scholarly journals ctDNA Detection in Microfluidic Platform: A Promising Biomarker for Personalized Cancer Chemotherapy

2020 ◽  
Vol 2020 ◽  
pp. 1-10
Author(s):  
Samla Gauri ◽  
Mohd R. Ahmad
Keyword(s):  
Cancer Chemotherapy ◽  
Liquid Biopsy ◽  
Treatment Resistance ◽  
Circulating Tumor Cell ◽  
Circulating Tumor Dna ◽  
Microfluidic System ◽  
Tumor Biopsy ◽  
Ctdna Analysis ◽  
Personalized Cancer

Early detection and characterization of circulating tumor DNA (ctDNA) can reveal mint of comprehensive biological insights from indicating the presence of tumor, identifying mutational changes of malignant cells, and allowing precision or targeted therapy together with monitoring disease progression, treatment resistance, and relapse of the disease. Apart from these, one of the greatest axiomatic implications of ctDNA detection is that it provides a new shed of light as noninvasive liquid biopsy as a replaceable procedure of surgical tumor biopsy. Despite the tremendous potential of ctDNA in cancer research, there remains a paucity of quantitative study on ctDNA detection and analysis. The majority of previously published microfluidic-based studies have focused on circulating tumor cell (CTC) detection and have failed to address the potential of ctDNA. The studies on microfluidic ctDNA detection are not consistent might be due to the complexity of ctDNA isolation as they present in low concentration in blood plasma. Researchers need to leverage the ability of microfluidic system for ctDNA analysis so that the significant enigma about cancer can be resolved effectively. This study, therefore, highlights the importance of ctDNA as cancer biomarker for liquid biopsy and provides an overview of the current laboratory as well as microfluidic techniques for ctDNA detection. This paper also attempts to show the emergence of new strands of microfluidic ctDNA detection and analysis for personalized cancer chemotherapy.

scholarly journals The Use of Microfluidic Technology for Cancer Applications and Liquid Biopsy

Micromachines ◽  
2018 ◽  
Vol 9 (8) ◽  
pp. 397 ◽  
Author(s):  
Arutha Kulasinghe ◽  
Hanjie Wu ◽  
Chamindie Punyadeera ◽  
Majid Warkiani
Keyword(s):  
Tumor Markers ◽  
Liquid Biopsy ◽  
Point Of Care ◽  
High Sensitivity ◽  
Circulating Tumor Dna ◽  
Diagnostic Tools ◽  
Tumor Biomarkers ◽  
Blood Draw ◽  
Tumor Biopsy ◽  
Microfluidic Technology

There is growing awareness for the need of early diagnostic tools to aid in point-of-care testing in cancer. Tumor biopsy remains the conventional means in which to sample a tumor and often presents with challenges and associated risks. Therefore, alternative sources of tumor biomarkers is needed. Liquid biopsy has gained attention due to its non-invasive sampling of tumor tissue and ability to serially assess disease via a simple blood draw over the course of treatment. Among the leading technologies developing liquid biopsy solutions, microfluidics has recently come to the fore. Microfluidic platforms offer cellular separation and analysis platforms that allow for high throughout, high sensitivity and specificity, low sample volumes and reagent costs and precise liquid controlling capabilities. These characteristics make microfluidic technology a promising tool in separating and analyzing circulating tumor biomarkers for diagnosis, prognosis and monitoring. In this review, the characteristics of three kinds of circulating tumor markers will be described in the context of cancer, circulating tumor cells (CTCs), exosomes, and circulating tumor DNA (ctDNA). The review will focus on how the introduction of microfluidic technologies has improved the separation and analysis of these circulating tumor markers.

The results of a study of the concordance of RAS status in liquid and invasive biopsies in patients with metastatic colorectal cancer in the Republic of Kazakhstan.

2020 ◽  
Vol 38 (15_suppl) ◽  
pp. e16017-e16017
Author(s):  
Kaldigul Smagulova ◽  
Dilyara Kaidarova ◽  
Yelena Ukolova ◽  
Madina Orazgalieva ◽  
Anel Kurmankulova
Keyword(s):  
Colorectal Cancer ◽  
Liquid Biopsy ◽  
Point Mutations ◽  
Diagnostic System ◽  
Circulating Tumor Dna ◽  
Diagnostic Methods ◽  
Molecular Diagnostic ◽  
Wild Type ◽  
Kras Gene ◽  
Tumor Biopsy

e16017 Background: Liquid biopsy is increasingly of interest as an alternative to invasive biopsy of solid tumors for predicting, making decisions about the treatment and monitoring of the disease. Particular preference is given to liquid biopsy in cases where it is not possible to obtain a sufficient amount of material or material of poor quality with a tumor biopsy. However, in order to find out the clinical significance of circulating tumor DNA (ctDNA), it is important to first establish the sensitivity of the method using tumor-plasma consistency studies. Methods: We selected 38 patients with a confirmed diagnosis of colorectal cancer (CRC), in whom was established the progression of the disease. All patients underwent two diagnostic methods, which we divided conditionally into 2 groups: A – invasive biopsy from available metastatic foci; to detect mutations in exons 2, 3, and 4 the KRAS gene used a reagent kit to detect 18 point mutations in codons 12,13,61,117,146 and a reagent kit to identify 10 mutations of the NRAS gene in codons 12,13,61,146 (Entrogen) on a Rotor-Gene 6000 Amplifier; B - liquid biopsy, to determine 21 mutations in the codons 12,13,59,61,117,146 of the KRAS gene, 18 mutations in the codons of 12,13,59,61,117,146 of the NRAS gene, was used Idylla automated molecular diagnostic system. Results: Of the 38 studied samples of group A: 22 (57.9%) had wild type KRAS, 16 (42.1%) were mutated, in group B: wild type had 25 (65.8%) patients, mutated - 13 (34, 2%). Thus, we see a discrepancy in the results in 3 (7.9%) of 38 cases. Conclusions: The results indicate a high degree of sensitivity (92.1%) of liquid biopsy as a diagnostic method, but confirmation of concordance with traditional tissue biopsy requires further in-depth study of this issue in a larger sample of patients.

scholarly journals Rational Development of Liquid Biopsy Analysis in Renal Cell Carcinoma

Cancers ◽  
2021 ◽  
Vol 13 (22) ◽  
pp. 5825
Author(s):  
Kate I. Glennon ◽  
Mahafarin Maralani ◽  
Narges Abdian ◽  
Antoine Paccard ◽  
Laura Montermini ◽  
...  
Keyword(s):  
Renal Cell Carcinoma ◽  
Cell Carcinoma ◽  
Liquid Biopsy ◽  
Renal Cell ◽  
Somatic Mutations ◽  
Circulating Tumor Dna ◽  
Precision Oncology ◽  
Liquid Biopsies ◽  
Disease Evolution ◽  
Ctdna Analysis

Renal cell carcinoma (RCC) is known for its variable clinical behavior and outcome, including heterogeneity in developing relapse or metastasis. Recent data highlighted the potential of somatic mutations as promising biomarkers for risk stratification in RCC. Likewise, the analysis of circulating tumor DNA (ctDNA) for such informative somatic mutations (liquid biopsy) is considered an important advance for precision oncology in RCC, allowing to monitor molecular disease evolution in real time. However, our knowledge about the utility of ctDNA analysis in RCC is limited, in part due to the lack of RCC-appropriate assays for ctDNA analysis. Here, by interrogating different blood compartments in xenograft models, we identified plasma cell-free (cf) DNA and extracellular vesicles (ev) DNA enriched for RCC-associated ctDNA. Additionally, we developed sensitive targeted sequencing and bioinformatics workflows capable of detecting somatic mutations in RCC-relevant genes with allele frequencies ≥ 0.5%. Applying this assay to patient-matched tumor and liquid biopsies, we captured tumor mutations in cf- and ev-DNA fractions isolated from the blood, highlighting the potentials of both fractions for ctDNA analysis. Overall, our study presents an RCC-appropriate sequencing assay and workflow for ctDNA analysis and provides a proof of principle as to the feasibility of detecting tumor-specific mutations in liquid biopsy in RCC patients.

scholarly journals Translational Application of Circulating DNA in Oncology: Review of the Last Decades Achievements

Cells ◽  
2019 ◽  
Vol 8 (10) ◽  
pp. 1251 ◽  
Author(s):  
Tuaeva ◽  
Falzone ◽  
Porozov ◽  
Nosyrev ◽  
Trukhan ◽  
...  
Keyword(s):  
Early Diagnosis ◽  
Liquid Biopsy ◽  
Prognostic Significance ◽  
Circulating Tumor Dna ◽  
Molecular Techniques ◽  
Unknown Primary ◽  
Diagnostic Strategies ◽  
Early Diagnosis Of Cancer ◽  
Mutational Status ◽  
Ctdna Analysis

In recent years, the introduction of new molecular techniques in experimental and clinical settings has allowed researchers and clinicians to propose circulating-tumor DNA (ctDNA) analysis and liquid biopsy as novel promising strategies for the early diagnosis of cancer and for the definition of patients’ prognosis. It was widely demonstrated that through the non-invasive analysis of ctDNA, it is possible to identify and characterize the mutational status of tumors while avoiding invasive diagnostic strategies. Although a number of studies on ctDNA in patients’ samples significantly contributed to the improvement of oncology practice, some investigations generated conflicting data about the diagnostic and prognostic significance of ctDNA. Hence, to highlight the relevant achievements obtained so far in this field, a clearer description of the current methodologies used, as well as the obtained results, are strongly needed. On these bases, this review discusses the most relevant studies on ctDNA analysis in cancer, as well as the future directions and applications of liquid biopsy. In particular, special attention was paid to the early diagnosis of primary cancer, to the diagnosis of tumors with an unknown primary location, and finally to the prognosis of cancer patients. Furthermore, the current limitations of ctDNA-based approaches and possible strategies to overcome these limitations are presented.

Circulating tumor DNA analysis of genomic alterations in metastatic urothelial carcinoma from NCT03113266 study.

2021 ◽  
Vol 39 (6_suppl) ◽  
pp. 486-486
Author(s):  
Haige Chen ◽  
Ruiyun Zhang ◽  
Feng Xie ◽  
Pan Du ◽  
Yue Zhang ◽  
...  
Keyword(s):  
Urothelial Carcinoma ◽  
Liquid Biopsy ◽  
Circulating Tumor Dna ◽  
Genomic Alterations ◽  
Invasive Approach ◽  
Synonymous Mutations ◽  
Therapeutic Decisions ◽  
Metastatic Urothelial Carcinoma ◽  
Ctdna Analysis ◽  
Tumor Dna

486 Background: Recent studies have suggested the predictive value of liquid biopsies for immune checkpoint inhibitors. NCT03113266 is a multicenter phase II trial to evaluate the safety and efficacy of toripalimab (anti-PD-1) in metastatic urothelial carcinoma (mUC). Here we report the initial circulating tumor DNA (ctDNA) analysis of genomic alterations from a single-institution biomarker cohort. Methods: Twenty-seven mUC patients receiving toripalimab (3 mg/kg Q2W) at Ren Ji Hospital were enrolled and consented to Institutional Review Board-approved protocols permitting biomaterial collection and genetic sequencing. Serial plasma specimens were obtained at baseline and every two cycles. The 600-gene panel (PredicineATLAS) liquid biopsy assay was applied to assess somatic variants and blood tumor mutational burden (bTMB). Results: The ctDNA assays were performed successfully for 100% of baseline samples (n = 27) with average read depth of 24,389 (range 14,000-31,700). A total of 571 non-synonymous mutations were identified, demonstrating prevalent aberrations in TP53 (63%), TERT promoter (30%), KDM2D (26%), PPM1D (26%), and KDM6A (26%). In 5 patients, FGFR3 variants were detected, including 6 missense sites and 4 FGFR3- TACC3 fusion events. Copy number gain ( FGFR1, ERBB2) and loss ( PTEN, BRCA2, CDKN2A) were pinpointed. TMB estimation revealed one case with an exceptionally high bTMB (62.6 mutations/Mb) and genomic features of microsatellite instability (MSI). Concordance with tumor-based genotyping and ctDNA kinetics during toripalimab treatment are being determined. Conclusions: Prospective ctDNA analysis using the PredicineATLAS liquid biopsy assay is feasible and represents a minimally invasive approach to detecting cancer-specific genetic landscape and potentially guiding personalized therapeutic decisions in mUC patients. Clinical trial information: NCT03113266 . Research Sponsor: Shanghai Junshi BioSciences; Huidu Shanghai Medical Sciences Ltd

Circulating Tumor DNA: A Step into the Future of Cancer Management

2019 ◽  
Vol 63 (6) ◽  
pp. 456-465 ◽  
Author(s):  
Joana Fernandes Marques ◽  
Joana Pereira Reis ◽  
Gabriela Fernandes ◽  
Venceslau Hespanhol ◽  
José Carlos Machado ◽  
...  
Keyword(s):  
Liquid Biopsy ◽  
Clinical Utility ◽  
New Technologies ◽  
Therapy Response ◽  
Circulating Tumor Dna ◽  
Sample Collection ◽  
Cancer Management ◽  
The Past ◽  
Ctdna Analysis ◽  
Tumor Dna

Liquid biopsy was introduced to the oncology field with the promise of revolutionizing the management of cancer patients, minimizing the exposure to invasive procedures such as tissue biopsy, and providing reliable information regarding therapy response and detection of disease relapse. Despite the significant increase in the number of published studies on circulating tumor DNA (ctDNA) in the past years, the emphasis of most studies is on the development of new technologies or on the clinical utility of ctDNA. This leaves a clear gap of knowledge concerning the biology of ctDNA, such as the fundamental mechanisms through which DNA from tumor cells is released into the circulation. Moreover, considering that ctDNA analysis is now currently being applied in clinical practice, the need for rigorous quality control is arising, and with it the necessity to standardize procedures, from sample collection to data analysis. This review focuses on the main aspects of ctDNA, including approaches currently available to evaluate tumor genetics, as well as the points that still require improvement in order to make liquid biopsy a key player in precision medicine.

scholarly journals Liquid Biopsy Detects Relapse Five Months Earlier than Regular Clinical Follow-Up and Guides Targeted Treatment in Breast Cancer

2019 ◽  
Vol 2019 ◽  
pp. 1-4
Author(s):  
Fiona Tsui-Fen Cheng ◽  
Nina Lapke ◽  
Chin-Chu Wu ◽  
Yen-Jung Lu ◽  
Shu-Jen Chen ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Early Detection ◽  
Liquid Biopsy ◽  
Digital Pcr ◽  
Circulating Tumor Dna ◽  
Genetic Alterations ◽  
Targeted Treatment ◽  
Breast Cancer Patients ◽  
Ctdna Analysis

Genetic alterations in circulating tumor DNA (ctDNA) are an emerging biomarker for the early detection of relapse and have the potential to guide targeted treatment. ctDNA analysis is often performed by droplet digital PCR; however, next-generation sequencing (NGS) allows multigene testing without having to access a tumor sample to identify target alterations. Here, we report the case of a stage III hormone receptor-positive breast cancer patient who remained symptomless after receiving surgery and adjuvant chemotherapy. Liquid biopsy analysis by NGS revealed the presence of a ctDNA PIK3CA N345K mutation five months before the detection of relapse with multiple liver metastases by regular clinical follow-up. To date, clinical implications of the PIK3CA N345K variant remain insufficiently investigated; however, everolimus treatment resulted in the shrinkage of tumor lesions and decreased the levels of tumor markers. Four months after treatment initiation, a second ctDNA analysis suggested a relapse, and the patient clinically progressed after five months of everolimus therapy. This case report demonstrates the value of ctDNA analysis by NGS for the early detection of relapse in breast cancer patients. The study further indicates its usefulness for the choice of targeted treatments, suggesting that the variant PIK3CA N345K might be associated with everolimus sensitivity.

scholarly journals Capturing Genomic Evolution of Lung Cancers through Liquid Biopsy for Circulating Tumor DNA

2017 ◽  
Vol 2017 ◽  
pp. 1-5 ◽  
Author(s):  
Michael Offin ◽  
Jacob J. Chabon ◽  
Pedram Razavi ◽  
James M. Isbell ◽  
Charles M. Rudin ◽  
...  
Keyword(s):  
Liquid Biopsy ◽  
Circulating Tumor Dna ◽  
Intratumoral Heterogeneity ◽  
Darwinian Evolution ◽  
Genomic Evolution ◽  
Current Standard ◽  
Genetic Sequencing ◽  
Lung Cancers ◽  
Ctdna Analysis ◽  
Tumor Dna

Genetic sequencing of malignancies has become increasingly important to uncover therapeutic targets and capture the tumor’s dynamic changes to drug sensitivity and resistance through genomic evolution. In lung cancers, the current standard of tissue biopsy at the time of diagnosis and progression is not always feasible or practical and may underestimate intratumoral heterogeneity. Technological advances in genetic sequencing have enabled the use of circulating tumor DNA (ctDNA) analysis to obtain information on both targetable mutations and capturing real-time Darwinian evolution of tumor clones and drug resistance mechanisms under selective therapeutic pressure. The ability to analyze ctDNA from plasma, CSF, or urine enables a comprehensive view of cancers as systemic diseases and captures intratumoral heterogeneity. Here, we describe these recent advances in the setting of lung cancers and advocate for further research and the incorporation of ctDNA analysis in clinical trials of targeted therapies. By capturing genomic evolution in a noninvasive manner, liquid biopsy for ctDNA analysis could accelerate therapeutic discovery and deliver the next leap forward in precision medicine for patients with lung cancers and other solid tumors.

Greater than two coexisting mutations in KRAS and NRAS identified in the circulating tumor DNA fraction of liquid biopsies by NGS and confirmed with ddPCR.

2020 ◽  
Vol 38 (15_suppl) ◽  
pp. e15563-e15563
Author(s):  
Hala Boulos ◽  
Robert Tell ◽  
Nike Beaubier ◽  
Richard Blidner
Keyword(s):  
Liquid Biopsy ◽  
Detection Threshold ◽  
Treatment Resistance ◽  
Digital Pcr ◽  
Circulating Tumor Dna ◽  
Precision Oncology ◽  
Single Nucleotide Variants ◽  
Liquid Biopsies ◽  
Low Frequencies ◽  
Tumor Dna

e15563 Background: Liquid biopsies are increasingly utilized as a non-invasive tool in precision oncology to assess tumor mutational profiles in order to select targeted therapies, detect treatment resistance, and monitor disease progression in cancer patients. Additionally, liquid biopsies may provide a more comprehensive representation of tumor heterogeneity than standard tissue biopsies. However, limitations such as scarcity of circulating tumor DNA (ctDNA) and/or variants at low frequencies can be technically challenging to detect by next-generation sequencing (NGS) assays. Here, we use NGS to detect greater than two KRAS/NRAS mutations coexisting in single samples at low variant allele frequencies (VAFs). Methods: The Tempus xF liquid biopsy NGS assay is designed to detect actionable oncologic targets spanning 105 genes in plasma. The assay was validated to reliably detect single-nucleotide variants at 0.25% VAF, indels and copy number variants at 0.5% VAF, and fusions at 1% VAF with 96.2%-100% specificity and 97.4%-100% sensitivity. Pre-designed digital PCR assays were modified to measure 10ng of cell-free DNA (cfDNA) on a droplet-digital PCR (ddPCR) platform. Results: Overall, we report 100% positive predictive value and high correlation between ddPCR results and xF VAF, as well as in individual variants, such as KRAS G12D. Unexpectedly, we detected more than two coexisting KRAS/NRAS mutations at a low VAF in the plasma samples. To orthogonally confirm these results, ddPCR was deployed to independently measure the presence of each cfDNA variant with a sensitivity of 0.09% VAF. Subsequent ddPCR analysis of all targeted variants were concordant with NGS results. Conclusions: The occurrence of multiple KRAS and NRAS mutations in a single sample is quite uncommon and may be falsely interpreted as an NGS artifact. However, verification of this phenomenon by ddPCR confirmed the validity of the NGS liquid biopsy approach. These results highlight the capability of the Tempus xF assay to detect low-frequency variants, including those that fall below the validated detection threshold, which is essential for the diagnosis of early disease.

Circulating tumor DNA (ctDNA) analysis predicts recurrence following surgery in patients with stage I-IIIA non-small-cell lung cancer (NSCLC): Results of GASTO1035 and GASTO1018.

2020 ◽  
Vol 38 (15_suppl) ◽  
pp. 9023-9023
Author(s):  
Si-Yu Wang ◽  
Ning Li ◽  
Wei Ou ◽  
Chao Cheng ◽  
Peng-Peng Kuang ◽  
...  
Keyword(s):  
High Risk ◽  
Early Stage ◽  
Disease Recurrence ◽  
Circulating Tumor Dna ◽  
Stage I ◽  
Disease Stage ◽  
Tissue Samples ◽  
Ctdna Analysis ◽  
Personalized Cancer ◽  
Tumor Dna

9023 Background: Circulating tumor DNA can be detected in the plasma and serum of patients with solid tumors and has emerged as a noninvasive biomarker for dynamically monitoring tumor. Postsurgical ctDNA analysis of early-stage NSCLC may identify patients at high risk of recurrence and facilitate early intervention and personalized cancer therapy. Methods: These studies recruited 123 patients with newly diagnosed resectable stage I-IIIA NSCLC. Preoperative and postoperative plasma and postoperative tissue samples were subjected to next-generation sequencing (Nanjing Shihe Jiyin Biotechnology Inc.) using a 425 cancer-related genes panel. Peripheral blood samples were collected before surgery, postoperatively within 1 month, and every 3-6 months for up to 3 years. Plasma samples with at least 1 variants detected in tissue samples were defined as ctDNA positive. Results: After 4 exclusions, 119 eligible patients were enrolled from June 2016 to February 2019. Presurgical ctDNA was detectable in 31 of 117 (26.5%) patients and was associated with inferior recurrence-free survival (HR, 3.90, 95% CI, 1.44-10.58, P = 0.004). Similarly, ctDNA was detected in 13 of 116 (11.2%) of the first postsurgical samples and was associated with shorter RFS (HR, 3.54, 95% CI, 1.22-10.23, P = 0.002). During surveillance after surgery, ctDNA-positive patients (38/119, 31.9%) were more than 9 times more likely to experience disease recurrence than ctDNA-negative patients (HR, 9.17, 95% CI, 2.60-32.42, P <0.001). Serial ctDNA detection preceded radiologic disease recurrence by a median lead time of 4.23 months (95% CI, 0.91-7.54 months). We also observed a positive correlation between the ctDNA detection rate and the disease stage. Conclusions: These results suggest that detection of ctDNA before and after surgery is associated with the identification of a high risk of disease recurrence of resectable NSCLC. Perioperative ctDNA analyses identify disease recurrence earlier than standard-of-care radiologic imaging, and thus could facilitate personalized cancer treatment at early time points. Clinical trial information: NCT03465241 and NCT03172156.

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