AA).

226 Background: Appendiceal adenocarcinoma (AA) is a rare and heterogenous cancer with marked differences in clinical course between high- and low-grade tumors. Unlike colorectal cancer (CRC) and other gastrointestinal malignancies, AA virtually never has hematogenous metastases, rather, metastasis is limited to the peritoneum. Here we present a retrospective, single institution study of AA to identify the prevalence of detectable ctDNA, evaluate the clinical predictive value of positive ctDNA, and assess what clinical, pathologic, or molecular features predict positive ctDNA. Methods: 160 blood samples from 147 patients with AA metastatic to the peritoneum were profiled with a CLIA approved 73 gene mutational panel as part of routine clinical practice. Paired tumor sequencing was available for 73 patients. Survival was measured starting from day ctDNA was drawn. Mutations that most likely represented clonal hematopoiesis were removed from analysis. Results: Out of 160 ctDNA samples, 120 were taken in the setting of radiographically apparent metastatic disease. Of these, 46 (38.3%) had any detectable mutation. 40 ctDNA tests were performed when patients had no radiographic evidence of disease (NED); 15 (37.5%) of which had any detectable mutation. High-grade tumors were more likely to have detectable ctDNA with detection rates of 10/46 (21.7%), 18/46 (39.1%), and 33/68 (48.5%) for well, moderately, and poorly-differentiated tumors, respectively. Restricting analysis to the 73 patients with paired tissue and blood samples and 73 genes sequenced in both, of 81 mutations detected in tumor only, 21 were detected in blood (sensitivity of 26%). Sensitivity was highest for mutation in TP53 (53.8%) suggesting these tumors may have a greater propensity to shed DNA into circulation. Overall, the sensitivity of ctDNA detection in metastatic AA was markedly less than what was observed in a cohort of 274 metastatic CRC patients from the same institution (288/581 = 49.6%). For AA patients with detectable ctDNA, variant allele frequency (VAF) in AA was significantly lower compared to CRC (median VAF 0.04% vs. 6%, p = &lt;0.0001). Detectable ctDNA was associated with shorter overall survival (46.2 mo for positive ctDNA vs. not-yet-reached for negative ctDNA, HR = 2.5, p = 0.016) and shorter disease free survival (DFS) (60 mo vs. not-yet-reached, HR = 3.4, p = 0.05). As expected, patients with radiographic evidence of disease did worse than patients with NED (HR = 2.1. p = 0.08), but of note this hazard ratio was less than that for positive ctDNA. Conclusions: In patients with AA, the presence of detectable ctDNA is associated with shorter overall and disease-free survival. Sensitivity of ctDNA detection in metastatic AA is overall markedly lower than CRC, with detection more likely in high-grade tumors and higher sensitivity in tumors containing TP53 mutation.

Loss of Heterozygosity in the Circulating Tumor DNA and CD138+ Bone Marrow Cells in Multiple Myeloma.

Multiple myeloma (MM) is characterized by heterogeneity of tumor cells. The study of tumor cells from blood, bone marrow, plasmacytoma, etc., allows us to identify similarities and differences in tumor lesions of various anatomical localizations. The aim of this study was to compare the loss of heterozygosity (LOH) by tumor cells by assessing STR profiles of different MM lesions. We examined paired samples of plasma circulating tumor DNA (ctDNA) and CD138+ bone marrow cells in MM patients. For patients with plasmacytomas (66% of 38 patients included), the STR profile of plasmacytomas was also studied when biopsy samples were available. Diverse patterns of LOH were found in lesions of different localization for most patients. LOH in plasma ctDNA, bone marrow, and plasmacytoma samples was found for 55%, 71%, and 100% of patients, respectively. One could expect a greater variety of STR profiles in aberrant loci for patients with plasmacytomas. This hypothesis was not confirmed-no difference in the frequency of LOH in MM patients with or without plasmacytomas was found. This indicates the genetic diversity of tumor clones in MM, regardless of the presence of extramedullar lesions. Therefore, we conclude that risk stratification based on molecular tests performed solely on bone marrow samples may not be sufficient for all MM patients, including those without plasmacytomas. Due to genetic heterogeneity of MM tumor cells from various lesions, the high diagnostic value of liquid biopsy approaches becomes obvious.

Application of ddPCR in detection of the status and abundance of EGFR T790M mutation in the plasma samples of non-small cell lung cancer patients.

The third-generation epidermal growth factor receptor (EGFR) -tyrosine kinase inhibitor (TKIs), such as osimertinib, designed for targeting the acquired drug-resistant mutation of EGFR T790M, was approved as the first-line therapy for advanced EGFR-mutated non-small cell lung cancer (NSCLC). Thus, detection of the EGFR T790M mutation for NSCLC is crucial. However, tissue samples are often difficult to obtain, especially in patients at advanced stages. This study assessed the performances of droplet digital polymerase chain reaction (ddPCR) and next-generation sequencing (NGS) in detecting EGFR T790M status and abundance in the plasma ctDNA samples of patients with NSCLC. We also explored the association between T790M status and abundance and the response to third-generation EGFR-TKIs. A total of 201 plasma samples with matched tissues, 821 plasma samples, and 56 patients who received third-generation EGFR-TKIs with response evaluation were included in this study. ddPCR and NGS were used to detect the mutation status and abundance of T790M in the tissues and/or blood samples. The results showed that the sensitivity and the specificity of EGFR T790M mutation status detected by ddPCR in plasma samples were 81.82% and 91.85%, respectively, compared with the tissue samples, with a consistency coefficient of 0.740. Among the 821 plasma samples, the positive rates of EGFR T790M detected by ddPCR and NGS were 34.2% (281/821) and 22.5% (185/821), respectively. With NGS results as the reference, the sensitivity and the specificity of ddPCR were 100% and 84.91%, respectively, and the consistency coefficient of the two methods was 0.717. In addition, we found that a higher EGFR T790M abundance was linked to a higher treatment response rate to the third-generation EGFR-TKIs regardless of the classification of the median value of 0.43% (P = 0.016) or average value of 3.16% (P = 0.010). Taking these data together, this study reveals that ddPCR is an alternatively potent method for the detection of EGFR T790M in the plasma samples of NSCLC patients.

Abstract PR007: Comprehensive ctDNA profiling reveals potential metastatic genomic signatures in treatment-naive early-stage breast cancer patients

Abstract Background: Genomic profiling has revolutionized precision oncology impacting the diagnosis, prognosis, and therapy decisions. Considering high spatiotemporal diversity and heterogenicity of breast tumor-cell genomes, small-gene panels often fail to capture rare but important genomic alterations. Conversely, comprehensive ctDNA sequencing approaches enable the identification of under characterized ‘long tailed driver’ genomic alterations and capture Intra and inter metastatic heterogeneity. Here, we demonstrate the clinical utility of comprehensive genome profiling with higher sensitivity to predict the possibility of metastasis in early-stage breast cancer patients. Methods: We retrospectively analyzed ctDNA and genomic DNA (gDNA) from FFPE samples as well as circulating tumor cells (CTC) in 10 treatment-naive hormone positive and HER2 negative, primary-stage breast cancer patients [GS1] using the OncoIndx comprehensive 600 gene panel. The panel captures all important cancer-relevant genomic alterations including Tumor Mutation Burden (TMB), Micro Satellite Instability (MSI), homologous recombination deficiency (HRD) prediction, and cfDNA tumor fraction (TF). CTCs were enumerated from 1.5 ml of blood using the OncoDiscover platform approved by the Drug Controller General of India having anti-EpCAM antibody-mediated immunomagnetic nanoparticles. CTCs were confirmed for cytokeratin 18+ and DAPI + markers and the absence of CD45. Results: Comprehensive genomic profile obtained from ctDNA and gDNA from FFPE of early-stage breast cancer patients predominantly exhibited the presence of alterations in PIK3CA and ESR1 signaling pathways. PIK3CA mutations were present in 77% and 44% of baseline ctDNA and gDNA samples, while ESR1 mutations were present in 44% and 22% of baseline ctDNA and gDNA, respectively. In addition, we observed about 70% additional driver mutations in ctDNA samples suggesting shedding of ctDNA together with CTC (80% positive), a likely positive biomarker of metastasis. About 50% of the patients showed higher TMB and HRD. Notably, TF representing ctDNA varied between 13% to 27% in blood samples with a corresponding ploidy range of 2.9 to 4.7. Surprisingly, ~50% of the patient population matched the mutation profile of clinically confirmed metastatic patients. All the patients harboring potential metastatic driver alterations showed the presence of CTCs in peripheral blood. Conclusions: Comprehensive ctDNA genomic profiling showed potential metastasis driving alterations suggesting the role of ctDNA-based liquid biopsy to predict metastasis in early breast cancer patients. We observed enhanced TF at the time of diagnosis, possibly due to the presence of distant metastasis, high disease burden, and aggressive tumor biology. Our results suggest that ctDNA dynamics at the time of disease presentation can predict early metastasis, and may demonstrate the divergent response of tumor heterogeneity to treatment in early-stage breast cancer. Citation Format: Gowhar Shafi, Manoj Dongare, Atul Bharde, Moubeen Fauzul, Kanchan Hariramani, Alain D’Souza, Bhagwat Jadhav, Trupti Kad, Sangeeta Prajapati, Vikas Jadhav, ManojKumar Kumaran, Sumit Haldar, Vatsal Mehra, Sujit Joshi, Gourishankar Aland, Richa Dave, Sreeja Jayant, Aravindan Vasudevan, Mohan Uttarwar, Jayant Khandare. Comprehensive ctDNA profiling reveals potential metastatic genomic signatures in treatment-naive early-stage breast cancer patients [abstract]. In: Proceedings of the AACR Special Conference: Cancer Metastasis; 2022 Nov 14-17; Portland, OR. Philadelphia (PA): AACR; Cancer Res 2022;83(2 Suppl_2):Abstract nr PR007.

Optimizing the number of variants tracked to follow disease burden with circulating tumor DNA assays in metastatic colorectal cancer.

The number of somatic mutations detectable in circulating tumor DNA (ctDNA) is highly heterogeneous in metastatic colorectal cancer (mCRC). The optimal number of mutations required to assess disease kinetics is relevant and remains poorly understood. To determine whether increasing panel breadth (the number of tracked variants in a ctDNA assay) would alter the sensitivity in detecting ctDNA in patients with mCRC. We used archival tissue sequencing to perform an in silico assessment of the optimal number of tracked mutations to detect and monitor disease kinetics in mCRC using sequencing data from the Canadian Cancer Trials Group CO.26 trial. For each patient, 1, 2, 4, 8, 12, or 16 of the most clonal (highest variant allele frequency) somatic variants were selected from archival tissue-based whole-exome sequencing and assessed for the proportion of variants detected in matched ctDNA at baseline, week 8, and progression timepoints. Data from 110 patients were analyzed. Genes most frequently encountered among the top four highest VAF variants in archival tissue were TP53 (51.9% of patients), APC (43.3%), KRAS (42.3%), and SMAD4 (9.6%). While the frequency of detecting at least one tracked variant increased when expanding beyond variant pool sizes of 1 and 2 in baseline (p = 0.0030) and progression (p = 0.0030) ctDNA samples, we observed no significant benefit to increases in variant pool size past four variants in any of the ctDNA timepoints (p < 0.05). While increasing panel breadth beyond two tracked variants improved variant re-detection in ctDNA samples from patients with treatment refractory mCRC, increases beyond four tracked variants yielded no significant improvement in variant re-detection.