ctDNAtools: An R package to work with sequencing data of circulating tumor DNA

AbstractSummarySequencing of cell-free DNA (cfDNA) including circulating tumor DNA (ctDNA) in minimally-invasive liquid biopsies is rapidly maturing towards clinical utility for cancer diagnostics. However, the publicly available bioinformatics tools for the specialized analysis of ctDNA sequencing data are still scarce. Here, we present the ctDNAtools R package, which provides functionalities for testing minimal residual disease (MRD) and analyzing cfDNA fragmentation. MRD detection in ctDNAtools utilizes a Monte Carlo sampling approach to test ctDNA positivity through tracking a set of pre-detected reporter mutations in follow-up samples. Additionally, ctDNAtools includes various functionalities to study cfDNA fragment size histograms, profiles and fragment ends patterns.AvailabilityThe ctDNAtools package is freely available under MIT license at https://github.com/alkodsi/ctDNAtools.

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Circulating tumor DNA is detectable in canine histiocytic sarcoma, oral malignant melanoma, and multicentric lymphoma

Scientific Reports ◽

10.1038/s41598-020-80332-y ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Anaïs Prouteau ◽

Jérôme Alexandre Denis ◽

Pauline De Fornel ◽

Edouard Cadieu ◽

Thomas Derrien ◽

...

Keyword(s):

Residual Disease ◽

Specific Antigen ◽

Point Mutations ◽

Antigen Receptor ◽

Digital Pcr ◽

Circulating Tumor Dna ◽

Histiocytic Sarcoma ◽

Oncology Research ◽

Tumor Dna

AbstractCirculating tumor DNA (ctDNA) has become an attractive biomarker in human oncology, and its use may be informative in canine cancer. Thus, we used droplet digital PCR or PCR for antigen receptor rearrangement, to explore tumor-specific point mutations, copy number alterations, and chromosomal rearrangements in the plasma of cancer-affected dogs. We detected ctDNA in 21/23 (91.3%) of histiocytic sarcoma (HS), 2/8 (25%) of oral melanoma, and 12/13 (92.3%) of lymphoma cases. The utility of ctDNA in diagnosing HS was explored in 133 dogs, including 49 with HS, and the screening of recurrent PTPN11 mutations in plasma had a specificity of 98.8% and a sensitivity between 42.8 and 77% according to the clinical presentation of HS. Sensitivity was greater in visceral forms and especially related to pulmonary location. Follow-up of four dogs by targeting lymphoma-specific antigen receptor rearrangement in plasma showed that minimal residual disease detection was concordant with clinical evaluation and treatment response. Thus, our study shows that ctDNA is detectable in the plasma of cancer-affected dogs and is a promising biomarker for diagnosis and clinical follow-up. ctDNA detection appears to be useful in comparative oncology research due to growing interest in the study of natural canine tumors and exploration of new therapies.

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ABEMUS: platform-specific and data-informed detection of somatic SNVs in cfDNA

Bioinformatics ◽

10.1093/bioinformatics/btaa016 ◽

2020 ◽

Vol 36 (9) ◽

pp. 2665-2674

Author(s):

Nicola Casiraghi ◽

Francesco Orlando ◽

Yari Ciani ◽

Jenny Xiang ◽

Andrea Sboner ◽

...

Keyword(s):

Cancer Patients ◽

R Package ◽

Circulating Tumor Dna ◽

Supplementary Information ◽

Sequencing Error ◽

Sequencing Data ◽

Single Nucleotide Variants ◽

Liquid Biopsies ◽

Non Invasive ◽

Cross Platform

Abstract Motivation The use of liquid biopsies for cancer patients enables the non-invasive tracking of treatment response and tumor dynamics through single or serial blood drawn tests. Next-generation sequencing assays allow for the simultaneous interrogation of extended sets of somatic single-nucleotide variants (SNVs) in circulating cell-free DNA (cfDNA), a mixture of DNA molecules originating both from normal and tumor tissue cells. However, low circulating tumor DNA (ctDNA) fractions together with sequencing background noise and potential tumor heterogeneity challenge the ability to confidently call SNVs. Results We present a computational methodology, called Adaptive Base Error Model in Ultra-deep Sequencing data (ABEMUS), which combines platform-specific genetic knowledge and empirical signal to readily detect and quantify somatic SNVs in cfDNA. We tested the capability of our method to analyze data generated using different platforms with distinct sequencing error properties and we compared ABEMUS performances with other popular SNV callers on both synthetic and real cancer patients sequencing data. Results show that ABEMUS performs better in most of the tested conditions proving its reliability in calling low variant allele frequencies somatic SNVs in low ctDNA levels plasma samples. Availability and implementation ABEMUS is cross-platform and can be installed as R package. The source code is maintained on Github at http://github.com/cibiobcg/abemus, and it is also available at CRAN official R repository. Supplementary information Supplementary data are available at Bioinformatics online.

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Clinical implications of monitoring circulating tumor DNA in early- and late-stage non-small cell lung cancer patients.

Journal of Clinical Oncology ◽

10.1200/jco.2019.37.15_suppl.e20607 ◽

2019 ◽

Vol 37 (15_suppl) ◽

pp. e20607-e20607

Author(s):

Muyun Peng ◽

Lihan Chin ◽

Qi Huang ◽

Wei Yin ◽

Sichuang Tan ◽

...

Keyword(s):

Squamous Cell Carcinoma ◽

Cell Carcinoma ◽

Squamous Cell ◽

Somatic Mutations ◽

Residual Disease ◽

Lung Squamous Cell Carcinoma ◽

Circulating Tumor Dna ◽

Small Cell Lung ◽

Tumor Dna

e20607 Background: Non-small cell lung cancer (NSCLC) accounts for about 85% of all lung cancers, and the most common types of NSCLC are squamous cell carcinoma, adenocarcinoma, and large cell carcinoma. The development of noninvasive methods to monitor circulating tumor DNA (ctDNA) continues to be a major challenge in NSCLC. Methods: We investigated if detection of ctDNA after resection of NSCLC identifies the patients with risk of relapse, and furthermore, informs about response to management.In this cohort study, high-throughput 168 target-gene capture technology and high-sensitivity circulating single molecule amplification and re-sequencing technology (cSMART) were used to detect the somatic mutations in tissues and plasma of patients with NSCLC, respectively. Moreover, ctDNA somatic mutations were used to monitor changes in minimal residual disease during a follow-up period. Results: A total of 169 patients with lung squamous cell carcinoma and adenocarcinoma were included. Detectable levels of ctDNA were present in 60.7% of patients with stage I and 68.8% of patients with late-stage. In patients not treated with adjuvant chemotherapy, ctDNA was detected preoperatively in 46 of 81 (56.8%) patients, 14 (30.4%) of whom had recurred at follow-up of 44 months; recurrence occurred in only 2 (5.7 %) of 35 patients with negative ctDNA. Serial ctDNA status changed from positive to negative during the initial phase of post operation in four patients. Then, ctDNA became positive again after 2 weeks to 3 months, all the four patients with relapse during the follow-up of 44 months. Conclusions: Detection of ctDNA supplies evidence of residual disease and identifies patients at risk of relapse. These observations have implications for the intervention of lung squamous cell carcinoma and adenocarcinoma patients.

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Circulating Tumor DNA Testing Opens New Perspectives in Melanoma Management

Cancers ◽

10.3390/cancers12102914 ◽

2020 ◽

Vol 12 (10) ◽

pp. 2914 ◽

Cited By ~ 1

Author(s):

Alessandra Sacco ◽

Laura Forgione ◽

Marianeve Carotenuto ◽

Antonella De Luca ◽

Paolo A. Ascierto ◽

...

Keyword(s):

Residual Disease ◽

Circulating Tumor Dna ◽

Resistance Mechanisms ◽

Prognostic Information ◽

Skin Cancers ◽

Highly Sensitive ◽

Ctdna Analysis ◽

Next Generation Sequencing Ngs ◽

Tumor Dna

Malignant melanoma accounts for about 1% of all skin cancers, but it causes most of the skin cancer-related deaths. Circulating tumor DNA (ctDNA) testing is emerging as a relevant tool for the diagnosis and monitoring of cancer. The availability of highly sensitive techniques, including next generation sequencing (NGS)-based panels, has increased the fields of application of ctDNA testing. While ctDNA-based tests for the early detection of melanoma are not available yet, perioperative ctDNA analysis in patients with surgically resectable melanoma offers relevant prognostic information: i) the detection of ctDNA before surgery correlates with the extent and the aggressiveness of the disease; ii) ctDNA testing after surgery/adjuvant therapy identifies minimal residual disease; iii) testing ctDNA during the follow-up can detect a tumor recurrence, anticipating clinical/radiological progression. In patients with advanced melanoma, several studies have demonstrated that the analysis of ctDNA can better depict tumor heterogeneity and provides relevant prognostic information. In addition, ctDNA testing during treatment allows assessing the response to systemic therapy and identifying resistance mechanisms. Although validation in prospective clinical trials is needed for most of these approaches, ctDNA testing opens up new scenarios in the management of melanoma patients that could lead to improvements in the diagnosis and therapy of this disease.

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Circulating tumor DNA (ctDNA) is not a good proxy for liquid biopsies of tumor tissues for early detection

Clinical Chemistry and Laboratory Medicine (CCLM) ◽

10.1515/cclm-2020-0083 ◽

2020 ◽

Vol 58 (10) ◽

pp. 1651-1653

Author(s):

Clare Fiala ◽

Eleftherios P. Diamandis

Keyword(s):

Early Detection ◽

Early Cancer ◽

Circulating Tumor Dna ◽

Cancer Diagnostics ◽

Clinical Value ◽

Liquid Biopsies ◽

Important Conclusion ◽

Tumor Tissues ◽

Good Proxy ◽

Tumor Dna

AbstractThe important conclusion that ctDNA is a mediocre proxy for liquid biopsies of tumor tissues for early detection was reached after new data were published recently in Nature Genetics. These data have shown that most mutations found in ctDNA are not related to tumor tissues but rather to the precancerous condition clonal hematopoiesis. Previously, our group has analyzed the sensitivity of the ctDNA test for early detection of cancer and concluded that the achievable sensitivity, especially for small tumors, is not enough to have clinical value. Now, the new data have shown a serious compromise in specificity. We believe that scientists who are interested in early cancer diagnostics should be aware of the limitations of this test, in both sensitivity and specificity. Our work may prompt further work aiming to alleviate these important issues in the cancer diagnostics field.

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Clinical utility of circulating tumor DNA as a response and follow-up marker in cancer therapy

Cancer and Metastasis Reviews ◽

10.1007/s10555-020-09876-9 ◽

2020 ◽

Vol 39 (3) ◽

pp. 999-1013 ◽

Cited By ~ 1

Author(s):

Pieter A. Boonstra ◽

Thijs T. Wind ◽

Michel van Kruchten ◽

Ed Schuuring ◽

Geke A. P. Hospers ◽

...

Keyword(s):

Cancer Therapy ◽

Treatment Response ◽

Clinical Utility ◽

Tumor Response ◽

Circulating Tumor Dna ◽

Tumor Burden ◽

Liquid Biopsies ◽

Secondary Resistance ◽

Tumor Dna

Abstract Response evaluation for cancer treatment consists primarily of clinical and radiological assessments. In addition, a limited number of serum biomarkers that assess treatment response are available for a small subset of malignancies. Through recent technological innovations, new methods for measuring tumor burden and treatment response are becoming available. By utilization of highly sensitive techniques, tumor-specific mutations in circulating DNA can be detected and circulating tumor DNA (ctDNA) can be quantified. These so-called liquid biopsies provide both molecular information about the genomic composition of the tumor and opportunities to evaluate tumor response during therapy. Quantification of tumor-specific mutations in plasma correlates well with tumor burden. Moreover, with liquid biopsies, it is also possible to detect mutations causing secondary resistance during treatment. This review focuses on the clinical utility of ctDNA as a response and follow-up marker in patients with non-small cell lung cancer, melanoma, colorectal cancer, and breast cancer. Relevant studies were retrieved from a literature search using PubMed database. An overview of the available literature is provided and the relevance of ctDNA as a response marker in anti-cancer therapy for clinical practice is discussed. We conclude that the use of plasma-derived ctDNA is a promising tool for treatment decision-making based on predictive testing, detection of resistance mechanisms, and monitoring tumor response. Necessary steps for translation to daily practice and future perspectives are discussed.

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Circulating Tumor DNA Detection by Digital-Droplet PCR in Pancreatic Ductal Adenocarcinoma: A Systematic Review

Cancers ◽

10.3390/cancers13050994 ◽

2021 ◽

Vol 13 (5) ◽

pp. 994

Author(s):

Marisol Huerta ◽

Susana Roselló ◽

Luis Sabater ◽

Ana Ferrer ◽

Noelia Tarazona ◽

...

Keyword(s):

Tumor Cells ◽

Residual Disease ◽

Malignant Tumors ◽

Circulating Tumor Dna ◽

Ductal Adenocarcinoma ◽

Epigenetic Alterations ◽

Non Invasive ◽

Droplet Pcr ◽

Tumor Dna

Pancreatic cancer (PC) is one of the most devastating malignant tumors, being the seventh leading cause of cancer-related death worldwide. Researchers and clinicians are endeavoring to develop strategies for the early detection of the disease and the improvement of treatment results. Adequate biopsy is still challenging because of the pancreas’s poor anatomic location. Recently, circulating tumor DNA (ctDNA) could be identified as a liquid biopsy tool with huge potential as a non-invasive biomarker in early diagnosis, prognosis and management of PC. ctDNA is released from apoptotic and necrotic cancer cells, as well as from living tumor cells and even circulating tumor cells, and it can reveal genetic and epigenetic alterations with tumor-specific and individual mutation and methylation profiles. However, ctDNA sensibility remains a limitation and the accuracy of ctDNA as a biomarker for PC is relatively low and cannot be currently used as a screening or diagnostic tool. Increasing evidence suggests that ctDNA is an interesting biomarker for predictive or prognosis studies, evaluating minimal residual disease, longitudinal follow-up and treatment management. Promising results have been published and therefore the objective of our review is to understand the current role and the future perspectives of ctDNA in PC.

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Aperture: Accurate detection of structural variations and viral integrations in circulating tumor DNA using an alignment-free algorithm

10.1101/2020.12.04.409508 ◽

2020 ◽

Author(s):

Hongchao Liu ◽

Huihui Yin ◽

Guangyu Li ◽

Junling Li ◽

Xiaoyue Wang

Keyword(s):

Fragment Size ◽

Repetitive Sequences ◽

High Sensitivity ◽

Circulating Tumor Dna ◽

Precision Oncology ◽

Sequencing Data ◽

Structural Variations ◽

Real Patient ◽

Alignment Free ◽

Tumor Dna

AbstractBackgroundThe identification of structural variations (SV) and viral integrations in circulating tumor DNA (ctDNA) is a key step in precision oncology that may assist clinicians for treatment selection and monitoring. However, it is challenging to accurately detect low frequency SVs or SVs involving complex junctions in ctDNA sequencing data due to the short fragment size of ctDNA.ResultsHere, we describe Aperture, a new fast SV caller that applies a unique strategy of k-mer based searching, breakpoint detection using binary labels and candidates clustering to detect SVs and viral integrations in high sensitivity, especially when junctions span repetitive regions, followed by a barcode-based filter to ensure specificity. We evaluated the performance of Aperture in stimulated, reference and real datasets. Aperture demonstrates superior sensitivity and specificity in all tests, especially for low dilution test, compared with existing methods. In addition, Aperture is able to predict sites of viral integration and identify complex SVs involving novel insertions and repetitive sequences in real patient data.ConclusionsUsing a novel alignment-free algorithm, Aperture achieves sensitive, specific and fast detection of structural variations and viral integrations, which may enhance the diagnostic value of ctDNA in clinical application. The executable file and source code are freely available at https://github.com/liuhc8/Aperture.

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Efficient detection and post-surgical monitoring of colon cancer with a multi-marker DNA methylation liquid biopsy

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2017421118 ◽

2021 ◽

Vol 118 (5) ◽

pp. e2017421118

Author(s):

Shengnan Jin ◽

Dewen Zhu ◽

Fanggui Shao ◽

Shiliang Chen ◽

Ying Guo ◽

...

Keyword(s):

Early Stage ◽

Cancer Recurrence ◽

Cost Effective ◽

Circulating Tumor Dna ◽

Plasma Samples ◽

Liquid Biopsies ◽

Efficient Detection ◽

Radiologic Imaging ◽

Tumor Dna

Multiplex assays, involving the simultaneous use of multiple circulating tumor DNA (ctDNA) markers, can improve the performance of liquid biopsies so that they are highly predictive of cancer recurrence. We have developed a single-tube methylation-specific quantitative PCR assay (mqMSP) that uses 10 different methylation markers and is capable of quantitative analysis of plasma samples with as little as 0.05% tumor DNA. In a cohort of 179 plasma samples from colorectal cancer (CRC) patients, adenoma patients, and healthy controls, the sensitivity and specificity of the mqMSP assay were 84.9% and 83.3%, respectively. In a head-to-head comparative study, the mqMSP assay also performed better for detecting early-stage (stage I and II) and premalignant polyps than a published SEPT9 assay. In an independent longitudinal cohort of 182 plasma samples (preoperative, postoperative, and follow-up) from 82 CRC patients, the mqMSP assay detected ctDNA in 73 (89.0%) of the preoperative plasma samples. Postoperative detection of ctDNA (within 2 wk of surgery) identified 11 of the 20 recurrence patients and was associated with poorer recurrence-free survival (hazard ratio, 4.20; P = 0.0005). With subsequent longitudinal monitoring, 14 patients (70%) had detectable ctDNA before recurrence, with a median lead time of 8.0 mo earlier than seen with radiologic imaging. The mqMSP assay is cost-effective and easily implementable for routine clinical monitoring of CRC recurrence, which can lead to better patient management after surgery.

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Liquid Biopsies in Hepatocellular Carcinoma: Are We Winning?

Journal of Clinical Medicine ◽

10.3390/jcm9051541 ◽

2020 ◽

Vol 9 (5) ◽

pp. 1541 ◽

Cited By ~ 4

Author(s):

Tudor Mocan ◽

André L. Simão ◽

Rui E. Castro ◽

Cecília M. P. Rodrigues ◽

Artur Słomka ◽

...

Keyword(s):

Hepatocellular Carcinoma ◽

Clinical Performance ◽

Circulating Tumor Dna ◽

Liquid Biopsies ◽

Disease Biomarkers ◽

Common Cancer ◽

Tumor Dna ◽

Tumor Proteins

Hepatocellular carcinoma (HCC) represents the sixth most common cancer worldwide and the third most common cause of cancer-related death. One of the major problems faced by researchers and clinicians in this area is the lack of reliable disease biomarkers, which would allow for an earlier diagnosis, follow-up or prediction of treatment response, among others. In this regard, the “HCC circulome”, defined as the pool of circulating molecules in the bloodstream derived from the primary tumor, represents an appealing target, the so called liquid biopsy. Such molecules encompass circulating tumor proteins, circulating tumor cells (CTCs), extracellular vesicles (EVs), tumor-educated platelets (TEPs), and circulating tumor nucleic acids, namely circulating tumor DNA (ctDNA) and circulating tumor RNA (ctRNA). In this article, we summarize recent findings highlighting the promising role of liquid biopsies as novel potential biomarkers in HCC, emphasizing on its clinical performance.

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