MA 11.02 Circulating Tumor DNA in Early Stage NSCLC: High Sensitivity Analysis in Low Burden Disease. LUCID Study Update

Abstract BACKGROUND The diagnosis of intracranial tumors relies on tissue specimens obtained by invasive surgery. Non-invasive diagnostic approaches, particularly for patients with brain tumours, provide an opportunity to avoid surgery and mitigate unnecessary risk to patients. We reasoned that DNA methylation profiles of circulating tumor DNA in blood can be used as a clinically useful biomarker for patients with brain tumors, given the specificity of DNA methylation profiles for cell-of-origin. METHODS We generated methylation profiles on the plasma of 608 patients with cancer (219 intracranial, 388 extracranial) and 60 healthy controls using a cell-free methylated DNA immunoprecipitation combined with deep sequencing (cfMeDIP-seq) approach. Using machine-learning approaches we generated and evaluated models to distinguish brain tumors from extracranial cancers that may metastasize to the brain, as well as additional models to discriminate common brain tumors included in the differential diagnosis of solitary extra-axial and intra-axial tumors. RESULTS We observed high sensitivity and discriminative capacity for our models to distinguish gliomas from other cancerous and healthy patients (AUC=0.99, 95%CI 0.96–1), with similar performance in IDH mutant and wildtype gliomas as well as in lower- and high-grade gliomas. Excluding non-malignant contributors to plasma methylation did not change model performance (AUC=0.982, 95%CI 0.93–1). Models generated to discriminate intracranial tumors from each other also demonstrated high accuracy for common extra-axial tumors (AUCmeningioma=0.89, 95%CI 0.80–0.97; AUChemangiopericytoma=0.95, 95%CI 0.73–1) as well as intra-axial tumors ranging from low-grade indolent glial-neuronal tumors (AUC 0.93, 95%CI 0.80 – 1) to diffuse intra-axial gliomas with distinct molecular composition (AUCIDH-mutant glioma = 0.82, 95%CI 0.66 -0.98; AUCIDH-wildtype-glioma = 0.71, 95%CI 0.53 – 0.9). Plasma cfMeDIP-seq signals originated from corresponding tumor tissue DNA methylation signals (r=0.37, p< 2.2e-16). CONCLUSIONS These results demonstrate the potential for cfMeDIP-seq profiles to not only detect circulating tumor DNA, but to accurately discriminate common intracranial tumors that share cell-of-origin lineages.

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Detection of KRAS Mutations in Circulating Tumor DNA by Digital PCR in Early Stages of Pancreatic Cancer

Clinical Chemistry ◽

10.1373/clinchem.2016.257469 ◽

2016 ◽

Vol 62 (11) ◽

pp. 1482-1491 ◽

Cited By ~ 55

Author(s):

Nora Brychta ◽

Thomas Krahn ◽

Oliver von Ahsen

Keyword(s):

Pancreatic Cancer ◽

Early Stage ◽

Digital Pcr ◽

Circulating Tumor Dna ◽

Surgical Removal ◽

Plasma Samples ◽

Kras Mutations ◽

Detection Rates ◽

Early Stages ◽

Tumor Dna

Abstract BACKGROUND Since surgical removal remains the only cure for pancreatic cancer, early detection is of utmost importance. Circulating biomarkers have potential as diagnostic tool for pancreatic cancer, which typically causes clinical symptoms only in advanced stage. Because of their high prevalence in pancreatic cancer, KRAS proto-oncogene, GTPase [KRAS (previous name: Kirsten rat sarcoma viral oncogene homolog)] mutations may be used to identify tumor-derived circulating plasma DNA. Here we tested the diagnostic sensitivity of chip based digital PCR for the detection of KRAS mutations in circulating tumor DNA (ctDNA) in early stage pancreatic cancer. METHODS We analyzed matched plasma (2 mL) and tumor samples from 50 patients with pancreatic cancer. Early stages (I and II) were predominant (41/50) in this cohort. DNA was extracted from tumor and plasma samples and tested for the common codon 12 mutations G12D, G12V, and G12C by chip-based digital PCR. RESULTS We identified KRAS mutations in 72% of the tumors. 44% of the tumors were positive for G12D, 20% for G12V, and 10% for G12C. One tumor was positive for G12D and G12V. Analysis of the mutations in matched plasma samples revealed detection rates of 36% for G12D, 50% for G12V, and 0% for G12C. The detection appeared to be correlated with total number of tumor cells in the primary tumor. No KRAS mutations were detected in 20 samples of healthy control plasma. CONCLUSIONS Our results support further evaluation of tumor specific mutations as early diagnostic biomarkers using plasma samples as liquid biopsy.

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MA07.06 Circulating Tumor DNA for Monitoring Minimal Residual Disease and Early Detection of Recurrence in Early Stage Lung Cancer

Journal of Thoracic Oncology ◽

10.1016/j.jtho.2021.08.144 ◽

2021 ◽

Vol 16 (10) ◽

pp. S907

Author(s):

A. Tan ◽

G. Lai ◽

S. Saw ◽

K. Chua ◽

A. Takano ◽

...

Keyword(s):

Lung Cancer ◽

Early Detection ◽

Minimal Residual Disease ◽

Residual Disease ◽

Early Stage ◽

Circulating Tumor Dna ◽

Early Stage Lung Cancer ◽

Tumor Dna ◽

Minimal Residual ◽

Stage Lung Cancer

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Targeted next-generation sequencing of endometrial cancer and matched circulating tumor DNA: identification of plasma-based, tumor-associated mutations in early stage patients

Modern Pathology ◽

10.1038/s41379-018-0158-8 ◽

2018 ◽

Vol 32 (3) ◽

pp. 405-414 ◽

Cited By ~ 12

Author(s):

Ana M. Bolivar ◽

Rajyalakshmi Luthra ◽

Meenakshi Mehrotra ◽

Wei Chen ◽

Bedia A. Barkoh ◽

...

Keyword(s):

Endometrial Cancer ◽

Next Generation Sequencing ◽

Early Stage ◽

Circulating Tumor Dna ◽

Next Generation ◽

Dna Identification ◽

Targeted Next Generation Sequencing ◽

Tumor Dna ◽

Generation Sequencing

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Electroanalytical Biosensors for Circulating Tumor DNA Detection—A Brief Review

10.20944/preprints202111.0357.v1 ◽

2021 ◽

Author(s):

Zhijia Peng ◽

Xiaogang Lin ◽

Weiqi Nian ◽

Xiaodong Zheng ◽

Jayne Wu

Keyword(s):

Real Time ◽

Point Of Care ◽

Low Cost ◽

High Sensitivity ◽

High Specificity ◽

Circulating Tumor Dna ◽

Minimal Invasive ◽

Diagnosis And Treatment ◽

Detection Technology ◽

Tumor Dna

Early diagnosis and treatment have always been highly desired in the fight against cancer, and detection of circulating tumor DNA (ctDNA) has recently been touted as highly promising for early cancer screening. Consequently, the detection of ctDNA in liquid biopsy gains much attention in the field of tumor diagnosis and treatment, which has also attracted research interest from the industry. However, traditional gene detection technology is difficult to achieve low cost, real-time and portable measurement of ctDNA. Electroanalytical biosensors have many unique advantages such as high sensitivity, high specificity, low cost and good portability. Therefore, this review aims to discuss the latest development of biosensors for minimal-invasive, rapid, and real-time ctDNA detection. Various ctDNA sensors are reviewed with respect to their choices of receptor probes, detection strategies and figures of merit. Aiming at the portable, real-time and non-destructive characteristics of biosensors, we analyze their development in the Internet of Things, point-of-care testing, big data and big health.

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Ultra-low Input Circulating Tumor DNA Detection by MED-Amp in Early-Stage Pancreatic Cancer

10.1101/2021.03.28.437388 ◽

2021 ◽

Author(s):

Erica D Pratt ◽

David B Zhen ◽

Robert W Cowan ◽

Heather Cameron ◽

Kara Schradle ◽

...

Keyword(s):

Early Stage ◽

Locally Advanced ◽

Progression Free Survival ◽

Circulating Tumor Dna ◽

Fold Change ◽

Diagnostic Sensitivity ◽

Ductal Adenocarcinoma ◽

Kras Mutations ◽

The Relationship ◽

Tumor Dna

Purpose: The clinical utility of circulating tumor DNA (ctDNA) has been shown in advanced pancreatic ductal adenocarcinoma (PDA). However, diagnostic sensitivity of many ctDNA assays is low in resectable and locally advanced disease, where tumor burden is substantially lower. We have previously described Multiplex Enrichment using Droplet Pre-Amplification (MED-Amp), a multiplexed panel for the detection of the most common oncogenic KRAS mutations in PDA. In this study, we aimed to assess the diagnostic sensitivity of MED-Amp for detection of rare mutant alleles present in the plasma of patients with localized PDA. Experimental Design: We retrospectively analyzed ninety-eight plasma samples from 51 patients with various stages of localized disease. For comparison, we measured ctDNA levels in 20 additional patients with metastatic PDA. The MED-Amp assay was used to measure the abundance of the four most common KRAS codon 12 mutations (G12C/D/R/V). We correlated the presence and quantity of ctDNA with overall survival (OS) as well as progression-free survival (PFS). Using serial plasma draws, we also assessed the relationship between changes in ctDNA allelic frequency and progression. Results: KRAS-positive ctDNA was detected in 52.9% of localized PDA and 75% of metastatic samples tested using DNA inputs as low as 2 ng. As previously reported, the presence of KRAS mutant ctDNA was correlated with worse OS for all disease stages (p = 0.02). In patients with localized PDA high ctDNA levels also correlated with significantly worse median OS (533 days vs 1090 days) and PFS (192 days vs 787 days). We also studied a small cohort of serial plasma draws to observe the relationship between ctDNA fold change and PFS. We found 83% of patients with increased fold change in mutant KRAS experienced disease progression (n=6). In contrast, 75% (n=4) of patients with decreased fold change remained disease-free (p=0.03). Conclusions: MED-Amp is a flexible and cost-effective approach for measurement of ctDNA in patients with localized cancer. Though this study focused on KRAS mutation detection, this assay could be adapted for a number of common oncogenic alterations.

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