Next-generation sequencing in liquid biopsy: cancer screening and early detection

Ming Chen, Hongyu Zhao, Ming Chen, Hongyu Zhao

Abstract

In recent years, the rapid development of next-generation sequencing (NGS) technologies has led to a significant reduction in sequencing cost with improved accuracy. In the area of liquid biopsy, NGS has been applied to sequence circulating tumor DNA (ctDNA). Since ctDNA is the DNA fragments released by tumor cells, it can provide a molecular profile of cancer. Liquid biopsy can be applied to all stages of cancer diagnosis and treatment, allowing non-invasive and real-time monitoring of disease development. The most promising aspects of liquid biopsy in cancer applications are cancer screening and early diagnosis because they can lead to better survival results and less disease burden. Although many ctDNA sequencing methods have enough sensitivity to detect extremely low levels of mutation frequency at the early stage of cancer, how to effectively implement them in population screening settings remains challenging. This paper focuses on the application of liquid biopsy in the early screening and diagnosis of cancer, introduces NGS-related methods, reviews recent progress, summarizes challenges, and discusses future research directions.

Keywords: Cancer screening; Early detection; Liquid biopsy; Next-generation sequencing.

Conflict of interest statement

The authors declare that they have no competing interests.

References

    1. World Health Organization. WHO. Cancer. 2019. , [Accessed 12 Sept 2018].
    1. Blumen H, Fitch K, Polkus V. Comparison of treatment costs for breast cancer, by tumor stage and type of service. Am Health Drug Benefits. 2016;9(1):23.
    1. Cipriano LE, Romanus D, Earle CC, Neville BA, Halpern EF, Gazelle GS, McMahon PM. Lung cancer treatment costs, including patient responsibility, by disease stage and treatment modality, 1992 to 2003. Value Health. 2011;14(1):41–52. doi: 10.1016/j.jval.2010.10.006.
    1. Center for Disease Control CDC and Prevention. How to prevent cancer or find it early: screening tests. 2019. .cdc.gov [Accessed 02 May 2018].
    1. Kwapisz D. The first liquid biopsy test approved. is it a new era of mutation testing for non-small cell lung cancer? Ann Transl Med. 2017;5(3):46. doi: 10.21037/atm.2017.01.32.
    1. Crowley E, Di Nicolantonio F, Loupakis F, Bardelli A. Liquid biopsy: monitoring cancer- genetics in the blood. Nat Rev Clin Oncol. 2013;10(8):472. doi: 10.1038/nrclinonc.2013.110.
    1. Yoshioka Y, Kosaka N, Konishi Y, Ohta H, Okamoto H, Sonoda H, Nonaka R, Yamamoto H, Ishii H, Mori M, et al. Ultra-sensitive liquid biopsy of circulating extracellular vesicles using exoscreen. Nat Commun. 2014;5:3591. doi: 10.1038/ncomms4591.
    1. Pantel K, Alix-Panabières C. Real-time liquid biopsy in cancer patients: fact or fiction? Cancer Res. 2013;73(21):6384–6388. doi: 10.1158/0008-5472.CAN-13-2030.
    1. Labib M, Mohamadi RM, Poudineh M, Ahmed SU, Ivanov I, Huang C-L, Moosavi M, Sargent EH, Kelley SO. Single-cell mrna cytometry via sequence-specific nanoparticle clustering and trapping. Nat Chem. 2018;10(5):1. doi: 10.1038/s41557-018-0025-8.
    1. Stroun M, Lyautey J, Lederrey C, Olson-Sand A, Anker P. About the possible origin and mechanism of circulating DNA: apoptosis and active DNA release. Clin Chim Acta. 2001;313(1–2):139–142. doi: 10.1016/S0009-8981(01)00665-9.
    1. Siena S, Sartore-Bianchi A, Garcia-Carbonero R, Karthaus M, Smith D, Tabernero J, Van Cutsem E, Guan X, Boedigheimer M, Ang A, et al. Dynamic molecular analysis and clinical correlates of tumor evolution within a phase ii trial of panitumumab-based therapy in metastatic colorectal cancer. Ann Oncol. 2017;29(1):119–126. doi: 10.1093/annonc/mdx504.
    1. Wan JCM, Massie C, Garcia-Corbacho J, Mouliere F, Brenton JD, Caldas C, Pacey S, Baird R, Rosenfeld N. Liquid biopsies come of age: towards implementation of circulating tumour DNA. Nat Rev Cancer. 2017;17(4):223. doi: 10.1038/nrc.2017.7.
    1. Tangvarasittichai O, Jaiwang W, Tangvarasittichai S. The plasma DNA concentration as a potential breast cancer screening marker. Indian J Clin Biochem. 2015;30(1):55–58. doi: 10.1007/s12291-013-0407-z.
    1. Lehmann-Werman R, Neiman D, Zemmour H, Moss J, Magenheim J, Vaknin-Dembinsky A, Rubertsson S, Nellgård B, Blennow K, Zetterberg H, et al. Identification of tissue-specific cell death using methylation patterns of circulating DNA. Proc Natl Acad Sci. 2016;113(13):E1826–E1834. doi: 10.1073/pnas.1519286113.
    1. Abbosh C, Birkbak NJ, Wilson GA, Jamal-Hanjani M, Constantin T, Salari R, Le Quesne J, Moore DA, Veeriah S, Rosenthal R, et al. Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution. Nature. 2017;545(7655):446. doi: 10.1038/nature22364.
    1. Phallen J, Sausen M, Adleff V, Leal A, Hruban C, White J, Anagnostou V, Fiksel J, Cristiano S, Papp E, et al. Direct detection of early-stage cancers using circulating tumor DNA. Sci Transl Med. 2017;9(403):eaan2415. doi: 10.1126/scitranslmed.aan2415.
    1. Cohen JD, Li L, Wang Y, Thoburn C, Afsari B, Danilova L, Douville C, Javed AA, Wong F, Mattox A, et al. Detection and localization of surgically resectable cancers with a multi-analyte blood test. Science. 2018;359(6378):eaar3247. doi: 10.1126/science.aar3247.
    1. Donaldson J, Park BH. Circulating tumor DNA: measurement and clinical utility. Ann Rev Med. 2018;69:223–234. doi: 10.1146/annurev-med-041316-085721.
    1. Mao L, Hruban RH, Boyle JO, Tockman M, Sidransky D. Detection of oncogene mutations in sputum precedes diagnosis of lung cancer. Cancer Res. 1994;54(7):1634–1637.
    1. Gormally E, Vineis P, Matullo G, Veglia F, Caboux E, Le Roux E, Peluso M, Garte S, Guarrera S, Munnia A, et al. Tp53 and kras2 mutations in plasma DNA of healthy subjects and subsequent cancer occurrence: a prospective study. Cancer Res. 2006;66(13):6871–6876. doi: 10.1158/0008-5472.CAN-05-4556.
    1. Gorgannezhad L, Umer M, Islam MN, Nguyen N-T, Shiddiky MJA. Circulating tumor DNA and liquid biopsy: opportunities, challenges, and recent advances in detection technologies. Lab Chip. 2018;18(8):1174–1196. doi: 10.1039/C8LC00100F.
    1. Ossandon MR, Agrawal L, Bernhard EJ, Conley BA, Dey SM, Divi RL, Guan P, Lively TG, McKee TC, Sorg BS, et al. Circulating tumor DNA assays in clinical cancer research. JNCI: J Natl Cancer Inst. 2018;110(9):929–934. doi: 10.1093/jnci/djy105.
    1. Church TR, Wandell M, Lofton-Day C, Mongin SJ, Burger M, Payne SR, Castaños-Vélez E, Blumenstein BA, Rösch T, Osborn N, et al. Prospective evaluation of methylated sept9 in plasma for detection of asymptomatic colorectal cancer. Gut. 2013;63(2):317–325. doi: 10.1136/gutjnl-2012-304149.
    1. Song L, Li Y. Sept9: a specific circulating biomarker for colorectal cancer. Adv Clin Chem. 2015;72:171–204. doi: 10.1016/bs.acc.2015.07.004.
    1. Song L, Jia J, Peng X, Xiao W, Li Y. The performance of the sept9 gene methylation assay and a comparison with other crc screening tests: a meta-analysis. Sci Rep. 2017;7(1):3032. doi: 10.1038/s41598-017-03321-8.
    1. Diehl F, Schmidt K, Choti MA, Romans K, Goodman S, Li M, Thornton K, Agrawal N, Sokoll L, Szabo SA, et al. Circulating mutant DNA to assess tumor dynamics. Nat Med. 2008;14(9):985. doi: 10.1038/nm.1789.
    1. European Medicines Agency. EMA. Tarceva. 2018. , [Accessed 27 July 2018].
    1. US Food FDA and Drug Administration. Premarket approval P150044 Cobas EGFR MUTATION TEST V2. 2018. [Accessed 27 July 2018].
    1. Goldberg SB, Narayan A, Kole AJ, Decker RH, Teysir J, Carriero NJ, Lee A, Nemati R, Nath SK, Mane SM, et al. Early assessment of lung cancer immunotherapy response via circulating tumor DNA. Clin Cancer Res. 2018;24(8):1341. doi: 10.1158/1078-0432.CCR-17-1341.
    1. Reinert T, Schøler LV, Thomsen R, Tobiasen H, Vang S, Nordentoft I, Lamy P, Kannerup A-S, Mortensen FV, Stribolt K, Hamilton-Dutoit S, Nielsen HJ, Laurberg S, Pallisgaard N, Pedersen JS, Ørntoft TF, Andersen CL. Analysis of circulating tumour DNA to monitor disease burden following colorectal cancer surgery. Gut. 2016;65(4):625–634. doi: 10.1136/gutjnl-2014-308859.
    1. Lecomte T, Berger A, Zinzindohoué F, Micard S, Landi B, Blons H, Beaune P, Cugnenc P-H, Laurent-Puig P. Detection of free-circulating tumor-associated DNA in plasma of colorectal cancer patients and its association with prognosis. Int J Cancer. 2002;100(5):542–548. doi: 10.1002/ijc.10526.
    1. Thierry AR, Mouliere F, Gongora C, Ollier J, Robert B, Ychou M, Del Rio M, Molina F. Origin and quantification of circulating DNA in mice with human colorectal cancer xenografts. Nucleic Acids Res. 2010;38(18):6159–6175. doi: 10.1093/nar/gkq421.
    1. Bettegowda C, Sausen M, Leary RJ, Kinde I, Wang Y, Agrawal N, Bartlett BR, Wang H, Luber B, Alani RM, et al. Detection of circulating tumor DNA in early-and late-stage human malignancies. Sci Transl Med. 2014;6(224):224ra24. doi: 10.1126/scitranslmed.3007094.
    1. Haque IS, Elemento O. Challenges in using ctDNA to achieve early detection of cancer. bioRxiv. 2017;237578.
    1. Inc. Grail. ESUMMIT Study. 2018. , [Accessed 21 Feb 2019].
    1. Inc. Guardant Health. Early detection LUNAR-2. 2018. , [Accessed 21 Feb 2019].
    1. Freenome. Clinical studies. 2019. [Accessed 21 Feb 2019].
    1. Inc. Biocept. Target Selector™ ctDNA EGFR Kit*. 2019. , [Accessed 21 Feb 2019].
    1. Inivata. Our products. 2019. .iniv [Accessed 21 Feb 2019].
    1. Inc. Cynvenio Biosystems. The LiquidBiopsy® Platform. 2019. .cynv [Accessed 21 Feb 2019].
    1. CellMax Life. FirstSightCRC. 2019. , [Accessed 21 Feb 2019].
    1. Exosome Diagnostics. Our diagnostics: for patients. 2019. [Accessed 21 Feb 2019].
    1. Inc. Biodesix. Genomic blood test. 2019. [Accessed 21 Feb 2019].
    1. Inc. Personal Genome Diagnostics. Liquid biopsy. 2019. , [Accessed 21 Feb 2019].
    1. Cui S, Cheng Z, Qin W, Jiang L. Exosomes as a liquid biopsy for lung cancer. Lung Cancer. 2018;116:46–54. doi: 10.1016/j.lungcan.2017.12.012.
    1. Köhn L, Johansson M, Grankvist K, Nilsson J. Liquid biopsies in lung cancer? time to implement research technologies in routine care? Ann Transl Med. 2017;5(13):278. doi: 10.21037/atm.2017.04.12.
    1. Sorber L, Zwaenepoel K, Deschoolmeester V, Van Schil PEY, Van Meerbeeck J, Lardon F, Rolfo C, Pauwels P. Circulating cell-free nucleic acids and platelets as a liquid biopsy in the provision of personalized therapy for lung cancer patients. Lung Cancer. 2017;107:100–107. doi: 10.1016/j.lungcan.2016.04.026.
    1. Santis G, Angell R, Nickless G, Quinn A, Herbert A, Cane P, Spicer J, Breen R, McLean E, Tobal K. Screening for egfr and kras mutations in endobronchial ultrasound derived transbronchial needle aspirates in non-small cell lung cancer using COLD-PCR. PLoS One. 2011;6(9):e25191. doi: 10.1371/journal.pone.0025191.
    1. Castellanos-Rizaldos E, Liu P, Milbury CA, Guha M, Brisci A, Cremonesi L, Ferrari M, Mamon H, Makrigiorgos GM. Temperature-tolerant cold-pcr eliminates temperature stringency and enables robust mutation enrichment. Clin Chem. 2012;58(7):1130–1138. doi: 10.1373/clinchem.2012.183095.
    1. Pérez-Callejo D, Romero A, Provencio M, Torrente M. Liquid biopsy based biomarkers in non-small cell lung cancer for diagnosis and treatment monitoring. Transl Lung Cancer Res. 2016;5(5):455. doi: 10.21037/tlcr.2016.10.07.
    1. Narayan A, Carriero NJ, Gettinger SN, Kluytenaar J, Kozak KR, Yock TI, Muscato NE, Ugarelli P, Decker RH, Patel AA. Ultrasensitive measurement of hotspot mutations in tumor DNA in blood using error-suppressed multiplexed deep sequencing. Cancer Res. 2012;72(14):3492–3498. doi: 10.1158/0008-5472.CAN-11-4037.
    1. Newman AM, Lovejoy AF, Klass DM, Kurtz DM, Chabon JJ, Scherer F, Stehr H, Liu CL, Bratman SV, Say C, et al. Integrated digital error suppression for improved detection of circulating tumor DNA. Nat Biotechnol. 2016;34(5):547. doi: 10.1038/nbt.3520.
    1. Dressman D, Yan H, Traverso G, Kinzler KW, Vogelstein B. Transforming single DNA molecules into fluorescent magnetic particles for detection and enumeration of genetic variations. Proc Natl Acad Sci. 2003;100(15):8817–8822. doi: 10.1073/pnas.1133470100.
    1. Mosko MJ, Nakorchevsky AA, Flores E, Metzler H, Ehrich M, van den Boom DJ, Sherwood JL, Nygren AOH. Ultrasensitive detection of multiplexed somatic mutations using maldi-tof mass spectrometry. J Mol Diagn. 2016;18(1):23–31. doi: 10.1016/j.jmoldx.2015.08.001.
    1. Baer C, Kern W, Koch S, Nadarajah N, Schindela S, Meggendorfer M, Haferlach C, Haferlach T. Ultra-deep sequencing leads to earlier and more sensitive detection of the tyrosine kinase inhibitor resistance mutation t315i in chronic myeloid leukemia. Haematologica. 2016;101(7):830–838. doi: 10.3324/haematol.2016.145888.
    1. Forshew T, Murtaza M, Parkinson C, Gale D, Tsui DWY, Kaper F, Dawson S-J, Piskorz AM, Jimenez-Linan M, Bentley D, et al. Noninvasive identification and monitoring of cancer mutations by targeted deep sequencing of plasma DNA. Sci Transl Med. 2012;4(136):136ra68. doi: 10.1126/scitranslmed.3003726.
    1. Gale D, Lawson ARJ, Howarth K, Madi M, Durham B, Smalley S, Calaway J, Blais S, Jones G, Clark J, et al. Development of a highly sensitive liquid biopsy platform to detect clinically-relevant cancer mutations at low allele fractions in cell-free DNA. PloS one. 2018;13(3):e0194630. doi: 10.1371/journal.pone.0194630.
    1. Kinde I, Wu J, Papadopoulos N, Kinzler KW, Vogelstein B. Detection and quantification of rare mutations with massively parallel sequencing. ProcNatl Acad Sci. 2011;108(23):9530–9535. doi: 10.1073/pnas.1105422108.
    1. Jeanne T, Kinde I, Wang Y, Wong HL, Roebert J, Christie M, Tacey M, Wong R, Singh M, Karapetis CS, et al. Circulating tumor DNA as an early marker of therapeutic response in patients with metastatic colorectal cancer. Ann Oncol. 2015;26(8):1715–1722. doi: 10.1093/annonc/mdv177.
    1. Chabon JJ, Simmons AD, Lovejoy AF, Esfahani MS, Newman AM, Haringsma HJ, Kurtz DM, Stehr H, Scherer F, Karlovich CA, et al. Circulating tumour DNA profiling reveals heterogeneity of egfr inhibitor resistance mechanisms in lung cancer patients. Nat Commun. 2016;7:11815. doi: 10.1038/ncomms11815.
    1. Newman AM, Bratman SV, Jacqueline To. Wynne JF, Eclov NCW, Modlin LA, Liu CL, Neal JW, Wakelee HA, Merritt RE, et al. An ultrasensitive method for quantitating circulating tumor DNA with broad patient coverage. Nat Med. 2014;20(5):548. doi: 10.1038/nm.3519.
    1. Thermo Fisher Scientific. Ion AmpliSeq Panels. 2019. , [Accessed 07 Feb 2019].
    1. Rothé F, Laes J-F, Lambrechts D, Smeets D, Vincent D, Maetens M, Fumagalli D, Michiels S, Drisis S, Moerman C, et al. Plasma circulating tumor DNA as an alternative to metastatic biopsies for mutational analysis in breast cancer. Ann Oncol. 2014;25(10):1959–1965. doi: 10.1093/annonc/mdu288.
    1. Lebofsky R, Decraene C, Bernard V, Kamal M, Blin A, Leroy Q, Frio TR, Pierron G, Callens C, Bieche I, 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. Mol Oncol. 2015;9(4):783–790. doi: 10.1016/j.molonc.2014.12.003.
    1. Guttery DS, Page K, Hills A, Woodley L, Marchese SD, Rghebi B, Hastings RK, Luo J, Pringle JH, Stebbing J, et al. Noninvasive detection of activating estrogen receptor 1 (esr1) mutations in estrogen receptor–positive metastatic breast cancer. Clin Chem. 2015;61(7):974–982. doi: 10.1373/clinchem.2015.238717.
    1. Leary RJ, Kinde I, Diehl F, Schmidt K, Clouser C, Duncan C, Antipova A, Lee C, McKernan K, Francisco M, et al. Development of personalized tumor biomarkers using massively parallel sequencing. Sci Transl Med. 2010;2(20):20ra14. doi: 10.1126/scitranslmed.3000702.
    1. Leary RJ, Sausen M, Kinde I, Papadopoulos N, Carpten JD, Craig D, O’shaughnessy J, Kinzler KW, Parmigiani G, Vogelstein B, et al. Detection of chromosomal alterations in the circulation of cancer patients with whole-genome sequencing. Sci Transl Med. 2012;4(162):162ra154. doi: 10.1126/scitranslmed.3004742.
    1. Wang T-L, Maierhofer C, Speicher MR, Lengauer C, Vogelstein B, Kinzler KW, Velculescu VE. Digital karyotyping. Proc Natl Acad Sci. 2002;99(25):16156–16161. doi: 10.1073/pnas.202610899.
    1. Boon K, Eberhart CG, Riggins GJ. Genomic amplification of orthodenticle homologue 2 in medulloblastomas. Cancer Res. 2005;65(3):703–707.
    1. Kinde I, Papadopoulos N, Kinzler KW, Vogelstein B. Fast-seqs: a simple and efficient method for the detection of aneuploidy by massively parallel sequencing. PloS one. 2012;7(7):e41162. doi: 10.1371/journal.pone.0041162.
    1. Belic J, Koch M, Ulz P, Auer M, Gerhalter T, Mohan S, Fischereder K, Petru E, Bauernhofer T, Geigl JB, et al. Rapid identification of plasma DNA samples with increased ctDNA levels by a modified fast-seqs approach. Clin Chem. 2015;61(6):838–849. doi: 10.1373/clinchem.2014.234286.
    1. Belic J, Koch M, Ulz P, Auer M, Gerhalter T, Mohan S, Fischereder K, Petru E, Bauernhofer T, Geigl JB, et al. mfast-seqs as a monitoring and pre-screening tool for tumor-specific aneuploidy in plasma DNA. Circ Nucleic Acids in Serum and Plasma–CNAPS IX. 2016;924:147–155. doi: 10.1007/978-3-319-42044-8_28.
    1. Shen SY, Singhania R, Fehringer G, Chakravarthy A, Roehrl MHA, Chadwick D, Zuzarte PC, Borgida A, Wang TT, Li T, et al. Sensitive tumour detection and classification using plasma cell-free DNA methylomes. Nature. 2018;563(7732):579. doi: 10.1038/s41586-018-0703-0.
    1. Cohen JD, Javed AA, Thoburn C, Wong F, Tie J, Gibbs P, Schmidt CM, Yip-Schneider MT, Allen PJ, Schattner M, et al. Combined circulating tumor DNA and protein biomarker-based liquid biopsy for the earlier detection of pancreatic cancers. Proc Natl Acad Sci. 2017;114:201704961.
    1. Xu R-h, Wei W, Krawczyk M, Wang W, Luo H, Flagg K, Yi S, Shi W, Quan Q, Li K, et al. Circulating tumour DNA methylation markers for diagnosis and prognosis of hepatocellular carcinoma. Nat Mater. 2017;16(11):1155. doi: 10.1038/nmat4997.
    1. Guo S, Diep D, Plongthongkum N, Fung H-L, Zhang K, Zhang K, et al. Nat Genet. 2017;49(4):635. doi: 10.1038/ng.3805.
    1. Hao X, Luo H, Krawczyk M, Wei W, Wang W, Wang J, Flagg K, Hou J, Zhang H, Yi S, et al. Dna methylation markers for diagnosis and prognosis of common cancers. Proc Natl Acad Sci. 2017;114(28):7414–7419. doi: 10.1073/pnas.1703577114.
    1. Taiwo O, Wilson GA, Morris T, Seisenberger S, Reik W, Pearce D, Beck S, Butcher LM. Methylome analysis using medip-seq with low DNA concentrations. Nat Protoc. 2012;7(4):617. doi: 10.1038/nprot.2012.012.
    1. Beikircher G, Pulverer W, Hofner M, Noehammer C, Weinhaeusel A. Multiplexed and sensitive DNA methylation testing using methylation-sensitive restriction enzymes “msre-qpcr”. In: DNA methylation protocols: Springer; 2018. p. 407–24.
    1. Kristiansen S, Nielsen D, Sölétormos G. Detection and monitoring of hypermethylated rassf1a in serum from patients with metastatic breast cancer. Clinical Epigenetics. 2016;8(1):35. doi: 10.1186/s13148-016-0199-0.
    1. Herman JG, Graff JR, Myöhänen SBDN, Nelkin BD, Baylin SB. Methylation-specific pcr: a novel pcr assay for methylation status of cpg islands. Proc Natl Acad Sci. 1996;93(18):9821–9826. doi: 10.1073/pnas.93.18.9821.
    1. Eads CA, Danenberg KD, Kawakami K, Saltz LB, Blake C, Shibata D, Danenberg PV, Laird PW. Methylight: a high-throughput assay to measure DNA methylation. Nucleic Acids Res. 2000;28(8):e32–e00. doi: 10.1093/nar/28.8.e32.
    1. Bibikova M, Lin Z, Zhou L, Chudin E, Garcia EW, Wu B, Doucet D, Thomas NJ, Wang Y, Vollmer E, et al. High-throughput DNA methylation profiling using universal bead arrays. Genome Res. 2006;16(3):383–393. doi: 10.1101/gr.4410706.
    1. Taylor KH, Kramer RS, Davis JW, Guo J, Duff DJ, Xu D, Caldwell CW, Shi H. Ultradeep bisulfite sequencing analysis of DNA methylation patterns in multiple gene promoters by 454 sequencing. Cancer Res. 2007;67(18):8511–8518. doi: 10.1158/0008-5472.CAN-07-1016.
    1. Meissner A, Gnirke A, Bell GW, Ramsahoye B, Lander ES, Jaenisch R. Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic acids Res. 2005;33(18):5868–5877. doi: 10.1093/nar/gki901.
    1. Deng J, Shoemaker R, Xie B, Gore A, LeProust EM, Antosiewicz-Bourget J, Egli D, Maherali N, Park I-H, Yu J, et al. Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming. Nat Biotechnol. 2009;27(4):353. doi: 10.1038/nbt.1530.
    1. Pisanic TR, Athamanolap P, Poh W, Chen C, Hulbert A, Brock MV, Herman JG, Wang T-H. Dreaming: a simple and ultrasensitive method for assessing intratumor epigenetic heterogeneity directly from liquid biopsies. Nucleic Acids Res. 2015;43(22):e154. doi: 10.1093/nar/gkv795.
    1. Sedlackova T, Repiska G, Celec P, Szemes T, Minarik G. Fragmentation of DNA affects the accuracy of the DNA quantitation by the commonly used methods. Biol Proced Online. 2013;15(1):5. doi: 10.1186/1480-9222-15-5.
    1. Thakur BK, Zhang H, Becker A, Matei I, Huang Y, Costa-Silva B, Zheng Y, Hoshino A, Brazier H, Xiang J, et al. Double-stranded DNA in exosomes: a novel biomarker in cancer detection. Cell Res. 2014;24(6):766. doi: 10.1038/cr.2014.44.
    1. Forbes SA, Bindal N, Bamford S, Cole C, Kok CY, Beare D, Jia M, Shepherd R, Leung K, Menzies A, et al. Cosmic: mining complete cancer genomes in the catalogue of somatic mutations in cancer. Nucleic Acids Res. 2010;39(suppl 1):D945–D950.
    1. Tomczak K, Czerwińska P, Wiznerowicz M. The Cancer Genome Atlas (TCGA): an immeasurable source of knowledge. Contemp Oncol. 2015;19(1A):A68.
    1. Merker JD, Oxnard GR, Compton C, Diehn M, Hurley P, Lazar AJ, Lindeman N, Lockwood CM, Rai AJ, Schilsky RL, et al. Circulating tumor DNA analysis in patients with cancer: American society of clinical oncology and college of american pathologists joint review. Arch Pathol Lab Med. 2018;142(10):1242–1253. doi: 10.5858/arpa.2018-0901-SA.
    1. Zhao H, Chen K-Z, Hui B-G, Zhang K, Yang F, Wang J. Role of circulating tumor DNA in the management of early-stage lung cancer. Thoracic Cancer. 2018;9(5):509–515. doi: 10.1111/1759-7714.12622.
    1. Kang Q, Henry NL, Paoletti C, Jiang H, Vats P, Chinnaiyan AM, Hayes DF, Merajver SD, Rae JM, Tewari M. Comparative analysis of circulating tumor DNA stability in k3edta, streck, and cellsave blood collection tubes. Clin Biochem. 2016;49(18):1354–1360. doi: 10.1016/j.clinbiochem.2016.03.012.
    1. Lam NYL, Rainer TH, Chiu RWK, Lo YMD. Edta is a better anticoagulant than heparin or citrate for delayed blood processing for plasma DNA analysis. Clin Chem. 2004;50(1):256–257. doi: 10.1373/clinchem.2003.026013.
    1. Xi L, Pham TH-T, Payabyab EC, Sherry RM, Rosenberg SA, Raffeld M. Circulating tumor DNA as an early indicator of response to T-cell transfer immunotherapy in metastatic melanoma. Clin Cancer Res. 2016;22(22):5480–5486. doi: 10.1158/1078-0432.CCR-16-0613.
    1. Wang R, Li X, Zhang H, Wang K, He J. Cell-free circulating tumor DNA analysis for breast cancer and its clinical utilization as a biomarker. Oncotarget. 2017;8(43):75742.
    1. Vandeputte C, Kehagias P, El Housni H, Ameye L, Laes J-F, Desmedt C, Sotiriou C, Deleporte A, Puleo F, Geboes K, et al. Circulating tumor DNA in early response assessment and monitoring of advanced colorectal cancer treated with a multi-kinase inhibitor. Oncotarget. 2018;9(25):17756. doi: 10.18632/oncotarget.24879.
    1. Dawson S-J, Tsui DWY, Murtaza M, Biggs H, Rueda OM, Chin S-F, Dunning MJ, Gale D, Forshew T, Mahler-Araujo B, et al. Analysis of circulating tumor DNA to monitor metastatic breast cancer. New England J Med. 2013;368(13):1199–1209. doi: 10.1056/NEJMoa1213261.
    1. Kuderer NM, Burton KA, Blau S, Rose AL, Parker S, Lyman GH, Blau CA. Comparison of 2 commercially available next-generation sequencing platforms in oncology. JAMA Oncol. 2017;3(7):996–998. doi: 10.1001/jamaoncol.2016.4983.
    1. Wyatt AW, Annala M, Aggarwal R, Beja K, Feng F, Youngren J, Foye A, Lloyd P, Nykter M, Beer TM, et al. Concordance of circulating tumor DNA and matched metastatic tissue biopsy in prostate cancer. JNCI: J Natl Cancer Inst. 2017;110(1):78–86.
    1. Guo Q, Wang J, Xiao J, Lin W, Hu X, Yu W, Song G, Lou J, Chen JF. Heterogeneous mutation pattern in tumor tissue and circulating tumor DNA warrants parallel ngs panel testing. Mol Cancer. 2018;17(1):131. doi: 10.1186/s12943-018-0875-0.
    1. Mok TS, Wu Y-L, Ahn M-J, Garassino MC, Kim HR, Ramalingam SS, Shepherd FA, He Y, Akamatsu H, Theelen WSME, et al. Osimertinib or platinum–pemetrexed in egfr t790m–positive lung cancer. New England J Med. 2017;376(7):629–640. doi: 10.1056/NEJMoa1612674.
    1. Douillard J-Y, Ostoros G, Cobo M, Ciuleanu T, Cole R, McWalter G, Walker J, Dearden S, Webster A, Milenkova T, et al. Gefitinib treatment in egfr mutated caucasian nsclc: circulating-free tumor DNA as a surrogate for determination of egfr status. J Thor Oncol. 2014;9(9):1345–1353. doi: 10.1097/JTO.0000000000000263.
    1. Jean-Yves D, Ostoros G, Cobo M, Ciuleanu T, McCormack R, Webster A, Milenkova T. First-line gefitinib in caucasian egfr mutation-positive nsclc patients: a phase-iv, open-label, single-arm study. Br J Cancer. 2014;110(1):55. doi: 10.1038/bjc.2013.721.
    1. Oxnard GR, Thress KS, Alden RS, Lawrance R, Paweletz CP, Cantarini M, Yang JC-H, Barrett JC, Jänne PA. Association between plasma genotyping and outcomes of treatment with osimertinib (azd9291) in advanced non–small-cell lung cancer. J Clin Oncol. 2016;34(28):3375. doi: 10.1200/JCO.2016.66.7162.
    1. Jing C-W, Wang Z, Cao H-X, Ma R, Wu J-Z. High resolution melting analysis for epidermal growth factor receptor mutations in formalin-fixed paraffin-embedded tissue and plasma free DNA from non-small cell lung cancer patients. Asian Pac J Cancer Prev. 2013;14(11):6619–6623. doi: 10.7314/APJCP.2013.14.11.6619.
    1. Guo N, Lou F, Ma Y, Li J, Yang B, Chen W, Ye H, Zhang J-B, Zhao M-Y, Wu W-J, et al. Circulating tumor DNA detection in lung cancer patients before and after surgery. Sci Rep. 2016;6:33519. doi: 10.1038/srep33519.
    1. Condello V, Macerola E, Ugolini C, De Napoli L, Romei C, Materazzi G, Elisei R, Basolo F. Analysis of circulating tumor DNA does not improve the clinical management of patients with locally advanced and metastatic papillary thyroid carcinoma. Head Neck. 2018;40(8):1752–1758.
    1. Chen K, Zhang J, Guan T, Yang F, Lou F, Chen W, Zhao M, Zhang J, Chen S, Wang J. Comparison of plasma to tissue DNA mutations in surgical patients with non–small cell lung cancer. J Thorac Cardiovasc Surg. 2017;154(3):1123–1131. doi: 10.1016/j.jtcvs.2017.04.073.
    1. The National Lung Screening Trial Research Team Reduced lung-cancer mortality with low-dose computed tomographic screening. New England J Med. 2011;365(5):395–409. doi: 10.1056/NEJMoa1102873.

Source: PubMed

Sponsoren und Mitarbeiter

Krankheiten

Drogeninterventionen

3
Abonnieren