Circulating tumor DNA: a promising biomarker in the liquid biopsy of cancer

Tissue biopsy is the standard diagnostic procedure for cancers and also provides a material for genotyping, which can assist in the targeted therapies of cancers. However, tissue biopsy-based cancer diagnostic procedures have limitations in their assessment of cancer development, prognosis and genotyping, due to tumor heterogeneity and evolution. Circulating tumor DNA (ctDNA) is single- or double-stranded DNA released by the tumor cells into the blood and it thus harbors the mutations of the original tumor. In recent years, liquid biopsy based on ctDNA analysis has shed a new light on the molecular diagnosis and monitoring of cancer. Studies found that the screening of genetic mutations using ctDNA is highly sensitive and specific, suggesting that ctDNA analysis may significantly improve current systems of tumor diagnosis, even facilitating early-stage detection. Moreover, ctDNA analysis is capable of accurately determining the tumor progression, prognosis and assisting in targeted therapy. Therefore, using ctDNA as a liquid biopsy may herald a revolution for tumor management. Herein, we review the biology of ctDNA, its detection methods and potential applications in tumor diagnosis, treatment and prognosis.

[1]  Qiang Hu,et al.  Circulating miR-148b and miR-133a as biomarkers for breast cancer detection , 2014, Oncotarget.

[2]  M. Tachibana,et al.  Serum carcinoembryonic antigen as a prognostic factor in resectable gastric cancer. , 1998, Journal of the American College of Surgeons.

[3]  N. Lindeman,et al.  Novel molecular insights from routine genotyping of colorectal carcinomas. , 2015, Human pathology.

[4]  C. Ding,et al.  Quantitative analysis of circulating methylated DNA as a biomarker for hepatocellular carcinoma. , 2008, Clinical chemistry.

[5]  W. Parson,et al.  The side population of ovarian cancer cells defines a heterogeneous compartment exhibiting stem cell characteristics , 2014, Oncotarget.

[6]  P. A. Futreal,et al.  Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. , 2012, The New England journal of medicine.

[7]  T. Yap,et al.  Circulating Tumor Cells: A Multifunctional Biomarker , 2014, Clinical Cancer Research.

[8]  Kun-He Zhang,et al.  Combined use of AFP, CEA, CA125 and CAl9-9 improves the sensitivity for the diagnosis of gastric cancer , 2013, BMC Gastroenterology.

[9]  I. Vajtai,et al.  Polymorphous oligodendroglioma of Zülch revisited: A genetically heterogeneous group of anaplastic gliomas including tumors of bona fide oligodendroglial differentiation , 2014, Neuropathology : official journal of the Japanese Society of Neuropathology.

[10]  M. Niederweis,et al.  Nanopore DNA sequencing with MspA , 2010, Proceedings of the National Academy of Sciences.

[11]  D. García-Olmo,et al.  Biological role of cell-free nucleic acids in cancer: the theory of genometastasis. , 2013, Critical reviews in oncogenesis.

[12]  J. García-Verdugo,et al.  Molecular and Cellular Pathobiology Cancer Research Cell-Free Nucleic Acids Circulating in the Plasma of Colorectal Cancer Patients Induce the Oncogenic Transformation of Susceptible Cultured Cells , 2010 .

[13]  U. Ballehaninna,et al.  Serum CA 19-9 as a Biomarker for Pancreatic Cancer—A Comprehensive Review , 2011, Indian journal of surgical oncology.

[14]  D. Welch,et al.  Breast cancer metastasis suppressor-1 promoter methylation in cell-free DNA provides prognostic information in non-small cell lung cancer , 2014, British Journal of Cancer.

[15]  A. King,et al.  Early detection of nasopharyngeal carcinoma by plasma Epstein‐Barr virus DNA analysis in a surveillance program , 2013, Cancer.

[16]  D. García-Olmo,et al.  Functionality of Circulating DNA , 2001 .

[17]  H. Shah,et al.  Personalized ovarian cancer disease surveillance and detection of candidate therapeutic drug target in circulating tumor DNA. , 2014, Neoplasia.

[18]  Claudia Peitzsch,et al.  Cancer biomarker discovery: Current status and future perspectives , 2014, International journal of radiation biology.

[19]  M. Duffy,et al.  Carcinoembryonic antigen as a marker for colorectal cancer: is it clinically useful? , 2001, Clinical chemistry.

[20]  Takahiro Ochiya,et al.  Circulating microRNA in body fluid: a new potential biomarker for cancer diagnosis and prognosis , 2010, Cancer science.

[21]  K. Nie,et al.  Cell-free circulating tumor DNA in plasma/serum of non-small cell lung cancer , 2014, Tumor Biology.

[22]  Andrew Menzies,et al.  The patterns and dynamics of genomic instability in metastatic pancreatic cancer , 2010, Nature.

[23]  H. Nielsen,et al.  Analysis of circulating tumour DNA to monitor disease burden following colorectal cancer surgery , 2015, Gut.

[24]  A Ruibal Morell,et al.  CEA serum levels in non-neoplastic disease. , 1992, The International journal of biological markers.

[25]  S. Leung,et al.  Quantitative analysis of cell-free Epstein-Barr virus DNA in plasma of patients with nasopharyngeal carcinoma. , 1999, Cancer research.

[26]  Brigitte Rack,et al.  Apoptosis-related deregulation of proteolytic activities and high serum levels of circulating nucleosomes and DNA in blood correlate with breast cancer progression , 2011, BMC Cancer.

[27]  L. Diaz,et al.  Liquid biopsies: genotyping circulating tumor DNA. , 2014, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[28]  M. Fleischhacker,et al.  Circulating nucleic acids (CNAs) and cancer--a survey. , 2007, Biochimica et biophysica acta.

[29]  Beatriz Bellosillo,et al.  Clonal evolution and resistance to EGFR blockade in the blood of colorectal cancer patients , 2015, Nature Medicine.

[30]  B. Shapiro,et al.  Free DNA in the serum of cancer patients and the effect of therapy. , 1977, Cancer research.

[31]  Qian Zhao,et al.  Serum SALL4 Is a Novel Prognosis Biomarker with Tumor Recurrence and Poor Survival of Patients in Hepatocellular Carcinoma , 2014, Journal of immunology research.

[32]  S. Goodman,et al.  Circulating mutant DNA to assess tumor dynamics , 2008, Nature Medicine.

[33]  W. Huh,et al.  Cost Effectiveness of Human Papillomavirus-16/18 Genotyping in Cervical Cancer Screening , 2014, Applied Health Economics and Health Policy.

[34]  Ash A. Alizadeh,et al.  An ultrasensitive method for quantitating circulating tumor DNA with broad patient coverage , 2013, Nature Medicine.

[35]  A. Schneeweiss,et al.  Plasma DNA integrity as a biomarker for primary and metastatic breast cancer and potential marker for early diagnosis , 2014, Breast Cancer Research and Treatment.

[36]  V. Heinemann,et al.  Clinical Relevance of Circulating Nucleosomes in Cancer , 2008, Annals of the New York Academy of Sciences.

[37]  Andre Marziali,et al.  Mutation profiling of tumor DNA from plasma and tumor tissue of colorectal cancer patients with a novel, high-sensitivity multiplexed mutation detection platform , 2014, Oncotarget.

[38]  Marius Ilie,et al.  Current challenges for detection of circulating tumor cells and cell-free circulating nucleic acids, and their characterization in non-small cell lung carcinoma patients. What is the best blood substrate for personalized medicine? , 2014, Annals of translational medicine.

[39]  D. Chan,et al.  Increased plasma DNA integrity in cancer patients. , 2003, Cancer research.

[40]  M. Spreeuwenberg,et al.  The Origin of Circulating Free DNA , 2007 .

[41]  Peiyong Jiang,et al.  Noninvasive detection of cancer-associated genome-wide hypomethylation and copy number aberrations by plasma DNA bisulfite sequencing , 2013, Proceedings of the National Academy of Sciences.

[42]  M. Stroun,et al.  About the possible origin and mechanism of circulating DNA apoptosis and active DNA release. , 2001, Clinica chimica acta; international journal of clinical chemistry.

[43]  Lin Xu,et al.  Circulating Tumor DNA Is Effective for the Detection of EGFR Mutation in Non–Small Cell Lung Cancer: A Meta-analysis , 2014, Cancer Epidemiology, Biomarkers & Prevention.

[44]  A. Dicker,et al.  Screening for prostate cancer: the current evidence and guidelines controversy. , 2011, The Canadian journal of urology.

[45]  Armando Varela-Ramírez,et al.  Serum dickkopf-1 is a novel serological biomarker for the diagnosis and prognosis of pancreatic cancer , 2015, Oncotarget.

[46]  V A Memoli,et al.  Soluble normal and mutated DNA sequences from single-copy genes in human blood. , 1994, Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology.

[47]  J. Castle,et al.  Mutant MHC class II epitopes drive therapeutic immune responses to cancer , 2015, Nature.

[48]  N. Rosenfeld,et al.  Non-invasive analysis of acquired resistance to cancer therapy by sequencing of plasma DNA , 2013, Nature.

[49]  N. Rosenfeld,et al.  Noninvasive Identification and Monitoring of Cancer Mutations by Targeted Deep Sequencing of Plasma DNA , 2012, Science Translational Medicine.

[50]  Alexander Dobrovic,et al.  Monitoring response to therapy in melanoma by quantifying circulating tumour DNA with droplet digital PCR for BRAF and NRAS mutations , 2015, Scientific Reports.

[51]  L. Steinbock,et al.  The emergence of nanopores in next-generation sequencing , 2015, Nanotechnology.

[52]  Drew M Pardoll,et al.  Circulating tumor DNA analysis as a real-time method for monitoring tumor burden in melanoma patients undergoing treatment with immune checkpoint blockade , 2014, Journal of Immunotherapy for Cancer.

[53]  E. Diamandis,et al.  The failure of protein cancer biomarkers to reach the clinic: why, and what can be done to address the problem? , 2012, BMC Medicine.

[54]  L. Staudt,et al.  Circulating tumour DNA and CT monitoring in patients with untreated diffuse large B-cell lymphoma: a correlative biomarker study. , 2015, The Lancet. Oncology.

[55]  I. Bièche,et al.  Circulating tumor DNA as a non‐invasive substitute to metastasis biopsy for tumor genotyping and personalized medicine in a prospective trial across all tumor types , 2015, Molecular oncology.

[56]  M. Ychou,et al.  High Fragmentation Characterizes Tumour-Derived Circulating DNA , 2011, PloS one.

[57]  Ken Chen,et al.  Recurring mutations found by sequencing an acute myeloid leukemia genome. , 2009, The New England journal of medicine.

[58]  M. Vallejo,et al.  Tumor DNA circulating in the plasma might play a role in metastasis. The hypothesis of the genometastasis. , 1999, Histology and histopathology.

[59]  Jorge S. Reis-Filho,et al.  Mutation tracking in circulating tumor DNA predicts relapse in early breast cancer , 2015, Science Translational Medicine.

[60]  P. J. Pretorius,et al.  The origin of circulating free DNA. , 2007, Clinical chemistry.

[61]  T. Jiang,et al.  Role of circulating-tumor DNA analysis in non-small cell lung cancer. , 2015, Lung cancer.

[62]  Jay Shendure,et al.  Decoding long nanopore sequencing reads of natural DNA , 2014, Nature Biotechnology.

[63]  W. Catalona,et al.  PSA enzymatic activity: A new biomarker for assessing prostate cancer aggressiveness , 2013, The Prostate.

[64]  Johannes G. Reiter,et al.  The molecular evolution of acquired resistance to targeted EGFR blockade in colorectal cancers , 2012, Nature.

[65]  Ed Yong,et al.  Cancer biomarkers: Written in blood , 2014, Nature.

[66]  P. Damkier CYP2D6 genotyping and tamoxifen in the treatment of post-menopausal breast cancer. , 2014, British journal of clinical pharmacology.

[67]  Diana Romero Breast cancer: Tracking ctDNA to evaluate relapse risk , 2015, Nature Reviews Clinical Oncology.

[68]  Bert Vogelstein,et al.  DETECTION OF CIRCULATING TUMOR DNA IN EARLY AND LATE STAGE HUMAN MALIGNANCIES , 2014 .

[69]  M. Ychou,et al.  Origin and quantification of circulating DNA in mice with human colorectal cancer xenografts , 2010, Nucleic acids research.

[70]  Tianhong Li,et al.  Genotyping and genomic profiling of non-small-cell lung cancer: implications for current and future therapies. , 2013, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[71]  V. Servois,et al.  Detection rate and prognostic value of circulating tumor cells and circulating tumor DNA in metastatic uveal melanoma , 2014, International journal of cancer.

[72]  H. Mulcahy,et al.  Detection of Circulating Tumour DNA in the Blood (Plasma/Serum) of Cancer Patients , 2004, Cancer and Metastasis Reviews.

[73]  Robert A. Weinberg,et al.  Tumor Metastasis: Molecular Insights and Evolving Paradigms , 2011, Cell.

[74]  Andrew Kasarskis,et al.  Validation of ITD mutations in FLT3 as a therapeutic target in human acute myeloid leukaemia , 2012, Nature.

[75]  R. Strausberg,et al.  Circulating tumor DNA as an early marker of therapeutic response in patients with metastatic colorectal cancer. , 2015, Annals of oncology : official journal of the European Society for Medical Oncology.

[76]  Valeri Vasioukhin,et al.  Point mutations of the N‐ras gene in the blood plasma DNA of patients with myelodysplastic syndrome or acute myelogenous leukaemia , 1994, British journal of haematology.

[77]  Kikuya Kato,et al.  Quantitative Detection of EGFR Mutations in Circulating Tumor DNA Derived from Lung Adenocarcinomas , 2011, Clinical Cancer Research.

[78]  Y. Doki,et al.  Monitoring gastric cancer progression with circulating tumour DNA , 2014, British Journal of Cancer.

[79]  Frank Diehl,et al.  Detection and quantification of mutations in the plasma of patients with colorectal tumors. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[80]  C. López-Otín,et al.  Emerging roles of proteases in tumour suppression , 2007, Nature Reviews Cancer.

[81]  T. Mok,et al.  Single-Molecule Detection of Epidermal Growth Factor Receptor Mutations in Plasma by Microfluidics Digital PCR in Non–Small Cell Lung Cancer Patients , 2009, Clinical Cancer Research.

[82]  J. Troge,et al.  Tumour evolution inferred by single-cell sequencing , 2011, Nature.

[83]  K. Kruglyak,et al.  Next-generation sequencing in precision oncology: challenges and opportunities , 2014, Expert review of molecular diagnostics.

[84]  A. Nicholson,et al.  Circulating tumor DNA outperforms circulating tumor cells for KRAS mutation detection in thoracic malignancies. , 2015, Clinical chemistry.

[85]  D. García-Olmo,et al.  Surgery and Hematogenous Dissemination: Comparison Between the Detection of Circulating Tumor Cells and of Tumor DNA in Plasma Before and After Tumor Resection in Rats , 2006, Annals of Surgical Oncology.

[86]  Jacob Rosenstein,et al.  The Promise of Nanopore Technology: Nanopore DNA sequencing represents a fundamental change in the way that genomic information is read, with potentially big savings. , 2014, IEEE Pulse.

[87]  H. Bayley Nanopore sequencing: from imagination to reality. , 2015, Clinical chemistry.

[88]  Ash A. Alizadeh,et al.  Predicting Radiotherapy Responses and Treatment Outcomes Through Analysis of Circulating Tumor DNA. , 2015, Seminars in radiation oncology.

[89]  A. Meller,et al.  DNA sequencing and bar‐coding using solid‐state nanopores , 2012, Electrophoresis.

[90]  D. Busam,et al.  An Integrated Genomic Analysis of Human Glioblastoma Multiforme , 2008, Science.

[91]  Olivier Lantz,et al.  Human Papillomavirus Mutational Insertion: Specific Marker of Circulating Tumor DNA in Cervical Cancer Patients , 2012, PloS one.

[92]  A. Morell CEA Serum Levels in Non-Neoplastic Disease , 1992 .

[93]  Peiyong Jiang,et al.  Cancer genome scanning in plasma: detection of tumor-associated copy number aberrations, single-nucleotide variants, and tumoral heterogeneity by massively parallel sequencing. , 2013, Clinical chemistry.

[94]  D. García-Olmo,et al.  Detection of circulating tumor cells and of tumor DNA in plasma during tumor progression in rats. , 2005, Cancer letters.

[95]  A. Hidalgo-Miranda,et al.  Cancer Progression Mediated by Horizontal Gene Transfer in an In Vivo Model , 2012, PloS one.

[96]  Nitzan Rosenfeld,et al.  Circulating tumor-derived DNA is shorter than somatic DNA in plasma , 2015, Proceedings of the National Academy of Sciences.

[97]  Johnny Lo,et al.  Circulating tumor DNA to monitor treatment response and detect acquired resistance in patients with metastatic melanoma , 2015, Oncotarget.

[98]  Hui-yuan Shao,et al.  Increased integrity of circulating cell-free DNA in plasma of patients with acute leukemia , 2010, Clinical chemistry and laboratory medicine.

[99]  V. Wong,et al.  Lengthening and shortening of plasma DNA in hepatocellular carcinoma patients , 2015, Proceedings of the National Academy of Sciences.

[100]  R Montironi,et al.  Prostate tissue and serum markers. , 2000, Advances in clinical pathology : the official journal of Adriatic Society of Pathology.

[101]  M. Stroun,et al.  The virtosome—a novel cytosolic informative entity and intercellular messenger , 2010, Cell biochemistry and function.

[102]  D. García-Olmo,et al.  Functionality of circulating DNA: the hypothesis of genometastasis. , 2001, Annals of the New York Academy of Sciences.

[103]  Carlos Caldas,et al.  Analysis of circulating tumor DNA to monitor metastatic breast cancer. , 2013, The New England journal of medicine.