Liquid Biopsy Specimens Research Articles

Abstract B056: Towards a generalized machine learning model for Raman spectroscopy-based liquid biopsy in cancer screening using self-supervised learning

Abstract Head and neck cancers, which encompass a range of malignancies affecting the oral cavity, pharynx, and larynx, are critical to address due to their high morbidity and impact on quality of life. This underscores the need for effective and non-invasive diagnostic tools. Raman spectroscopy-based liquid biopsy detects cancers by analyzing intrinsic Raman fingerprints in biofluids without the need for molecular labels, making it a promising point-of-care screening method. However, Raman scattering is weak, and interpreting spectra from biological samples is challenging due to overlapping peaks, fluorescence background, cosmic rays, and instrument noise, which obscure the signal. Extensive preprocessing and advanced analytical techniques are usually needed to isolate the true Raman signal. While machine learning models have shown promise in classifying cancer status from Raman spectra, variations in Raman systems, lack of standardized protocols, and small patient cohorts limit their clinical utility. Our goal is to develop a model for Raman spectroscopy-based liquid biopsy that generalizes across different measurement conditions and clinical indications. A key challenge is the high cost of acquiring extensive labeled training data. To overcome this, we use a Siamese-based, self-supervised model trained on unlabeled spectral data. The model generates synthetic spectra that mimic real variations across Raman systems and measurement protocols by preprocessing the input and adding simulated factors like fluorescence background, noise, and cosmic rays. By maximizing the cosine similarity between the embeddings of the generated spectra and their originals, the model learns meaningful features of the Raman spectra. This approach not only expands the training set but also enhances the model’s stability across different instruments. In our preliminary study, we analyzed thousands of Raman spectra measured on liquid biopsy specimens (blood plasma and saliva) collected from a cohort of 71 head and neck cancer patients (spread across early and late-stage disease) and 44 non-cancerous controls. Spectra were divided into training and test sets with an 80:20 ratio. Each specimen was drop cast onto a quartz substrate and 25 repeated Raman point scans were performed in a grid over the dried spot. We augmented the training set to reach 9,200 spectra, and t-SNE plots of the embeddings of the test set (1,150 spectra) showed clear clustering separated by sample type, with distinct clusters for healthy individuals and cancer patients. Despite the excellent performance for cancer vs control, separation among cancer patients at different stages remains limited, but will be the target of future work building on this study. These results suggest that our label-free approach can effectively distinguish between healthy and cancerous samples using unlabeled data, advancing the potential for the widespread clinical application of Raman-based liquid biopsy powered by machine learning. Citation Format: Yifei Gu, Kwan Lun Chiu, Andrés Muñoz-Jaramillo, Andrew C. Birkeland, Maria Navas-Moreno, Randy Carney. Towards a generalized machine learning model for Raman spectroscopy-based liquid biopsy in cancer screening using self-supervised learning [abstract]. In: Proceedings of the AACR Special Conference: Liquid Biopsy: From Discovery to Clinical Implementation; 2024 Nov 13-16; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(21_Suppl):Abstract nr B056.

Comparative targeted genome profiling between solid and liquid biopsies in gastroenteropancreatic neuroendocrine neoplasms (GEP-NENs): a proof-of-concept pilot study.

Clinical presentation and genetic profile of gastro-entero-pancreatic neuroendocrine tumors (GEP-NETs) are highly variable, hampering their management. Sequencing of circulating tumor DNA (ctDNA) from liquid biopsy (LB) has been proposed as a less invasive alternative to solid biopsy (SB). Our aim is to compare the mutational profile (MP) provided by LB with that deriving from SB in GEP-NETs. SB and LB derived simultaneously from 6 GEP-NETs patients. A comparative targeted Next Generation Sequencing (NGS) analysis was performed on DNA from SB and LB to evaluate the mutational status of 11 genes (MEN1, DAXX, ATRX, MUTYH, SETD2, DEPDC5, TSC2, ARID1A, CHECK2, MTOR, PTEN). Patients (M:F =2:1; median age 64 yrs) included 3 with pancreatic and 3 with ileal NETs. NGS detected a median number of 55 variants/sample in SB and 66.5 variants/sample in LB specimens (mutational burden: 0.2-1.9 and 0.3-1.8 mut/Mb, respectively). Missense and nonsense mutations were prevalent in both, mainly represented by C>T transitions. ARID1A, MTOR, and ATRX were consistently mutated in SB and ARID1A, TSC2, MEN1, PTEN, SETD2, and MUTYH were consistently mutated in LB. DAXX mutations were absent in LB. 17 recurrent mutations were shared between SB and LB; in particular, MTOR single nucleotide variants (SNVs) c.G4731A and c.C2997T were shared by 5 out of 6 patients. Hierarchical clustering supported genetic similarity between SB and LB. This pilot study explores the applicability of LB in GEP-NETs MP evaluation. Further studies with larger cohorts are needed to validate LB and to define the clinical impact.

Flushing fluid of post-bronchoscopic biopsy as a novel liquid biopsy specimen for genome profiling in advanced lung cancer.

e15038 Background: Tumour tissue is the primary substrate for molecular testing in advanced NSCLC. However, obtaining sufficient tissue samples from biopsy for molecular testing can often be challenging. Flushing fluid of post-bronchoscopic biopsy, which contains tumor-derived DNA, may serve as a supplement for genotyping. The aim of this study is to assess the efficacy and precision of detecting gene alterations in flushing fluid samples and evaluate their clinical potential. Methods: Flushing fluid, matched tissue (TIS), and whole blood were prospectively collected from 25 patients with stage III-IV NSCLC between June 2022 and December 2023. Ten milliliters of flushing fluid and whole blood were used to prepare flushing fluid supernatant (FFS) and plasma (PLA), respectively. Capture-based targeted sequencing of TIS, FFS and PLA samples was performed using a universal oncology panel. Results: In this cohort of 25 patients, there was a male predominance (22 out of 25) and the mean age was 60.2 years. The majority of patients were diagnosed with lung adenocarcinoma (23 out of 25), and smokers outnumbered non-smokers (16 out of 25). Furthermore, 18 out of 25 patients presented with metastatic disease at diagnosis. The performance of three sample types regarding key quality control indices was evaluated first. FFS exhibited a maximum allelic fraction similar to TIS, while PLA showed a significantly lower than TIS and FFS. Subsequently, we compared the positive detection rates, with TIS, FFS, and PLA achieving respective rates of 100%, 96%, and 80%. A total of 495 mutation events were detected from the three samples (FFP:209, FFS:196, PLA:90), Among these, 161 were concordant between TIS and FFS samples, and 72 were concordant between TIS and PLA samples. The sensitivity and positive predictive value (PPV) of detecting eight established driver alterations in NSCLC were compared using TIS as the gold standard with the two liquid biopsies. FFS demonstrated superior sensitivity and PPV compared to PLA (80.5% vs. 56.1%, 97% vs. 88.5%) and showed equivalent performance for EGFR mutation. Furthermore, estimates of tumor mutational burden (TMB) based on TIS and FFS were highly correlated (Pearson r= 0.97). Conclusions: Our study demonstrated that FFS performs comparably to matched TIS and superiorly to PLA for genotyping advanced NSCLC. FFS emerges as a valuable specimen source, especially in patients with insufficient tumor tissue.

Spectrum of HER2 alterations in NSCLC: Comparative analysis of tissue and liquid biopsies in lung cancer.

e20602 Background: Non-Small Cell Lung Cancer (NSCLC) exhibits a spectrum of molecular alterations that play a crucial role in understanding its heterogeneity and tailoring targeted therapies. Among these alterations, HER2 aberrations have gained significance as potential therapeutic targets. This study aims to explore the diversity of HER2 changes in NSCLC through tissue and liquid biopsies, providing valuable insights into the feasibility and accuracy of either method. Methods: Data from next generation sequencing of 799 tissues and 1380 liquid biopsy specimens was retrospectively analyzed. The study sought to elucidate the prevalence of HER2 alterations with these two methodologies, evaluating their respective strengths and limitations in detecting HER2 changes in NSCLC. Results: HER2 mutations were identified in 2.1% (17/799) of tissue, mirroring the prevalence observed in the TCGA cohort (2%). The liquid biopsy cohort identified Her2 mutations with similar prevalence and was positive for Her2 mutations in 2.2% (30/1380). Within Her2 mutations, HER2 exon 20 insertion mutations emerged as the predominant variant, accounting for all variants in tissue samples and 93.3% (28/30) in liquid biopsies. The most frequent HER2 exon 20 variant was p.Y772_A775dup variant (76.5% in tissue, 71.4% in liquid biopsy), followed by p.E770_A771insAYVM (17.6% in tissue and 7.1% in liquid). Less frequent HER2 mutations included p.G776delinsLC, p.G776delinsVC, p.V777_G778insGSP, p.A775_G776insYVMA. HER2 amplification was detected in 1.4% (5/352) of tissue and 1.3% (8/617) of liquid biopsy samples; concurrent HER2 mutation and Her2 amplification were detected in 3 liquid biopsy samples. 11/60 cases had concurrent targetable alterations in other targetable genes. Most common concurrent alterations were in EGFR followed by KRAS. Concurrent EGFR sensitizing alterations were observed in 7 patients ( 6 EGFR Exon 19 deletion and one EGFR L858R). Only 2/7 patients showed concurrent EGFR/HER2 alterations at baseline, the remaining 5/7 patients had received prior EGFR TKI therapy. Conclusions: Our results demonstrate equivalent Her2 alteration detection rate with liquid biopsy as compared to tissue molecular profiling in NSCLC. Our results support utility of liquid biopsy for Her2 profiling in the primary setting as well as to detect acquired Her2 alterations like in patients post EGFR-TKI therapy. It highlights that HER2mutations coexist with HER2 amplification in subset of advanced NSCLC patients. [Table: see text]

Molecular profiling of serial liquid biopsy specimens utilizing cell free DNA (cfDNA) and circulating tumor cells (CTCs) in TBCRC041: A phase II study of alisertib in endocrine resistant metastatic breast cancer (MBC).

1037 Background: TBCRC041, a randomized phase 2 trial of alisertib (A) ± fulvestrant (F) in women with HR+/HER2- MBC demonstrated promising clinical activity for alisertib (1). Interrogation of baseline (PreC1) and end of cycle 1 (EOC1) cfDNA and CTCs may identify biomarkers associated with response to A±F. Methods: Plasma cfDNA was sequenced using the Guardant INFINITY platform, which includes genomic and methylated tumor fraction (mTF) analysis. Pathogenic variants were determined using publicly available databases and Mayo Clinic annotation pipelines. CTCs were identified as nucleated, EpCAM+/ cytokeratin+/ CD45- cells and assessed for ER/HER2 staining (RareCyte, Seattle). PFS was defined as the time from randomization to progression or death. EOC1-PFS differs from PFS as time starts at C2D1. Stratified log-rank tests and conditional Cox modeling were used to assess whether PFS or EOC1-PFS differed by mutations in ESR1 or PIK3CA, pre-CTC ≥ 5, or mTF>1%. Results: Of the 91 eligible pts, 84 progressed, and 73 were deceased. In the 86 pts with PreC1-cfDNA results, variants were identified in ESR1 (42; 48.8%), PIK3CA (36; 41.9%), AKT1 (7; 8.1%), PTEN(7; 8.1%), BRCA1 (4; 4.7%), and BRCA2 (7; 8.1%). Pts with a PIK3CAmut had significantly decreased PFS (HR 1.8; 95%CI: 1.1 -2.9, p=0.014) but not by ESR1mut status (p=0.583). PreC1 and EOC1-mTF were determined for 78 and 76 pts, respectively. PreC1-mTF was 0-1% in 21; 1.1-10.0% in 27; and 10.1-100% in 30. mTF levels remained between 0-1% in 17 pts fell to 0-1% in 11 pts, and was 0-1% in 5 pts without a preC1-mTF determination. PFS did not differ with respect to PreC1-mTF (p=0.210), but EOC1-PFS was worse in pts with mTF >1% (HR 3.0; 95%CI: 1.6 -5.2, p<0.001). PreC1 and EOC1-CTC were determined for 78 and 76 pts. 36 (46.2%) pts had a PreC1 CTC count ≥ 5. EOC1-CTC levels remained at (n=17) or increased to (n=1) ≥ 5 and was ≥ 5 in 2 pts without a preC1-CTC determination. EOC1-PFS was not significantly different for EOC1-CTC ≥ 5 (p=0.065), but was significantly decreased in pts with PreC1-CTC≥5 (HR=1.8; 95%CI: 1.1-3.0; p=0.018). Broader cfDNA NGS panel and CTC-derived ER/HER2 staining results will be presented at the meeting. Conclusions: Among patients receiving A±F, PFS varied based on the PIK3CAmutation status. cfDNA and CTC assessment PreC1 and EOC1 provided complementary information. Further validation in larger datasets is needed. 1. JAMA Oncol 2023;9:815. Clinical trial information: NCT02860000 .

Abstract 5023: Analytical validation of the Oncomine™ Dx Express Test using liquid biopsy samples as an IUO assay in a CAP/CLIA lab

Abstract Introduction: The Oncomine™ Dx Express Test (ODxET) is a next-generation sequencing (NGS) test. It can be used as an investigational use only (IUO**) test to detect somatic DNA and RNA alterations in human cell-free total nucleic acid (cfTNA) isolated from plasma samples. This study outlines the analytical validation of the ODxET for relevant single nucleotide variants (SNV) and insertion/deletions (INDEL) in liquid biopsy specimens. The Ion Torrent Genexus™ platform has a short turnaround time with minimal operator input. This study was performed in a College of American Pathologists (CAP™) accredited and Clinical Laboratory Improvement Act (CLIA) licensed laboratory. Methods: Forty-seven unique samples (39 clinical, 3 derived, 2 reference and 3 commercially available DNA controls) were analyzed. All experiments began with sample extraction, except the lower input limit of detection (LLOD). We evaluated limit of detection, variant calling accuracy, and precision. Two control NIST™ samples were sequenced with 3 technical replicates each for INDEL and SNVs analytical accuracy. The LOD was evaluated at both the target input of 2ng/µl (40ng), and the minimum input,0.33ng/µl (6.6ng) with allele frequency (AF) levels at 1%, 0.5%, and 0.25%. The 39 clinical plasma samples were used for variant calling accuracy. Inter-assay reproducibility was assessed by sequencing DNA controls across four runs by different operators over multiple days/systems. Intra-assay repeatability was assessed by sequencing 4 samples in replicate on the same run by one operator on the same day/system. Results: The analytical accuracy and NPV was 100% for SNV/INDEL variants. The 40ng input LOD sensitivity was 96% for SNVs at 0.5% AF and 100% for INDELs at 0.25% Minimum AF. The lower input LOD sensitivity was 89% for SNVs and 100% for INDEL at 1% AF. Variant calling accuracy on samples with pre-characterized data was 100% for the 13 positive samples. Specificity was >99% for all samples including both healthy donor and positive samples. Repeatability was 100% for INDELs and >96% for SNVs, reproducibility was 100% for both variant classes. Conclusion: This validation study to estimate analytical accuracy, limit of detection, variant calling accuracy and precision has demonstrated that the ODxET assay is highly robust in detecting SNV and INDEL mutations in plasma samples and is suitable for use in a CAP/CLIA laboratory as an IUO assay.**=In Vitro Diagnostic use only. Not available in all regions including North America. Citation Format: Juan C. Espinoza, Rajendra Ramsamooj, Akemi Yuki, John Williamson, Diarra Hassell, Madhu Jasti, Suzanne Salazar, David Ginzinger. Analytical validation of the Oncomine™ Dx Express Test using liquid biopsy samples as an IUO assay in a CAP/CLIA lab [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 5023.

Abstract 3706: Single cell and cell-free nucleic acid analyses of liquid biopsy specimens from a blood collection tube using a new droplet digital PCR system

Abstract Introduction: Liquid biopsy-based testing has increasingly been adopted by oncologists for biomarker-driven diagnostics, therapy selection, and patient monitoring. Unlike tissue-based approaches, the target analytes in blood specimens are often rare events that must be discriminated from a background of non-tumor derived material. Droplet digital PCR (ddPCR) is an ideal platform for detection of rare nucleic acid markers in the clinic, because it is highly sensitive and specific, robust, and quantitative. Additionally, the workflow is simple to adopt and execute. The QX600 System is a new ddPCR instrument designed for advanced multiplexing which enables simultaneous detection of up to 6 unique fluorophores in a single well. This capability can decrease the sub-sampling needed for detection of multiple analytes. The objective of our study was to develop multiplexed ddPCR assays for detection of cell-based and cell-free circulating biomarkers from a single tube of whole blood. Methods: Tumor cells were enriched from the buffy coat fraction of whole blood collected in fixative-containing cfDNA BCT based on size and morphology using a microfluidics-based system. Enriched tumor cells were enumerated by immunofluorescence (DAPI+/Pan-CK+/CD45-), and gene expression was measured using the QX600 for a panel of cytokeratins (CK) and PD-L1 in CTC negative, NSCLC donor specimens (n=8). Results were compared to CTC positive, contrived specimens (whole blood spiked with breast tumor cell line MCF7 cells; n=5). For ctDNA analysis of the plasma fraction, a multiplexed ddPCR assay was designed to test for five actionable mutations prevalent in NSCLC, including EGFR del19, L858R, T790M, KRAS G12C, BRAF V600E, and wildtype EGFR. To evaluate performance of the multiplexed assay, concordance evaluation was conducted using cfDNA from 8 mutation-positive NSCLC donors on the QX600 and compared to single assays run on the QX200 system. Results: CK8 and CK19 were differentially expressed in the cells enriched from the CTC negative NSCLC cohort as compared to the contrived positives (p=0.0058, and p=0.0049, respectively). All the NSCLC cfDNA samples were positive for the reference variant, and linear regression analysis of the minor variant frequency for ctDNA biomarkers showed good concordance between QX systems (R2=0.8847). Conclusions: These studies demonstrate proof of concept for single cell and cell-free analysis from a single blood draw into a cfDNA BCT using the QX600 system. Liquid biopsy analysis of CTCs and ctDNA can enable minimally invasive, comprehensive decision making in the diagnostic workup of patients. Future studies will focus on further optimizing the cell enrichment methodology from cfDNA BCT and development of additional multiplexed ddPCR assays for NSCLC-relevant biomarkers on the QX600. Citation Format: Leisa Jackson, Colin Cochran, Claire Gould, Sarah Kreston, Jazmin Bello, Brittany D’Alessio, Janice Riley, Alisa Tubbs, Gary A. Pestano. Single cell and cell-free nucleic acid analyses of liquid biopsy specimens from a blood collection tube using a new droplet digital PCR system [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 3706.

Abstract 2283: A targeted mutation calling workflow - end to end - from FASTQ to clinical report for single cells

Abstract Molecular profiling of rare cancer cells derived from liquid biopsy holds promise to monitor systemic cancer progression and guide personalized therapy interventions. However, this necessitates reliable and comprehensive profiling of samples at the single cell level and requires whole genome amplification (WGA), which adds amplification errors and bias to common sequencing errors. Therefore, we established a single-cell mutation calling workflow that can identify clinically actionable somatic mutations in rare single cell DNA with high sensitivity and accuracy. Our workflow is an end-to-end solution which can take FASTQ reads from any Panel Sequencing (PanelSeq) data and gives out single nucleotide variations (SNVs), insertion-deletions (InDels), and copy number variations (CNVs) in single cells alongside with mutation specific information from ClinVar, OncoKB, pathogenicity scores, conservations scores as well as known association to drug response and resistance. We incorporated a Bayesian Neural Network (NN) based Classifier algorithm that assigns a single statistical confidence score to the mutations, enabling prioritization of the mutations in a robust manner. On the training dataset including MDA-MB-453, BT474, BT549 and ZR-75.1 cell lines, the classifier achieved 91% sensitivity and 96% specificity (AUC=0.98), while on the independent test collective including HCC1395/HCC1395BL cell lines it achieved 84% sensitivity and 96% specificity (AUC=0.90). We applied the workflow to patient samples suffering from advanced metastatic Triple Negative Breast Cancer (TNBC) assayed with in-house single-cell Integrated Mutation Profiling of Actionable Cancer Targets (scIMPACT) and single-cell Whole Exome Sequencing (scWES). Using our method, we detected clinically actionable SNVs with pathogenic relevance in primary tumor, metastatic specimens, circulating tumor cells (CTCs) from blood and disseminated cancer cells (DCC) from pleural effusions, as well as the matched CTC-derived in vivo models (CDX). Notably, functional in vitro drug screens performed on CDX models uncovered susceptibility to approved drug treatments conferred by mutations detected in the samples. In summary, we introduce a novel mutation calling workflow facilitating detection of SNVs, Indels and CNVs in rare single cells with high sensitivity and precision. Confident scores assigned by the NN classifier enables identification of functionally actionable mutations. The workflow was executed in GDPR compliant fashion and follows all data protection standards imposed by the European laws. Accordingly, the method is well suited for molecular profiling, therapeutic target selection and longitudinal monitoring of liquid biopsy specimens in diagnostic environments. Citation Format: Adithi Ravikumar Varadarajan, Thomas Ragg, Jonas Grote, Vadim Dechand, Steffi Treitschke, Clara Chaiban, Christoph Klein, Zbigniew Czyz, Jens Warfsmann. A targeted mutation calling workflow - end to end - from FASTQ to clinical report for single cells [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 2283.

Intersections of focused ultrasound and extracellular vesicles: Toward diversified biomarker enrichment and discovery

Extracellular vesicles (EVs) are heterogeneous, membrane-bound structures shed by most fluid-interfacing cell types and play a critical role in orchestrating pathophysiological processes. With the advancement of liquid biopsy for cancer diagnosis and surveillance, EVs have burgeoned as a powerful asset toward circulating biomarker discovery owing to their diverse cargo (i.e., proteins, metabolites, nucleic acids, lipids). With the advent of focused ultrasound (FUS) technology as a tool for “sonobiopsy” in solid tumors, we recognize the increasing importance of deconvolving how the diverse bioeffects of FUS may influence EV quantity and quality. We have examined the impacts of thermal and mechanical FUS regimens on EV release and profile across cancer and immune cell contexts. Our observations suggest that both hyperthermia and microbubble-assisted FUS augment EV release acutely. On closer examination, hyperthermia-exposed EVs also display shifts in proteomic profile and differential immunomodulatory capacity. Ongoing studies are interrogating the impact of other FUS regimens on EV biology. Meanwhile, we are also directly investigating EVs from liquid biopsy specimens spanning murine cancer models, veterinary oncology (spontaneous canine cancers), and clinical trials. We expect that a continued work at the functional intersection of FUS and EVs will yield important, timely insight for this rapidly evolving field.

Development and application of an ultra-sensitive ctDNA mutation profiling assay in monitoring therapy response and drug resistance.

264 Background: Next-generation sequencing (NGS) assays offer efficient high-throughput profiling methods for analyzing circulating tumor DNA (ctDNA) in blood or other liquid biopsy specimens. The ctDNA mutant allele fractions of patients after treatment is often very low and below the detection limit of regular cfDNA assays. Here we report the development and clinical application of a CLIA-certified ultra-sensitive NGS cfDNA assay in detecting the low-frequency ctDNA mutations and monitoring therapy response and drug resistance in patients with metastatic gastroesophageal adenocarcinoma under combined blockade treatments. Methods: PredicineCARE ULTRA cfDNA assay with 100,000X sequencing depth was validated under CLIA settings. Limit of blank (LoB) and limit of detection (LoD) were established by profiling 38 healthy donor plasma samples, 23 contrived human cfDNAs samples from patients with various cancers, and 30 replicates of well-established ctDNA reference standards. In silico down-sampling of FASTQ files was carried out to test the sensitivity of this assay with a lower coverage (50,000X). This assay was then adopted for longitudinal sequencing of 57 serial plasmas from 6 patients with HER2+ gastroesophageal adenocarcinomas (GEC) who underwent combined treatments (capecitabine, oxaliplatin, bevacizumab and trastuzumab) at different time points (baseline, response, and progression). Results: PredicineCARE ULTRA cfDNA assay exhibited exceptional sensitivity in calling single-nucleotide variants and indels, with a 98.0% detection rate at a LoD of 0.075% mutant allele frequency (MAF) for 60 ng cfDNA. This is significantly lower than the LoD (0.25% MAF) of a standard PredicineCARE cfDNA assay. The ultra-sensitive assay also displayed decent analytical specificity (>99.99%) and precision (intra-assay 100%; inter-assay 99.41%). In 6 GEC patients’ longitudinal samples, PredicineCARE ULTRA cfDNA assay detected 36 additional somatic mutations with the MAFs spanning in a range from 0.024% to 0.1% beyond 124 baseline mutations identified using standard PredicineCARE. In two representative cases presented here, all baseline mutations (genes TP53 and PIK3CA etc.) were consistently reported in the follow-up time points with a noticeable MAF reduction (lowest MAFs from 0.046% to 0.024%) during response. Subsequent elevations were observed in more genes, including low-frequency mutations (KRAS and ERBB2) not detected at baseline or only detected in PredicineCARE ULTRA. Conclusions: This study demonstrated the promise and clinical utility of the ultra-sensitive cfDNA molecular profiling at 100,000X sequencing depth in treatment selection, therapy monitoring, and drug resistance studies.

Technical evaluation of a novel digital PCR platform for detecting EGFR/KRAS mutations in NSCLC archived plasma specimens

IntroductionKRAS p.G12C hot spot mutations has rapidly modified diagnostic algorithm for lung cancer patients electing Non-Small Cell Lung Cancer (NSCLC) patients to target treatment. As regards, patients that harbor this hallmark showed a clinical benefit in terms of progression-free survival (PFS) and overall survival (OS) in comparison with control group under target treatment. In this scenario, KRAS p.G12C mutation requires optimized testing strategy in diagnostic routine practice. Although the widespread diffusion of NGS platforms, a not negligible percentage of Italian diagnostic institutions adopt singleplex technology (RT-PCR, dPCR) for molecular testing. Here, we aim to technically validate a novel dPCR system (QIAcuity™ Digital PCR System, Qiagen; Hilden, Germany) on a retrospective series of cfDNA samples from previously tested with a custom NGS system. (1,2)Methods: n = 50 liquid biopsy specimens (n = 25 KRAS/EGFR mutated and n = 25 wild type for actionable KRAS/EGFR mutations) from diagnostic routine NSCLC patients previously tested with a custom NGS panel were retrieved from our internal archival. Each sample was tested by adopting n = 5 KRAS and n = 3 EGFR commercially available dPCR assays on QIAcuity™ Digital PCR System (Qiagen; Hilden, Germany); an ultra-deep dPCR walk-away platform that automatizes molecular analysis. Technical sensitivity, technical specificity, and concordance rate between “gold standard” NGS system and QIAcuity™ Digital PCR System (Qiagen; Hilden, Germany) were assessed. ResultsOverall, all specimens were successfully analyzed with dPCR system. In details, 24 out of 25 mutated and 21 out of 24 wild type cases were detected. A technical sensitivity, specificity, and a concordance rate of 96.0 % (24/25), 88.0 % (22/25) and 92.0 % (46/50) were evaluated taking into account a MAF cut-off ≥ 0.2 % and a partition number of 100 positive partitions in wild-type channel. ConclusionQiacuity (Qiagen; Hilden, Germany) platform enables accurate molecular analysis of diagnostic routine specimens. Optimized technical workflow is required to technically implement this platform in diagnostic routine setting.

Usefulness of Liquid Biopsy for Veteran Patients with Metastatic Lung Cancer

Abstract Introduction/Objective The National Comprehensive Cancer Network (NCCN) non-small cell lung cancer (NSCLC) Guidelines Panel strongly advises the use of broad molecular tumor profiling to identify rare driver mutations in patients with advanced or metastatic disease. This testing could either be performed on the tumor sample itself or from liquid biopsy with next generation sequencing. Liquid biopsy presents a minimally invasive opportunity to obtain molecular information from circulating tumor cells (CTC) that may impact treatment. However, the literature of metastatic lung cancers targeted by liquid biopsies and the mutations found is sparse, particularly for the veteran population. Methods/Case Report A retrospective review was performed of all patients with a submitted liquid biopsy specimen at a Veteran Affairs Medical Center (VAMC) from November 26th, 2019, to March 3rd, 2023, to exa mine those patients with metastatic lung cancer. Information on mutations detected was collected. Results (if a Case Study enter NA) There were a total of 35 patient specimens with a history of metastatic lung cancer, from which 34 cases had an available liquid biopsy report. The first liquid biopsy for a patient with metastatic lung cancer was sent on November 26th, 2019. Some of the more common mutations identified through the liquid biopsy included KRAS (7/34), TP53 (15/34), and TERT promoter (3/34). 5 of these 34 cases had no reportable genomic alterations detected. Conclusion Liquid biopsies are a non-invasive, powerful diagnostic tool that is highly useful for broad molecular tumor profiling for precise management and for appropriate counseling of patients on treatment as per the standard of care clinical practice guidelines (such as from the NCCN).

Liquid Biopsy as a Powerful Therapeutic Tool in Veteran Patients with Prostate Carcinoma

Abstract Introduction/Objective The National Comprehensive Cancer Network (NCCN) guidelines currently recommend somatic tumor molecular testing for alterations in homologous recombination (HR) DNA repair genes in patients with metastatic prostate cancer, which can be performed on either the sampled tumor tissue itself or by liquid biopsy. Particularly when the sampled tumor tissue may be limited, liquid biopsy with next generation sequencing is a recently available attractive alternative that is minimally invasive (requiring just phlebotomy). Based on the information gathered from circulating tumor cells (CTC), a tumor molecular profile can be obtained that can impact treatment, particularly if a HR DNA repair mutation is found as that may predict response to a poly (ADP-ribose) polymerase (PARP) enzyme inhibitor such as Olaparib. However, the literature of metastatic prostate cancers targeted by liquid biopsies and the mutations found is sparse, particularly for the veteran population. Methods/Case Report A retrospective review was performed of all patients with a submitted liquid biopsy specimen at a Veteran Affairs Medical Center (VAMC) October 23rd, 2019, to March 3rd, 2023 to examine those patients with metastatic prostate cancer. Information on mutations detected was collected. Results (if a Case Study enter NA) There were a total of 64 patient specimens with a history of metastatic prostate cancer, from which 56 had an available liquid biopsy report with the first liquid biopsy collection occurring on October 23rd, 2019. HR DNA repair mutations found included CHEK2 (6/56), ATM (4/56), and BRCA1 (1/56). Outside of HR DNA repair genes, relatively common detected mutations were found in TP53 (25/56), PTEN (6/56), BRAF (4/56), and an AR amplification (4/56). 7 of the 56 reports had no reportable genomic alterations detected. Conclusion Liquid biopsies continues to be a minimally invasive, highly useful powerful therapeutic tool in veteran patients with metastatic prostate carcinoma for molecular profiling. Not uncommonly in the Veteran population, these molecular findings include mutations in HR DNA repair genes that as noted by the NCCN may predict response to PARP inhibitor chemotherapy.

Veteran Healthcare System: A Unique Healthcare Setting Providing Equitable Access to all Patients with Metastatic Lung Cancer in the Era of Precision Diagnostics

Abstract Introduction/Objective The National Comprehensive Cancer Network (NCCN) Non-Small Cell Lung Cancer (NSCLC) Guidelines Panel strongly advises broad molecular tumor profiling to identify mutations that help guide precision- based patient tailored therapy and subsequent patient counseling. Liquid biopsy with next generation sequencing represents a powerful tool to obtain this information through phlebotomy but is costly and only recently available. Although ethnic minorities may not have the same access to health care resources, studies of ethnic access to liquid biopsies in the setting of Veteran patients at a Veteran Affairs Medical Center (VAMC) with metastatic lung cancer have not been well studied. Methods/Case Report A retrospective review was performed of all patients with a submitted liquid biopsy specimen at a VAMC and a history of metastatic lung cancer from November 26th, 2019, to March 3rd, 2023. Demographic data was collected for each patient specimen and compared with the ethnic proportions noted in the census of the city where the VAMC is located. Results (if a Case Study enter NA) There were a total of 35 patient specimens, with the first liquid biopsy collection occurring on November 26th, 2019. The mean age of the patients was 70. The ethnic composition of the population was as follows: 16 were African American (45.7%), 16 were Caucasian American (45.7%), 2 mixed ethnicity (5.7%), and 1 declined to answer or were of unknown ethnicity (2.9%). The census of the surrounding metropolitan area demonstrated a general population ethnic composition of 43.6% African American and 44.4% Caucasian American. Conclusion The proportion of Veteran patients of each ethnicity with metastatic lung cancer that received liquid biopsy testing was similar to the ethnic distribution of the general population of the surrounding metropolitan area. This demonstrates that there was equitable access to this testing modality at the VAMC with potential to deliver best cancer care to the veterans by detection, prognosis, and monitoring treatment outcomes.

Liquid Biopsy: A Highly Useful Tool to Decide Personalized Therapy in Veteran Patients with Metastatic Pancreaticobiliary Cancer

Abstract Introduction/Objective Pancreatic cancer is one of the leading causes of death in Veteran patients. Early detection and treatment of the pancreatic cancers are key to the successful management of pancreatic cancer with good patient outcome. The National Comprehensive Cancer Network (NCCN) recommends tumor molecular profiling in all patient cases of unresectable or metastatic pancreatic adenocarcinomas and biliary tract cancers who are candidates for chemotherapy. This testing can be performed using liquid biopsy to obtain this molecular profiling from circulating tumor cells (CTC) to obtain information that may impact treatment. However, the literature of metastatic pancreaticobiliary cancers targeted by liquid biopsies and the mutations found is sparse, particularly for the veteran population. Methods/Case Report A retrospective review was performed of all patients with a submitted liquid biopsy specimen at a Veteran Affairs Medical Center (VAMC) from April 2020 to March 3rd, 2023, to examine those patients with metastatic pancreaticobiliary cancers, specifically pancreatic adenocarcinoma, and cholangiocarcinoma. Information on mutations detected was collected. Results (if a Case Study enter NA) There were a total of 5 patient specimens with a history of metastatic pancreatic adenocarcinoma (4 cases/5) and cholangiocarcinoma (1 case/5). The first liquid biopsy from a patient with a history of metastatic pancreaticobiliary cancer was sent on April 14th, 2020, and the last was sent on November 12th, 2021. TP53 was detected on all the successfully tested pancreatic adenocarcinoma cases. Other mutations detected in the individual pancreatic adenocarcinoma cases were KRAS, TET2 BCOR, DNMT3A, FUBP1, RAD21, and STAG2. The mutations found on the single cholangiocarcinoma case included DNMT3A and TP53. 1 of the 4 cases sent on a patient with pancreatic adenocarcinoma resulted in a sample failure. Conclusion Liquid biopsies provided comprehensive molecular profiling in cases of metastatic pancreatic adenocarcinoma and biliary tract cancer in the veteran population treated at a local VAMC to help decide on personalized therapy, in compliance with the recommendations of the NCCN. The results of this pilot quality assurance study help highlight the potential of liquid biopsies to detect most commonly mutated genes such as KRAS and T53 in pancreatic cancer.

SAT587 Methylation-based Machine Learning Classifiers Discriminate Sellar Tumors By Lobe Origin Using Liquid Biopsy Or Surgical Specimens

Abstract Disclosure: G.A. Herrgott: None. K.P. Asmaro: None. M. Wells: None. K. Nelson: None. B. Thomas: None. L.A. Hasselbach: None. A. Transou: None. S. Cazacu: None. K.M. Tundo: None. S. Nadimidla: None. L. Scarpace: None. J. Barnholtz-Sloan: None. A.E. Sloan: None. W.R. Selman: None. A.C. deCarvalho: None. A. Mukherjee: None. A.M. Robin: None. I.Y. Lee: None. J. Craig: None. S. Kalkanis: None. J. Snyder: None. T. Walbert: None. J. Rock: None. H. Noushmehr: None. A.B. Castro: None. Background: The differential diagnosis of challenging sellar tumor cases can be inconclusive through imaging features and could benefit from noninvasive diagnostic approaches, such as liquid biopsy (LB). Similar to tissue, LB specimens carry tumor-specific DNA methylation signatures amenable to the construction of accurate machine learning models able to discriminate CNS tumors. We aimed to develop methylation-based classifiers which classify sellar tumors by lobe of origin, using either LB or tumor tissue specimens. Methodology: We analyzed the DNA methylome (EPIC array) of tumor tissue (T) and LB specimens from adult patients with tumors representing each of the three pituitary lobes (Anterior: T=177; LB=37; Intermediate: T= 7; LB: 10 and Posterior: T=44, LB=2 cases). Using the most variably methylated CpG probes derived from the unsupervised variance-based analyses across tumors from different lobes, we applied multi-class linear discriminant analysis to construct machine learning models to classify sellar tumor tissue and/or LB specimens. Results: We generated classifiers based on lobe-specific methylation signatures that were able to discriminate across sellar tumors either using tissue and/or LB specimens (500 and 600 CpGs, respectively) with observed accuracies of ∼99% across independent validation. DISCUSSION/CONCLUSION: Our findings suggest that methylation-based classifiers constitute an accurate diagnostic approach to discriminate sellar tumors according to the lobe origin, either pre-surgically through a blood draw or through surgical tumor specimens. These classifiers are objective approaches that could complement imaging and pathology reports for an accurate diagnosis of inconclusive cases, ultimately leading to optimal management of the patients with these diseases. Presentation: Saturday, June 17, 2023

Influencing Best Practices for Genomic and Germline Testing in Urology.

To evaluate germline and somatic testing practices and compare results from tissue and liquid biopsy specimens in a large community urology setting. A retrospective analysis was performed on advanced prostate cancer patients from a single community practice between June 2016 and September 2021. Clinical data and sequencing results from tissue and liquid biopsy specimens were available for 389 patients. Genomic data were available for 81 tissues and 74 liquid biopsy specimens. Comparison of genomic findings included 81 tissues and 27 liquid biopsy specimens. The number of actionable biomarkers and patients screened and enrolled in clinical trials was assessed from germline and somatic testing. Frequency of pathogenically altered genes, alteration types, and biomarkers were assessed from tissue and liquid specimens. Alteration frequency was compared between specimen types for the top 25 altered genes. Clinically relevant alterations were found from germline and somatic testing in both tissue and liquid biopsy specimens. The frequency of microsatellite instability-high, tumor mutational burden-high, or alterations in homologous recombination repair genes was consistent with published findings. Concordance between tissue and liquid findings varied with low circulating tumor DNA. Germline and somatic testing is critical for treatment decisions and should be standard of care for community practices. Liquid biopsy is a viable alternative when circulating tumor DNA is high.

Detection of diagnostic and prognostic methylation-based signatures in liquid biopsy specimens from patients with meningiomas

Recurrence of meningiomas is unpredictable by current invasive methods based on surgically removed specimens. Identification of patients likely to recur using noninvasive approaches could inform treatment strategy, whether intervention or monitoring. In this study, we analyze the DNA methylation levels in blood (serum and plasma) and tissue samples from 155 meningioma patients, compared to other central nervous system tumor and non-tumor entities. We discover DNA methylation markers unique to meningiomas and use artificial intelligence to create accurate and universal models for identifying and predicting meningioma recurrence, using either blood or tissue samples. Here we show that liquid biopsy is a potential noninvasive and reliable tool for diagnosing and predicting outcomes in meningioma patients. This approach can improve personalized management strategies for these patients.

Detection of methylation-based prognostic signatures in liquid biopsy specimens from patients with meningiomas.

2073 Background: Detection of distinct epigenetic biomarkers in circulating cell-free DNA (cfDNA) of liquid biopsy (LB) specimens (e.g. blood) fosters opportunity for prognostication of central nervous system (CNS) tumors and has not been thoroughly explored in patients with meningiomas. Methods: We profiled the cfDNA methylome (EPIC array) in serum from patients with meningiomas (MNG; n = 93) and harnessed internal and external meningioma tissue methylome data with reported follow up (n = 77). To predict recurrence risk (RR), we consolidated a tissue cohort with at least 5 years of follow up and divided them into confirmed recurrence (CR; either reported progressive disease in post-surgical imaging, or additional resections following initial surgery) and confirmed no-recurrence (CNR: no confirmed disease progression w/in at least 5-years of follow-up). Then through application of an iterative process consisting of multiple tissue- and serum-based supervised analyses, we identified risk-specific methylation markers with potential for serum application. which, when inputted into a random forest algorithm allowed for segregation of both tumor tissue and liquid biopsy specimens according to recurrence risk. We estimated immune cell composition using MethylCIBERSORT, where a reference methylome atlas of chosen immune cell types was utilized to deconvolute the MNG samples. Results: The resulting recurrence risk classifier demonstrated an appreciable predictive power in classifying samples as high or low recurrence risk across the tumor tissue cohort (ACC: 87.7%, CUI+: 86.4%). When compared to another classifier of rivaling purpose, our model demonstrated statistically significant agreement across primary meningioma samples (κ = 0.269, p = 0.01), and more accurately predicted samples to recur across expanded time windows (time to recurrence > 5 yrs). Across resulting liquid biopsy classifications, recurrence risk subgroups were analogous with reported risk factors, including WHO grade, extent of resection, and tumor location. Recurrence risk subgroups also demonstrated differential estimated immune cell contributions, with low-risk samples exhibiting a “hot” profile, or enrichment of B-Cells, CD56- and CD4 T-Cells, and natural killer cells. Notably, the estimated neutrophil to lymphocyte ratio, previously purported to be relevant to tumor prognosis, was appreciably higher for those meningioma samples with the highest recurrence risk. Conclusions: DNA methylation markers identified in the serum are suitable for the development of machine learning-based models which present high predictive power to prognosticate patients with meningioma and estimate a differential immune profile across recurrence risk groups. After validation in an external cohort, this noninvasive approach may improve the presurgical therapeutic management of patients with meningiomas.

Multiplex Digital Methylation-Specific PCR for Noninvasive Screening of Lung Cancer.

There remains tremendous interest in developing liquid biopsy assays for detection of cancer-specific alterations, such as mutations and DNA methylation, in cell-free DNA (cfDNA) obtained through noninvasive blood draws. However, liquid biopsy analysis is often challenging due to exceedingly low fractions of circulating tumor DNA (ctDNA), necessitating the use of extended tumor biomarker panels. While multiplexed PCR strategies provide advantages such as higher throughput, their implementation is often hindered by challenges such as primer-dimers and PCR competition. Alternatively, digital PCR (dPCR) approaches generally offer superior performance, but with constrained multiplexing capability. This paper describes development and validation of the first multiplex digital methylation-specific PCR (mdMSP) platform for simultaneous analysis of four methylation biomarkers for liquid-biopsy-based detection of non-small cell lung cancer (NSCLC). mdMSP employs a microfluidic device containing four independent, but identical modules, housing a total of 40 160 nanowells. Analytical validation of the mdMSP platform demonstrates multiplex detection at analytical specificities as low as 0.0005%. The clinical utility of mdMSP is also demonstrated in a cohort of 72 clinical samples of low-volume liquid biopsy specimens from patients with computed tomography(CT)-scan indeterminant pulmonary nodules, exhibiting superior clinical performance when compared to traditional MSP assays for noninvasive detection of early-stage NSCLC.