scholarly journals Clinical relevance of blood-based ctDNA analysis: mutation detection and beyond

2020 ◽  
Author(s):  
Laura Keller ◽  
Yassine Belloum ◽  
Harriet Wikman ◽  
Klaus Pantel
Keyword(s):  
Cancer Patients ◽  
Mutation Detection ◽  
Methylation Status ◽  
High Sensitivity ◽  
Resistance Mechanisms ◽  
Noninvasive Detection ◽  
Solid Malignancies ◽  
Ctdna Analysis ◽  
Detection Of Mutations ◽  
Circulating Tumour Dna

Abstract Cell-free DNA (cfDNA) derived from tumours is present in the plasma of cancer patients. The majority of currently available studies on the use of this circulating tumour DNA (ctDNA) deal with the detection of mutations. The analysis of cfDNA is often discussed in the context of the noninvasive detection of mutations that lead to resistance mechanisms and therapeutic and disease monitoring in cancer patients. Indeed, substantial advances have been made in this area, with the development of methods that reach high sensitivity and can interrogate a large number of genes. Interestingly, however, cfDNA can also be used to analyse different features of DNA, such as methylation status, size fragment patterns, transcriptomics and viral load, which open new avenues for the analysis of liquid biopsy samples from cancer patients. This review will focus on the new perspectives and challenges of cfDNA analysis from mutation detection in patients with solid malignancies.

scholarly journals Expanding the clinical uses of ctDNA

2021 ◽  
Vol 22 (1) ◽  
pp. 41-47
Author(s):  
A.S. Zhabina
Keyword(s):  
Cancer Patients ◽  
High Sensitivity ◽  
Resistance Mechanisms ◽  
Noninvasive Detection ◽  
Disease Monitoring ◽  
Number Of Genes ◽  
Detection Of Mutations ◽  
Circulating Tumour Dna ◽  
Made In

The majority of currently available studies on the use of this circulating tumour DNA (ctDNA) deal with the detection of mutations. The analysis of cfDNA is often discussed in the context of the noninvasive detection of mutations that lead to resistance mechanisms and therapeutic and disease monitoring in cancer patients. Indeed, substantial advances have been made in this area, with the development of methods that reach high sensitivity and can interrogate a large number of genes.

scholarly journals Mutation profiling of tumor DNA from plasma and tumor tissue of colorectal cancer patients with a novel, high-sensitivity multiplexed mutation detection platform

Oncotarget ◽  
2014 ◽  
Vol 6 (4) ◽  
pp. 2549-2561 ◽  
Author(s):  
Evelyn Kidess ◽  
Kyra Heirich ◽  
Matthew Wiggin ◽  
Valentina Vysotskaia ◽  
Brendan C. Visser ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Cancer Patients ◽  
Tumor Tissue ◽  
Mutation Detection ◽  
High Sensitivity ◽  
Colorectal Cancer Patients ◽  
Tumor Dna ◽  
Mutation Profiling

scholarly journals Development of circulating tumour DNA analysis for gastrointestinal cancers

ESMO Open ◽  
2020 ◽  
Vol 5 (Suppl 1) ◽  
pp. e000600 ◽  
Author(s):  
Yoshiaki Nakamura ◽  
Kohei Shitara
Keyword(s):  
Dna Analysis ◽  
Residual Disease ◽  
Turnaround Time ◽  
Resistance Mechanisms ◽  
Detection Methods ◽  
Comprehensive Genomic Profiling ◽  
Gi Cancers ◽  
Ctdna Analysis ◽  
Next Generation Sequencing Ngs ◽  
Circulating Tumour Dna

Comprehensive genomic profiling using next-generation sequencing (NGS) enables the identification of multiple genomic biomarkers established in advanced gastrointestinal (GI) cancers. However, tissue-based NGS has limitations, such as long turnaround time and failure to detect tumour heterogeneity. Recently, the analysis of circulating tumour DNA (ctDNA) using polymerase chain reaction-based or NGS-based methods has demonstrated the capability to detect genomic alterations with high accuracy compared with tumour tissue analysis with short turnaround time and identify heterogeneous resistance mechanisms. Furthermore, ctDNA analysis can be repeatedly performed on disease progression to clarify resistant clones. Clinical trials that test the outcome of a selected targeted therapy based on a ctDNA result are ongoing to prospectively evaluate the clinical utility of ctDNA analysis. Furthermore, the improvement of ctDNA analysis beyond current technical limits of mutation-based ctDNA detection methods has expanded the potential for detecting the presence of tumours in patients with no clinically evident disease, such as minimal residual disease and early cancer. Although a careful understanding of the advantages and limitations are required and further prospective studies are needed, the ctDNA analysis has the potential to overcome several challenges in the treatment of various types of cancers at all stages, including GI cancers.

Blood-based screening for methylation changes in colorectal cancer patients using novel nanotechnologies.

2013 ◽  
Vol 31 (4_suppl) ◽  
pp. 384-384
Author(s):  
Nita Ahuja ◽  
Ruby Kwak ◽  
Brian Keeley ◽  
Alejandro Stark ◽  
Angela Anna Guzzetta ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Cancer Screening ◽  
Cancer Patients ◽  
Methylation Status ◽  
High Sensitivity ◽  
Single Copy ◽  
Tissue Samples ◽  
Methylation Frequency ◽  
Colorectal Cancer Patients ◽  
Cancer Tissues

384 Background: Identification of blood-based biomarkers for cancer screening is essential in order to develop novel and minimally invasive methods for colorectal cancer screening. Our lab has successfully applied a novel nanotechnology that allows us to detect and amplify a single tumor DNA fragment in a plasma sample. This DNA is tested for methylation of several genes including TFPI2 which has shown to be highly sensitive and specific for the detection colorectal cancer in stool. Methods: Whole blood was obtained from 18 colorectal cancer patients and plasma was isolated. Plasma was processed using Methylation On Beads nanotechnology (MOB) and bisulfate treated. Methylation status was determined via quantitative PCR method. Results: Two genes, TFPI2 and IGFBP3, were detected with a high sensitivity. TFPI2, demonstrated a methylation frequency of 94.4%, which is concordant with the TFPI2 methylation frequency of 99% in primary colorectal cancer tissues. IGFBP3 showed the methylation frequency of 61.1%, which corresponds with the methylation frequency of 52% in retrospective colorectal cancer tissues in previous studies. Quantification using standard curves indicated a single copy level of DNA found in plasma. Conclusions: Blood-based screening is challenging due to extremely low quantities of circulating DNA in blood. Utilizing a novel nanotechnology that detects DNA at a single copy level, the methylation changes in colorectal cancer were successfully detected in plasmas at similar frequencies as in tissue samples. This study has demonstrated the feasablility and applicability to blood-based screening. Future studies will focus on improving the sensitivity and determining the specificity of this method.

scholarly journals Circulating tumour DNA profiling reveals heterogeneity of EGFR inhibitor resistance mechanisms in lung cancer patients

2016 ◽  
Vol 7 (1) ◽  
Author(s):  
Jacob J. Chabon ◽  
Andrew D. Simmons ◽  
Alexander F. Lovejoy ◽  
Mohammad S. Esfahani ◽  
Aaron M. Newman ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Resistance Mechanism ◽  
Growth Factor Receptor ◽  
Resistance Mechanisms ◽  
Egfr Inhibitor ◽  
Tumour Heterogeneity ◽  
Lung Cancer Patients ◽  
Ctdna Analysis ◽  
Inhibitor Resistance ◽  
Circulating Tumour Dna

Abstract Circulating tumour DNA (ctDNA) analysis facilitates studies of tumour heterogeneity. Here we employ CAPP-Seq ctDNA analysis to study resistance mechanisms in 43 non-small cell lung cancer (NSCLC) patients treated with the third-generation epidermal growth factor receptor (EGFR) inhibitor rociletinib. We observe multiple resistance mechanisms in 46% of patients after treatment with first-line inhibitors, indicating frequent intra-patient heterogeneity. Rociletinib resistance recurrently involves MET, EGFR, PIK3CA, ERRB2, KRAS and RB1. We describe a novel EGFR L798I mutation and find that EGFR C797S, which arises in ∼33% of patients after osimertinib treatment, occurs in <3% after rociletinib. Increased MET copy number is the most frequent rociletinib resistance mechanism in this cohort and patients with multiple pre-existing mechanisms (T790M and MET) experience inferior responses. Similarly, rociletinib-resistant xenografts develop MET amplification that can be overcome with the MET inhibitor crizotinib. These results underscore the importance of tumour heterogeneity in NSCLC and the utility of ctDNA-based resistance mechanism assessment.

scholarly journals Clinical impact of PTEN methylation status as a prognostic marker for breast cancer

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Amal Ramadan ◽  
Maha Hashim ◽  
Amr Abouzid ◽  
Menha Swellam
Keyword(s):  
Breast Cancer ◽  
Cancer Patients ◽  
Tumor Markers ◽  
Prognostic Marker ◽  
Methylation Status ◽  
Clinical Impact ◽  
Breast Cancer Patients ◽  
Duct Carcinoma ◽  
Cancer Group ◽  
And Control

Abstract Background Aberrant DNA methylation of phosphatase and tensin homolog (PTEN) gene has been found in many cancers. The object of this study was to evaluate the clinical impact of PTEN methylation as a prognostic marker in breast cancer. The study includes 153 newly diagnosed females, and they were divided according to their clinical diagnosis into breast cancer patients (n = 112) and females with benign breast lesion (n = 41). A group of healthy individuals (n = 25) were recruited as control individuals. Breast cancer patients were categorized into early stage (0–I, n = 48) and late stage (II–III, n = 64), and graded into low grade (I–II, n = 42) and high grade (III, n = 70). Their pathological types were invasive duct carcinoma (IDC) (n = 66) and duct carcinoma in situ (DCI) (n = 46). Tumor markers (CEA and CA15.3) were detected using ELISA. DNA was taken away from the blood, and the PTEN promoter methylation level was evaluated using the EpiTect Methyl II PCR method. Results The findings revealed the superiority of PTEN methylation status as a good discriminator of the cancer group from the other two groups (benign and control) with its highest AUC and increased sensitivity (96.4%) and specificity (100%) over tumor markers (50% and 84% for CEA and 49.1% and 86.4% for CA15.3), respectively. The frequency of PTEN methylation was 96.4% of breast cancer patients and none of the benign and controls showed PTEN methylation and the means of PTEN methylation (87 ± 0.6) were significantly increased in blood samples of breast cancer group as compared to both benign and control groups (25 ± 0.7 and 12.6 ± 0.3), respectively. Methylation levels of PTEN were higher in the blood of patients with ER-positive than in patients with ER-negative cancers (P = 0.007) and in HER2 positive vs. HER2 negative tumors (P = 0.001). The Kaplan-Meier analysis recognizes PTEN methylation status as a significant forecaster of bad progression-free survival (PFS) and overall survival (OS), after 40 months follow-up. Conclusions PETN methylation could be supposed as one of the epigenetic aspects influencing the breast cancer prognosis that might foretell more aggressive actions and worse results in breast cancer patients.

scholarly journals Enhanced specificity of clinical high-sensitivity tumor mutation profiling in cell-free DNA via paired normal sequencing using MSK-ACCESS

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
A. Rose Brannon ◽  
Gowtham Jayakumaran ◽  
Monica Diosdado ◽  
Juber Patel ◽  
Anna Razumova ◽  
...  
Keyword(s):  
Cancer Patients ◽  
De Novo ◽  
Low Frequency ◽  
High Sensitivity ◽  
Clinical Analysis ◽  
De Novo Mutation ◽  
Cell Free Dna ◽  
Free Dna ◽  
Somatic Alterations ◽  
Mutation Profiling

AbstractCirculating cell-free DNA from blood plasma of cancer patients can be used to non-invasively interrogate somatic tumor alterations. Here we develop MSK-ACCESS (Memorial Sloan Kettering - Analysis of Circulating cfDNA to Examine Somatic Status), an NGS assay for detection of very low frequency somatic alterations in 129 genes. Analytical validation demonstrated 92% sensitivity in de-novo mutation calling down to 0.5% allele frequency and 99% for a priori mutation profiling. To evaluate the performance of MSK-ACCESS, we report results from 681 prospective blood samples that underwent clinical analysis to guide patient management. Somatic alterations are detected in 73% of the samples, 56% of which have clinically actionable alterations. The utilization of matched normal sequencing allows retention of somatic alterations while removing over 10,000 germline and clonal hematopoiesis variants. Our experience illustrates the importance of analyzing matched normal samples when interpreting cfDNA results and highlights the importance of cfDNA as a genomic profiling source for cancer patients.

scholarly journals Sensitivity, specificity, and accuracy of a liquid biopsy approach utilizing molecular amplification pools

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jessica Garcia ◽  
Nick Kamps-Hughes ◽  
Florence Geiguer ◽  
Sébastien Couraud ◽  
Brice Sarver ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Cancer Patients ◽  
Clinical Setting ◽  
High Sensitivity ◽  
Sequencing Error ◽  
Lung Cancer Patients ◽  
Mutation Discovery ◽  
Sensitivity Specificity ◽  
Next Generation Sequencing Ngs ◽  
Digital Polymerase Chain Reaction

AbstractCirculating cell-free DNA (cfDNA) has the potential to be a specific biomarker for the therapeutic management of lung cancer patients. Here, a new sequencing error-reduction method based on molecular amplification pools (MAPs) was utilized to analyze cfDNA in lung cancer patients. We determined the accuracy of MAPs plasma sequencing with respect to droplet digital polymerase chain reaction assays (ddPCR), and tested whether actionable mutation discovery is improved by next-generation sequencing (NGS) in a clinical setting. This study reports data from 356 lung cancer patients receiving plasma testing as part of routine clinical management. Sequencing of cfDNA via MAPs had a sensitivity of 98.5% and specificity 98.9%. The ddPCR assay was used as the reference, since it is an established, accurate assay that can be performed contemporaneously on the same plasma sample. MAPs sequencing detected somatic variants in 261 of 356 samples (73%). Non-actionable clonal hematopoiesis-associated variants were identified via sequencing in 21% of samples. The accuracy of this cfDNA sequencing approach was similar to that of ddPCR assays in a clinical setting, down to an allele frequency of 0.1%. Due to broader coverage and high sensitivity for insertions and deletions, sequencing via MAPs afforded important detection of additional actionable mutations.

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