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):224ra224.
Article
Google Scholar
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):446–51.
Article
CAS
Google Scholar
Forshew T, Murtaza M, Parkinson C, Gale D, Tsui DW, Kaper F, Dawson SJ, 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):136ra168.
Article
Google Scholar
Diehl F, Li M, Dressman D, He Y, Shen D, Szabo S, Diaz LA Jr, Goodman SN, David KA, Juhl H, et al. Detection and quantification of mutations in the plasma of patients with colorectal tumors. Proc Natl Acad Sci USA. 2005;102(45):16368–73.
Article
CAS
Google Scholar
Siravegna G, Mussolin B, Venesio T, Marsoni S, Seoane J, Dive C, Papadopoulos N, Kopetz S, Corcoran RB, Siu LL, et al. How liquid biopsies can change clinical practice in oncology. Ann Oncol. 2019;30:1580–90.
Article
CAS
Google Scholar
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):223–38.
Article
CAS
Google Scholar
Chen M, Zhao H. Next-generation sequencing in liquid biopsy: cancer screening and early detection. Hum Genom. 2019;13(1):34.
Article
Google Scholar
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):926–30.
Article
CAS
Google Scholar
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.
Article
Google Scholar
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):547–55.
Article
CAS
Google Scholar
Chung J, Son DS, Jeon HJ, Kim KM, Park G, Ryu GH, Park WY, Park D. The minimal amount of starting DNA for Agilent’s hybrid capture-based targeted massively parallel sequencing. Sci Rep. 2016;6:26732.
Article
CAS
Google Scholar
Shin SH, Kim YJ, Lee D, Cho D, Ko YH, Cho J, Park WY, Park D, Kim SJ, Kim WS. Analysis of circulating tumor DNA by targeted ultra-deep sequencing across various non-Hodgkin lymphoma subtypes. Leuk Lymphoma. 2019;60:2237–46.
Article
CAS
Google Scholar
Newman AM, Bratman SV, To J, Wynne JF, Eclov NC, 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):548–54.
Article
CAS
Google Scholar
Park G, Park JK, Son DS, Shin SH, Kim YJ, Jeon HJ, Lee J, Park WY, Lee KH, Park D. Utility of targeted deep sequencing for detecting circulating tumor DNA in pancreatic cancer patients. Sci Rep. 2018;8(1):11631.
Article
Google Scholar
Park G, Park JK, Shin SH, Jeon HJ, Kim NKD, Kim YJ, Shin HT, Lee E, Lee KH, Son DS, et al. Characterization of background noise in capture-based targeted sequencing data. Genome Biol. 2017;18(1):136.
Article
Google Scholar
Schmitt MW, Kennedy SR, Salk JJ, Fox EJ, Hiatt JB, Loeb LA. Detection of ultra-rare mutations by next-generation sequencing. Proc Natl Acad Sci USA. 2012;109(36):14508–13.
Article
CAS
Google Scholar
Kinde I, Wu J, Papadopoulos N, Kinzler KW, Vogelstein B. Detection and quantification of rare mutations with massively parallel sequencing. Proc Natl Acad Sci USA. 2011;108(23):9530–5.
Article
Google Scholar
Kim J, Kim D, Lim JS, Maeng JH, Son H, Kang H-C, Nam H, Lee JH, Kim S. The use of technical replication for detection of low-level somatic mutations in next-generation sequencing. Nat Commun. 2019;10(1):1047.
Article
Google Scholar
Yeom H, Lee Y, Ryu T, Noh J, Lee AC, Lee H-B, Kang E, Song SW, Kwon S. Barcode-free next-generation sequencing error validation for ultra-rare variant detection. Nat Commun. 2019;10(1):977.
Article
Google Scholar
Chen L, Liu P, Evans TC Jr, Ettwiller LM. DNA damage is a pervasive cause of sequencing errors, directly confounding variant identification. Science. 2017;355(6326):752–6.
Article
CAS
Google Scholar
Chen G, Mosier S, Gocke CD, Lin MT, Eshleman JR. Cytosine deamination is a major cause of baseline noise in next-generation sequencing. Mol Diagn Ther. 2014;18(5):587–93.
Article
CAS
Google Scholar
Do H, Wong SQ, Li J, Dobrovic A. Reducing sequence artifacts in amplicon-based massively parallel sequencing of formalin-fixed paraffin-embedded DNA by enzymatic depletion of uracil-containing templates. Clin Chem. 2013;59(9):1376–83.
Article
CAS
Google Scholar
Costello M, Pugh TJ, Fennell TJ, Stewart C, Lichtenstein L, Meldrim JC, Fostel JL, Friedrich DC, Perrin D, Dionne D, et al. Discovery and characterization of artifactual mutations in deep coverage targeted capture sequencing data due to oxidative DNA damage during sample preparation. Nucleic Acids Res. 2013;41(6):e67.
Article
CAS
Google Scholar
Laehnemann D, Borkhardt A, McHardy AC. Denoising DNA deep sequencing data-high-throughput sequencing errors and their correction. Brief Bioinform. 2016;17(1):154–79.
Article
CAS
Google Scholar
Wong SQ, Li J, Salemi R, Sheppard KE, Do H, Tothill RW, McArthur GA, Dobrovic A. Targeted-capture massively-parallel sequencing enables robust detection of clinically informative mutations from formalin-fixed tumours. Sci Rep. 2013;3:3494.
Article
Google Scholar
Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics. 2010;26(5):589–95.
Article
Google Scholar
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25(16):2078–9.
Article
Google Scholar
McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Dalyl M. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Gen Res. 2010;20(9):1297–303.
Article
CAS
Google Scholar
Team RC: R: A language and environment for statistical computing. 2013.
Tate JG, Bamford S, Jubb HC, Sondka Z, Beare DM, Bindal N, Boutselakis H, Cole CG, Creatore C, Dawson E. COSMIC: the catalogue of somatic mutations in cancer. Nucleic Acid Res. 2019;47(D1):D941–7.
Article
CAS
Google Scholar
McBride TJ, Preston BD, Loeb LA. Mutagenic spectrum resulting from DNA damage by oxygen radicals. Biochemistry. 1991;30(1):207–13.
Article
CAS
Google Scholar
Valentine MR, Rodriguez H, Termini J. Mutagenesis by peroxy radical is dominated by transversions at deoxyguanosine: evidence for the lack of involvement of 8-oxo-dG1 and/or abasic site formation. Biochemistry. 1998;37(19):7030–8.
Article
CAS
Google Scholar
Schirmer M, Ijaz UZ, D’Amore R, Hall N, Sloan WT, Quince C. Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform. Nucleic Acids Res. 2015;43(6):e37.
Article
Google Scholar