Advertisement

Cell-free Nucleic Acids in Cancer

Current Approaches, Challenges, and Future Directions
      Tumors shed fragmented DNA and nucleic acids into the blood, generally during apoptosis.

      Keywords

      To read this article in full you will need to make a payment

      Purchase one-time access:

      Academic & Personal: 24 hour online accessCorporate R&D Professionals: 24 hour online access
      One-time access price info
      • For academic or personal research use, select 'Academic and Personal'
      • For corporate R&D use, select 'Corporate R&D Professionals'

      Subscribers receive full online access to your subscription and archive of back issues up to and including 2002.

      Content published before 2002 is available via pay-per-view purchase only.

      Subscribe:

      Subscribe to Clinics in Laboratory Medicine
      Already a print subscriber? Claim online access
      Already an online subscriber? Sign in
      Institutional Access: Sign in to ScienceDirect

      References

        • American College of Obstetrics and Gynecologists’ Committee on Practices: Bulletins-Obstetrics, American College of Obstetrics and Gynecologists’ Committee on Genetics, Society of Maternal-fetal Medicine
        Screening for Fetal Chromosomal Abnormalities: ACOG Practice Bulletin, Number 226.
        Obstet Gynecol. 2020; 136: e48-e69
        • Lo Y.M.
        • Corbetta N.
        • Chamberlain P.F.
        • et al.
        Presence of fetal DNA in maternal plasma and serum.
        Lancet. 1997; 350: 485-487
        • Bronkhorst A.J.
        • Ungerer V.
        • Holdenrieder S.
        The emerging role of cell-free DNA as a molecular marker for cancer management.
        Biomol Detect Quantif. 2019; 17: 100087
        • Snyder M.W.
        • Kircher M.
        • Hill A.J.
        • et al.
        Cell-free DNA Comprises an In Vivo Nucleosome Footprint that Informs Its Tissues-Of-Origin.
        Cell. 2016; 164: 57-68
        • Bettegowda C.
        • Sausen M.
        • Leary R.J.
        • et al.
        Detection of circulating tumor DNA in early- and late-stage human malignancies.
        Sci Transl Med. 2014; 6: 224ra224
        • Bronkhorst A.J.
        • Ungerer V.
        • Holdenrieder S.
        Comparison of methods for the isolation of cell-free DNA from cell culture supernatant.
        Tumour Biol. 2020; 42 (1010428320916314)
        • Ungerer V.
        • Bronkhorst A.J.
        • Holdenrieder S.
        Preanalytical variables that affect the outcome of cell-free DNA measurements.
        Crit Rev Clin Lab Sci. 2020; 57: 484-507
        • Fettke H.
        • Kwan E.M.
        • Azad A.A.
        Cell-free DNA in cancer: current insights.
        Cell Oncol. 2019; 42: 13-28
        • Peng M.
        • Chen C.
        • Hulbert A.
        • et al.
        Non-blood circulating tumor DNA detection in cancer.
        Oncotarget. 2017; 8: 69162-69173
        • Lampignano R.
        • Kloten V.
        • Krahn T.
        • et al.
        Integrating circulating miRNA analysis in the clinical management of lung cancer: Present or future?.
        Mol Aspects Med. 2020; 72: 100844
        • Schneegans S.
        • Luck L.
        • Besler K.
        • et al.
        Pre-analytical factors affecting the establishment of a single tube assay for multiparameter liquid biopsy detection in melanoma patients.
        Mol Oncol. 2020; 14: 1001-1015
        • Greytak S.R.
        • Engel K.B.
        • Parpart-Li S.
        • et al.
        Harmonizing Cell-Free DNA Collection and Processing Practices through Evidence-Based Guidance.
        Clin Cancer Res. 2020; 26: 3104-3109
        • Sorber L.
        • Zwaenepoel K.
        • Jacobs J.
        • et al.
        Specialized Blood Collection Tubes for Liquid Biopsy: Improving the Pre-analytical Conditions.
        Mol Diagn Ther. 2020; 24: 113-124
        • van Dessel L.F.
        • Beije N.
        • Helmijr J.C.
        • et al.
        Application of circulating tumor DNA in prospective clinical oncology trials - standardization of preanalytical conditions.
        Mol Oncol. 2017; 11: 295-304
        • van Dessel L.F.
        • Martens J.W.M.
        • Lolkema M.P.
        Fundamentals of liquid biopsies in metastatic prostate cancer: from characterization to stratification.
        Curr Opin Oncol. 2020; 32: 527-534
        • Risberg B.
        • Tsui D.W.Y.
        • Biggs H.
        • et al.
        Effects of Collection and Processing Procedures on Plasma Circulating Cell-Free DNA from Cancer Patients.
        J Mol Diagn. 2018; 20: 883-892
        • Bronkhorst A.J.
        • Ungerer V.
        • Holdenrieder S.
        Early detection of cancer using circulating tumor DNA: biological, physiological and analytical considerations.
        Crit Rev Clin Lab Sci. 2019; : 1-17
        • Alborelli I.
        • Generali D.
        • Jermann P.
        • et al.
        Cell-free DNA analysis in healthy individuals by next-generation sequencing: a proof of concept and technical validation study.
        Cell Death Dis. 2019; 10: 534
        • de Kock R.
        • Deiman B.
        • Kraaijvanger R.
        • et al.
        Optimized (Pre) Analytical Conditions and Workflow for Droplet Digital PCR Analysis of Cell-Free DNA from Patients with Suspected Lung Carcinoma.
        J Mol Diagn. 2019; 21: 895-902
        • Barrett A.N.
        • Thadani H.A.
        • Laureano-Asibal C.
        • et al.
        Stability of cell-free DNA from maternal plasma isolated following a single centrifugation step.
        Prenat Diagn. 2014; 34: 1283-1288
        • Cavallone L.
        • Aldamry M.
        • Lafleur J.
        • et al.
        A Study of Pre-Analytical Variables and Optimization of Extraction Method for Circulating Tumor DNA Measurements by Digital Droplet PCR.
        Cancer Epidemiol Biomarkers Prev. 2019; 28: 909-916
        • Swinkels D.W.
        • Wiegerinck E.
        • Steegers E.A.
        • et al.
        Effects of blood-processing protocols on cell-free DNA quantification in plasma.
        Clin Chem. 2003; 49: 525-526
        • Beije N.
        • Martens J.W.M.
        • Sleijfer S.
        Incorporating liquid biopsies into treatment decision-making: obstacles and possibilities.
        Drug Discov Today. 2019; 24: 1715-1719
        • van Dessel L.F.
        • Vitale S.R.
        • Helmijr J.C.A.
        • et al.
        High-throughput isolation of circulating tumor DNA: a comparison of automated platforms.
        Mol Oncol. 2019; 13: 392-402
        • Diefenbach R.J.
        • Lee J.H.
        • Kefford R.F.
        • et al.
        Evaluation of commercial kits for purification of circulating free DNA.
        Cancer Genet. 2018; 228-229: 21-27
        • Diaz Jr., L.A.
        • Bardelli A.
        Liquid biopsies: genotyping circulating tumor DNA.
        J Clin Oncol. 2014; 32: 579-586
        • Heitzer E.
        • Haque I.S.
        • Roberts C.E.S.
        • et al.
        Current and future perspectives of liquid biopsies in genomics-driven oncology.
        Nat Rev Genet. 2019; 20: 71-88
        • Elazezy M.
        • Joosse S.A.
        Techniques of using circulating tumor DNA as a liquid biopsy component in cancer management.
        Comput Struct Biotechnol J. 2018; 16: 370-378
        • Hindson B.J.
        • Ness K.D.
        • Masquelier D.A.
        • et al.
        High-throughput droplet digital PCR system for absolute quantitation of DNA copy number.
        Anal Chem. 2011; 83: 8604-8610
        • Chaudhuri A.A.
        • Chabon J.J.
        • Lovejoy A.F.
        • et al.
        Early Detection of Molecular Residual Disease in Localized Lung Cancer by Circulating Tumor DNA Profiling.
        Cancer Discov. 2017; 7: 1394-1403
        • Newman A.M.
        • Bratman S.V.
        • To J.
        • et al.
        An ultrasensitive method for quantitating circulating tumor DNA with broad patient coverage.
        Nat Med. 2014; 20: 548-554
        • Newman A.M.
        • Lovejoy A.F.
        • Klass D.M.
        • et al.
        Integrated digital error suppression for improved detection of circulating tumor DNA.
        Nat Biotechnol. 2016; 34: 547-555
        • Phallen J.
        • Sausen M.
        • Adleff V.
        • et al.
        Direct detection of early-stage cancers using circulating tumor DNA.
        Sci Transl Med. 2017; 9: eaan2415
        • Abbosh C.
        • Birkbak N.J.
        • Swanton C.
        Early stage NSCLC - challenges to implementing ctDNA-based screening and MRD detection.
        Nat Rev Clin Oncol. 2018; 15: 577-586
        • Forshew T.
        • Murtaza M.
        • Parkinson C.
        • et al.
        Noninvasive identification and monitoring of cancer mutations by targeted deep sequencing of plasma DNA.
        Sci Transl Med. 2012; 4: 136ra168
        • Cohen J.D.
        • Li L.
        • Wang Y.
        • et al.
        Detection and localization of surgically resectable cancers with a multi-analyte blood test.
        Science. 2018; 359: 926-930
        • Guo S.
        • Diep D.
        • Plongthongkum N.
        • et al.
        Identification of methylation haplotype blocks aids in deconvolution of heterogeneous tissue samples and tumor tissue-of-origin mapping from plasma DNA.
        Nat Genet. 2017; 49: 635-642
        • Zeng H.
        • He B.
        • Yi C.
        • et al.
        Liquid biopsies: DNA methylation analyses in circulating cell-free DNA.
        J Genet Genomics. 2018; 45: 185-192
        • Legendre C.
        • Gooden G.C.
        • Johnson K.
        • et al.
        Whole-genome bisulfite sequencing of cell-free DNA identifies signature associated with metastatic breast cancer.
        Clin Epigenet. 2015; 7: 100
        • Wen L.
        • Li J.
        • Guo H.
        • et al.
        Genome-scale detection of hypermethylated CpG islands in circulating cell-free DNA of hepatocellular carcinoma patients.
        Cell Res. 2015; 25: 1250-1264
        • Liu M.C.
        • Oxnard G.R.
        • Klein E.A.
        • et al.
        Sensitive and specific multi-cancer detection and localization using methylation signatures in cell-free DNA.
        Ann Oncol. 2020; 31: 745-759
        • He F.C.
        • Meng W.W.
        • Qu Y.H.
        • et al.
        Expression of circulating microRNA-20a and let-7a in esophageal squamous cell carcinoma.
        World J Gastroenterol. 2015; 21: 4660-4665
        • Lan H.
        • Lu H.
        • Wang X.
        • et al.
        MicroRNAs as potential biomarkers in cancer: opportunities and challenges.
        Biomed Res Int. 2015; 2015: 125094
        • Markou A.
        • Liang Y.
        • Lianidou E.
        Prognostic, therapeutic and diagnostic potential of microRNAs in non-small cell lung cancer.
        Clin Chem Lab Med. 2011; 49: 1591-1603
        • de Planell-Saguer M.
        • Rodicio M.C.
        Detection methods for microRNAs in clinic practice.
        Clin Biochem. 2013; 46: 869-878
      1. Detecting Cancers Earlier Through Elective Plasma-based CancerSEEK Testing (ASCEND).
        (Available at:)
        https://clinicaltrials.gov/ct2/show/NCT04213326
        Date: 2021
        Date accessed: April 28, 2021
        • Ignatiadis M.
        • Sledge G.W.
        • Jeffrey S.S.
        Liquid biopsy enters the clinic - implementation issues and future challenges.
        Nat Rev Clin Oncol. 2021; 18: 297-312
        • Kalinich M.
        • Haber D.A.
        Cancer detection: Seeking signals in blood.
        Science. 2018; 359: 866-867
        • Liu M.C.
        Transforming the landscape of early cancer detection using blood tests-Commentary on current methodologies and future prospects.
        Br J Cancer. 2021; 124: 1475-1477
        • Lennon A.M.
        • Buchanan A.H.
        • Kinde I.
        • et al.
        Feasibility of blood testing combined with PET-CT to screen for cancer and guide intervention.
        Science. 2020; : 369
        • GRAIL Clinical Research Program
        (Available at:)
        https://grail.com/clinical-studies/
        Date: 2020
        Date accessed: April 28, 2001
        • Cristiano S.
        • Leal A.
        • Phallen J.
        • et al.
        Genome-wide cell-free DNA fragmentation in patients with cancer.
        Nature. 2019; 570: 385-389
        • Potter N.T.
        • Hurban P.
        • White M.N.
        • et al.
        Validation of a real-time PCR-based qualitative assay for the detection of methylated SEPT9 DNA in human plasma.
        Clin Chem. 2014; 60: 1183-1191
        • Chabon J.J.
        • Hamilton E.G.
        • Kurtz D.M.
        • et al.
        Integrating genomic features for non-invasive early lung cancer detection.
        Nature. 2020; 580: 245-251
        • Network NCC
        NCCN Guidelines Non-Small Cell Lung Cancer v4.2021.
        (Available at:)
        • Malapelle U.
        • Sirera R.
        • Jantus-Lewintre E.
        • et al.
        Profile of the Roche cobas(R) EGFR mutation test v2 for non-small cell lung cancer.
        Expert Rev Mol Diagn. 2017; 17: 209-215
        • Aggarwal C.
        • Rolfo C.D.
        • Oxnard G.R.
        • et al.
        Strategies for the successful implementation of plasma-based NSCLC genotyping in clinical practice.
        Nat Rev Clin Oncol. 2021; 18: 56-62
        • Leighl N.B.
        • Page R.D.
        • Raymond V.M.
        • et al.
        Clinical Utility of Comprehensive Cell-free DNA Analysis to Identify Genomic Biomarkers in Patients with Newly Diagnosed Metastatic Non-small Cell Lung Cancer.
        Clin Cancer Res. 2019; 25: 4691-4700
        • Andre F.
        • Ciruelos E.
        • Rubovszky G.
        • et al.
        Alpelisib for PIK3CA-Mutated, Hormone Receptor-Positive Advanced Breast Cancer.
        N Engl J Med. 2019; 380: 1929-1940
        • Teyssonneau D.
        • Margot H.
        • Cabart M.
        • et al.
        Prostate cancer and PARP inhibitors: progress and challenges.
        J Hematol Oncol. 2021; 14: 51
        • Garcia-Murillas I.
        • Schiavon G.
        • Weigelt B.
        • et al.
        Mutation tracking in circulating tumor DNA predicts relapse in early breast cancer.
        Sci Transl Med. 2015; 7: 302ra133
        • Garcia-Murillas I.
        • Chopra N.
        • Comino-Mendez I.
        • et al.
        Assessment of Molecular Relapse Detection in Early-Stage Breast Cancer.
        JAMA Oncol. 2019; 5: 1473-1478
        • Abbosh C.
        • Birkbak N.J.
        • Wilson G.A.
        • et al.
        Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution.
        Nature. 2017; 545: 446-451
        • Christensen E.
        • Birkenkamp-Demtroder K.
        • Sethi H.
        • et al.
        Early Detection of Metastatic Relapse and Monitoring of Therapeutic Efficacy by Ultra-Deep Sequencing of Plasma Cell-Free DNA in Patients With Urothelial Bladder Carcinoma.
        J Clin Oncol. 2019; 37: 1547-1557
        • Coombes R.C.
        • Page K.
        • Salari R.
        • et al.
        Personalized Detection of Circulating Tumor DNA Antedates Breast Cancer Metastatic Recurrence.
        Clin Cancer Res. 2019; 25: 4255-4263
        • Bratman S.V.
        • Yang S.Y.C.
        • Iafolla M.A.J.
        • et al.
        Personalized circulating tumor DNA analysis as a predictive biomarker in solid tumor patients treated with pembrolizumab.
        Nat Cancer. 2020; 1: 873-881
        • Parikh A.R.
        • Leshchiner I.
        • Elagina L.
        • et al.
        Liquid versus tissue biopsy for detecting acquired resistance and tumor heterogeneity in gastrointestinal cancers.
        Nat Med. 2019; 25: 1415-1421
        • Cavallone L.
        • Aguilar-Mahecha A.
        • Lafleur J.
        • et al.
        Prognostic and predictive value of circulating tumor DNA during neoadjuvant chemotherapy for triple negative breast cancer.
        Sci Rep. 2020; 10: 14704
        • Steensma D.P.
        • Bejar R.
        • Jaiswal S.
        • et al.
        Clonal hematopoiesis of indeterminate potential and its distinction from myelodysplastic syndromes.
        Blood. 2015; 126: 9-16
        • Jaiswal S.
        • Fontanillas P.
        • Flannick J.
        • et al.
        Age-related clonal hematopoiesis associated with adverse outcomes.
        N Engl J Med. 2014; 371: 2488-2498
        • Jaiswal S.
        • Natarajan P.
        • Silver A.J.
        • et al.
        Clonal Hematopoiesis and Risk of Atherosclerotic Cardiovascular Disease.
        N Engl J Med. 2017; 377: 111-121
        • Gondek L.P.
        • DeZern A.E.
        Assessing clonal haematopoiesis: clinical burdens and benefits of diagnosing myelodysplastic syndrome precursor states.
        Lancet Haematol. 2020; 7: e73-e81
        • Zhang W.
        • Xu J.
        DNA methyltransferases and their roles in tumorigenesis.
        Biol Res. 2017; 5: 1
        • Kuderer N.M.
        • Burton K.A.
        • Blau S.
        • et al.
        Comparison of 2 Commercially Available Next-Generation Sequencing Platforms in Oncology.
        JAMA Oncol. 2017; 3: 996-998
        • Stetson D.
        • Ahmed A.
        • Xu X.
        • et al.
        Orthogonal Comparison of Four Plasma NGS Tests With Tumor Suggests Technical Factors are a Major Source of Assay Discordance.
        JCO Precision Oncol. 2019; : 1-9
        • Godsey J.H.
        • Silvestro A.
        • Barrett J.C.
        • et al.
        Generic Protocols for the Analytical Validation of Next-Generation Sequencing-Based ctDNA Assays: A Joint Consensus Recommendation of the BloodPAC’s Analytical Variables Working Group.
        Clin Chem. 2020; 66: 1156-1166
        • IJzerman M.J.
        • de Boer J.
        • Azad A.
        • et al.
        Towards Routine Implementation of Liquid Biopsies in Cancer Management: It Is Always Too Early, until Suddenly It Is Too Late.
        Diagnostics. 2021; 11: 103
        • Merker J.D.
        • Oxnard G.R.
        • Compton C.
        • et al.
        Circulating Tumor DNA Analysis in Patients With Cancer: American Society of Clinical Oncology and College of American Pathologists Joint Review.
        J Clin Oncol. 2018; 36: 1631-1641
        • Weber S.
        • Spiegl B.
        • Perakis S.O.
        • et al.
        Technical Evaluation of Commercial Mutation Analysis Platforms and Reference Materials for Liquid Biopsy Profiling.
        Cancers (Basel). 2020; 12
        • Connors D.
        • Allen J.
        • Alvarez J.D.
        • et al.
        International liquid biopsy standardization alliance white paper.
        Crit Rev Oncol Hematol. 2020; 156: 103112
        • Verma S.
        • Moore M.W.
        • Ringler R.
        • et al.
        Analytical performance evaluation of a commercial next generation sequencing liquid biopsy platform using plasma ctDNA, reference standards, and synthetic serial dilution samples derived from normal plasma.
        BMC Cancer. 2020; 20: 945
        • Fettke H.
        • Steen J.A.
        • Kwan E.M.
        • et al.
        Analytical validation of an error-corrected ultra-sensitive ctDNA next-generation sequencing assay.
        BioTechniques. 2020; 69: 133-140
        • Johansson G.
        • Andersson D.
        • Filges S.
        • et al.
        Considerations and quality controls when analyzing cell-free tumor DNA.
        Biomol Detect Quantif. 2019; 17: 100078
        • Yu Q.
        • Huang F.
        • Zhang M.
        • et al.
        Multiplex picoliter-droplet digital PCR for quantitative assessment of EGFR mutations in circulating cell-free DNA derived from advanced non-small cell lung cancer patients.
        Mol Med Rep. 2017; 16: 1157-1166
        • Douglas M.P.
        • Gray S.W.
        • Phillips K.A.
        Private Payer and Medicare Coverage for Circulating Tumor DNA Testing: A Historical Analysis of Coverage Policies From 2015 to 2019.
        J Natl Compr Canc Netw. 2020; 18: 866-872
        • Sanchez-Calderon D.
        • Pedraza A.
        • Mancera Urrego C.
        • et al.
        Analysis of the Cost-Effectiveness of Liquid Biopsy to Determine Treatment Change in Patients with Her2-Positive Advanced Breast Cancer in Colombia.
        Clin Outcomes Res. 2020; 12: 115-122
        • Mandel P.
        • Metais P.
        Nuclear Acids In Human Blood Plasma.
        C R Seances Soc Biol Fil. 1948; 142: 241-243