Cancer Genome Atlas Research N, Weinstein JN, Collisson EA, Mills GB, Shaw KR, Ozenberger BA, Ellrott K, Shmulevich I, Sander C, Stuart JM. The Cancer genome atlas pan-Cancer analysis project. Nat Genet. 2013;45(10):1113–20.
Article
Google Scholar
Hoadley KA, Yau C, Wolf DM, Cherniack AD, Tamborero D, Ng S, Leiserson MDM, Niu B, McLellan MD, Uzunangelov V, et al. Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin. Cell. 2014;158(4):929–44.
Article
CAS
Google Scholar
Cancer Genome Atlas Research N. Integrated genomic analyses of ovarian carcinoma. Nature. 2011;474(7353):609–15.
Article
Google Scholar
Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, et al. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med. 2015;17(5):405–24.
Article
Google Scholar
Forbes SA, Beare D, Boutselakis H, Bamford S, Bindal N, Tate J, Cole CG, Ward S, Dawson E, Ponting L, et al. COSMIC: somatic cancer genetics at high-resolution. Nucleic Acids Res. 2017;45(D1):D777–83.
Article
CAS
Google Scholar
Mertes F, Elsharawy A, Sauer S, van Helvoort JM, van der Zaag PJ, Franke A, Nilsson M, Lehrach H, Brookes AJ. Targeted enrichment of genomic DNA regions for next-generation sequencing. Brief Funct Genomics. 2011;10(6):374–86.
Article
CAS
Google Scholar
Rohland N, Reich D. Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture. Genome Res. 2012;22(5):939–46.
Article
CAS
Google Scholar
Brunham LR, Hayden MR. Medicine. Whole-genome sequencing: the new standard of care? Science. 2012;336(6085):1112–3.
Article
CAS
Google Scholar
Iglesias A, Anyane-Yeboa K, Wynn J, Wilson A, Truitt Cho M, Guzman E, Sisson R, Egan C, Chung WK. The usefulness of whole-exome sequencing in routine clinical practice. Genet Med. 2014;16(12):922–31.
Article
Google Scholar
Sausen M, Phallen J, Adleff V, Jones S, Leary RJ, Barrett MT, Anagnostou V, Parpart-Li S, Murphy D, Kay Li Q, et al. Clinical implications of genomic alterations in the tumour and circulation of pancreatic cancer patients. Nat Commun. 2015;6:7686.
Article
Google Scholar
Xuan J, Yu Y, Qing T, Guo L, Shi L. Next-generation sequencing in the clinic: promises and challenges. Cancer Lett. 2013;340(2):284–95.
Article
CAS
Google Scholar
Sims D, Sudbery I, Ilott NE, Heger A, Ponting CP. Sequencing depth and coverage: key considerations in genomic analyses. Nat Rev Genet. 2014;15(2):121–32.
Article
CAS
Google Scholar
Meynert AM, Ansari M, FitzPatrick DR, Taylor MS. Variant detection sensitivity and biases in whole genome and exome sequencing. BMC Bioinformatics. 2014;15:247.
Article
Google Scholar
Shin HT, Choi YL, Yun JW, Kim NKD, Kim SY, Jeon HJ, Nam JY, Lee C, Ryu D, Kim SC, et al. Prevalence and detection of low-allele-fraction variants in clinical cancer samples. Nat Commun. 2017;8(1):1377.
Article
Google Scholar
Hata AN, Niederst MJ, Archibald HL, Gomez-Caraballo M, Siddiqui FM, Mulvey HE, Maruvka YE, Ji F, Bhang HE, Krishnamurthy Radhakrishna V, et al. Tumor cells can follow distinct evolutionary paths to become resistant to epidermal growth factor receptor inhibition. Nat Med. 2016;22(3):262–9.
Article
CAS
Google Scholar
Al-Kateb H, Nguyen TT, Steger-May K, Pfeifer JD. Identification of major factors associated with failed clinical molecular oncology testing performed by next generation sequencing (NGS). Mol Oncol. 2015;9(9):1737–43.
Article
CAS
Google Scholar
Murtaza M, Dawson SJ, Tsui DW, Gale D, Forshew T, Piskorz AM, Parkinson C, Chin SF, Kingsbury Z, Wong AS, et al. Non-invasive analysis of acquired resistance to cancer therapy by sequencing of plasma DNA. Nature. 2013;497(7447):108–12.
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
Volik S, Alcaide M, Morin RD, Collins C. Cell-free DNA (cfDNA): clinical significance and utility in Cancer shaped by emerging technologies. Mol Cancer Res. 2016;14(10):898–908.
Article
CAS
Google Scholar
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
Gnirke A, Melnikov A, Maguire J, Rogov P, LeProust EM, Brockman W, Fennell T, Giannoukos G, Fisher S, Russ C, et al. Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat Biotechnol. 2009;27(2):182–9.
Article
CAS
Google Scholar
Summerer D. Enabling technologies of genomic-scale sequence enrichment for targeted high-throughput sequencing. Genomics. 2009;94(6):363–8.
Article
CAS
Google Scholar
Kivioja T, Vaharautio A, Karlsson K, Bonke M, Enge M, Linnarsson S, Taipale J. Counting absolute numbers of molecules using unique molecular identifiers. Nat Methods. 2011;9(1):72–4.
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 U S A. 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 U S A. 2011;108(23):9530–5.
Article
Google Scholar
Islam S, Zeisel A, Joost S, La Manno G, Zajac P, Kasper M, Lonnerberg P, Linnarsson S. Quantitative single-cell RNA-seq with unique molecular identifiers. Nat Methods. 2014;11(2):163–6.
Article
CAS
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
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.
Article
Google Scholar
Scolnick JA, Dimon M, Wang IC, Huelga SC, Amorese DA. An efficient method for identifying gene fusions by targeted RNA sequencing from fresh frozen and FFPE samples. PLoS One. 2015;10(7):e0128916.
Article
Google Scholar
Zheng Z, Liebers M, Zhelyazkova B, Cao Y, Panditi D, Lynch KD, Chen J, Robinson HE, Shim HS, Chmielecki J, et al. Anchored multiplex PCR for targeted next-generation sequencing. Nat Med. 2014;20(12):1479–84.
Article
CAS
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
Smith T, Heger A, Sudbery I. UMI-tools: modeling sequencing errors in unique molecular identifiers to improve quantification accuracy. Genome Res. 2017;27(3):491–9.
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
Data Analysis Center [https://www.qiagen.com/kr/shop/genes-and-pathways/data-analysis-center-overview-page/].
Xu C, Nezami Ranjbar MR, Wu Z, DiCarlo J, Wang Y. Detecting very low allele fraction variants using targeted DNA sequencing and a novel molecular barcode-aware variant caller. BMC Genomics. 2017;18(1):5.
Article
Google Scholar
Wilm A, Aw PP, Bertrand D, Yeo GH, Ong SH, Wong CH, Khor CC, Petric R, Hibberd ML, Nagarajan N. LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets. Nucleic Acids Res. 2012;40(22):11189–201.
Article
CAS
Google Scholar
Ye K, Schulz MH, Long Q, Apweiler R, Ning Z. Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics. 2009;25(21):2865–71.
Article
CAS
Google Scholar
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. Genome project data processing S: 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, Daly M, et al. The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20(9):1297–303.
Article
CAS
Google Scholar