The next generation sequencing technology and its application in cancer research

Chinese Journal of Lung Cancer

Volumn 13, Issue 2, 2010, Pages 154-159

  Chen, Chen ^a   Wan, Haisu ^a   Zhou, Qinghua ^a  

^a TIANJIN MEDICAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

CANCER RESEARCH; FLUORESCENCE RESONANCE ENERGY TRANSFER; METHYLATION; PYROSEQUENCING; SEQUENCE ANALYSIS; SHORT SURVEY;

GENOME, HUMAN; HUMANS; MODELS, THEORETICAL; NEOPLASMS; SEQUENCE ANALYSIS, DNA;

EID: 77949283354     PISSN: 10093419     EISSN: 19996187     Source Type: Journal    
DOI: 10.3779/j.issn.1009-3419.2010.02.15     Document Type: Short Survey

References (47)

1. Sanger F, Nicklen S, Coulson AR. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA, 1977, 74(12): 5463-5467.
2. Chu T, Bunce K, Hogge WA, et al. Statistical model for whole genome sequencing and its application to minimally invasive diagnosis of fetal genetic disease. Bioinformatics, 2009, 25(10): 1244-1250.
3. Metzker ML. Emerging technologies in DNA sequencing. Genome Res, 2005, 15(12): 1767-1776.
4. Fullwood MJ, Wei CL, Liu ET, et al. Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. Genome Res, 2009, 19(4): 521-532.
5. Pearson T, Okinaka RT, Foster JT, et al. Phylogenetic understanding of clonal populations in an era of whole genome sequencing. Infect Genet Evol, 2009, 9(5): 1010-1019.
6. Wheat CW. Rapidly developing functional genomics in ecological modelsystems via 454 transcriptome sequencing. Genetica, 2008, 10.1007/s10709-008-9326-y. 7 Droege M, Hill B. The Genome Sequencer FLX System-Longer reads, more applications, straight forward bioinformatics and more complete data sets. J Biotechnol, 2008, 136(1-2): 3-10.
7. Imelfort M, Duran C, Batley J, et al. Discovering genetic polymorphisms in next-generation sequencing data. Plant Biotechnol J, 2009, 7(4): 312-317.
8. Mardis ER. The impact of next-generationsequencing technology on genetics. Trends Genet, 2008, 24(3): 133-141.
9. Matsumura H, Krüger DH, Kahl G, et al. Super SAGE: a modern platform for genome-wide quantitative transcript profiling. Curr Pharm Biotechnol, 2008, 9(5): 368-374.
10. Clarke J, Wu HC, Jayasinghe L, et al. Continuous base identification for single-molecule nanopore DNA sequencing. Nat Nanotechnol, 2009, 4(4): 265-270.
11. Milos PM. Emergence of single-molecule sequencing and potential for molecular diagnostic applications. Expert Rev Mol Diagn, 2009, 9(7): 659-666.
12. Blom J, Albaum SP, Doppmeier D, et al. EDGAR: a software framework for the comparative analysis of prokaryotic genomes. BMC Bioinformatics, 2009, 10: 154.
13. Kofler R, Teixeira Torres T, Lelley T, et al. PanGEA: Identification of allele specific gene expression using the 454 technology. BMC Bioinformatics, 2009, 10: 143.
14. Hackenberg M, Sturm M, Langenberger D, et al. miRanalyzer: a microRNA detection and analysis tool for next-generation sequencing experiments. Nucleic Acids Res, 2009, 37(Web Server issue): W68-76.
15. Quail MA, Swerdlow H, Turner DJ. Improved protocols for the illumina genome analyzer sequencing system. Curr Protoc Hum Genet, 2009, 18: 18.2.
16. Huang X, Feng Q, Qian Q, et al. High-throughput genotyping by whole-genome resequencing. Genome Res, 2009, 19(6): 1068-1076.
17. Saunier JL, Irwin JA, Strouss KM, et al. Mitochondrial control region sequences from an Egyptian population sample. Forensic Sci Int Genet, 2009, 3(3): e97-103.
18. Tang F, Barbacioru C, Wang Y, et al. mRNA-Seq whole-transcriptome analysis of a single cell. Nat Methods, 2009, 6(5): 377-382.
19. Hormozdiari F, Alkan C, Eichler EE, et al. Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes. Genome Res, 2009, 19(7): 1270-1278.
20. Hoberman R, Dias J, Ge B, et al. A probabilistic approach for SNP discovery in high-throughput human resequencing data. Genome Res, 2009, 19(9): 1542-1552.
21. Zheng J, Moorhead M, Weng L, et al. High-throughput, high-accuracy array-based resequencing. Proc Natl Acad Sci USA, 2009, 106(16): 6712-6717.
22. Cao W, Sun B, Feitelson MA, et al. Gene expression and hepatitis C virus infection. Int J Cancer, 2009, 124(12): 2886-2892.
23. Ramírez O, Gigli E, Bover P, et al. Paleogenomics in a temperate environment: shotgun sequencing from an extinct mediterranean caprine. PLoS One, 2009, 4(5): e5670.
24. Tsibris AM, Korber B, Arnaout R, et al. Quantitative deep sequencing reveals dynamic HIV-1 escape and large population shifts during CCR5 antagonist therapy in vivo. PLoS One, 2009, 4(5): e5683.
25. Morrison M, Pope PB, Denman SE, et al. Plant biomass degradation by gut microbiomes: more of the same or something new? Curr Opin Biotechnol, 2009, 20(3): 358-363.
26. Erlich Y, Chang K, Gordon A, et al. DNA Sudoku-harnessing high-throughput sequencing for multiplexed specimen analysis. Genome Res, 2009, 19(7): 1243-1253.
27. Tyner JW, Deininger MW, Loriaux MM, et al. RNAi screen for rapid therapeutic target identification in leukemia patients. Proc Natl Acad Sci USA, 2009, 106(21): 8695-8700.
28. Morrissy AS, Morin RD, Delaney A, et al. Next-generation tag sequencing for cancer gene expression profiling. Genome Res, 2009, 19(10): 1825-35.
29. Pan Q, Shai O, Lee LJ, et al. Addendum: Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet, 2009, 41(6): 762.
30. Hillier LW, Marth GT, Quinlan AR, et al. Whole-genome sequencing and variant discovery in C. elegans. Nat Methods, 2008, 5(2): 183-188.
31. Prabhu S, Pe'er I. Overlapping pools for high-throughput targeted resequencing. Genome Res, 2009, 19(7): 1254-1261.
32. Pfeifer GP, Besaratinia A. Mutational spectra of human cancer. Hum Genet, 2009, 125(5-6): 493-506.
33. Gorlov IP, Meyer P, Liloglou T, et al. Seizure 6-like (SEZ6L) gene and risk for lung cancer. Cancer Res, 2007, 67(17): 8406-8411.
34. Mortazavi A, Williams BA, McCue K, et al. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods, 2008, 5(7): 621-628.
35. Balwierz PJ, Carninci P, Daub CO, et al. Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deep CAGE data. Genome Biol, 2009, 10(7): R79.
36. Kreuze JF, Perez A, Untiveros M, et al. Complete viral genome sequence and discovery of novel viruses by deep sequencing of small RNAs: a generic method for diagnosis, discovery and sequencing of viruses. Virology, 2009, 388(1): 1-7.
37. Armisen J, Gilchrist MJ, Wilczynska A, et al. Abundant and dynamically expressed miRNAs, piRNAs and other small RNAs in the African clawed frog Xenopus tropicalis. Genome Res, 2009, 19(10): 1766-1775.
38. Li J, Gao F, Li N, et al. An improved method for genome wide DNA methylation profiling correlated to transcription and genomic instability in two breast cancer cell lines. BMC Genomics, 2009, 10: 223.
39. Xie H, Wang M, Bonaldo Mde F, et al. High-throughput sequence-based epigenomic analysis of Alu repeats in human cerebellum. Nucleic Acids Res, 2009, 37(13): 4331-4340.
40. White HE, Durston VJ, Harvey JF, et al. Quantitative analysis of SNRPN (correction of SRNPN) gene methylation by pyrosequencing as a diagnostic test for Prader-Willi syndrome and Angelman syndrome. Clin Chem, 2006, 52(6): 1005-1013.
41. Shaw RJ, Akufo-Te+eh EK, Risk JM, et al. Methylation enrichment pyrosequencing: combining the specificity of MSP with validation by pyrosequencing. Nucleic Acids Res, 2006, 34(11): e78.
42. Taylor KH, Kramer RS, Davis JW, et al. Ultradeep bisulfite sequencing analysis of DNA methylation patterns in multiple gene promoters by 454 sequencing. Cancer Res, 2007, 67(18): 8511-8518.
43. Wold B, Myers RM. Sequence census methods for functional genomics. Nat Methods, 2008, 5(1): 19-21.
44. Zang C, Schones DE, Zeng C, et al. A clustering approach for identification of enriched domains from histone modification ChIP-Seq data. Bioinformatics, 2009, 25(15): 1952-1958.
45. Gattiker A, Hermida L, Liechti R, et al. MIMAS 3.0 is a Multiomics Information Management and Annotation System. BMC Bioinformatics, 2009, 10: 151.
46. Zheng S, Chen L. A hierarchical Bayesian model for comparing transcriptomes at the individual transcript isoform level. Nucleic Acids Res, 2009, 37(10): e75.
47. Biesecker L, Mullikin JC, Facio F, et al. The ClinSeq Project: Piloting largescale genome sequencing for research in genomic medicine. Genome Res, 2009, 19: 1665-1674.