Detection of a novel panel of somatic mutations in plasma cell-free DNA and its diagnostic value in hepatocellular carcinoma

References

• Torre LA, Bray F, Siegel RL, Ferlay J, Lortet-Tieulent J, Jemal A. Global cancer statistics, 2012. CA Cancer J Clin. 2015;65(2):87–108. doi:10.3322/caac.2126225651787
   PubMed Web of Science ®Google Scholar
• Parkin DM. Global cancer statistics in the year 2000. Lancet Oncol. 2001;2(9):533–543. doi:10.1016/S1470-2045(01)00486-711905707
   PubMed Web of Science ®Google Scholar
• Yao DF, Dong ZZ, Yao M. Specific molecular markers in hepatocellular carcinoma. Hepatobiliary Pancreat Dis Int. 2007;6(3):241–247. 17548245
   PubMed Web of Science ®Google Scholar
• Lok AS, Sterling RK, Everhart JE, et al. Des-gamma-carboxy prothrombin and alpha-fetoprotein as biomarkers for the early detection of hepatocellular carcinoma. Gastroenterology. 2010;138(2):493–502. doi:10.1053/j.gastro.2009.10.03119852963
   PubMed Web of Science ®Google Scholar
• Mandel P, Metais P. Les acides nucléiques du plasma sanguin chez l’Homme [Nucleic acids of blood plasma in humans]. C R Seances Soc Biol Fil. 1948;142(3–4):241–243. 18875018
   PubMedGoogle Scholar
• Fleischhacker M, Schmidt B. Circulating nucleic acids (CNAs) and cancer – a survey. Biochim Biophys Acta. 2007;1775(1):181–232. doi:10.1016/j.bbcan.2006.10.00117137717
   PubMed Web of Science ®Google Scholar
• Shaw JA, Page K, Blighe K, et al. Genomic analysis of circulating cell-free DNA infers breast cancer dormancy. Genome Res. 2012;22(2):220–231. doi:10.1101/gr.123497.11121990379
   PubMed Web of Science ®Google Scholar
• Jung K, Fleischhacker M, Rabien A. Cell-free DNA in the blood as a solid tumor biomarker – a critical appraisal of the literature. Clin Chim Acta. 2010;411(21–22):1611–1624. doi:10.1016/j.cca.2010.07.03220688053
   PubMed Web of Science ®Google Scholar
• Murtaza M, Dawson SJ, Tsui DW, et al. Non-invasive analysis of acquired resistance to cancer therapy by sequencing of plasma DNA. Nature. 2013;497(7447):108–112. doi:10.1038/nature1206523563269
   PubMed Web of Science ®Google Scholar
• Bettegowda C, Sausen M, Leary RJ, et al. Detection of circulating tumor DNA in early- and late-stage human malignancies. Sci Transl Med. 2014;6(224):224ra224. doi:10.1126/scitranslmed.3007094
   Web of Science ®Google Scholar
• Frenel JS, Carreira S, Goodall J, et al. Serial next-generation sequencing of circulating cell-free DNA evaluating tumor clone response to molecularly targeted drug administration. Clin Cancer Res. 2015;21(20):4586–4596. doi:10.1158/1078-0432.CCR-15-058426085511
   PubMed Web of Science ®Google Scholar
• Maheswaran S, Sequist LV, Nagrath S, et al. Detection of mutations in EGFR in circulating lung-cancer cells. N Engl J Med. 2008;359(4):366–377. doi:10.1056/NEJMoa080066818596266
   PubMed Web of Science ®Google Scholar
• Scher HI, Heller G, Molina A, et al. Circulating tumor cell biomarker panel as an individual-level surrogate for survival in metastatic castration-resistant prostate cancer. J Clin Oncol. 2015;33(12):1348–1355. doi:10.1200/JCO.2014.55.348725800753
   PubMed Web of Science ®Google Scholar
• Schwarzenbach H, Alix-Panabieres C, Muller I, et al. Cell-free tumor DNA in blood plasma as a marker for circulating tumor cells in prostate cancer. Clin Cancer Res. 2009;15(3):1032–1038. doi:10.1158/1078-0432.CCR-08-191019188176
   PubMed Web of Science ®Google Scholar
• Thierry AR, Mouliere F, El Messaoudi S, et al. Clinical validation of the detection of KRAS and BRAF mutations from circulating tumor DNA. Nat Med. 2014;20(4):430–435. doi:10.1038/nm.351124658074
   PubMed Web of Science ®Google Scholar
• Thompson JC, Yee SS, Troxel AB, et al. Detection of therapeutically targetable driver and resistance mutations in lung cancer patients by next-generation sequencing of cell-free circulating tumor DNA. Clin Cancer Res. 2016;22(23):5772–5782. doi:10.1158/1078-0432.CCR-16-123127601595
   PubMed Web of Science ®Google Scholar
• Schwaederle MC, Patel SP, Husain H, et al. Utility of genomic assessment of blood-derived circulating tumor DNA (ctDNA) in patients with advanced lung adenocarcinoma. Clin Cancer Res. 2017;23(17):5101–5111. doi:10.1158/1078-0432.CCR-16-249728539465
   PubMed Web of Science ®Google Scholar
• Paweletz CP, Sacher AG, Raymond CK, et al. Bias-corrected targeted next-generation sequencing for rapid, multiplexed detection of actionable alterations in cell-free DNA from advanced lung cancer patients. Clin Cancer Res. 2016;22(4):915–922. doi:10.1158/1078-0432.CCR-15-1627-T26459174
   PubMed Web of Science ®Google Scholar
• Martincorena I, Campbell PJ. Somatic mutation in cancer and normal cells. Science. 2015;349:1483–1490. doi:10.1126/science.aab408226404825
   PubMed Web of Science ®Google Scholar
• Primary Liver Cancer Diagnosis and Treatment Expert Panel of the Chinese Ministry of Health. Guidelines on the diagnosis and treatment of primary liver cancer (2011 edition). Chin Clin Oncol. 2012;1:10. 25842068
   PubMedGoogle Scholar
• Newman AM, Bratman SV, To J, et al. An ultrasensitive method for quantitating circulating tumor DNA with broad patient coverage. Nat Med. 2014;20(5):548–554. doi:10.1038/nm.351924705333
   PubMed Web of Science ®Google Scholar
• Forbes SA, Bindal N, Bamford S, et al. COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer. Nucleic Acids Res. 2011;39(Database issue):D945–950. doi:10.1093/nar/gkq92920952405
   PubMed Web of Science ®Google Scholar
• Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25(14):1754–1760. doi:10.1093/bioinformatics/btp32419451168
   PubMed Web of Science ®Google Scholar
• Li H. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics. 2011;27(21):2987–2993. doi:10.1093/bioinformatics/btr50921903627
   PubMed Web of Science ®Google Scholar
• Hochberg Y, Benjamini Y. More powerful procedures for multiple significance testing. Stat Med. 1990;9(7):811–818. 2218183
   PubMed Web of Science ®Google Scholar
• Dennis G Jr, Sherman BT, Hosack DA, et al. DAVID: database for annotation, visualization, and integrated discovery. Genome Biol. 2003;4(5):P3. doi:10.1186/gb-2003-4-5-p312734009
   PubMed Web of Science ®Google Scholar
• Youn A, Simon R. Identifying cancer driver genes in tumor genome sequencing studies. Bioinformatics. 2011;27(2):175–181. doi:10.1093/bioinformatics/btq63021169372
   PubMed Web of Science ®Google Scholar
• Kan Z, Zheng H, Liu X, et al. Whole-genome sequencing identifies recurrent mutations in hepatocellular carcinoma. Genome Res. 2013;23(9):1422–1433. doi:10.1101/gr.154492.11323788652
   PubMed Web of Science ®Google Scholar
• Neuveut C, Wei Y, Buendia MA. Mechanisms of HBV-related hepatocarcinogenesis. J Hepatol. 2010;52(4):594–604. doi:10.1016/j.jhep.2009.10.03320185200
   PubMed Web of Science ®Google Scholar
• Marrero JA. Screening tests for hepatocellular carcinoma. Clin Liver Dis. 2005;9(2):235–251, vi. doi:10.1016/j.cld.2004.12.00615831271
   PubMedGoogle Scholar
• Chen H, Sun LY, Zheng HQ, Zhang QF, Jin XM. Total serum DNA and DNA integrity: diagnostic value in patients with hepatitis B virus-related hepatocellular carcinoma. Pathology. 2012;44(4):318–324. doi:10.1097/PAT.0b013e328353a24c
   Web of Science ®Google Scholar
• Ren N, Qin LX, Tu H, Liu YK, Zhang BH, Tang ZY. The prognostic value of circulating plasma DNA level and its allelic imbalance on chromosome 8p in patients with hepatocellular carcinoma. J Cancer Res Clin Oncol. 2006;132(6):399–407. doi:10.1007/s00432-005-0049-516502316
   PubMed Web of Science ®Google Scholar
• Zhou J, Shi YH, Fan J. Circulating cell-free nucleic acids: promising biomarkers of hepatocellular carcinoma. Semin Oncol. 2012;39(4):440–448. doi:10.1053/j.seminoncol.2012.05.01322846861
   PubMed Web of Science ®Google Scholar
• Tokuhisa Y, Iizuka N, Sakaida I, et al. Circulating cell-free DNA as a predictive marker for distant metastasis of hepatitis C virus-related hepatocellular carcinoma. Br J Cancer. 2007;97(10):1399–1403. doi:10.1038/sj.bjc.660403417940509
   PubMed Web of Science ®Google Scholar