연구동향 분석
박사

Droplet digital PCR-based EGFR mutation detection with an internal quality control index to determine the quality of DNA

김성수 2018년

논문상세정보
인용/피인용
' Droplet digital PCR-based EGFR mutation detection with an internal quality control index to determine the quality of DNA' 의 주제별 논문영향력
논문영향력 선정 방법
논문영향력 요약
주제
  • 약리학과 치료학
  • Circulating tumor DNA
  • DIN
  • DNA integrity number
  • Droplet digital PCR
  • EGFR
  • Formalin fixed paraffin embedded
  • Genetic mutation detection
  • Liquid biopsy
  • ctdna
  • ddPCR
  • epidermal growth factor receptor
  • ffpe
  • iQC
  • internal quality control
동일주제 총논문수 논문피인용 총횟수 주제별 논문영향력의 평균
902 0

0.0%

' Droplet digital PCR-based EGFR mutation detection with an internal quality control index to determine the quality of DNA' 의 참고문헌

  • Zsikla V, Baumann M, Cathomas G. Effect of buffered formalin on amplification of DNA from paraffin wax embedded small biopsies using real-time pcr. Journal of clinical pathology 2004;57:654-6.
  • Zhou C, Wu YL, Chen G, Feng J, Liu XQ, Wang C, et al. Erlotinib versus chemotherapy as first-line treatment for patients with advanced egfr mutation-positive non-small-cell lung cancer (optimal, ctong-0802): A multicentre, open-label, randomised, phase 3 study. The Lancet Oncology 2011;12:735-42.
  • Yung TK, Chan KC, Mok TS, Tong J, To KF, Lo YM. Single-molecule detection of epidermal growth factor receptor mutations in plasma by microfluidics digital pcr in non-small cell lung cancer patients. Clinical cancer research : an official journal of the American Association for Cancer Research 2009;15:2076-84.
  • Yu HA, Arcila ME, Rekhtman N, Sima CS, Zakowski MF, Pao W, et al. Analysis of tumor specimens at the time of acquired resistance to egfr-tki therapy in 155 patients with egfr-mutant lung cancers. Clinical cancer research : an official journal of the American Association for Cancer Research 2013;19:2240-7.
  • Ye X, Zhu ZZ, Zhong L, Lu Y, Sun Y, Yin X, et al. High t790m detection rate in tkinaive nsclc with egfr sensitive mutation: Truth or artifact? Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer 2013;8:1118-20.
  • Wu YL, Zhou C, Hu CP, Feng J, Lu S, Huang Y, et al. Afatinib versus cisplatin plus gemcitabine for first-line treatment of asian patients with advanced non-small-cell lung cancer harbouring egfr mutations (lux-lung 6): An open-label, randomised phase 3 trial. The Lancet Oncology 2014;15:213-22.
  • Wu L, Patten N, Yamashiro CT, Chui B. Extraction and amplification of DNA from formalin-fixed, paraffin-embedded tissues. Applied immunohistochemistry & molecular morphology : AIMM 2002;10:269-74.
  • Wong SQ, Li J, Tan AY, Vedururu R, Pang JM, Do H, et al. Sequence artefacts in a prospective series of formalin-fixed tumours tested for mutations in hotspot regions by massively parallel sequencing. BMC medical genomics 2014;7:23.
  • White RA, 3rd, Blainey PC, Fan HC, Quake SR. Digital pcr provides sensitive and absolute calibration for high throughput sequencing. BMC genomics 2009;10:116.
  • Walsh K, Wallace WA, Butler R, Mackean MJ, Harrison DJ, Stirling D, Oniscu A. A cautionary lesson on the use of targeted methods for egfr mutation analysis: A case report. Journal of clinical pathology 2014;67:734-5.
  • Vivanco I, Robins HI, Rohle D, Campos C, Grommes C, Nghiemphu PL, et al. Differential sensitivity of glioma- versus lung cancer-specific egfr mutations to egfr kinase inhibitors. Cancer discovery 2012;2:458-71.
  • Ulivi P, Mercatali L, Casoni GL, Scarpi E, Bucchi L, Silvestrini R, et al. Multiple marker detection in peripheral blood for nsclc diagnosis. PloS one 2013;8:e57401.
  • Tsiatis AC, Norris-Kirby A, Rich RG, Hafez MJ, Gocke CD, Eshleman JR, Murphy KM. Comparison of sanger sequencing, pyrosequencing, and melting curve analysis for the detection of kras mutations: Diagnostic and clinical implications. The Journal of molecular diagnostics : JMD 2010;12:425-32.
  • Thress KS, Paweletz CP, Felip E, Cho BC, Stetson D, Dougherty B, et al. Acquired egfr c797s mutation mediates resistance to azd9291 in non-small cell lung cancer harboring egfr t790m. Nature medicine 2015;21:560-2.
  • Thierry AR, Mouliere F, Gongora C, Ollier J, Robert B, Ychou M, et al. Origin and quantification of circulating DNA in mice with human colorectal cancer xenografts. Nucleic acids research 2010;38:6159-75.
  • Thatcher N, Chang A, Parikh P, Rodrigues Pereira J, Ciuleanu T, von Pawel J, et al. Gefitinib plus best supportive care in previously treated patients with refractory advanced non-small-cell lung cancer: Results from a randomised, placebo-controlled, multicentre study (iressa survival evaluation in lung cancer). Lancet 2005;366:1527-37.
  • Taniguchi K, Uchida J, Nishino K, Kumagai T, Okuyama T, Okami J, et al. Quantitative detection of egfr mutations in circulating tumor DNA derived from lung adenocarcinomas. Clinical cancer research : an official journal of the American Association for Cancer Research 2011;17:7808-15.
  • Taly V, Pekin D, Benhaim L, Kotsopoulos SK, Le Corre D, Li X, et al. Multiplex picodroplet digital pcr to detect kras mutations in circulating DNA from the plasma of colorectal cancer patients. Clinical chemistry 2013;59:1722-31.
  • Suzuki T, Ohsumi S, Makino K. Mechanistic studies on depurination and apurinic site chain breakage in oligodeoxyribonucleotides. Nucleic acids research 1994;22:4997- 5003.
  • Su KY, Chen HY, Li KC, Kuo ML, Yang JC, Chan WK, et al. Pretreatment epidermal growth factor receptor (egfr) t790m mutation predicts shorter egfr tyrosine kinase inhibitor response duration in patients with non-small-cell lung cancer. Journal of clinical oncology : official journal of the American Society of Clinical Oncology 2012;30:433-40.
  • Speit G, Schutz P, Merk O. Induction and repair of formaldehyde-induced DNA-protein crosslinks in repair-deficient human cell lines. Mutagenesis 2000;15:85-90.
  • Specht K, Richter T, Muller U, Walch A, Werner M, Hofler H. Quantitative gene expression analysis in microdissected archival formalin-fixed and paraffin-embedded tumor tissue. The American journal of pathology 2001;158:419-29.
  • Sorenson GD. Detection of mutated kras2 sequences as tumor markers in plasma/serum of patients with gastrointestinal cancer. Clinical cancer research : an official journal of the American Association for Cancer Research 2000;6:2129-37.
  • Sorenson GD. A review of studies on the detection of mutated kras2 sequences as tumor markers in plasma/serum of patients with gastrointestinal cancer. Annals of the New York Academy of Sciences 2000;906:13-6.
  • Slamon DJ, Leyland-Jones B, Shak S, Fuchs H, Paton V, Bajamonde A, et al. Use of chemotherapy plus a monoclonal antibody against her2 for metastatic breast cancer that overexpresses her2. The New England journal of medicine 2001;344:783-92.
  • Sikorsky JA, Primerano DA, Fenger TW, Denvir J. DNA damage reduces taq DNA polymerase fidelity and pcr amplification efficiency. Biochemical and biophysical research communications 2007;355:431-7.
  • Shi SR, Cote RJ, Wu L, Liu C, Datar R, Shi Y, et al. DNA extraction from archival formalin-fixed, paraffin-embedded tissue sections based on the antigen retrieval principle: Heating under the influence of ph. The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society 2002;50:1005-11.
  • Serizawa M, Yokota T, Hosokawa A, Kusafuka K, Sugiyama T, Tsubosa Y, et al. The efficacy of uracil DNA glycosylase pretreatment in amplicon-based massively parallel sequencing with DNA extracted from archived formalin-fixed paraffin-embedded esophageal cancer tissues. Cancer Genet 2015;208:415-27.
  • Sequist LV, Yang JC, Yamamoto N, O'Byrne K, Hirsh V, Mok T, et al. Phase iii study of afatinib or cisplatin plus pemetrexed in patients with metastatic lung adenocarcinoma with egfr mutations. Journal of clinical oncology : official journal of the American Society of Clinical Oncology 2013;31:3327-34.
  • Sequist LV, Waltman BA, Dias-Santagata D, Digumarthy S, Turke AB, Fidias P, et al. Genotypic and histological evolution of lung cancers acquiring resistance to egfr inhibitors. Science translational medicine 2011;3:75ra26.
  • Sequist LV, Soria JC, Goldman JW, Wakelee HA, Gadgeel SM, Varga A, et al. Rociletinib in egfr-mutated non-small-cell lung cancer. The New England journal of medicine 2015;372:1700-9.
  • Sepp R, Szabo I, Uda H, Sakamoto H. Rapid techniques for DNA extraction from routinely processed archival tissue for use in pcr. Journal of clinical pathology 1994;47:318-23.
  • Schormann N, Ricciardi R, Chattopadhyay D. Uracil-DNA glycosylases-structural and functional perspectives on an essential family of DNA repair enzymes. Protein science : a publication of the Protein Society 2014;23:1667-85.
  • Sakurada A, Lara-Guerra H, Liu N, Shepherd FA, Tsao MS. Tissue heterogeneity of egfr mutation in lung adenocarcinoma. Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer 2008;3:527- 9.
  • Sah S, Chen L, Houghton J, Kemppainen J, Marko AC, Zeigler R, Latham GJ. Functional DNA quantification guides accurate next-generation sequencing mutation detection in formalin-fixed, paraffin-embedded tumor biopsies. Genome medicine 2013;5:77.
  • Rosell R, Moran T, Queralt C, Porta R, Cardenal F, Camps C, et al. Screening for epidermal growth factor receptor mutations in lung cancer. The New England journal of medicine 2009;361:958-67.
  • Rosell R, Carcereny E, Gervais R, Vergnenegre A, Massuti B, Felip E, et al. Erlotinib versus standard chemotherapy as first-line treatment for european patients with advanced egfr mutation-positive non-small-cell lung cancer (eurtac): A multicentre, open-label, randomised phase 3 trial. The Lancet Oncology 2012;13:239-46.
  • Rosell R, Bivona TG, Karachaliou N. Genetics and biomarkers in personalisation of lung cancer treatment. Lancet 2013;382:720-31.
  • Rajasekaran N, Oh MR, Kim SS, Kim SE, Kim YD, Choi HJ, et al. Employing digital droplet pcr to detect braf v600e mutations in formalin-fixed paraffin-embedded reference standard cell lines. Journal of visualized experiments : JoVE 2015.
  • Pinheiro LB, Coleman VA, Hindson CM, Herrmann J, Hindson BJ, Bhat S, Emslie KR. Evaluation of a droplet digital polymerase chain reaction format for DNA copy number quantification. Analytical chemistry 2012;84:1003-11.
  • Permenter J, Ishwar A, Rounsavall A, Smith M, Faske J, Sailey CJ, Alfaro MP. Quantitative analysis of genomic DNA degradation in whole blood under various storage conditions for molecular diagnostic testing. Molecular and cellular probes 2015;29:449-53.
  • Penzel R, Sers C, Chen Y, Lehmann-Muhlenhoff U, Merkelbach-Bruse S, Jung A, et al. Egfr mutation detection in nsclc--assessment of diagnostic application and recommendations of the german panel for mutation testing in nsclc. Virchows Arch 2011;458:95-8.
  • Park K, Han JY, Kim DW, Bazhenova LA, Ou SH, Pang YK, et al. 190tip: Eluxa 1: Phase ii study of bi 1482694 (hm61713) in patients (pts) with t790m-positive non-small cell lung cancer (nsclc) after treatment with an epidermal growth factor receptor tyrosine kinase inhibitor (egfr tki). Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer 2016;11:S139.
  • Pao W, Miller VA, Politi KA, Riely GJ, Somwar R, Zakowski MF, et al. Acquired resistance of lung adenocarcinomas to gefitinib or erlotinib is associated with a second mutation in the egfr kinase domain. PLoS medicine 2005;2:e73.
  • Paez JG, Janne PA, Lee JC, Tracy S, Greulich H, Gabriel S, et al. EGFR mutations in lung cancer: correlation with clinical response to gefitinib therapy. Science 2004,304:1497-500
  • Oxnard GR, Paweletz CP, Kuang Y, Mach SL, O'Connell A, Messineo MM, et al. Noninvasive detection of response and resistance in egfr-mutant lung cancer using quantitative next-generation genotyping of cell-free plasma DNA. Clinical cancer research : an official journal of the American Association for Cancer Research 2014;20:1698-705.
  • Ono A, Kenmotsu H, Watanabe M, Serizawa M, Mori K, Imai H, et al. Mutant allele frequency predicts the efficacy of egfr-tkis in lung adenocarcinoma harboring the l858r mutation. Annals of oncology : official journal of the European Society for Medical Oncology / ESMO 2014;25:1948-53.
  • Oh E, Choi YL, Kwon MJ, Kim RN, Kim YJ, Song JY, et al. Comparison of accuracy of whole-exome sequencing with formalin-fixed paraffin-embedded and fresh frozen tissue samples. PloS one 2015;10:e0144162.
  • Ofner R, Ritter C, Ugurel S, Cerroni L, Stiller M, Bogenrieder T, et al. Nonreproducible sequence artifacts in ffpe tissue: An experience report. Journal of cancer research and clinical oncology 2017.
  • O'Donnell P, Ferguson J, Shyu J, Current R, Rehage T, Tsai J, et al. Analytic performance studies and clinical reproducibility of a real-time pcr assay for the detection of epidermal growth factor receptor gene mutations in formalin-fixed paraffin-embedded tissue specimens of non-small cell lung cancer. BMC cancer 2013;13:210.
  • Nakahara Y, Takagi Y, Hosomi Y, Kagei A, Yamamoto T, Sawada T, et al. Noninvasive monitoring of the genetic evolution of egfr-mutant non-small-cell lung cancer by analyzing circulating tumor DNA during combination chemotherapy with gefitinib and pemetrexed or s-1. OncoTargets and therapy 2016;9:5287-95.
  • Nagai Y, Miyazawa H, Huqun, Tanaka T, Udagawa K, Kato M, et al. Genetic heterogeneity of the epidermal growth factor receptor in non-small cell lung cancer cell lines revealed by a rapid and sensitive detection system, the peptide nucleic acid-locked nucleic acid pcr clamp. Cancer research 2005;65:7276-82.
  • Mouliere F, Robert B, Arnau Peyrotte E, Del Rio M, Ychou M, Molina F, et al. High fragmentation characterizes tumour-derived circulating DNA. PloS one 2011;6:e23418.
  • Mok TS. Personalized medicine in lung cancer: What we need to know. Nature reviews Clinical oncology 2011;8:661-8.
  • Mok TS, Wu YL, Thongprasert S, Yang CH, Chu DT, Saijo N, et al. Gefitinib or carboplatin-paclitaxel in pulmonary adenocarcinoma. The New England journal of medicine 2009;361:947-57.
  • Mok TS, Wu YL, Ahn MJ, Garassino MC, Kim HR, Ramalingam SS, et al. Osimertinib or platinum-pemetrexed in egfr t790m-positive lung cancer. The New England journal of medicine 2017;376:629-40.
  • Mitsudomi T, Morita S, Yatabe Y, Negoro S, Okamoto I, Tsurutani J, et al. Gefitinib versus cisplatin plus docetaxel in patients with non-small-cell lung cancer harbouring mutations of the epidermal growth factor receptor (wjtog3405): An open label, randomised phase 3 trial. The Lancet Oncology 2010;11:121-8.
  • Misale S, Yaeger R, Hobor S, Scala E, Janakiraman M, Liska D, et al. Emergence of kras mutations and acquired resistance to anti-egfr therapy in colorectal cancer. Nature 2012;486:532-6.
  • Minari R, Bordi P, Tiseo M. Third-generation epidermal growth factor receptor-tyrosine kinase inhibitors in t790m-positive non-small cell lung cancer: Review on emerged mechanisms of resistance. Translational lung cancer research 2016;5:695-708.
  • Merk O, Speit G. Significance of formaldehyde-induced DNA-protein crosslinks for mutagenesis. Environmental and molecular mutagenesis 1998;32:260-8.
  • Mendelsohn J, Baselga J. Status of epidermal growth factor receptor antagonists in the biology and treatment of cancer. Journal of clinical oncology : official journal of the American Society of Clinical Oncology 2003;21:2787-99.
  • McGhee JD, von Hippel PH. Formaldehyde as a probe of DNA structure. Ii. Reaction with endocyclic imino groups of DNA bases. Biochemistry 1975;14:1297-303.
  • Maheswaran S, Sequist LV, Nagrath S, Ulkus L, Brannigan B, Collura CV, et al. Detection of mutations in egfr in circulating lung-cancer cells. The New England journal of medicine 2008;359:366-77.
  • Maemondo M, Inoue A, Kobayashi K, Sugawara S, Oizumi S, Isobe H, et al. Gefitinib or chemotherapy for non-small-cell lung cancer with mutated egfr. The New England journal of medicine 2010;362:2380-8.
  • Lynch TJ, Bell DW, Sordella R, Gurubhagavatula S, Okimoto RA, Brannigan BW, et al. Activating mutations in the epidermal growth factor receptor underlying responsiveness of non-small-cell lung cancer to gefitinib. The New England journal of medicine 2004;350:2129-39.
  • Ludyga N, Grunwald B, Azimzadeh O, Englert S, Hofler H, Tapio S, Aubele M. Nucleic acids from long-term preserved ffpe tissues are suitable for downstream analyses. Virchows Arch 2012;460:131-40.
  • Lopez-Rios F, Angulo B, Gomez B, Mair D, Martinez R, Conde E, et al. Comparison of molecular testing methods for the detection of egfr mutations in formalin-fixed paraffin-embedded tissue specimens of non-small cell lung cancer. Journal of clinical pathology 2013;66:381-5.
  • Lin J, Kennedy SH, Svarovsky T, Rogers J, Kemnitz JW, Xu A, Zondervan KT. Highquality genomic DNA extraction from formalin-fixed and paraffin-embedded samples deparaffinized using mineral oil. Analytical biochemistry 2009;395:265-7.
  • Libermann TA, Nusbaum HR, Razon N, Kris R, Lax I, Soreq H, et al. Amplification, enhanced expression and possible rearrangement of egf receptor gene in primary human brain tumours of glial origin. Nature 1985;313:144-7.
  • Liao BC, Lin CC, Lee JH, Yang JC. Update on recent preclinical and clinical studies of t790m mutant-specific irreversible epidermal growth factor receptor tyrosine kinase inhibitors. Journal of biomedical science 2016;23:86.
  • Lehmann A, Schewe C, Hennig G, Denkert C, Weichert W, Budczies J, Dietel M. Applicability of a system for fully automated nucleic acid extraction from formalinfixed paraffin-embedded sections for routine kras mutation testing. Diagnostic molecular pathology : the American journal of surgical pathology, part B 2012;21:114- 9.
  • Lee Y, Lee GK, Lee YS, Zhang W, Hwang JA, Nam BH, et al. Clinical outcome according to the level of preexisting epidermal growth factor receptor t790m mutation in patients with lung cancer harboring sensitive epidermal growth factor receptor mutations. Cancer 2014;120:2090-8.
  • Lee JC, Vivanco I, Beroukhim R, Huang JH, Feng WL, DeBiasi RM, et al. Epidermal growth factor receptor activation in glioblastoma through novel missense mutations in the extracellular domain. PLoS medicine 2006;3:e485.
  • Leary RJ, Sausen M, Kinde I, Papadopoulos N, Carpten JD, Craig D, et al. Detection of chromosomal alterations in the circulation of cancer patients with whole-genome sequencing. Science translational medicine 2012;4:162ra54.
  • Krokan HE, Drablos F, Slupphaug G. Uracil in DNA--occurrence, consequences and repair. Oncogene 2002;21:8935-48.
  • Kosaka T, Yatabe Y, Endoh H, Yoshida K, Hida T, Tsuboi M, et al. Analysis of epidermal growth factor receptor gene mutation in patients with non-small cell lung cancer and acquired resistance to gefitinib. Clinical cancer research : an official journal of the American Association for Cancer Research 2006;12:5764-9.
  • Kosaka T, Yatabe Y, Endoh H, Kuwano H, Takahashi T, Mitsudomi T. Mutations of the epidermal growth factor receptor gene in lung cancer: Biological and clinical implications. Cancer research 2004;64:8919-23.
  • Kimura H, Ohira T, Uchida O, Matsubayashi J, Shimizu S, Nagao T, et al. Analytical performance of the cobas egfr mutation assay for japanese non-small-cell lung cancer. Lung cancer 2014;83:329-33.
  • Kimura H, Kasahara K, Kawaishi M, Kunitoh H, Tamura T, Holloway B, Nishio K. Detection of epidermal growth factor receptor mutations in serum as a predictor of the response to gefitinib in patients with non-small-cell lung cancer. Clinical cancer research : an official journal of the American Association for Cancer Research 2006;12:3915-21.
  • Kim S, Park C, Ji Y, Kim DG, Bae H, van Vrancken M, et al. Deamination effects in formalin-fixed, paraffin-embedded tissue samples in the era of precision medicine. The Journal of molecular diagnostics : JMD 2017;19:137-46.
  • Kim ES. Olmutinib: First global approval. Drugs 2016;76:1153-7.
  • Jia Y, Juarez J, Li J, Manuia M, Niederst MJ, Tompkins C, et al. Egf816 exerts anticancer effects in non-small cell lung cancer by irreversibly and selectively targeting primary and acquired activating mutations in the egf receptor. Cancer research 2016;76:1591-602.
  • Janne PA, Yang JC, Kim DW, Planchard D, Ohe Y, Ramalingam SS, et al. Azd9291 in egfr inhibitor-resistant non-small-cell lung cancer. The New England journal of medicine 2015;372:1689-99.
  • Janne PA, Engelman JA, Johnson BE. Epidermal growth factor receptor mutations in non-small-cell lung cancer: Implications for treatment and tumor biology. Journal of clinical oncology : official journal of the American Society of Clinical Oncology 2005;23:3227-34.
  • Jahr S, Hentze H, Englisch S, Hardt D, Fackelmayer FO, Hesch RD, Knippers R. DNA fragments in the blood plasma of cancer patients: Quantitations and evidence for their origin from apoptotic and necrotic cells. Cancer research 2001;61:1659-65.
  • Jackson V. Studies on histone organization in the nucleosome using formaldehyde as a reversible cross-linking agent. Cell 1978;15:945-54.
  • Ishii H, Azuma K, Sakai K, Kawahara A, Yamada K, Tokito T, et al. Digital pcr analysis of plasma cell-free DNA for non-invasive detection of drug resistance mechanisms in egfr mutant nsclc: Correlation with paired tumor samples. Oncotarget 2015;6:30850-8.
  • Inukai M, Toyooka S, Ito S, Asano H, Ichihara S, Soh J, et al. Presence of epidermal growth factor receptor gene t790m mutation as a minor clone in non-small cell lung cancer. Cancer research 2006;66:7854-8.
  • Inoue T, Nabeshima K, Kataoka H, Koono M. Feasibility of archival non-buffered formalin-fixed and paraffin-embedded tissues for pcr amplification: An analysis of resected gastric carcinoma. Pathology international 1996;46:997-1004.
  • Horiike A, Kimura H, Nishio K, Ohyanagi F, Satoh Y, Okumura S, et al. Detection of epidermal growth factor receptor mutation in transbronchial needle aspirates of nonsmall cell lung cancer. Chest 2007;131:1628-34.
  • Hindson CM, Chevillet JR, Briggs HA, Gallichotte EN, Ruf IK, Hindson BJ, et al. Absolute quantification by droplet digital pcr versus analog real-time pcr. Nature methods 2013;10:1003-5.
  • Hindson BJ, Ness KD, Masquelier DA, Belgrader P, Heredia NJ, Makarewicz AJ, et al. High-throughput droplet digital pcr system for absolute quantitation of DNA copy number. Analytical chemistry 2011;83:8604-10.
  • Heyn P, Stenzel U, Briggs AW, Kircher M, Hofreiter M, Meyer M. Road blocks on paleogenomes--polymerase extension profiling reveals the frequency of blocking lesions in ancient DNA. Nucleic acids research 2010;38:e161.
  • Hewitt SM, Lewis FA, Cao Y, Conrad RC, Cronin M, Danenberg KD, et al. Tissue handling and specimen preparation in surgical pathology: Issues concerning the recovery of nucleic acids from formalin-fixed, paraffin-embedded tissue. Archives of pathology & laboratory medicine 2008;132:1929-35.
  • Herbst RS, Maddox AM, Rothenberg ML, Small EJ, Rubin EH, Baselga J, et al. Selective oral epidermal growth factor receptor tyrosine kinase inhibitor zd1839 is generally well-tolerated and has activity in non-small-cell lung cancer and other solid tumors: Results of a phase i trial. Journal of clinical oncology : official journal of the American Society of Clinical Oncology 2002;20:3815-25.
  • Hennig G, Gehrmann M, Stropp U, Brauch H, Fritz P, Eichelbaum M, et al. Automated extraction of DNA and rna from a single formalin-fixed paraffin-embedded tissue section for analysis of both single-nucleotide polymorphisms and mrna expression. Clinical chemistry 2010;56:1845-53.
  • He C, Liu M, Zhou C, Zhang J, Ouyang M, Zhong N, Xu J. Detection of epidermal growth factor receptor mutations in plasma by mutant-enriched pcr assay for prediction of the response to gefitinib in patients with non-small-cell lung cancer. International journal of cancer 2009;125:2393-9.
  • Han SW, Kim TY, Hwang PG, Jeong S, Kim J, Choi IS, et al. Predictive and prognostic impact of epidermal growth factor receptor mutation in non-small-cell lung cancer patients treated with gefitinib. Journal of clinical oncology : official journal of the American Society of Clinical Oncology 2005;23:2493-501.
  • Hadd AG, Houghton J, Choudhary A, Sah S, Chen L, Marko AC, et al. Targeted, highdepth, next-generation sequencing of cancer genes in formalin-fixed, paraffinembedded and fine-needle aspiration tumor specimens. The Journal of molecular diagnostics : JMD 2013;15:234-47.
  • Giordano P, Manzo A, Montanino A, Costanzo R, Sandomenico C, Piccirillo MC, et al. Afatinib: An overview of its clinical development in non-small-cell lung cancer and other tumors. Critical reviews in oncology/hematology 2016;97:143-51.
  • Gillio-Tos A, De Marco L, Fiano V, Garcia-Bragado F, Dikshit R, Boffetta P, Merletti F. Efficient DNA extraction from 25-year-old paraffin-embedded tissues: Study of 365 samples. Pathology 2007;39:345-8.
  • Gilbert Y, Le Bihan Y, Aubry G, Veillette M, Duchaine C, Lessard P. Microbiological and molecular characterization of denitrification in biofilters treating pig manure. Bioresource technology 2008;99:4495-502.
  • Gallegos Ruiz MI, Floor K, Rijmen F, Grunberg K, Rodriguez JA, Giaccone G. Egfr and k-ras mutation analysis in non-small cell lung cancer: Comparison of paraffin embedded versus frozen specimens. Cellular oncology : the official journal of the International Society for Cellular Oncology 2007;29:257-64.
  • Fukuoka M, Wu YL, Thongprasert S, Sunpaweravong P, Leong SS, Sriuranpong V, et al. Biomarker analyses and final overall survival results from a phase iii, randomized, open-label, first-line study of gefitinib versus carboplatin/paclitaxel in clinically selected patients with advanced non-small-cell lung cancer in asia (ipass). Journal of clinical oncology : official journal of the American Society of Clinical Oncology 2011;29:2866-74.
  • Frattini M, Gallino G, Signoroni S, Balestra D, Lusa L, Battaglia L, et al. Quantitative and qualitative characterization of plasma DNA identifies primary and recurrent colorectal cancer. Cancer letters 2008;263:170-81.
  • Fraenkel-Conrat H, Olcott HS. The reaction of formaldehyde with proteins; crosslinking between amino and primary amide or guanidyl groups. Journal of the American Chemical Society 1948;70:2673-84.
  • Forshew T, Murtaza M, Parkinson C, Gale D, Tsui DW, Kaper F, et al. Noninvasive identification and monitoring of cancer mutations by targeted deep sequencing of plasma DNA. Science translational medicine 2012;4:136ra68.
  • Fang S, Wang Z. Egfr mutations as a prognostic and predictive marker in non-smallcell lung cancer. Drug design, development and therapy 2014;8:1595-611.
  • Dong L, Cordova-Kreylos AL, Yang J, Yuan H, Scow KM. Humic acids buffer the effects of urea on soil ammonia oxidizers and potential nitrification. Soil biology & biochemistry 2009;41:1612-21.
  • 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. Clinical chemistry 2013;59:1376-83.
  • Do H, Dobrovic A. Sequence artifacts in DNA from formalin-fixed tissues: Causes and strategies for minimization. Clinical chemistry 2015;61:64-71.
  • Do H, Dobrovic A. Limited copy number-high resolution melting (lcn-hrm) enables the detection and identification by sequencing of low level mutations in cancer biopsies. Molecular cancer 2009;8:82.
  • Do H, Dobrovic A. Dramatic reduction of sequence artefacts from DNA isolated from formalin-fixed cancer biopsies by treatment with uracil- DNA glycosylase. Oncotarget 2012;3:546-58.
  • Diehl F, Li M, Dressman D, He Y, Shen D, Szabo S, et al. Detection and quantification of mutations in the plasma of patients with colorectal tumors. Proceedings of the National Academy of Sciences of the United States of America 2005;102:16368-73.
  • Didelot A, Kotsopoulos SK, Lupo A, Pekin D, Li X, Atochin I, et al. Multiplex picoliter-droplet digital pcr for quantitative assessment of DNA integrity in clinical samples. Clinical chemistry 2013;59:815-23.
  • Denis MG, Vallee A, Theoleyre S. Egfr t790m resistance mutation in non small-cell lung carcinoma. Clinica chimica acta; international journal of clinical chemistry 2015;444:81-5.
  • Cross DA, Ashton SE, Ghiorghiu S, Eberlein C, Nebhan CA, Spitzler PJ, et al. Azd9291, an irreversible egfr tki, overcomes t790m-mediated resistance to egfr inhibitors in lung cancer. Cancer discovery 2014;4:1046-61.
  • Chi A, Remick S, Tse W. Egfr inhibition in non-small cell lung cancer: Current evidence and future directions. Biomarker research 2013;1:2.
  • Chen XQ, Stroun M, Magnenat JL, Nicod LP, Kurt AM, Lyautey J, et al. Microsatellite alterations in plasma DNA of small cell lung cancer patients. Nature medicine 1996;2:1033-5.
  • Chen L, Liu P, Evans TC, Jr., Ettwiller LM. DNA damage is a pervasive cause of sequencing errors, directly confounding variant identification. Science 2017;355:752- 6.
  • Chan KC, Jiang P, Zheng YW, Liao GJ, Sun H, Wong J, et al. Cancer genome scanning in plasma: Detection of tumor-associated copy number aberrations, single-nucleotide variants, and tumoral heterogeneity by massively parallel sequencing. Clinical chemistry 2013;59:211-24.
  • Catarino R, Coelho A, Araujo A, Gomes M, Nogueira A, Lopes C, Medeiros R. Circulating DNA: Diagnostic tool and predictive marker for overall survival of nsclc patients. PloS one 2012;7:e38559.
  • Cataldo VD, Gibbons DL, Perez-Soler R, Quintas-Cardama A. Treatment of non-small113 cell lung cancer with erlotinib or gefitinib. The New England journal of medicine 2011;364:947-55.
  • Carrick DM, Mehaffey MG, Sachs MC, Altekruse S, Camalier C, Chuaqui R, et al. Robustness of next generation sequencing on older formalin-fixed paraffin-embedded tissue. PloS one 2015;10:e0127353.
  • Breathnach OS, Freidlin B, Conley B, Green MR, Johnson DH, Gandara DR, et al. Twenty-two years of phase iii trials for patients with advanced non-small-cell lung cancer: Sobering results. Journal of clinical oncology : official journal of the American Society of Clinical Oncology 2001;19:1734-42.
  • Brambilla E, Travis WD, Colby TV, Corrin B, Shimosato Y. The new world health organization classification of lung tumours. The European respiratory journal 2001;18:1059-68.
  • Bourgon R, Lu S, Yan Y, Lackner MR, Wang W, Weigman V, et al. High-throughput detection of clinically relevant mutations in archived tumor samples by multiplexed pcr and next-generation sequencing. Clinical cancer research : an official journal of the American Association for Cancer Research 2014;20:2080-91.
  • Blackhall F, Ranson M, Thatcher N. Where next for gefitinib in patients with lung cancer? The Lancet Oncology 2006;7:499-507.
  • Benlloch S, Botero ML, Beltran-Alamillo J, Mayo C, Gimenez-Capitan A, de Aguirre I, et al. Clinical validation of a pcr assay for the detection of egfr mutations in nonsmall- cell lung cancer: Retrospective testing of specimens from the eurtac trial. PloS one 2014;9:e89518.
  • Bellon E, Ligtenberg MJ, Tejpar S, Cox K, de Hertogh G, de Stricker K, et al. External quality assessment for kras testing is needed: Setup of a european program and report of the first joined regional quality assessment rounds. The oncologist 2011;16:467-78.
  • Becker KF, Schott C, Hipp S, Metzger V, Porschewski P, Beck R, et al. Quantitative protein analysis from formalin-fixed tissues: Implications for translational clinical research and nanoscale molecular diagnosis. The Journal of pathology 2007;211:370-8.
  • Beaver JA, Jelovac D, Balukrishna S, Cochran RL, Croessmann S, Zabransky DJ, et al. Detection of cancer DNA in plasma of patients with early-stage breast cancer. Clinical cancer research : an official journal of the American Association for Cancer Research 2014;20:2643-50.
  • Beau-Faller M, Degeorges A, Rolland E, Mounawar M, Antoine M, Poulot V, et al. Cross-validation study for epidermal growth factor receptor and kras mutation detection in 74 blinded non-small cell lung carcinoma samples: A total of 5550 exons sequenced by 15 molecular french laboratories (evaluation of the egfr mutation status for the administration of egfr-tkis in non-small cell lung carcinoma [ermetic] project--part 1). Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer 2011;6:1006-15.
  • Aung KL, Board RE, Ellison G, Donald E, Ward T, Clack G, et al. Current status and future potential of somatic mutation testing from circulating free DNA in patients with solid tumours. The HUGO journal 2010;4:11-21.
  • Astolfi A, Urbini M, Indio V, Nannini M, Genovese CG, Santini D, et al. Whole exome sequencing (wes) on formalin-fixed, paraffin-embedded (ffpe) tumor tissue in gastrointestinal stromal tumors (gist). BMC genomics 2015;16:892.
  • Arteaga CL, Sliwkowski MX, Osborne CK, Perez EA, Puglisi F, Gianni L. Treatment of her2-positive breast cancer: Current status and future perspectives. Nature reviews Clinical oncology 2012;9:16-32.
  • Armbruster DA, Pry T. Limit of blank, limit of detection and limit of quantitation. The Clinical biochemist Reviews 2008;29 Suppl 1:S49-52.
  • Ardakani NM, Giardina T, Grieu-Iacopetta F, Tesfai Y, Carrello A, Taylor J, et al. Detection of epidermal growth factor receptor mutations in lung adenocarcinoma: Comparing cobas 4800 egfr assay with sanger bidirectional sequencing. Clinical lung cancer 2016;17:e113-e9.
  • Arcila ME, Oxnard GR, Nafa K, Riely GJ, Solomon SB, Zakowski MF, et al. Rebiopsy of lung cancer patients with acquired resistance to egfr inhibitors and enhanced detection of the t790m mutation using a locked nucleic acid-based assay. Clinical cancer research : an official journal of the American Association for Cancer Research 2011;17:1169-80.
  • Anderson S, Bloom KJ, Vallera DU, Rueschoff J, Meldrum C, Schilling R, et al. Multisite analytic performance studies of a real-time polymerase chain reaction assay for the detection of braf v600e mutations in formalin-fixed, paraffin-embedded tissue specimens of malignant melanoma. Archives of pathology & laboratory medicine 2012;136:1385-91.
  • Alix-Panabieres C, Pantel K. Circulating tumor cells: Liquid biopsy of cancer. Clinical chemistry 2013;59:110-8.