From genome sequencing to the discovery of potential biomarkers in liver disease

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참고문헌 (107)

1. Luo P, "A Large-scale, multicenter serum metabolite biomarker identification study for the early detection of hepatocellular carcinoma", Hepatology, 67, pp.662~675 (2018)
2. Miao R, "Identification of prognostic biomarkers in hepatitis B virus-related hepatocellular carcinoma and stratification by integrative multiomics analysis", J Hepatol, 61, pp.840~849 (2014)
3. Wu Z, "Genomic subtyping of liver cancers with prognostic application", BMC Cancer, 20, pp.84~ (2020)
4. Tahmasebi S, "Translation deregulation in human disease", Nat Rev Mol Cell Biol, 19, pp.791~807 (2018)
5. Ng SB, "Targeted capture and massively parallel sequencing of 12 human exomes", Nature, 461, pp.272~276 (2009)
6. Brunner SF, "Somatic mutations and clonal dynamics in healthy and cirrhotic human liver", Nature, 574, pp.538~542 (2019)
7. Letouze E, "Mutational signatures reveal the dynamic interplay of risk factors and cellular processes during liver tumorigenesis", Nat Commun, 8, pp.1315~ (2017)
8. Genomes Project C, "A map of human genome variation from population-scale sequencing", Nature, 467, pp.1061~1073 (2010)
9. Sepanlou SG, "The global, regional, and national burden of cirrhosis by cause in 195 countries and territories, 1990–2017 : a systematic analysis for the Global Burden of Disease Study 2017", Lancet Gastroenterol Hepatol, 5, pp.245~266 (2020)
10. Pellicoro A, "Liver fibrosis and repair : immune regulation of wound healing in a solid organ", Nat Rev Immunol, 14, pp.181~194 (2014)
11. Kentepozidou E, "Clustered CTCF binding is an evolutionary mechanism to maintain topologically associating domains", Genome Biol, 21, pp.5~ (2020)
12. Schwarzer W, "Two independent modes of chromatin organization revealed by cohesin removal", Nature, 551, pp.51~56 (2017)
13. Caruso S, "Analysis of Liver Cancer Cell Lines Identifies Agents With Likely Efficacy Against Hepatocellular Carcinoma and Markers of Response", Gastroenterology, 157, pp.760~776 (2019)
14. Sakai M, "Liver-Derived Signals Sequentially Reprogram Myeloid Enhancers to Initiate and Maintain Kupffer Cell Identity", Immunity, 51, pp.655~670 e658 (2019)
15. Brosch M, "Epigenomic map of human liver reveals principles of zonated morphogenic and metabolic control", Nat Commun, 9, pp.4150~ (2018)
16. Sanger F, "DNA sequencing with chain-terminating inhibitors", Proc Natl Acad Sci U S A, 74, pp.5463~5467 (1977)
17. Turnbull C, "The 100000 Genomes Project : bringing whole genome sequencing to the NHS", BMJ, 361, pp.k1687~ (2018)
18. Berger MF, "The emerging clinical relevance of genomics in cancer medicine", Nat Rev Clin Oncol, 15, pp.353~365 (2018)
19. Myllykangas S, "Efficient targeted resequencing of human germline and cancer genomes by oligonucleotide-selective sequencing", Nat Biotechnol, 29, pp.1024~1027 (2011)
20. Ahn EH, "Detection of Low-Frequency Mutations and Identification of Heat-Induced Artifactual Mutations Using Duplex Sequencing", Int J Mol Sci, 20 (2019)
21. Carlson KD, "MIPSTR : a method for multiplex genotyping of germline and somatic STR variation across many individuals", Genome Res, 25, pp.750~761 (2015)
22. van Opijnen T, "Tn-seq : high-throughput parallel sequencing for fitness and genetic interaction studies in microorganisms", Nat Methods, 6, pp.767~772 (2009)
23. Schauer SN, "L1retrotransposition is a common feature of mammalian hepatocarcinogenesis", Genome Res, 28, pp.639~653 (2018)
24. Davey JW, "RADSeq : next-generation population genetics", Brief Funct Genomics, 9, pp.416~423 (2010)
25. Sun X, "SLAF-seq : an efficient method of large-scale de novo SNP discovery and genotyping using high-throughput sequencing", PLoS One, 8, pp.e58700~ (2013)
26. Ali OA, "RAD Capture(Rapture) : Flexible and Efficient Sequence-Based Genotyping", Genetics, 202, pp.389~400 (2016)
27. Masser DR, "Focused, high accuracy 5-methylcytosine quantitation with base resolution by benchtop next-generation sequencing", Epigenetics Chromatin, 6, pp.33~ (2013)
28. Meissner A, "Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis", Nucleic Acids Res, 33, pp.5868~5877 (2005)
29. Neri F, "Methylation-assisted bisulfite sequencing to simultaneously map 5fC and 5caC on a genome-wide scale for DNA demethylation analysis", Nat Protoc, 11, pp.1191~1205 (2016)
30. Hansen RS, "Sequencing newly replicated DNA reveals widespread plasticity in human replication timing", Proc Natl Acad Sci U S A, 107, pp.139~144 (2010)
31. Mesner LD, "Bubble-seq analysis of the human genome reveals distinct chromatin-mediated mechanisms for regulating early-and late-firing origins", Genome Res, 23, pp.1774~1788 (2013)
32. Foulk MS, "Characterizing and controlling intrinsic biases of lambda exonuclease in nascent strand sequencing reveals phasing between nucleosomes and G-quadruplex motifs around a subset of human replication origins", Genome Res, 25, pp.725~735 (2015)
33. Kunnev D, "Isolation and sequencing of active origins of DNA replication by nascent strand capture and release(NSCR)", J Biol Methods, 2, pp.e33~ (2015)
34. Baranello L, "DNA break mapping reveals topoisomerase II activity genomewide", Int J Mol Sci, 15, pp.13111~13122 (2014)
35. Crosetto N, "Nucleotideresolution DNA double-strand break mapping by nextgeneration sequencing", Nat Methods, 10, pp.361~365 (2013)
36. Tsai SQ, "GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases", Nat Biotechnol, 33, pp.187~197 (2015)
37. Schones DE, "Dynamic regulation of nucleosome positioning in the human genome", Cell, 132, pp.887~898 (2008)
38. Ishii H, "MPE-seq, a new method for the genome-wide analysis of chromatin structure", Proc Natl Acad Sci U S A, 112, pp.E3457~3465 (2015)
39. Deal RB, "Genomewide kinetics of nucleosome turnover determined by metabolic labeling of histones", Science, 328, pp.1161~1164 (2010)
40. Giresi PG, "FAIRE(Formaldehyde-Assisted Isolation of Regulatory Elements)isolates active regulatory elements from human chromatin", Genome Res, 17, pp.877~885 (2007)
41. Sos BC, "Characterization of chromatin accessibility with a transposome hypersensitive sites sequencing(THS-seq)assay", Genome Biol, 17, pp.20~ (2016)
42. Klein DC, "Genomic methods in profiling DNA accessibility and factor localization", Chromosome Res, 28, pp.69~85 (2019)
43. Zentner GE, "High-resolution digital profiling of the epigenome", Nat Rev Genet, 15, pp.814~827 (2014)
44. Anders L, "Genome-wide localization of small molecules", Nat Biotechnol, 32, pp.92~96 (2014)
45. Riley TR, "SELEX-seq : a method for characterizing the complete repertoire of binding site preferences for transcription factor complexes", Methods Mol Biol, 1196, pp.255~278 (2014)
46. Li G, "Chromatin Interaction Analysis with Paired-End Tag(ChIA-PET)sequencing technology and application", BMC Genomics, 15(Suppl 12), pp.S11~S11 (2014)
47. Harewood L, "Hi-C as a tool for precise detection and characterisation of chromosomal rearrangements and copy number variation in human tumours", Genome Biol, 18, pp.125~ (2017)
48. Davies JO, "Multiplexed analysis of chromosome conformation at vastly improved sensitivity", Nat Methods, 13, pp.74~80 (2016)
49. Kalhor R, "Genome architectures revealed by tethered chromosome conformation capture and population-based modeling", Nat Biotechnol, 30, pp.90~98 (2011)
50. Li G, "Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation", Cell, 148, pp.84~98 (2012)
51. Wang Z, "RNA-Seq : a revolutionary tool for transcriptomics", Nat Rev Genet, 10, pp.57~63 (2009)
52. Li H, "RASL-seq for massively parallel and quantitative analysis of gene expression", Curr Protoc Mol Biol, (Chapter 4), pp.4 13 11~4 13 19 (2012)
53. Mercer TR, "Targeted sequencing for gene discovery and quantification using RNA CaptureSeq", Nat Protoc, 9, pp.989~1009 (2014)
54. Routh A, "ClickSeq : Fragmentation-Free Next-Generation Sequencing via Click Ligation of Adaptors to Stochastically Terminated 3'-Azido cDNAs", J Mol Biol, 427, pp.2610~2616 (2015)
55. Motameny S, "Next Generation Sequencing of miRNAs - Strategies, Resources and Methods", Genes (Basel), 1, pp.70~84 (2010)
56. Hashimshony T, "CEL-Seq : single-cell RNA-Seq by multiplexed linear amplification", Cell Rep, 2, pp.666~673 (2012)
57. Macosko EZ, "Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets", Cell, 161, pp.1202~1214 (2015)
58. Kawaji H, "Comparison of CAGE and RNA-seq transcriptome profiling using clonally amplified and single-molecule next-generation sequencing", Genome Res, 24, pp.708~717 (2014)
59. Park D, "Simultaneous mapping of transcript ends at single-nucleotide resolution and identification of widespread promoterassociated non-coding RNA governed by TATA elements", Nucleic Acids Res, 42, pp.3736~3749 (2014)
60. Arribere JA, "Roles for transcript leaders in translation and mRNA decay revealed by transcript leader sequencing", Genome Res, 23, pp.977~987 (2013)
61. Chang H, "TAIL-seq : genome-wide determination of poly(A)tail length and 3'end modifications", Mol Cell, 53, pp.1044~1052 (2014)
62. Mahat DB, "Base-pairresolution genome-wide mapping of active RNA polymerases using precision nuclear run-on(PRO-seq)", Nat Protoc, 11, pp.1455~1476 (2016)
63. Paulsen MT, "Coordinated regulation of synthesis and stability of RNA during the acute TNF-induced proinflammatory response", Proc Natl Acad Sci U S A, 110, pp.2240~2245 (2013)
64. Franco HL, "Enhancer transcription reveals subtype-specific gene expression programs controlling breast cancer pathogenesis", Genome Res, 28, pp.159~170 (2018)
65. Chu C, "Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions", Mol Cell, 44, pp.667~678 (2011)
66. Zhao J, "Genome-wide identification of polycomb-associated RNAs by RIP-seq", Mol Cell, 40, pp.939~953 (2010)
67. McMahon AC, "TRIBE : Hijacking an RNA-Editing Enzyme to Identify Cell-Specific Targets of RNA-Binding Proteins", Cell, 165, pp.742~753 (2016)
68. Ingolia NT, "Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling", Science, 324, pp.218~ (2009)
69. Jiao Y, "Cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control", Mol Syst Biol, 6, pp.419~ (2010)
70. Delaunay S, "RNA modifications regulating cell fate in cancer", Nat Cell Biol, 21, pp.552~559 (2019)
71. Panneerdoss S, "Crosstalk among writers, readers, and erasers of m(6)A regulates cancer growth and progression", Science Advances, pp.eaar8263~eaar8263 (2018)
72. Linder B, "Single-nucleotideresolution mapping of m6A and m6Am throughout the transcriptome", Nat Methods, 12, pp.767~772 (2015)
73. German MA, "Construction of Parallel Analysis of RNA Ends(PARE)libraries for the study of cleaved miRNA targets and the RNA degradome", Nat Protoc, 4, pp.356~362 (2009)
74. Yu X, "Genome-Wide Mapping of Uncapped and Cleaved Transcripts Reveals a Role for the Nuclear mRNA Cap-Binding Complex in Cotranslational RNA Decay in Arabidopsis", Plant Cell, 28, pp.2385~2397 (2016)
75. Lucks JB, "Multiplexed RNA structure characterization with selective 2'-hydroxyl acylation analyzed by primer extension sequencing(SHAPE-Seq)", Proc Natl Acad Sci U S A, 108, pp.11063~11068 (2011)
76. Fang R, "Probing Xist RNA Structure in Cells Using Targeted Structure-Seq", PLoS Genet, 11, pp.e1005668~ (2015)
77. Wan Y, "Genomewide mapping of RNA structure using nuclease digestion and high-throughput sequencing", Nat Protoc, 8, pp.849~869 (2013)
78. Castven D, "Application of patient-derived liver cancer cells for phenotypic characterization and therapeutic target identification", Int J Cancer, 144, pp.2782~2794 (2019)
79. Guo W, "A LIN28B Tumor-Specific Transcript in Cancer", Cell Rep, 22, pp.2016~2025 (2018)
80. Yao Z, "ZKSCAN1 gene and its related circular RNA(circZKSCAN1)both inhibit hepatocellular carcinoma cell growth, migration, and invasion but through different signaling pathways", Mol Oncol, 11, pp.422~437 (2017)
81. Sookoian S, "Serum aminotransferases in nonalcoholic fatty liver disease are a signature of liver metabolic perturbations at the amino acid and Krebs cycle level", Am J Clin Nutr, 103, pp.422~434 (2016)
82. Qiu C, "Multi-omics Data Integration for Identifying Osteoporosis Biomarkers and Their Biological Interaction and Causal Mechanisms", iScience, 23, pp.100847~ (2020)
83. Cleary SP, "Identification of driver genes in hepatocellular carcinoma by exome sequencing", Hepatology, 58, pp.1693~1702 (2013)
84. Zhu M, "Somatic Mutations Increase Hepatic Clonal Fitness and Regeneration in Chronic Liver Disease", Cell, 177, pp.608~621 e612 (2019)
85. Singal AG, "Hepatocellular Carcinoma From Epidemiology to Prevention : Translating Knowledge into Practice", Clin Gastroenterol Hepatol, 13, pp.2140~2151 (2015)
86. Gerstung M, "The evolutionary history of 2, 658 cancers", Nature, 578, pp.122~128 (2020)
87. Lee S, "Network analyses identify liver-specific targets for treating liver diseases", Mol Syst Biol, 13, pp.938~ (2017)
88. Zheng J, "Characterization of hepatocellular adenoma and carcinoma using microRNA profiling and targeted gene sequencing", PLoS One, 13, pp.e0200776~ (2018)
89. Wang Y, "Serum exosomal microRNAs combined with alpha-fetoprotein as diagnostic markers of hepatocellular carcinoma", Cancer Med, 7, pp.1670~1679 (2018)
90. Mizuguchi Y, "Sequencing and bioinformatics-based analyses of the microRNA transcriptome in hepatitis B-related hepatocellular carcinoma", PLoS One, 6, pp.e15304~ (2011)
91. Yang Y, "Recurrently deregulated lncRNAs in hepatocellular carcinoma", Nat Commun, 8, pp.14421~ (2017)
92. Zhang J, "Cancer Specific Long Noncoding RNAs Show Differential Expression Patterns and Competing Endogenous RNA Potential in Hepatocellular Carcinoma", PLoS One, 10, pp.e0141042~ (2015)
93. Dehghani Amirabad A, "Transgenic expression of the RNA binding protein IMP2 stabilizes miRNA targets in murine microsteatosis", Biochim Biophys Acta Mol Basis Dis, 1864, pp.3099~3108 (2018)
94. Lu M, "The crucial role of multiomic approach in cancer research and clinically relevant outcomes", EPMA J, 9, pp.77~102 (2018)
95. Gallo Cantafio ME, "From Single Level Analysis to Multi-Omics Integrative Approaches : A Powerful Strategy towards the Precision Oncology", High Throughput, 7, pp.33~ (2018)
96. Schulze K, "Genetic profiling of hepatocellular carcinoma using next-generation sequencing", J Hepatol, 65, pp.1031~1042 (2016)
97. Cazaly E, "Making Sense of the Epigenome Using Data Integration Approaches", Front Pharmacol, 10, pp.126~ (2019)
98. Sommars MA, "Dynamic repression by BCL6 controls the genomewide liver response to fasting and steatosis", Elife, 8, pp.e43922~ (2019)
99. Huang J, "Dissecting superenhancer hierarchy based on chromatin interactions", Nat Commun, 9, pp.943~ (2018)
100. Koohy H, "A comparison of peak callers used for DNase-Seq data", PLoS One, 9, pp.e96303~ (2014)
101. Shiraishi Y, "Integrated analysis of whole genome and transcriptome sequencing reveals diverse transcriptomic aberrations driven by somatic genomic changes in liver cancers", PLoS One, 9, pp.e114263~ (2014)
102. Calderaro J, "Histological subtypes of hepatocellular carcinoma are related to gene mutations and molecular tumour classification", J Hepatol, 67, pp.727~738 (2017)
103. Sakai K, "Targeted DNA and RNA sequencing of fine-needle biopsy FFPE specimens in patients with unresectable hepatocellular carcinoma treated with sorafenib", Oncotarget, 6, pp.21636~21644 (2015)
104. Gutierrez Sanchez LH, "Perinatal Nutritional Reprogramming of the Epigenome Promotes Subsequent Development of Nonalcoholic Steatohepatitis", Hepatol Commun, 2, pp.1493~1512 (2018)
105. Matsushita J, "The DNA methylation profile of liver tumors in C3H mice and identification of differentially methylated regions involved in the regulation of tumorigenic genes", BMC Cancer, 18, pp.317~ (2018)
106. Beck A, "Overexpression of UHRF1 promotes silencing of tumor suppressor genes and predicts outcome in hepatoblastoma", Clin Epigenetics, 10, pp.27~ (2018)
107. Caliskan M, "Genetic and Epigenetic Fine Mapping of Complex Trait Associated Loci in the Human Liver", Am J Hum Genet, 105, pp.89~107 (2019)

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