연구동향 분석
박사

Genome-wide analysis of hepatocellular carcinoma cell lines by next-generation sequencing : 차세대 염기서열 분석법을 이용한 간세포암 세포주의 유전체 연구

Eun-Goo Jeong 2015년

논문상세정보
인용/피인용
' Genome-wide analysis of hepatocellular carcinoma cell lines by next-generation sequencing : 차세대 염기서열 분석법을 이용한 간세포암 세포주의 유전체 연구' 의 주제별 논문영향력
논문영향력 선정 방법
논문영향력 요약
주제
  • hepatocellular carcinoma
  • molecular target agents
  • targeted sequencing
  • transcriptome sequencing
동일주제 총논문수 논문피인용 총횟수 주제별 논문영향력의 평균
199 0

0.0%

' Genome-wide analysis of hepatocellular carcinoma cell lines by next-generation sequencing : 차세대 염기서열 분석법을 이용한 간세포암 세포주의 유전체 연구' 의 참고문헌

  • Yang JD, Roberts LR. Hepatocellular carcinoma: A global view. Nature reviews Gastroenterology & hepatology. 2010;7(8):448-58.
  • Wu TD, Nacu S. Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics. 2010;26(7):873-81.
  • Wilhelm SM, Carter C, Tang L, Wilkie D, McNabola A, Rong H, et al. BAY 43-9006 exhibits broad spectrum oral antitumor activity and targets the RAF/MEK/ERK pathway and receptor tyrosine kinases involved in tumor progression and angiogenesis. Cancer Res. 2004;64(19):7099-109.
  • Wagle N, Berger MF, Davis MJ, Blumenstiel B, Defelice M, Pochanard P, et al. High-throughput detection of actionable genomic alterations in clinical tumor samples by targeted, massively parallel sequencing. Cancer discovery. 2012;2(1):82-93.
  • Tsukui Y, Mochizuki H, Hoshino Y, Kawakami S, Kuno T, Fukasawa Y, et al. Factors contributing to the overall survival in patients with hepatocellular carcinoma treated by sorafenib. Hepatogastroenterology. 2012;59(120):2536-9.
  • Tran B, Dancey JE, Kamel-Reid S, McPherson JD, Bedard PL, Brown AM, et al. Cancer genomics: technology, discovery, and translation. Journal of clinical oncology : official journal of the American Society of Clinical Oncology. 2012;30(6):647-60.
  • Totoki Y, Tatsuno K, Covington KR, Ueda H, Creighton CJ, Kato M, et al. Trans-ancestry mutational landscape of hepatocellular carcinoma genomes. Nat Genet. 2014;46(12):1267-73.
  • Tangkijvanich P, Anukulkarnkusol N, Suwangool P, Lertmaharit S, Hanvivatvong O, Kullavanijaya P, et al. Clinical characteristics and prognosis of hepatocellular carcinoma: analysis based on serum alpha-fetoprotein levels. Journal of clinical gastroenterology. 2000;31(4):302-8.
  • Strebhardt K, Ullrich A. Paul Ehrlich's magic bullet concept: 100 years of progress. Nat Rev Cancer. 2008;8(6):473-80.
  • Song TJ, Eisenberg DP, Adusumilli PS, Hezel M, Fong Y. Oncolytic herpes viral therapy is effective in the treatment of hepatocellular carcinoma cell lines. Journal of gastrointestinal surgery : official journal of the Society for Surgery of the Alimentary Tract. 2006;10(4):532-42.
  • Schultz J, Milpetz F, Bork P, Ponting CP. SMART, a simple modular architecture research tool: identification of signaling domains. Proc Natl Acad Sci U S A. 1998;95(11):5857-64.
  • Sardiello M, Palmieri M, di Ronza A, Medina DL, Valenza M, Gennarino VA, et al. A gene network regulating lysosomal biogenesis and function. Science. 2009;325(5939):473-7.
  • Sakurai M, Yano T, Kawabata H, Ueda H, Suzuki T. Inosine cyanoethylation identifies A-to-I RNA editing sites in the human transcriptome. Nat Chem Biol. 2010;6(10):733-40.
  • Roychowdhury S, Iyer MK, Robinson DR, Lonigro RJ, Wu YM, Cao X, et al. Personalized oncology through integrative high-throughput sequencing: a pilot study. Science translational medicine. 2011;3(111):111ra21.
  • Ramaswami G, Zhang R, Piskol R, Keegan LP, Deng P, O'Connell MA, et al. Identifying RNA editing sites using RNA sequencing data alone. Nat Methods. 2013;10(2):128-32.
  • Portolani N, Coniglio A, Ghidoni S, Giovanelli M, Benetti A, Tiberio GA, et al. Early and late recurrence after liver resection for hepatocellular carcinoma: prognostic and therapeutic implications. Annals of surgery. 2006;243(2):229-35.
  • Piccart-Gebhart MJ, Procter M, Leyland-Jones B, Goldhirsch A, Untch M, Smith I, et al. Trastuzumab after adjuvant chemotherapy in HER2-positive breast cancer. N Engl J Med. 2005;353(16):1659-72.
  • Pelak K, Shianna KV, Ge D, Maia JM, Zhu M, Smith JP, et al. The characterization of twenty sequenced human genomes. PLoS Genet. 2010;6(9):e1001111.
  • Paz N, Levanon EY, Amariglio N, Heimberger AB, Ram Z, Constantini S, et al. Altered adenosine-to-inosine RNA editing in human cancer. Genome Res. 2007;17(11):1586-95.
  • Park JG, Lee JH, Kang MS, Park KJ, Jeon YM, Lee HJ, et al. Characterization of cell lines established from human hepatocellular carcinoma. International journal of cancer Journal international du cancer. 1995;62(3):276-82.
  • Park E, Williams B, Wold BJ, Mortazavi A. RNA editing in the human ENCODE RNA-seq data. Genome Res. 2012;22(9):1626-33.
  • Okumoto K, Hattori E, Tamura K, Kiso S, Watanabe H, Saito K, et al. Possible contribution of circulating transforming growth factor-beta1 to immunity and prognosis in unresectable hepatocellular carcinoma. Liver international : official journal of the International Association for the Study of the Liver. 2004;24(1):21-8.
  • Nishikura K. Functions and regulation of RNA editing by ADAR deaminases. Annu Rev Biochem. 2010;79:321-49.
  • Nguyen VT, Law MG, Dore GJ. Hepatitis B-related hepatocellular carcinoma: epidemiological characteristics and disease burden. Journal of viral hepatitis. 2009;16(7):453-63.
  • Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods. 2008;5(7):621-8.
  • Moore B, Hu H, Singleton M, De La Vega FM, Reese MG, Yandell M. Global analysis of disease-related DNA sequence variation in 10 healthy individuals: implications for whole genome-based clinical diagnostics. Genet Med. 2011;13(3):210-7.
  • Meyerson M, Gabriel S, Getz G. Advances in understanding cancer genomes through second-generation sequencing. Nature reviews Genetics. 2010;11(10):685-96.
  • Mehler MF, Mattick JS. Noncoding RNAs and RNA editing in brain development, functional diversification, and neurological disease. Physiol Rev. 2007;87(3):799-823.
  • MacConaill LE, Campbell CD, Kehoe SM, Bass AJ, Hatton C, Niu L, et al. Profiling critical cancer gene mutations in clinical tumor samples. PLoS One. 2009;4(11):e7887.
  • Maas S, Patt S, Schrey M, Rich A. Underediting of glutamate receptor GluR-B mRNA in malignant gliomas. Proc Natl Acad Sci U S A. 2001;98(25):14687-92.
  • Llovet JM, Ricci S, Mazzaferro V, Hilgard P, Gane E, Blanc JF, et al. Sorafenib in advanced hepatocellular carcinoma. N Engl J Med. 2008;359(4):378-90.
  • Llovet JM, Pena CE, Lathia CD, Shan M, Meinhardt G, Bruix J, et al. Plasma biomarkers as predictors of outcome in patients with advanced hepatocellular carcinoma. Clin Cancer Res. 2012;18(8):2290-300.
  • Llovet JM, Bruix J. Molecular targeted therapies in hepatocellular carcinoma. Hepatology. 2008;48(4):1312-27.
  • Li M, Zhao H, Zhang X, Wood LD, Anders RA, Choti MA, et al. Inactivating mutations of the chromatin remodeling gene ARID2 in hepatocellular carcinoma. Nat Genet. 2011;43(9):828-9.
  • Li M, Wang IX, Li Y, Bruzel A, Richards AL, Toung JM, et al. Widespread RNA and DNA sequence differences in the human transcriptome. Science. 2011;333(6038):53-8.
  • Letunic I, Doerks T, Bork P. SMART: recent updates, new developments and status in 2015. Nucleic Acids Res. 2015;43(Database issue):D257-60.
  • Lee JH, Ku JL, Park YJ, Lee KU, Kim WH, Park JG. Establishment and characterization of four human hepatocellular carcinoma cell lines containing hepatitis B virus DNA. World journal of gastroenterology : WJG. 1999;5(4):289-95.
  • Kumar P, Henikoff S, Ng PC. Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc. 2009;4(7):1073-81.
  • Ku JL, Park JG. Biology of SNU cell lines. Cancer research and treatment : official journal of Korean Cancer Association. 2005;37(1):1-19.
  • Knowles BB, Howe CC, Aden DP. Human hepatocellular carcinoma cell lines secrete the major plasma proteins and hepatitis B surface antigen. Science. 1980;209(4455):497-9.
  • Kim JI, Ju YS, Park H, Kim S, Lee S, Yi JH, et al. A highly annotated whole-genome sequence of a Korean individual. Nature. 2009;460(7258):1011-5.
  • Kim JG, Kang MJ, Yoon YK, Kim HP, Park J, Song SH, et al. Heterodimerization of glycosylated insulin-like growth factor-1 receptors and insulin receptors in cancer cells sensitive to anti-IGF1R antibody. PLoS One. 2012;7(3):e33322.
  • Kim HP, Han SW, Song SH, Jeong EG, Lee MY, Hwang D, et al. Testican-1-mediated epithelial-mesenchymal transition signaling confers acquired resistance to lapatinib in HER2-positive gastric cancer. Oncogene. 2014;33(25):3334-41.
  • Kim HP, Cho GA, Han SW, Shin JY, Jeong EG, Song SH, et al. Novel fusion transcripts in human gastric cancer revealed by transcriptome analysis. Oncogene. 2014;33(47):5434-41.
  • Karapetis CS, Khambata-Ford S, Jonker DJ, O'Callaghan CJ, Tu D, Tebbutt NC, et al. K-ras mutations and benefit from cetuximab in advanced colorectal cancer. N Engl J Med. 2008;359(17):1757-65.
  • Kanehisa M, Goto S, Sato Y, Kawashima M, Furumichi M, Tanabe M. Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic Acids Res. 2014;42(Database issue):D199-205.
  • Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M. The KEGG resource for deciphering the genome. Nucleic Acids Res. 2004;32(Database issue):D277-80.
  • Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita KF, Itoh M, Kawashima S, et al. From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res. 2006;34(Database issue):D354-7.
  • Kandoth C, McLellan MD, Vandin F, Ye K, Niu B, Lu C, et al. Mutational landscape and significance across 12 major cancer types. Nature. 2013;502(7471):333-9.
  • Kan Z, Zheng H, Liu X, Li S, Barber TD, Gong Z, et al. Whole-genome sequencing identifies recurrent mutations in hepatocellular carcinoma. Genome Res. 2013;23(9):1422-33.
  • Ju YS, Kim JI, Kim S, Hong D, Park H, Shin JY, et al. Extensive genomic and transcriptional diversity identified through massively parallel DNA and RNA sequencing of eighteen Korean individuals. Nature genetics. 2011;43(8):745-52.
  • Jiang Z, Jhunjhunwala S, Liu J, Haverty PM, Kennemer MI, Guan Y, et al. The effects of hepatitis B virus integration into the genomes of hepatocellular carcinoma patients. Genome research. 2012;22(4):593-601.
  • Jiang C, Zhao Z. Mutational spectrum in the recent human genome inferred by single nucleotide polymorphisms. Genomics. 2006;88(5):527-34.
  • Jia N, Liou I, Halldorson J, Carithers R, Perkins J, Reyes J, et al. Phase I adjuvant trial of sorafenib in patients with hepatocellular carcinoma after orthotopic liver transplantation. Anticancer Res. 2013;33(6):2797-800.
  • Iavarone M, Cabibbo G, Piscaglia F, Zavaglia C, Grieco A, Villa E, et al. Field-practice study of sorafenib therapy for hepatocellular carcinoma: a prospective multicenter study in Italy. Hepatology. 2011;54(6):2055-63.
  • Huang J, Deng Q, Wang Q, Li KY, Dai JH, Li N, et al. Exome sequencing of hepatitis B virus-associated hepatocellular carcinoma. Nat Genet. 2012;44(10):1117-21.
  • Hoshida Y, Toffanin S, Lachenmayer A, Villanueva A, Minguez B, Llovet JM. Molecular classification and novel targets in hepatocellular carcinoma: recent advancements. Semin Liver Dis. 2010;30(1):35-51.
  • Henikoff S, Henikoff JG. Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci U S A. 1992;89(22):10915-9.
  • Han SW, Kim HP, Shin JY, Jeong EG, Lee WC, Kim KY, et al. RNA editing in RHOQ promotes invasion potential in colorectal cancer. J Exp Med. 2014;211(4):613-21.
  • Guichard C, Amaddeo G, Imbeaud S, Ladeiro Y, Pelletier L, Maad IB, et al. Integrated analysis of somatic mutations and focal copy-number changes identifies key genes and pathways in hepatocellular carcinoma. Nat Genet. 2012;44(6):694-8.
  • Greenman C, Stephens P, Smith R, Dalgliesh GL, Hunter C, Bignell G, et al. Patterns of somatic mutation in human cancer genomes. Nature. 2007;446(7132):153-8.
  • Fujimoto A, Totoki Y, Abe T, Boroevich KA, Hosoda F, Nguyen HH, et al. Whole-genome sequencing of liver cancers identifies etiological influences on mutation patterns and recurrent mutations in chromatin regulators. Nature genetics. 2012;44(7):760-4.
  • Forbes SA, Beare D, Gunasekaran P, Leung K, Bindal N, Boutselakis H, et al. COSMIC: exploring the world's knowledge of somatic mutations in human cancer. Nucleic Acids Res. 2015;43(Database issue):D805-11.
  • Farazi PA, DePinho RA. Hepatocellular carcinoma pathogenesis: from genes to environment. Nat Rev Cancer. 2006;6(9):674-87.
  • El-Serag HB. Hepatocellular carcinoma. N Engl J Med. 2011;365(12):1118-27.
  • El-Serag HB, Rudolph KL. Hepatocellular carcinoma: epidemiology and molecular carcinogenesis. Gastroenterology. 2007;132(7):2557-76.
  • DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, etal. A framework for variation discovery and genotyping using nextgenerationDNA sequencing data. Nat Genet. 2011;43(5):491-8.
  • Davis IJ, Hsi BL, Arroyo JD, Vargas SO, Yeh YA, Motyckova G, et al. Cloning of an Alpha-TFEB fusion in renal tumors harboring the t(6;11)(p21;q13) chromosome translocation. Proc Natl Acad Sci U S A. 2003;100(10):6051-6.
  • Dai X, Schlemmer HP, Schmidt B, Hoh K, Xu K, Ganten TM, et al. Quantitative therapy response assessment by volumetric iodine-uptake measurement: initial experience in patients with advanced hepatocellular carcinoma treated with sorafenib. Eur J Radiol. 2013;82(2):327-34.
  • Cleary SP, Jeck WR, Zhao X, Chen K, Selitsky SR, Savich GL, et al. Identification of driver genes in hepatocellular carcinoma by exome sequencing. Hepatology. 2013;58(5):1693-702.
  • Cheng AL, Kang YK, Chen Z, Tsao CJ, Qin S, Kim JS, et al. Efficacy and safety of sorafenib in patients in the Asia-Pacific region with advanced hepatocellular carcinoma: a phase III randomised, double-blind, placebo-controlled trial. Lancet Oncol. 2009;10(1):25-34.
  • Chen L, Li Y, Lin CH, Chan TH, Chow RK, Song Y, et al. Recoding RNA editing of AZIN1 predisposes to hepatocellular carcinoma. Nat Med. 2013;19(2):209-16.
  • Chan TH, Lin CH, Qi L, Fei J, Li Y, Yong KJ, et al. A disrupted RNA editing balance mediated by ADARs (Adenosine DeAminases that act on RNA) in human hepatocellular carcinoma. Gut. 2014;63(5):832-43.
  • Cenci C, Barzotti R, Galeano F, Corbelli S, Rota R, Massimi L, et al. Down-regulation of RNA editing in pediatric astrocytomas: ADAR2 editing activity inhibits cell migration and proliferation. J Biol Chem. 2008;283(11):7251-60.
  • Brunocilla PR, Brunello F, Carucci P, Gaia S, Rolle E, Cantamessa A, et al. Sorafenib in hepatocellular carcinoma: prospective study on adverse events, quality of life, and related feasibility under daily conditions. Med Oncol. 2013;30(1):345.
  • Boom R, Sol CJ, Salimans MM, Jansen CL, Wertheim-van Dillen PM, van der Noordaa J. Rapid and simple method for purification of nucleic acids. Journal of clinical microbiology. 1990;28(3):495-503.
  • Balsom SM, Li X, Trolli E, Rose J, Bloomston M, Patel T, et al. A single-institute experience with sorafenib in untreated and previously treated patients with advanced hepatocellular carcinoma. Oncology. 2010;78(3-4):210-2.
  • Bahn JH, Lee JH, Li G, Greer C, Peng G, Xiao X. Accurate identification of A-to-I RNA editing in human by transcriptome sequencing. Genome Res. 2012;22(1):142-50.
  • Argani P, Hawkins A, Griffin CA, Goldstein JD, Haas M, Beckwith JB, et al. A distinctive pediatric renal neoplasm characterized by epithelioid morphology, basement membrane production, focal HMB45 immunoreactivity, and t(6;11)(p21.1;q12) chromosome translocation. Am J Pathol. 2001;158(6):2089-96.
  • Ahn SM, Jang SJ, Shim JH, Kim D, Hong SM, Sung CO, et al. Genomic portrait of resectable hepatocellular carcinomas: implications of RB1 and FGF19 aberrations for patient stratification. Hepatology. 2014;60(6):1972-82.