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

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.

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

2020 ◽  
Author(s):  
Amjad Alkodsi ◽  
Leo Meriranta ◽  
Annika Pasanen ◽  
Sirpa Leppä
Keyword(s):  
Residual Disease ◽  
Fragment Size ◽  
R Package ◽  
Monte Carlo Sampling ◽  
Circulating Tumor Dna ◽  
Cancer Diagnostics ◽  
Sequencing Data ◽  
Liquid Biopsies ◽  
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.

scholarly journals Liquid Biopsy in Gastrointestinal Cancers

Diagnostics ◽  
2018 ◽  
Vol 8 (4) ◽  
pp. 75 ◽  
Author(s):  
Aman Saini ◽  
Yash Pershad ◽  
Hassan Albadawi ◽  
Malia Kuo ◽  
Sadeer Alzubaidi ◽  
...  
Keyword(s):  
Liquid Biopsy ◽  
Disease Surveillance ◽  
Biological Fluid ◽  
Genetic Material ◽  
Circulating Tumor Dna ◽  
Cancer Diagnostics ◽  
Gastrointestinal Cancers ◽  
New Paradigm ◽  
Liquid Biopsies ◽  
Biopsy Material

Liquid biopsy is the sampling of any biological fluid in an effort to enrich and analyze a tumor’s genetic material. Peripheral blood remains the most studied liquid biopsy material, with circulating tumor cells (CTC’s) and circulating tumor DNA (ctDNA) allowing the examination and longitudinal monitoring of a tumors genetic landscape. With applications in cancer screening, prognostic stratification, therapy selection and disease surveillance, liquid biopsy represents an exciting new paradigm in the field of cancer diagnostics and offers a less invasive and more comprehensive alternative to conventional tissue biopsy. Here, we examine liquid biopsies in gastrointestinal cancers, specifically colorectal, gastric, and pancreatic cancers, with an emphasis on applications in diagnostics, prognostics and therapeutics.

scholarly journals Detection of Cell Types Contributing to Cancer From Circulating, Cell-Free Methylated DNA

2021 ◽  
Vol 12 ◽  
Author(s):  
Megan E. Barefoot ◽  
Netanel Loyfer ◽  
Amber J. Kiliti ◽  
A. Patrick McDeed ◽  
Tommy Kaplan ◽  
...  
Keyword(s):  
Cancer Cells ◽  
Cell Types ◽  
Circulating Tumor Dna ◽  
Cancer Diagnostics ◽  
Tissue Homeostasis ◽  
Specific Cell ◽  
Cell Type ◽  
Liquid Biopsies ◽  
Methylated Dna ◽  
Cell Type Specific

Detection of cellular changes in tissue biopsies has been the basis for cancer diagnostics. However, tissue biopsies are invasive and limited by inaccuracies due to sampling locations, restricted sampling frequency, and poor representation of tissue heterogeneity. Liquid biopsies are emerging as a complementary approach to traditional tissue biopsies to detect dynamic changes in specific cell populations. Cell-free DNA (cfDNA) fragments released into the circulation from dying cells can be traced back to the tissues and cell types they originated from using DNA methylation, an epigenetic regulatory mechanism that is highly cell-type specific. Decoding changes in the cellular origins of cfDNA over time can reveal altered host tissue homeostasis due to local cancer invasion and metastatic spread to distant organs as well as treatment responses. In addition to host-derived cfDNA, changes in cancer cells can be detected from cell-free, circulating tumor DNA (ctDNA) by monitoring DNA mutations carried by cancer cells. Here, we will discuss computational approaches to identify and validate robust biomarkers of changed tissue homeostasis using cell-free, methylated DNA in the circulation. We highlight studies performing genome-wide profiling of cfDNA methylation and those that combine genetic and epigenetic markers to further identify cell-type specific signatures. Finally, we discuss opportunities and current limitations of these approaches for implementation in clinical oncology.

scholarly journals Prognostic Utility of Pre- and Postoperative Circulating Tumor DNA Liquid Biopsies in Patients with Peritoneal Metastases

2020 ◽  
Vol 27 (9) ◽  
pp. 3259-3267
Author(s):  
Joel M. Baumgartner ◽  
Paul Riviere ◽  
Richard B. Lanman ◽  
Kaitlyn J. Kelly ◽  
Jula Veerapong ◽  
...  
Keyword(s):  
Circulating Tumor Dna ◽  
Peritoneal Metastases ◽  
Liquid Biopsies ◽  
Prognostic Utility ◽  
Tumor Dna

scholarly journals Toward liquid biopsies in cancer treatment: application of circulating tumor DNA

Apmis ◽  
2019 ◽  
Vol 127 (5) ◽  
pp. 329-336 ◽  
Author(s):  
Lise Barlebo Ahlborn ◽  
Olga Østrup
Keyword(s):  
Cancer Treatment ◽  
Circulating Tumor Dna ◽  
Liquid Biopsies ◽  
Tumor Dna ◽  
Treatment Application

scholarly journals Circulating Tumor DNA Biomarkers for Early Detection of Oligometastasis

2020 ◽  
Vol 26 (2) ◽  
pp. 116-123 ◽  
Author(s):  
David M. Routman ◽  
Bhishamjit S. Chera ◽  
Gaorav P. Gupta
Keyword(s):  
Early Detection ◽  
Circulating Tumor Dna ◽  
Tumor Dna
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