Multiplex parallel pair-end-ditag sequencing approaches in system biology

Wiley Interdisciplinary Reviews: Systems Biology and Medicine

Volumn 2, Issue 2, 2010, Pages 224-234

  Ruan, Yijun ^a   Wei, Chia Lin ^a  

^a GENOME INSTITUTE OF SINGAPORE   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL; DNA SEQUENCE; FORECASTING; GENOME; GENOMICS; HUMAN; HUMAN GENOME; METHODOLOGY; NUCLEOTIDE SEQUENCE; REVIEW; SYSTEMS BIOLOGY;

ANIMALS; BASE SEQUENCE; FORECASTING; GENOME; GENOME, HUMAN; GENOMICS; HUMANS; SEQUENCE ANALYSIS, DNA; SYSTEMS BIOLOGY;

EID: 79952115329     PISSN: 19395094     EISSN: 1939005X     Source Type: Journal    
DOI: 10.1002/wsbm.40     Document Type: Article

References (59)

1. Levy S, Sutton G, Ng PC, Feuk L, Halpern AL, et al. The diploid genome sequence of an individual human. PLoS Biol 2007, 5:e254.
2. The ENCODE consortium (ENCyclopedia Of DNA Elements) Project. Science 2004, 306:636-640.
3. Birney E, Stamatoyannopoulos JA, Dutta A, Guigo R, Gingeras TR, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 2007, 447:799-816.
4. Brenner S, Johnson M, Bridgham J, Golda G, Lloyd DH, et al. Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat Biotechnol 2000, 18:630-634.
5. Strausberg RL, Feingold EA, Grouse LH, Derge JG, Klausner RD, et al. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proc Natl Acad Sci U S A 2002, 99:16899-16903.
6. Velculescu VE, Zhang L, Vogelstein B, Kinzler KW. Serial analysis of gene expression. Science 1995, 270:484-487.
7. Shoemaker DD, Schadt EE, Armour CD, He YD, Garrett-Engele P, et al. Experimental annotation of the human genome using microarray technology. Nature 2001, 409:922-927.
8. Wu J, Smith LT, Plass C, Huang TH. ChIP-chip comes of age for genome-wide functional analysis. Cancer Res 2006, 66:6899-6902.
9. Harris TD, Buzby PR, Babcock H, Beer E, Bowers J, et al. Single-molecule DNA sequencing of a viral genome. Science 2008, 320:106-109.
10. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, et al. Genome sequencing in microfabricated highdensity picolitre reactors. Nature 2005, 437:376-380.
11. Shendure J, Porreca GJ, Reppas NB, Lin X, McCutcheon JP, et al. Accurate multiplex polony sequencing of an evolved bacterial genome. Science 2005, 309:1728-1732.
12. Johnson DS, Mortazavi A, Myers RM, Wold B. Genome-wide mapping of in vivo protein-DNA interactions. Science 2007, 316:1497-1502.
13. Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 2007, 448:553-560.
14. Ng P, Tan JJ, Ooi HS, Lee YL, Chiu KP, et al. Multiplex sequencing of paired-end ditags (MS-PET): a strategy for the ultra-high-throughput analysis of transcriptomes and genomes. Nucleic Acids Res 2006, 34:e84.
15. Ng P, Wei CL, Sung WK, Chiu KP, Lipovich L, et al. Gene identification signature (GIS) analysis for transcriptome characterization and genome annotation. Nat Methods 2005, 2:105-111.
16. Ruan Y, Ooi HS, Choo SW, Chiu KP, Zhao XD, et al. Fusion transcripts and transcribed retrotransposed loci discovered through comprehensive transcriptome analysis using Paired-End diTags (PETs). Genome Res 2007, 17:828-838.
17. Korbel JO, Urban AE, Affourtit JP, Godwin B, Grubert F, et al. Paired-end mapping reveals extensive structural variation in the human genome. Science 2007a, 318:420-426.
18. Wei CL, Wu Q, Vega VB, Chiu KP, Ng P, et al. A global map of p53 transcription-factor binding sites in the human genome. Cell 2006, 124:207-219.
19. Zhao XD, Han X, Chew JL, Liu J, Chiu KP, et al. Whole-genome mapping of histone h3 lys4 and 27 trimethylations reveals distinct genomic compartments in human embryonic stem cells. Cell Stem Cell 2007, 1:286-298.
20. Chiu KP, Wong CH, Chen Q, Ariyaratne P, Ooi HS, et al. PET-Tool: a software suite for comprehensive processing and managing of Paired-End diTag (PET) sequence data. BMC Bioinformatics 2006, 7:390.
21. Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, et al. High-resolution profiling of histone methylations in the human genome. Cell 2007, 129:823-837.
22. Carninci P, Hayashizaki Y.: High-efficiency full-length cDNA cloning. Methods Enzymol 1999, 303:19-44.
23. Adams MD, Dubnick M, Kerlavage AR, Moreno R, Kelley JM, et al. Sequence identification of 2,375 human brain genes. Nature 1992, 355:632-634.
24. Kodzius R, Kojima M, Nishiyori H, Nakamura M, Fukuda S, et al. CAGE: cap analysis of gene expression. Nat Methods 2006, 3:211-222.
25. Wei CL, Ng P, Chiu KP, Wong CH, Ang CC, et al. 5'Long serial analysis of gene expression (LongSAGE) and 3'LongSAGE for transcriptome characterization and genome annotation. Proc Natl Acad Sci U S A 2004, 101:11701-11706.
26. Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, et al. The transcriptional landscape of the mammalian genome. Science 2005, 309:1559-1563.
27. Mitelman F, Johansson B, Mertens F. Fusion genes and rearranged genes as a linear function of chromosome aberrations in cancer. Nat Genet 2004, 36:331-334.
28. Mauro MJ, O'Dwyer M, Heinrich MC, Druker BJ. STI571: a paradigm of new agents for cancer therapeutics. J Clin Oncol 2002, 20:325-334.
29. Sultan M, Schulz MH, Richard H, Magen A, Klingenhoff A, et al. A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science 2008, 321:956-960.
30. Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 2009, 10:57-63.
31. Korbel JO, Urban AE, Affourtit JP, Godwin B, Grubert F, Simons JF, Kim PM, Palejev D, Carriero NJ, Du L. Paired-End Mapping Reveals Extensive Structural Variation in the Human Genome. Science 2007b, 318:420-426.
32. Iafrate AJ, Feuk L, Rivera MN, Listewnik ML, Donahoe PK, et al. Detection of large-scale variation in the human genome. Nat Genet 2004, 36:949-951.
33. Sebat J, Lakshmi B, Troge J, Alexander J, Young J, et al. Large-scale copy number polymorphism in the human genome. Science 2004, 305:525-528.
34. Wang TL, Maierhofer C, Speicher MR, Lengauer C, Vogelstein B, et al. Digital karyotyping. Proc Natl Acad Sci U S A 2002, 99:16156-16161.
35. Schrock E, Padilla-Nash H.: Spectral karyotyping and multicolor fluorescence in situ hybridization reveal new tumor-specific chromosomal aberrations. Semin Hematol 2000, 37:334-347.
36. Knutsen T, Gobu V, Knaus R, Padilla-Nash H, Augustus M, et al. The interactive online SKY/M-FISH & CGH database and the Entrez cancer chromosomes search database: linkage of chromosomal aberrations with the genome sequence. Genes Chromosomes Cancer 2005, 44:52-64.
37. Tibiletti MG. Specificity of interphase fluorescence in situ hybridization for detection of chromosome aberrations in tumor pathology. Cancer Genet Cytogenet 2004, 155:143-148.
38. Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 2008, 456:53-59.
39. Greenman C, Stephens P, Smith R, Dalgliesh GL, Hunter C, et al. Patterns of somatic mutation in human cancer genomes. Nature 2007, 446:153-158.
40. Sjoblom T, Jones S, Wood LD, Parsons DW, Lin J, et al. The consensus coding sequences of human breast and colorectal cancers. Science 2006, 314:268-274.
41. Kidd JM, Cooper GM, Donahue WF, Hayden HS, Sampas N, et al. Mapping and sequencing of structural variation from eight human genomes. Nature 2008, 453:56-64.
42. Tuzun E, Sharp AJ, Bailey JA, Kaul R, Morrison VA, et al. Fine-scale structural variation of the human genome. Nat Genet 2005, 37:727-732.
43. Campbell PJ, Stephens PJ, Pleasance ED, O'Meara S, Li H, et al. Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nat Genet 2008, 40:722-729.
44. Parada L, Misteli T. Chromosome positioning in the interphase nucleus. Trends Cell Biol 2002, 12:425-432.
45. Cockell M, Gasser SM.: Nuclear compartments and gene regulation. Curr Opin Genet Dev 1999, 9:199-205.
46. Boyer LA, Lee TI, Cole MF, Johnstone SE, Levine SS, et al. Core transcriptional regulatory circuitry in human embryonic stem cells. Cell 2005, 122:947-956.
47. Kim TH, Ren B. Genome-wide analysis of protein-DNA interactions. Annu Rev Genomics Hum Genet 2006, 7:81-102.
48. Kuo MH, Allis CD. In vivo cross-linking and immunoprecipitation for studying dynamic Protein:DNA associations in a chromatin environment. Methods 1999, 19:425-433.
49. Orlando V. Mapping chromosomal proteins in vivo by formaldehyde-crosslinked-chromatin immunoprecipitation. Trends Biochem Sci 2000, 25:99-104.
50. Iyer VR, Horak CE, Scafe CS, Botstein D, Snyder M, et al. Genomic binding sites of the yeast cellcycle transcription factors SBF andMBF. Nature 2001, 409:533-538.
51. Ren B, Robert F, Wyrick JJ, Aparicio O, Jennings EG, et al. Genome-wide location and function of DNA binding proteins. Science 2000, 290:2306-2309.
52. Bourque G, Leong B, Vega VB, Chen X, Lee YL, et al. Evolution of the mammalian transcription factor binding repertoire via transposable elements. Genome Res 2008, 18:1752-1762.
53. Loh YH, Wu Q, Chew JL, Vega VB, Zhang W, et al. The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells. Nat Genet 2006, 38:431-440.
54. Euskirchen GM, Rozowsky JS, Wei CL, Lee WH, Zhang ZD, et al.Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologies. Genome Res 2007, 17:898-909.
55. Chen X, Xu H, Yuan P, Fang F, Huss M, et al. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 2008, 133:1106-1117.
56. Carter D, Chakalova L, Osborne CS, Dai YF, Fraser P. Long-range chromatin regulatory interactions in vivo. Nat Genet 2002, 32:623-626.
57. Dekker J, Rippe K, Dekker M, Kleckner N. Capturing chromosome conformation. Science 2002, 295:1306-1311.
58. Dostie J, Richmond TA, Arnaout RA, Selzer RR, Lee WL, et al. Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res 2006, 16:1299-1309.
59. Zhao Z, Tavoosidana G, SjolinderM, Gondor A, Mariano P, et al. Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions. Nat Genet 2006, 38:1341-1347.