Mean Variant Allele Frequency Research Articles

Circulating tumor DNA as a predictive biomarker for pathologic response after treatment with neoadjuvant immunotherapy for localized dMMR/MSI-H colorectal cancer.

3612 Background: Neoadjuvant immunotherapy (IO) has shown promise as a potential non-surgical, curative therapy in pts with localized dMMR/MSI-H CRC. However, response assessment to IO is challenging due to difficulty measuring luminal tumors, the invasive nature of endoscopy, and known discordance between these assessment modalities. ctDNA may serve as an important, novel marker of response in this population. We evaluated pre-treatment ctDNA and ctDNA clearance and their association with pathologic complete response (pCR) in pts with localized dMMR/MSI-H CRC treated with IO. Methods: We performed a 70-gene, tumor-agnostic, NGS-based ctDNA assay (LB-70) to detect somatic mutations in a CLIA setting on 49 plasma samples collected serially from 13 pts with localized dMMR/MSI-H CRC treated with neoadjuvant pembrolizumab (mean and median cycles per pt was 8; range 1 - 16) prior to definitive surgery as part of a prospective phase 2 trial (NCT04082572). NGS was also performed on each pt’s tumor tissue to confirm mutations identified in ctDNA were tumor-specific. We defined “ctDNA clearance” as a reduction in mutational variant allele frequency (VAF) to a threshold below LB-70’s limit of detection (<0.3% VAF) after neoadjuvant IO in mutations that were present in both plasma and tumor tissue. We conducted a descriptive analysis to evaluate the association between the presence of pre-treatment (“baseline”) ctDNA, ctDNA clearance, and pCR. Results: On a median number of 3 samples per pt, mutations in baseline ctDNA were detected in 7/13 pts and were confirmed orthogonally in all pts with matched tumor tissue. The mean and median VAF was 8.5% and 0.7% (range 0.3% - 26.9%). Among 10/13 pts with a pCR, none recurred clinically after median follow-up 29.7 mo. Three pts did not experience a pCR, 1 of whom had disease recurrence after surgery. pCR was observed in 6/6 pts without detectable ctDNA at baseline, while only 4/7 pts with detectable ctDNA at baseline had a pCR (100% vs 57%). Of the 7 pts with detectable ctDNA at baseline, 5 cleared their ctDNA in the neoadjuvant period, among whom, 4 had a pCR (80% likelihood of pCR with ctDNA clearance). Notably, the 1 pt who did not have a pCR despite clearing ctDNA had a near-pCR (carcinoma identified in 1/91 lymph nodes, none in cecum or colon). The mean and median number of cycles to ctDNA clearance was 2.8 and 2 (range 1 - 8). For the 2 pts who did not clear their ctDNA, neither (0%) had a pCR. Conclusions: Clearance of ctDNA following neoadjuvant IO appears to predict pCR in this pilot analysis of pts with localized dMMR/MSI-H CRC, even after a median of 2 cycles. The absence of detectable ctDNA at baseline, perhaps a surrogate for lower tumor burden at initial diagnosis, may also predict a higher likelihood for pCR. Our work suggests utility of ctDNA as a biomarker for improving risk-stratification and response assessment sensitivity.

Liquid biopsy-based prediction of clinical benefit from immune checkpoint inhibitors in advanced biliary tract cancer.

e16179 Background: Immune checkpoint inhibitors (ICIs) show promising efficacy as first-line therapy for advanced biliary tract cancer (aBTC), but validated predictive biomarkers are lacking. Here, we identified liquid biopsy-based biomarkers and developed a prediction model. Methods: aBTC patients who received ICIs-based combination therapy as the first-line treatment were prospectively enrolled in this study (NCT06074029). Plasma samples were collected before the first and second immunotherapy infusion to perform cell-free DNA (cfDNA) sequencing of 1021 genes. Circulating tumor DNA (ctDNA) concentration was calculated by multiplying the mean variant allele frequency by the cfDNA concentration and ctDNA fold change was calculated by dividing on-treatment ctDNA concentration by the pre-treatment ctDNA concentration. Tumor mutation burden (TMB) was normalized using the cfDNA concentration. In addition, RNA was extracted from peripheral blood mononuclear cells to profile the leukocyte transcriptome using whole transcriptome sequencing, and the relative proportions of immune cells in leukocytes was deconvoluted using CIBERSORT algorithm. Log-rank and univariate Cox regression were used to evaluate the relationship between features and progression-free survival (PFS). Results: 37 patients were enrolled, with 62.2% having intrahepatic cholangiocarcinoma. The median age was 61 years and 54.1% of patients were females. The median PFS was 4.4 months. Variables related to PFS with the log-rank p value smaller than 0.05 (Table) were entered into a multivariate Cox regression using a stepwise approach for final variable selection. As a result, ctDNA fold change, KRAS mutation, and resting memory CD4 T cell level were used to construct a COX regression model to predict clinical benefit from ICIs. The model predicting 6-month PFS demonstrated an AUC of 0.909 (95% CI, 0.795-1.024). Internal validation, performed through a bootstrap analysis with 100 iterations, yielded an optimism-adjusted AUC estimate of 0.859. Conclusions: Our preliminary results support the excellent performance of this liquid biopsy-based multivariable model to early predict durable benefit from ICIs in aBTC. A large sample size and verifying this model with internal and external data are warranted. Clinical trial information: NCT06074029 . [Table: see text]

DNMT3A-mutant clonal haematopoiesis and the recovery of patients with acute ST-elevation myocardial infarction

Abstract Funding Acknowledgements Type of funding sources: Foundation. Main funding source(s): British Heart foundation Background Haematopoietic stem cells can acquire mutations and produce mutant blood cells. When this occurs in the absence of overt blood disease, it is clonal haematopoiesis of indeterminate potential (CHIP). CHIP is a novel, independent risk factor for ischaemic heart disease and heart failure (HF)(1). However, the molecular mechanisms are poorly understood. Myocardial infarction (MI) is a leading cause of HF due to ventricular remodelling and scar formation(2). We postulate CHIP mutations result in aberrant inflammation that contributes to maladaptive ventricular remodelling following MI. We investigated clinical outcomes and immune cell biology in CHIP and non-CHIP patients (pts) with acute ST-segment elevation MI (STEMI). Purpose Identify and quantify mutations with variant allele frequency (VAF)≥1% in STEMI pts. Assess leukocyte mutational burden. Investigate transcription profiles and leukocyte function in CHIP and non-CHIP STEMI pts. Methods 119 pts diagnosed with STEMI were prospectively recruited (REC19/SC/0362). We collected clinical data, including echocardiogram (echo) parameters and isolated plasma and peripheral blood mononucleated cells (PBMCs) from blood collected 48-96 hours post onset of chest pain. PBMCs were screened for mutations and analysed by flow cytometry. We assessed CHIP VAF with digital droplet PCR in flow-sorted monocytes (Mono), T and B-cells. We performed single-cell RNAseq (10x Genomics) on PBMCs. Luminex or ELISA kits were used to measure plasma proteins. Results 59/119 recruited pts had CHIP (VAF≥1%). CHIP pts were significantly older than non-CHIP pts. DNMT3A was the most commonly mutated gene (28%), followed by TET2 (17%) and ASXL1 (5.3%). 53 pts had impaired LV ejection fraction (LVEF) at admission and a follow-up Echo at median 4.6 months (2.5-8 IQR) post STEMI. They were classified as responder (R) n=24, Δ LVEF≥5% or non-responder (NR) n=29, ΔLVEF<5%. Pts with DNMT3A CHIP were 12 times more likely to be NR (p=0.02). Baseline LVEF was similar in CHIP and non-CHIP pts, but ΔLVEF was significantly reduced in DNMT3A vs non-CHIP pts (p<0.01). DNMT3A mutations were highest in Mono (mean VAF 6.3%), present in B cells (3%) but rare in T cells (1.7%). Within the Mono population, DNMT3A mutant pts had significantly higher proportions of classical Mono compared to non-CHIP (p=0.02). Using scRNAseq, we computed Mono trajectories and differential gene expression. Compared to non-CHIP, DNMT3A-mutant samples upregulated receptor for advanced glycation end-products (RAGE) and toll-like receptor signaling gene signatures. Despite this, we did not observe raised leukocyte count or detect increased levels of inflammatory cytokines in DNMT3A-mutant pts plasma samples. Conclusions DNMT3A CHIP is associated with poor LVEF recovery post-STEMI due to a dysregulated inflammatory response to acute myocardial injury. Furthermore, our data suggests that this may occur via different mechanisms than non-CHIP NR.

Myelodysplastic Neoplasms (MDS) with Ring Sideroblasts or SF3B1 Mutations: The Improved Clinical Utility of World Health Organization and International Consensus Classification 2022 Definitions, a Single-Centre Retrospective Chart Review.

Myelodysplastic neoplasms (MDS) with ring sideroblasts (RS) are diagnosed via bone marrow aspiration in the presence of either (i) ≥15% RS or (ii) 5-14% RS and an SF3B1 mutation. In the MEDALIST trial and in an interim analysis of the COMMANDS trial, lower-risk MDS-RS patients had decreased transfusion dependency with luspatercept treatment. A total of 6817 patients with suspected hematologic malignancies underwent molecular testing using a next-generation-sequencing-based genetic assay and 395 MDS patients, seen at our centre from 1 January 2018 to 31 May 2023, were reviewed. Of these, we identified 39 evaluable patients as having lower-risk MDS with SF3B1 mutations: there were 20 (51.3%) males and 19 (48.7%) females, with a median age of 77 years (range of 57 to 92). Nineteen (48.7%) patients had an isolated SF3B1 mutation with a mean variant allele frequency of 35.2% +/- 8.1%, ranging from 7.4% to 46.0%. There were 29 (74.4%) patients with ≥15% RS, 6 (15.4%) with 5 to 14% RS, one (2.6%) with 1% RS, and 3 (7.7%) with no RS. Our study suggests that a quarter of patients would be missed based on the morphologic criterion of only using RS greater than 15% and supports the revised 2022 definitions of the World Health Organization (WHO) and International Consensus Classification (ICC), which shift toward molecularly defined subtypes of MDS and appropriate testing.

Natural history of clonal haematopoiesis seen in real-world haematology settings.

Recursive partitioning of healthy consortia led to the development of the Clonal Hematopoiesis Risk Score (CHRS) for clonal haematopoiesis (CH); however, in the practical setting, most cases of CH are diagnosed after patients present with cytopenias or related symptoms. To address this real-world population, we characterize the clinical trajectories of 94 patients with CH and distinguish CH harbouring canonical DNMT3A/TET2/ASXL1 mutations alone ('sole DTA') versus all other groups ('non-sole DTA'). TET2, rather than DNMT3A, was the most prevalent mutation in the real-world setting. Sole DTA patients did not progress to myeloid neoplasm (MN) in the absence of acquisition of other mutations. Contrastingly, 14 (20.1%) of 67 non-sole DTA patients progressed to MN. CHRS assessment showed a higher frequency of high-risk CH in non-sole DTA (vs. sole DTA) patients and in progressors (vs. non-progressors). RUNX1 mutation conferred the strongest risk for progression to MN (odds ratio [OR] 10.27, 95% CI 2.00-52.69, p = 0.0053). The mean variant allele frequency across all genes was higher in progressors than in non-progressors (36.9% ± 4.62% vs. 24.1% ± 1.67%, p = 0.0064). This analysis in the post-CHRS era underscores the natural history of CH, providing insight into patterns of progression to MN.

Abstract 5016: Building better contrived samples to properly evaluate Next-generation MRD and LBx assays

Abstract Circulating tumor DNA (ctDNA) is a component of cell-free DNA (cfDNA) that originates from tumor tissue in the plasma of cancer patients. Although ctDNA is a broadly applicable tumor biomarker, the absolute amount of ctDNA varies across indication and stage, with the level of ctDNA present reflective of tumor volume. As novel methods for the characterization of ctDNA develop, there is need to evaluate these assays with appropriate samples. But current commercial reference standards, generated from modified cell lines or oligonucleotides lack important features such as DNA methylation, fragmentation pattern and nucleosome positioning, whilst clinical trial samples lack the required volume to perform multiple tests and often lack proper consent. We have created a framework for generating contrived samples containing the biological features of clinical samples and the attributes of a reference standard. The plasma-in-plasma contrived samples are generated from commercially purchased and fully consented matched tumor and plasma from cancer patients with age and gender matched healthy donor plasma. Samples are characterized by an internally validated 700 gene NGS panel to identify somatic variants and copy number alterations, which establishes ‘ground truth’. A contrived plasma dilution range based on the mean variant allele frequency (VAF) of the concordant somatic variants identified is generated. Using these methods, we have been able to generate sample sets for pan-cancer and disease specific evaluations. We have tested these samples through many novel high sensitivity assays that utilize both tumor-informed and tumor agnostic methods. We have confirmed that plasma-in-plasma contrived samples are amenable to all evaluated assays to date. The FFPE tumor tissue provide results matching clinical trial samples and the extraction yields of cfDNA are within the range of plasma samples from clinical trial data. Each dilution can be generated with replicates for reproducibility metrics. Current models of the sample dilutions have been generated to increase the number of replicates at relevant levels of tumor burden (i.e., 0.01% VAF). Negative samples consisting of the background plasma were also generated for each sample used. These plasma-in-plasma contrived samples have greater commutability to clinical samples than other commercial reference standards, however there are limitations. The complexity of generating these samples restrict the number of unique patients that can be utilized. Also, due to the volume of healthy plasma used as diluent, it is difficult to generate volumes greater than 4ml. To our knowledge, this is the first report examining the generation and usage of a contrived sample set that can be applied to evaluating novel high sensitivity MRD assays with clinical sample commutability. Citation Format: Paul Labrousse, Hugh Russell, David Shera, Daniel Stetson, Barrett Nuttall, Brian Dougherty, Darren Hodgson, James Hadfield. Building better contrived samples to properly evaluate Next-generation MRD and LBx assays [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 5016.

Abstract 977: Germline BRCA1/2 mutations detected by circulating tumor DNA testing in breast cancer patients: A retrospective mutiinstitutional analysis

Abstract Background: The use of circulating tumor (ct) DNA testing allows to detect resistant and actionable somatic alterations and it could be associated with the incidental identification of germline mutations. An univocal variant allele frequency (VAF) threshold to distinguish germinal form somatic mutations has not been assessed yet. We aimed to correlate BRCA1/2 ctdNA detected mutations with germline mutational status to determine potential VAF cutoff. Materials and methods:We retrospectively analyzed the incidence of both somatic (s) and germinal (g) BRCA1/2 alterations in a multiinstitutional retrospective breast cancer (BC) cohort to assess the VAF threshold for the likelihood of germline mutations’ detection by ctDNA next-generation sequencing (Guardant 360) testing. Clinical variables were analyzed using descriptive analyses and receiving operating characteristic (ROC) curves were generated to determine the VAF cutoff. Results: Two hundred and fourteen patients (pts) with sBRCA1/2 mutations (including variant of uncertain significant and synonymous) detected by ctDNA testing, referred to the enrolling centers between January 2015 to May 2023 were included in the analysis. The median age at diagnosis was 50 years old (Interquartile range (IQR)43,5-61.5), 43% had a family history of cancer. Hormone receptor positive/HER2 negative was the most represented subtype (68%) followed by the HER2 positive (16%) and triple negative (16%) ones. At ctDNA baseline, 95.8% of pts had a metastatic disease; the main sites of metastases were bone (67.4%) and visceral (59.3%). Ninetyfour (43.9%) and 137 (64%) pts had a sBRCA1 and sBRCA2 alterations respectively, while 17 (7.9%) had a co-mutation in BRCA1 and BRCA2. The mean VAF value for sBRCA1 alterations was 10.1% (standard deviation (SD) 19.5%, range [0.04%-84.3%]) while for sBRCA2 alterations was 10.8% (SD 18.9%, range [0.21%-80.3%]). The germinal testing, performed per standard of care, was available for 100 pts (46.7%). Among these, 42 (42%) had at least a pathogenic variant detected. A gBRCA1 mutation was present in 11 (11%) pts while 25 (25%) had a gBRCA2 mutation. Comparing the somatic and germinal testing, 9/100 pts had a concordance for BRCA1 detection, the 2 discordant cases had both a low allele frequency sBRCA2 alterations; the concordance for BRCA2 detection was instead 100%. An optimal cutoff of 38.4% (AUC 0.98) for BRCA1 and 19.5% (AUC 0.96) for BRCA2 was assessed by ROC analysis as the likelihood of a germline meaning of a somatic mutation detected by ctDNA analysis. Conclusion: The identification of BRCA1/2 alterations in ctDNA could guide the use of germline testing. The VAF cutoff identified for the likelihood of a germinal mutation is lower than expected, suggesting that a wider population should be screened for germinal mutation with relevant impact on the therapeutic choices and family screening. Citation Format: Letizia Pontolillo, Carolina Reduzzi, Andrew A. Davis, Arielle J. Medford, Annika Putur, Lorenzo Gerratana, Katherine Clifton, Whitney L. Hensing, Marko Velimirovic, Surbhi Warrior, Mara S. Serafini, Eleonora Nicolò, Laura Munoz-Arcos, Jeannine Donahue, Charles S. Dai, Jennifer C. Keenan, Amir Behdad, William J. Gradishar, Diana Giannarelli, Emilio Bria, Cynthia X. Ma, Aditya Bardia, Massimo Cristofanilli. Germline BRCA1/2 mutations detected by circulating tumor DNA testing in breast cancer patients: A retrospective mutiinstitutional analysis [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 977.

Abstract 6443: Enhanced detection of ctDNA molecular response for immunotherapy treated non-small cell lung cancer through analyses of cell-free and matched white blood cell DNA

Abstract Introduction: Immune checkpoint inhibitors (ICIs) have greatly improved clinical outcomes for patients with non-small cell lung cancer (NSCLC), however, programmed death-ligand 1 (PD-L1) and tumor mutation burden (TMB) have failed to consistently predict therapeutic response and outcomes in this population. There remains a critical unmet need to identify patients who are likely to experience clinical benefit from treatment, particularly as additional treatment regimens become available. Longitudinal cell-free tumor DNA (ctDNA) assessments have recently been applied as a strategy to identify molecular response (mR) and better predict long term clinical response. Through this real-world analysis of NSCLC, we explore the technical and biological considerations associated with determination of ctDNA mR through matched cell-free and white blood cell (WBC) DNA analyses and apply this optimized approach to assess therapeutic response to ICIs. Methods: Plasma from 50 patients with advanced or metastatic NSCLC who received ICIs from 2017-2019 at Hospital del Mar had detectable pre-treatment ctDNA and underwent analysis using the 521 gene PGDx elio plasma complete liquid biopsy assay. Patient blood was collected prior to the start of ICI therapy, early on-treatment (median 4 weeks; range 2.4-9 weeks) and longitudinally throughout clinical follow-up and disease progression. Matched WBCs were also analyzed for each patient to identify alterations arising from germline polymorphisms and clonal hematopoiesis (CH). mR was calculated as the percent change in mean variant allele frequency of the tumor-specific alterations assessed at the early on-treatment timepoint compared to the pre-treatment timepoint, and compared to radiographic response, progression-free, and overall survival (OS). Results: Best overall response for patients within the cohort was 4% complete response, 26% partial response, 34% stable disease, and 36% progressive disease. The removal of germline or CH variants allowed for improved characterization of tumor-specific somatic alterations and associations with radiographic and survival-based endpoints. With the integrated ctDNA and matched WBC approach, we observed a mR rate of 34% (17/50) with a median OS of 36.8 months compared to 9.2 months for patients experiencing molecular progression at the early on-treatment timepoint (HR 5.6, 95% CI 2.4-12.7, p<0.001, log-rank test). Specifically, of all patients that survived ≤12 months after initiation of treatment, 84% (21/25) were categorized as experiencing molecular progression through early on-treatment ctDNA analyses. Conclusions: This real-world study of ICI treated, advanced NSCLC highlights the opportunity afforded through integrated analyses of ctDNA and matched WBCs to accurately determine mR and the associations with radiographic response and OS. Citation Format: Jennifer B. Jackson, Pedro Rocha, James R. White, Andrew P. Georgiadis, Ellen L. Verner, Amy Greer, Rafael Bach Mora, Laura Masfarré Pintó, Nil Navarro, Álvaro Taus, Beatriz Bellosillo Paricio, Sergi Clavé, Mark T. Sausen, Edurne Arriola. Enhanced detection of ctDNA molecular response for immunotherapy treated non-small cell lung cancer through analyses of cell-free and matched white blood cell DNA [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 6443.

Correlation between variant allele frequency and mean tumor molecules with tumor burden in patients with solidtumors.

Several studies have demonstrated the prognostic value of circulating tumor DNA (ctDNA); however, the correlation of mean tumor molecules (MTM)/ml of plasma and mean variant allele frequency (mVAF; %) with clinical parameters is yet to be understood. In this study, we analyzed ctDNA data in a pan-cancer cohort of 23 543 patients who had ctDNA testing performed using a personalized, tumor-informed assay (Signatera™, mPCR-NGS assay). For ctDNA-positive patients, the correlation between MTM/ml and mVAF was examined. Two subanalyses were performed: (a) to establish the association of ctDNA with tumor volume and (b) to assess the correlation between ctDNA dynamics and patient outcomes. On a global cohort, a positive correlation between MTM/ml and mVAF was observed. Among 18 426 patients with longitudinal ctDNA measurements, 13.3% had discordant trajectories between MTM/ml and mVAF at subsequent time points. In metastatic patients receiving immunotherapy (N = 51), changes in ctDNA levels expressed both in MTM/ml and mVAF showed a statistically significant association with progression-free survival; however, the correlation with MTM/ml was numerically stronger.

Low-Frequency PPM1D Gene Mutations Affect Treatment Response to CD19-Targeted CAR T-Cell Therapy in Large B-Cell Lymphoma.

Chimeric antigen receptor T (CAR T)-cell therapy has become a standard treatment option for patients with relapsed or refractory diffuse large B-cell lymphoma (r/r DLBCL). Mutations in the PPM1D gene, a frequent driver alteration in clonal hematopoiesis (CH), lead to a gain of function of PPM1D/Wip1 phosphatase, impairing p53-dependent G1 checkpoint and promoting cell proliferation. The presence of PPM1D mutations has been correlated with reduced response to standard chemotherapy in lymphoma patients. In this study, we analyzed the impact of low-frequency PPM1D mutations on the safety and efficacy of CD19-targeted CAR T-cell therapy in a cohort of 85 r/r DLBCL patients. In this cohort, the prevalence of PPM1D gene mutations was 20% with a mean variant allele frequency (VAF) of 0.052 and a median VAF of 0.036. CAR T-induced cytokine release syndrome (CRS) and immune effector cell-associated neuro-toxicities (ICANS) occurred at similar frequencies in patients with and without PPM1D mutations. Clinical outcomes were globally worse in the PPM1D mutated (PPM1Dmut) vs. PPM1D wild type (PPM1Dwt) subset. While the prevalent treatment outcome within the PPM1Dwt subgroup was complete remission (56%), the majority of patients within the PPM1Dmut subgroup had only partial remission (60%). Median progression-free survival (PFS) was 3 vs. 12 months (p = 0.07) and median overall survival (OS) was 5 vs. 37 months (p = 0.004) for the PPM1Dmut and PPM1Dwt cohort, respectively. Our data suggest that the occurrence of PPM1D mutations in the context of CH may predict worse outcomes after CD19-targeted CAR T-cell therapy in patients with r/r DLBCL.

Abstract B045: Ataxia telangiectasia- and Rad3-related kinase inhibitor (ATRi) camonsertib in combination with low dose gemcitabine in patients with solid tumors with DNA damage response (DDR) aberrations: Preclinical and Phase 1b results

Abstract Background: Antitumor activity and good tolerability of camonsertib (cam) monotherapy in patients (pts) with recurrent solid tumors was previously reported. Preclinical data showed that cam-related tumor cell death is potentiated by the replication stress-inducing agent gemcitabine (gem) even at low doses, resulting in synergistic combination activity. We evaluated safety/tolerability and efficacy of cam+gem in this Ph1b trial (TRESR; NCT04497116). Methods: A tumor xenograft (Granta-519; ATM loss of function) was tested with a range of cam+gem doses. Pts >18yr, ECOG 0-1, with advanced solid tumors with deleterious DDR alterations were enrolled. Cam (80-120mg) + de-escalating gem doses (1000-100mg/m2) were given over 21- or 28-day (d) cycles (cam d1-2/3 and d8-9/10 or d15-16/17; gem d1 and d8 or d15). Dose decisions followed BOIN methodology. Endpoints were safety/tolerability, recommended Ph2 dose (RP2D), response rate (RECIST v1.1, CA-125 [GCIG], or PSA [PCWG3]), clinical benefit rate (CBR; response or treatment [Tx] duration ≥16 weeks [w] without progression), ctDNA molecular response rate (MRR; best reduction in mean variant allele frequency ≥50%), and cam PK. Replication stress markers were analyzed in surrogate normal tissue. Results: In a tumor xenograft model, low doses of cam (1/3 of maximum tolerated dose [MTD]) and gem (1/20 of MTD) resulted in tumor regression not observed in single agent arms, with good tolerability. As of May 2023, 54 pts were treated with cam+gem in TRESR (ovarian [n=19], pancreatic [n=8], breast [n=6], other [n=21] tumors); enrollment genes included ATM (n=12), BRCA1 (n=18), BRCA2 (n=16), other (n=8). No drug-drug interactions were noted. RECIST v1.1 or CA-125 responses were observed in 5 pts (40 evaluable): 3 cPR, 1 uPR in pts with ovarian (n=2; 1 ATM, 1 BRCA1), endometrial (gPALB2), and breast (gBRCA1) cancers; 1 CA-125 response in a pt (ovarian/gBRCA1) with SD (on Tx 21w+). Four additional pts (uterine carcinosarcoma, ovarian, liver, lung) with SD were on Tx ≥6 months. CBR was 42.4% (14/33) in evaluable pts and 66.7% (8/12) in pts with gynecological cancers. MRR was 58% (7/12) in evaluable pts. Myelotoxicity, the most frequent Tx-related toxicity, improved with decreasing gem doses. Responses were maintained in the 3 pts with cPR following reductions to ≤200mg/m2 gem; the pts with the uPR and CA-125 responses started Tx at 200 and 100mg/m2 gem, respectively. Preliminary RP2D is 80mg cam (50% of monotherapy RP2D) + 400mg/m2 gem, 28d cycle (1w on/1w off). Related Grade 3+ neutropenia, anemia, and thrombocytopenia occurred in 44%, 11%, and 0% pts, respectively (n=9). Importantly, neutrophil nadir occurred in the 1w off Tx with quick rebound, alleviating the need for dose modifications. Conclusion: The synergy of low doses of cam+gem, demonstrated in preclinical studies, was confirmed in the clinical setting. A safe and tolerable dose and schedule of the combination was identified. The antitumor efficacy supports further development in pts with gynecological cancers; evaluation at RP2D is ongoing. Citation Format: Ezra Rosen, Timothy A Yap, Elisa Fontana, Elizabeth K Lee, Devalingam Mahalingam, Martin Højgaard, Niharika B Mettu, Gregory M Cote, Ruth Plummer, Ian M Silverman, Joseph D Schonhoft, Emeline Bacque, Adrian J Fretland, Gabriela Gomez, Danielle Ulanet, Kezhen Fei, Julia Yang, Maria Koehler, Anne Roulston, Li Li, Michal Zimmermann, Benedito A Carneiro, Stephanie Lheureux. Ataxia telangiectasia- and Rad3-related kinase inhibitor (ATRi) camonsertib in combination with low dose gemcitabine in patients with solid tumors with DNA damage response (DDR) aberrations: Preclinical and Phase 1b results [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr B045.

Clonal Dynamics of Gene Mutations during Oral Azacitidine Maintenance Therapy in Patients with Acute Myeloid Leukemia (AML): Outcomes from the QUAZAR AML-001 Trial

Background: Acute myeloid leukemia (AML) is a genetically heterogeneous disease and despite some patients (pts) achieving remission with frontline intensive chemotherapy (IC), most eventually relapse. In the QUAZAR trial (NCT01757535), oral azacitidine (Oral-AZA) prolonged overall survival and relapse-free survival (RFS) vs placebo (PBO) in older pts with AML in remission post IC (Wei et al, N Engl J Med 2020). Here, we studied the molecular landscape and clonal dynamics of pts treated with Oral-AZA/PBO in the QUAZAR study. The mutational landscape for older patients with AML in remission after IC may be confounded by persistence of pre-leukemic (PL) or age-related clonal hematopoietic (CH) variants. The implications of these residual mutations on disease relapse and treatment (Tx) outcome are largely unknown. Aims: 1) characterize the mutational landscape from remission bone marrow at baseline (BL) prior to Oral-AZA maintenance (i.e., in remission post-IC); 2) determine the fate of variants over time and at relapse in the Oral-AZA vs PBO arms; 3) examine associations between mutational landscape and relapse risk between Tx arms. Methods: In QUAZAR, 472 pts (≥55 years) with AML with intermediate- or poor-risk cytogenetics in remission after IC (BL) were randomized 1:1 to Oral-AZA or PBO. Among pts who consented to biomarker analyses (n=310), targeted NGS (37 myeloid genes) was performed on bone marrow DNA at BL (Oral-AZA/PBO: n=165/145), cycle 6 (n=107/79) and relapse (n=83/77). Mean NGS coverage was 13K reads and median minimal detectable variant allele frequency (VAF) was 0.12% (range: 0.02-2.79). Clonal variants were categorized by the longitudinal association between VAF and blast percentage (slope of leukemic variants >0.1; PL/CHIP <0.1). RFS was computed from time of randomization to relapse (≥5% BM blasts) or death, estimated by Kaplan-Meier methods. Hazard ratios (HR) and 95% confidence intervals (CI) were obtained from Cox regression models. Nominal P values were derived from log-rank tests. Results: In the NGS cohort (n=310), median RFS (mRFS) for Oral-AZA vs PBO was 10.2 vs 4.7 months (mo), respectively. At BL, prior to maintenance Tx, 221 (71.3%) had detectable mutations, the most frequently occurring mutations (>5% of pts) were in DNMT3A (28.4%), TP53 (15.5%), IDH2 (12.3%), TET2 (11.9%), SRSF2 (11.0%), IDH1 (6.1%) and ASXL1 (5.5%). At BL, 110/310 (35.5%) pts had VAF >5%, potentially representing persistence of PL/CH variants in remission. Comparative analysis of all gene variants at BL and relapse revealed that some VAFs increased with blast frequency, while other variants remained largely static. Applying a variant classification algorithm, 97/258 pts had potential leukemic variants detected at BL. These involved DNMT3A (16.1%), SRSF2 (7.1%), TP53 (7.1%) and IDH2 (5.7%). PL/CH variants included DNMT3A (17.5%), TP53 (8%), IDH2 (5.7%) or TET2 (5.7%). TP53 was detected in 19.4% PL/CH variants (mean VAF 1.7%; range 0.2-13.4). Notably, when analyses were limited to potential leukemic variants at BL (<5% VAF), their presence was correlated with worse RFS (PBO: mRFS for 0, 1 or 2+ mutations was 6.1, 4.7 or 1.9 mo, respectively). The presence of ≥2 leukemic mutations was associated with shorter RFS only in PBO arm (mRFS vs <2 mutations: 1.9 vs 5.7 mo, P=0.02; Oral-AZA: 10.2 vs 10.2 mo). RFS favored Oral-AZA in pts with low mutational burden at BL (<2 mutations: mRFS 10.2 vs 5.7 mo [ P=0.003]; n=145 vs 122 [PBO]), and in a small subset of pts with higher mutational burden (≥2 mutations: mRFS 10.2 vs 1.9 mo [ P=0.008]; n=14 vs 13 [PBO]). Oral-AZA prolonged RFS vs PBO in pts across most mutational subtypes, when assessed for mutations that were deemed potentially leukemic (Figure). At relapse, the frequency of mutations, hotspots variants and co-mutations were comparable between Tx arms. Mutation-based pathway analysis indicated Ras pathway genes were enriched at relapse in PBO (28.6%) vs Oral-AZA arm (14.5%, P=0.03). Summary: In pts with AML in remission post IC, post-hoc analyses showed that Oral-AZA improved RFS vs PBO regardless of the mutational landscape at baseline. The spectrum of mutations at relapse was similar between Tx arms, suggesting that Oral-AZA maintenance prolongs remission without altering mutational heterogeneity.

Sole DNMT3A/TET2/ASXL1 Mutations Define a Distinct Clinical Trajectory for Patients with Clonal Hematopoiesis

Background: Clonal hematopoiesis of indeterminate potential (CHIP) is a clinically defined entity that is recognized by the 2022 International Consensus Classification and the 5 th Edition of the WHO. While the Clonal Hematopoiesis Risk Score (CHRS) incorporates 8 variables that underlie a prognostic framework for prediction of risk for progression to myeloid neoplasm (MN) (Weeks LD et al., NEJM Evidence 2023), there remains debate as to the role of mutations in epigenetic regulators, such as DNMT3A, TET2 and ASXL1 (“DTA”), with respect to clinical outcomes in the real-world setting. Although DTA mutations often occur early in myeloid pathogenesis, the persistence of these mutations as age-related clonal hematopoiesis (CH) might not significantly influence clinical course (Jongen-Lavrencic M et al., NEJM 2018). We have previously observed impaired clearance of DTA-mutant clones with hypomethylating agent or intensive chemotherapy for myelodysplastic neoplasms and acute myeloid leukemia (ASH abstract 4122; Blood (2022) 140 (Supplement 1): 9150-9151), and we now seek to understand the impact of sole DTA mutations in patients with CH. Methods: We studied a pre-selected group of patients who had an indication for undergoing bone marrow evaluation. Such indications included cytopenia(s), elevated blood cell count(s), staging/workup for lymphoma, and radiographic marrow abnormalities. Patients with CH were identified via concurrent morphologic, cytogenetic, and molecular diagnostics of bone marrow aspirates reviewed by UMass and Stanford Hematopathology from 2013 to 2023. CH was defined as presence of a somatic mutation with variant allele frequency (VAF) ≥ 2% on molecular diagnostics or non-myelodysplastic syndrome (MDS)-defining clonal cytogenetic aberration in a patient without morphologic evidence of MN. A total of 79 patients with CH were identified, then segregated based on presence or absence of sole DTA mutations. Results: We assessed the clinical trajectory of patients with CH who did not exclusively have DTA mutations (“non-sole DTA;” n = 58) (Panel A) compared to patients with CH who had DTA mutations alone without any other concurrent mutations (“sole DTA;” n = 21) (Panel B). The median age at detection of CH for sole DTA vs. non-sole DTA was 71.0 ± 2.11 years vs. 71.5 ± 1.45 years, respectively ( p = 0.454). Median number of mutations for sole DTA vs. non-sole DTA patients was 1.24 ± 1.2 vs. 2.24 ± 0.18, respectively ( p < 0.0001). Median follow-up for all patients was 450 days, and the median overall survival was not reached for either group. For non-sole DTA patients, 44 of 58 patients (76%) did not progress, while 14 of 58 patients (24%) progressed to frank MN at the time of analysis. Types of frank MN in the 14 progressors included MDS (50%), MDS/myeloproliferative neoplasm (MPN) overlap (28.6%), AML (14.3%), and MPN (7.1%). For sole DTA patients, 0 of 21 patients (0%) progressed. Regarding distribution of VAFs for sole DTA patients vs. non-sole DTA patients, mean VAF was 13.5% ± 1.91% vs. 31.6% ± 2.18%, respectively ( p < 0.001). For patients with both DTA mutations plus additional mutations, mean VAF for non-progressors vs. progressors was 30.4% ±1.47% vs. 38.6% ± 2.97%, respectively ( p = 0.206). For patients without any DTA mutations but with other somatic mutations, mean VAF for non-progressors vs. progressors was 29.7% ±1.67% vs. 35.2% ± 2.26%, respectively ( p = 0.160). Conclusion: In this study of pre-selected patients with CH, DTA mutations alone were insufficient for progression to frank MN. Progressors included patients with either (1) DTA mutations plus concurrent mutations, or (2) patients without DTA mutations but presence of mutations in other gene clusters. The clinical trajectory of patients with CH in our study differs from that of patients from large consortia possibly because our patients presented with an indication for testing, reflecting real-world data. A limitation of our analysis is the variability in time to recognition and diagnosis of CH, which reflects the high heterogeneity of these patients. Still, our data suggest the need for large-scale studies in the real-world setting to better prognosticate the relevance of DTA mutations for this patient population.

Clinical Implications of CSF-Ctdna in CNS Involvement of Newly Diagnosed Diffuse Large B Cell Lymphoma: An Improvement of Diagnosis, Treatment and Evaluation

Background: CNS involvement (CNSi) is a rare and often fatal event, occurring in around 5% of patients (pts) with diffuse large B-cell lymphoma (DLBCL) during primary treatment or shortly after completion (SCNSL). Furthermore, the potential mechanisms of CNS dissemination were limited. Circulating tumor DNA from cerebrospinal fluid (CSF-ctDNA) has played an important part in the application of liquid biopsy in CNS cancers. In this study, we provided new insights into the feasibility of using CSF-ctDNA as an essential tool for CNSi diagnosis, treatment, and evaluation specifically in newly diagnosed (ND) DLBCL pts. Methods : Between December 2021 and April 2023, 168 ND DLBCL pts and 24 ND PCNSL pts have been treated in our center. One hundred DLBCL pts were enrolled in the training cohort while the other 68 pts refused to enter in our study. Another 26 ND DLBCL pts diagnosed between May 2023 and June 2023 were entered into a validation cohort. The flow of treatment and samples collections were according to the study protocol shown in Figure 1A. CSF-ctDNA positive (CSF-ctDNA(+)) criteria: (1) CSF-ctDNA detected mutations consistent with tissue; (2) Mutations detected in CSF-ctDNA were inconsistent with tissues, but were classified as grade I and grade II mutations; (3) At least one mutation was detected with an abundance >0.5%. The criteria of CNSi positive (CNSi(+)) were CSF-ctDNA(+) or/and other evidences detected by conventional methods (CM, including MRI, PET-CT, routine inspection analysis of CSF). Results: In the training cohort, 25 pts (25%) were diagnosed with CSF-ctDNA (+) while 21 pts were according to the first criteria and 4 pts were according to the second criteria. Among the 25 pts (25.0%) who were finally diagnosed with CNSi (+), only 3 pts (12.0%) have evidences of CNSi both in CM and CSF-ctDNA while similar results were shown in validation cohort ( Figure 1B). The unique mutations detected in CSF were rare compared with plasma and tissue mainly due to early detection with no clone evolution ( Figure 1C). The mean variant allele frequency was significantly higher in tumor tissue than CSF in SCNSL ( Figure 1D). The pretreatment ctDNA burden was significantly higher in CSF of PCNSL while higher in plasma of SCNSL ( Figure 1F). The distributions of gene subtypes for the 25 CNSi (+) DLBCL pts were shown in Figure 1E. Only 11 pts (44%) were MCD subtype while nearly 80% PCNSL pts were MCD subtype. There existed significant differences of gene mutation profile between SCNSL and PCNSL ( Figure 1G). We explored the association of clinical and biological factors with CNSi in ND DLBCL pts . Of note, high plasma ctDNA burden (≥2.18) were significantly related to CNSi (+) (Figure 1H). In multivariable analyses, CSF protein level ≥0.4, high plasma ctDNA burden (≥2.18) and high risk CNSi sites involvement were independent risk factors for CNSi ( Figure 1I). We use these 3 risk factors to build CNSi-IPI model which can significantly better predict CNSi than CNS-IPI ( Figure 1I). According to CNSi-IPI, pts were stratified into low-risk (0-1), intermediate-risk (2) and high-risk (3). CNSi (+) were observed in 5.0%, 48.3% and 72.7% in the training cohort and 5.9%, 50.0% and 100.0% in the validation cohort in the 3 risk groups ( Figure 1J). Pts with CARD11, JAK2, ID3, and PLCG2 mutation were more predominant with CNSi while FAT4 mutation seemed to promote tumor cells disseminating to CNS ( Figure 1K). Furthermore, the down-regulated genes of CNSi DLBCL pts significantly enriched in PI3K-AKT signaling pathway, focal adhesion, regulation of action cytoskeleton and tight junction pathways, which might be the potential mechanisms promoting CNS dissemination in ND DLBCL ( Figure 1L). The dynamic change of disease status and ctDNA burden of all the 25 CNSi (+) pts were shown in Table 1. Conclusion :In summary, our study highlighted the clinical implications of CSF-ctDNA in CNSi detection of ND DLBCL pts ( Figure 1M): (1) CSF-ctDNA exhibits higher sensitivity than CM in detecting CNSi in ND DLBCL. (2) Different genomic and clinical landscapes were observed between SCNSL and PCNSL. (3) The CNSi-IPI is a robust, highly reproducible tool that can be used to estimate the risk of CNSi in ND DLBCL. (4) Down-regulation of PI3K-AKT signaling pathway, focal adhesion, regulation of action cytoskeleton and tight junction pathways contribute to CNS dissemination in ND DLBCL. (5) Furthermore, CSF-ctDNA can be used to monitor CNS tumor burden and response to treatment.

Tumour-agnostic plasma assay for circulating tumour DNA predicts outcome in recurrent and/or metastatic squamous cell carcinoma of the head and neck treated with a PD-1 inhibitor

BackgroundOnly 15–20% of recurrent and/or metastatic squamous cell carcinoma of the head and neck (R/M SCCHN) patients derive long-term benefit from nivolumab or pembrolizumab. We developed a circulating tumour DNA (ctDNA) tumour-agnostic assay aimed at the early prediction of single agent programmed cell death 1 (PD1) inhibitor efficacy in R/M SCCHN. Patients and methodsOur tumour-agnostic assay included 37 genes frequently mutated in R/M SCCHN and two HPV16 genes. Primary endpoint was the concordance between ctDNA kinetics (ΔctDNA) and the best overall response according to Response Evaluation Criteria in Solid Tumors version 1.1. ΔctDNA was defined as the difference in mean variant allele frequency (VAF) between the on-treatment sample harvested 6–10 weeks (FU1) after PD1 inhibitor initiation and the pre-treatment plasma sample (ΔctDNA = mean FU1 VAF - mean pre-treatment VAF). ResultsctDNA was detected in 35/44 (80%) of the pre-treatment plasma samples. The concordance between ΔctDNA and imaging response was observed in 74%. Median progression-free survival was 8.6 months in the favourable ΔctDNA group and 2.5 months in the unfavourable ΔctDNA group (p = 0.057). Median overall survival (OS) was 18.1 and 8.2 months in the favourable and unfavourable ΔctDNA groups, respectively (p = 0.13). In patients with PD-L1 expressing SCCHN (Combined Positive Score ≥1), OS was significantly better in patients with favourable ΔctDNA compared with patients with unfavourable ΔctDNA: median OS was 41.5 and 8.4 months (p = 0.033), respectively. ConclusionsTumour-agnostic ctDNA analysis for human papillomavirus (HPV)-negative and HPV-positive R/M SCCHN is feasible. ctDNA kinetics show promising results in predicting the efficacy of PD1 inhibitors in R/M SCCHN.

Targeted next-generation sequencing for detection of PIK3CA mutations in archival tissues from patients with Klippel–Trenaunay syndrome in an Asian population

BackgroundKlippel–Trenaunay syndrome (KTS) is a rare slow-flow combined vascular malformation with limb hypertrophy. KTS is thought to lie on the PIK3CA-related overgrowth spectrum, but reports are limited. PIK3CA encodes p110α, a catalytic subunit of phosphatidylinositol 3-kinase (PI3K) that plays an essential role in the PI3K/AKT/mammalian target of rapamycin (mTOR) signaling pathway. We aimed to demonstrate the clinical utility of targeted next-generation sequencing (NGS) in identifying PIK3CA mosaicism in archival formalin-fixed paraffin-embedded (FFPE) tissues from patients with KTS.ResultsParticipants were 9 female and 5 male patients with KTS diagnosed as capillaro-venous malformation (CVM) or capillaro-lymphatico-venous malformation (CLVM). Median age at resection was 14 years (range, 5–57 years). Median archival period before DNA extraction from FFPE tissues was 5.4 years (range, 3–7 years). NGS-based sequencing of PIK3CA achieved an amplicon mean coverage of 119,000x. PIK3CA missense mutations were found in 12 of 14 patients (85.7%; 6/8 CVM and 6/6 CLVM), with 8 patients showing the hotspot variants E542K, E545K, H1047R, and H1047L. The non-hotspot PIK3CA variants C420R, Q546K, and Q546R were identified in 4 patients. Overall, the mean variant allele frequency for identified PIK3CA variants was 6.9% (range, 1.6–17.4%). All patients with geographic capillary malformation, histopathological lymphatic malformation or macrodactyly of the foot had PIK3CA variants. No genotype–phenotype association between hotspot and non-hotspot PIK3CA variants was found. Histologically, the vessels and adipose tissues of the lesions showed phosphorylation of the proteins in the PI3K/AKT/mTOR signaling pathway, including p-AKT, p-mTOR, and p-4EBP1.ConclusionsThe PI3K/AKT/mTOR pathway in mesenchymal tissues was activated in patients with KTS. Amplicon-based targeted NGS could identify low-level mosaicism from low-input DNA extracted from FFPE tissues, potentially providing a diagnostic option for personalized medicine with inhibitors of the PI3K/AKT/mTOR signaling pathway.

Early Circulating Tumor DNA Dynamics and Efficacy of Lorlatinib in Patients With Treatment-Naive, Advanced, ALK-Positive NSCLC

IntroductionCirculating tumor DNA (ctDNA) has been used as a biomarker for prognostication and response to treatment. Here, we evaluate ctDNA as a potential biomarker for response to lorlatinib, a third-generation ALK tyrosine kinase inhibitor in patients with treatment-naive, advanced, ALK-positive NSCLC in the ongoing phase 3 CROWN study (NCT03052608). MethodsMolecular responses were calculated using mean variant allele frequency (VAF), longitudinal mean change in VAF (dVAF), and ratio to baseline. Efficacy assessments (progression-free survival [PFS] and objective response rate) were paired with individual patient ctDNA and analyzed for association. ResultsCompared with baseline, mean VAF at week 4 was decreased in both treatment arms. Considering all detected somatic variants, a reduction in dVAF (≤0) was associated with a longer PFS in the lorlatinib arm. The hazard ratio (HR) for a dVAF less than or equal to 0 versus more than 0 was 0.50 (95% confidence interval [CI]: 0.23–1.12) in the lorlatinib arm. A similar association was not observed for crizotinib (HR = 1.00, 95% CI: 0.49–2.03). Comparing molecular responders with nonresponders, patients treated with lorlatinib who had a molecular response had longer PFS (HR = 0.37, 95% CI: 0.16–0.85); patients treated with crizotinib who had a molecular response had similar PFS as those without a molecular response (HR = 1.48, 95% CI: 0.67–3.30). ConclusionsIn patients with treatment-naive, advanced, ALK-positive NSCLC, early ctDNA dynamics predicted better outcome with lorlatinib but not with crizotinib. These results suggest that ctDNA may be used to monitor and potentially predict efficacy of lorlatinib treatment.

Liquid biopsy identification of ERBB2 amplified and HER2 expressing metastatic breast cancer: Comparison and combination of cell and cell-free platforms.

3061 Background: Liquid biopsies are a non-invasive diagnostic approach for detecting circulating tumor cells (CTCs) or circulating tumor DNA (ctDNA) that may provide clinically actionable information for treatment decisions for metastatic breast cancer (MBC) patients when a conventional biopsy is otherwise infeasible. Here we report a comprehensive liquid biopsy platform including: 1) quantitative immunofluorescent HER2 and ER protein expression in CTCs (ctcIF), 2) determination of ERBB2 amplification and the number of Large-scale State transitions (LST) by single-cells CTC genomics (ctcDNA) and 3) alterations in plasma ctDNA. Methods: Blood samples from 457 progressing metastatic breast cancer patients and 25 healthy donors (HDs) as controls were collected for cell & cell-free DNA analysis. After plasma isolation, nucleated cells were plated, & slides were bio-banked for Immunofluorescent staining & subsequent imaging. CTCs were identified using Epic Sciences digital imaging & machine learning algorithms, and individual CTCs were sequenced for genomic quantification of LSTs and Copy Number Variants (CNV). Bio-banked plasma was analyzed to detect ctDNA alterations with high clinical relevance (Class IA). Results: Within this cohort of 457 MBC patients, the presence of CTCs, ctcDNA (LST+) and ctDNA alterations were detected in 98%, 58%, and 42%, respectively, while no CTCs and no ctDNA alterations were detected in the HD cohort, suggesting high specificity. ctcDNA genomics was more sensitive than ctDNA in detecting ERBB2amp in MBC patients (16%, and 2%, respectively). A mean variant allele frequency (VAF) of < 25%, which is the threshold for detecting a two-fold ERBB2 amplification by ctDNA, was present in 20% and 80% of ERBB2amp MBC detected by the ctDNA and ctcDNA platform, respectively, suggesting that the ctcDNA platform can identify the majority of ERBB2amp among patients with a low ctDNA fraction. HER2exp or ERexp expression by ctcIF were detected in 67% and 67% of MBC patients, respectively. A liquid biopsy classification of HER2 status by combining the three platforms (ctcIF, ctcDNA, and ctDNA) identified that in the tested population, 16% were ERBB2amp, 52% were HER2 expressing (HER2exp and ERBB2nonamp), and 27% were HER2neg (HER2- and ERBB2nonamp). To identify MBC patients that may potentially change treatment as a result of the test we identified a small cohort of MBC patients (n=46) with HER2- disease and tissue biopsy IHC=0, 74% of these patients had HER2exp CTC consistent with HER2 low expression which may aid therapeutic decisions in later line MBC. Conclusions: Here we report a comprehensive liquid biopsy profile combining ctcIF, ctcDNA, and ctDNA platforms with high sensitivity and specificity in determining clinically actionable HER2 and ER biomarker status that may impact therapeutic decision-making in MBC patients.

Early Circulating Tumor DNA Dynamics Predict Neoadjuvant Therapy Response and Recurrence in Colorectal Liver Metastases: A Prospective Study.

For patients with colorectal liver metastases (CRLM) who receive neoadjuvant therapy (NAT), reliable indicators that can early and accurately predict treatment response are lacking. This study was conducted to prospectively investigate the potential of early circulating tumor DNA (ctDNA) dynamics as a precise predictor of NAT response and recurrence in CRLM. This study prospectively enrolled 34 patients with CRLM who received NAT, with blood samples collected and subjected to deep targeted panel sequencing at two time points: 1 day before the first and the second cycles of NAT. Correlations of ctDNA mean variant allele frequency (mVAF) dynamics and treatment response were assessed. The performance of early ctDNA dynamics in predicting treatment response was assessed and compared with those of carcinoembryonic antigen (CEA) and cancer antigen 19-9 (CA19-9). The baseline ctDNA mVAF was significantly associated with pre-NAT tumor diameter (r = 0.65; P < 0.0001). After one cycle of NAT, the ctDNA mVAF declined remarkably (P < 0.0001). The dynamic change in ctDNA mVAF of 50% or more was significantly correlated with better NAT responses. The discriminatory capacity of ctDNA mVAF changes was superior to that of CEA or CA19-9 in predicting radiologic response (area under the curve [AUC], 0.90 vs 0.71 vs 0.61) and pathologic tumor regression grade (AUC, 0.83 vs 0.64 vs 0.67). The early changes in ctDNA mVAF but not CEA or CA19-9 were an independent indicator of recurrence-free survival (RFS) (hazard ratio, 4.0; P = 0.023). For CRLM patients receiving NAT, an early ctDNA change is a superior predictor of treatment response and recurrence compared with conventional tumor markers.

Application of circulating tumour DNA in terms of prognosis prediction in Chinese follicular lymphoma patients.

Background: Follicular lymphoma (FL), an indolent non-Hodgkin lymphoma (NHL), is generally incurable. Favourable prognosis and durable remission are crucial for FL patients. The genetic mutation spectrum provides novel biomarkers for determining the prognosis of FL patients, but its detection is easily affected by the collection of tumour tissue biopsies. In this study, we aimed to describe the mutational landscape of FL using circulating tumour DNA (ctDNA) samples and to explore the relationship between mutations and prognostic indicators of clinical outcome in patients with newly diagnosed follicular lymphoma and the prognostic value of such mutations. Methods: A total of 28 patients with newly diagnosed FL were included in this study. A targeted NGS-based 59-gene panel was used to assess the ctDNA mutation profiles. Differences in clinical factors between patients carrying mutations and those without mutations were analysed. We also explored the relationship between gene mutation status, mean VAFs (variant allele frequencies) and clinical factors. The Kaplan‒Meier method was applied to analyse the overall survival (OS) and progression-free survival (PFS) of patients carrying mutations and those without mutations. Results: ctDNA mutations were detectable in 21 (75%) patients. The most commonly mutated genes were CREBBP (54%, 15/28), KMT2D (50%, 14/28), STAT6 (29%, 8/28), CARD11 (18%, 5/28), PCLO (14%, 4/28), EP300 (14%, 4/28), BCL2 (11%, 3/28), and TNFAIP3 (11%, 3/28), with a mutation frequency of >10%. Patients with detectable ctDNA mutation tended to present with advanced Ann Arbor stage (III-IV) (p = 0.009), high FLIPI risk (3-5) (p = 0.023) and severe lymph node involvement (No. of involved areas ≥5) (p = 0.02). In addition, we found that the mean VAF was significantly higher in patients with advanced Ann Arbor stage, high-risk FLIPI, elevated lactate dehydrogenase (LDH: 0-248U/L), advanced pathology grade, bone marrow involvement (BMI) and lymph node involvement. Additionally, KMT2D, EP300, and STAT6 mutations were associated with inferior PFS (p < 0.05). Conclusion: We described the ctDNA mutation landscapes in Chinese patients with newly diagnosed FL and found that ctDNA VAF means reflect tumour burden. Moreover, PFS was shorter in patients with KMT2D, EP300 and STAT6 mutations.