Emerging DNA sequencing technologies for human genomic medicine

Drug Discovery Today

Volumn 13, Issue 13-14, 2008, Pages 569-577

  Strausberg, Robert L ^a   Levy, Samuel ^a   Rogers, Yu Hui ^a  

^a J CRAIG VENTER INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; EPIDERMAL GROWTH FACTOR RECEPTOR; FIBROBLAST GROWTH FACTOR RECEPTOR 1; RNA POLYMERASE II;

ELECTROPHORESIS; EXPRESSED SEQUENCE TAG; GENE MUTATION; GENETIC PROCEDURES; HUMAN; HUMAN GENOME; MYCOPLASMA GENITALIUM; POLYMERASE CHAIN REACTION; PYROSEQUENCING; REVIEW; SANGER ELECTROPHORESIS; SANGER SEQUENCING TECHNOLOGY; SEQUENCE ANALYSIS; SERIAL ANALYSIS OF GENE EXPRESSION; SINGLE NUCLEOTIDE POLYMORPHISM; SOLEXA SEQUENCING TECHNOLOGY; SUPPORTED OLIGONUCLEOTIDE LIGATION AND DETECTION PLATFORM TECHNOLOGY;

ANIMALS; BIOMEDICAL TECHNOLOGY; GENOME, HUMAN; HUMANS; SEQUENCE ANALYSIS, DNA;

EID: 45849130924     PISSN: 13596446     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.drudis.2008.03.025     Document Type: Review

References (70)

1. Venter J.C., et al. The sequence of the human genome. Science 291 (2001) 1304-1351
2. Lander E.S., et al. Initial sequencing and analysis of the human genome. Nature 409 (2001) 860-921
3. Frazer K.A., et al. A second generation human haplotype map of over 3.1 million SNPs. Nature 449 (2007) 851-861
4. Levy S., et al. The diploid genome sequence of an individual human. PLoS Biol. 5 (2007) e254
5. Sanger F., et al. DNA sequencing with chain-terminating inhibitors. Proc. Natl. Acad. Sci. U. S. A. 74 (1977) 5463-5467
6. Maxam A.M., and Gilbert W. A new method for sequencing DNA. Proc. Natl. Acad. Sci. U. S. A. 74 (1977) 560-564
7. Smith L.M., et al. Fluorescence detection in automated DNA sequence analysis. Nature 321 (1986) 674-679
8. Bashkin J., et al. DNA sequencing by capillary electrophoresis with a hydroxyethylcellulose sieving buffer. Appl. Theor. Electrophor. 6 (1996) 23-28
9. Bashkin J.S., et al. Implementation of a capillary array electrophoresis instrument. J. Capillary Electrophor. 3 (1996) 61-68
10. Behr S., et al. A fully automated multicapillary electrophoresis device for DNA analysis. Electrophoresis 20 (1999) 1492-1507
11. Prober J.M., et al. A system for rapid DNA sequencing with fluorescent chain-terminating dideoxynucleotides. Science 238 (1987) 336-341
12. McCombie W.R., et al. Rapid and reliable fluorescent cycle sequencing of double-stranded templates. DNA Seq. 2 (1992) 289-296
13. Ju J., et al. Fluorescence energy transfer dye-labeled primers for DNA sequencing and analysis. Proc. Natl. Acad. Sci. U. S. A. 92 (1995) 4347-4351
14. Lee L.G., et al. New energy transfer dyes for DNA sequencing. Nucleic Acids Res. 25 (1997) 2816-2822
15. Hall N. Advanced sequencing technologies and their wider impact in microbiology. J. Exp. Biol. 210 (2007) 1518-1525
16. Myers E.W., et al. A whole-genome assembly of Drosophila. Science 287 (2000) 2196-2204
17. Adams M.D., et al. Complementary-DNA sequencing - expressed sequence tags and human genome project. Science 252 (1991) 1651-1656
18. Porter D., et al. SAGE and related approaches for cancer target identification. Drug Discov. Today 11 (2006) 110-118
19. Kodzius R., et al. CAGE: cap analysis of gene expression. Nat. Methods 3 (2006) 211-222
20. Wang T.L., et al. Digital karyotyping. Proc. Natl. Acad. Sci. U. S. A. 99 (2002) 16156-16161
21. Margulies M., et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437 (2005) 376-380
22. Shendure J., et al. Accurate multiplex polony sequencing of an evolved bacterial genome. Science 309 (2005) 1728-1732
23. Braslavsky I., et al. Sequence information can be obtained from single DNA molecules. Proc. Natl. Acad. Sci. U. S. A. 100 (2003) 3960-3964
24. Bentley D.R. Whole-genome re-sequencing. Curr. Opin. Genet. Dev. 16 (2006) 545-552
25. Ronaghi M., et al. Analyses of secondary structures in DNA by pyrosequencing. Anal. Biochem. 267 (1999) 65-71
26. Ronaghi M., et al. PCR-introduced loop structure as primer in DNA sequencing. Biotechniques 25 (1998) 876-878
27. Nyren P., et al. Solid phase DNA minisequencing by an enzymatic luminometric inorganic pyrophosphate detection assay. Anal. Biochem. 208 (1993) 171-175
28. Dressman D., et al. Transforming single DNA molecules into fluorescent magnetic particles for detection and enumeration of genetic variations. PNAS 100 (2003) 8817-8822
29. Smith A.D., et al. Using quality scores and longer reads improves accuracy of Solexa read mapping. BMC Bioinformatics 9 (2008) 128
30. Huse S.M., et al. Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biol. 8 (2007) R143
31. Brockman W., et al. Quality scores and SNP detection in sequencing-by-synthesis systems. Genome Res. (2008)
32. Ewing B., et al. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8 (1998) 175-185
33. Bainbridge M.N., et al. Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach. BMC Genomics 7 (2006) 246
34. Thomas R.K., et al. Sensitive mutation detection in heterogeneous cancer specimens by massively parallel picoliter reactor sequencing. Nat. Med. 12 (2006) 852-855
35. Hopkins K.L., et al. Rapid detection of gyrA and parC mutations in quinolone-resistant Salmonella enterica using Pyrosequencing (R) technology. J. Microbiol. Methods 68 (2007) 163-171
36. Edvinsson B., et al. Rapid genotyping of Toxoplasma gondii by pyrosequencing. Clin. Microbiol. Infect. 13 (2007) 424-429
37. Hefler L.A., et al. Vascular endothelial growth factor gene polymorphisms are associated with prognosis in ovarian cancer. Clin. Cancer Res. 13 (2007) 898-901
38. van der Straaten R., et al. Exploratory analysis of four polymorphisms in human GGH and FPGS genes and their effect in metho trexate-treated rheumatoid arthritis patients. Pharmacogenomics 8 (2007) 141-150
39. Braicu E.I., et al. Polymorphism of IL-1 alpha, IL-1 beta and IL-10 in patients with advanced ovarian cancer: results of a prospective study with 147 patients. Gynecol. Oncol. 104 (2007) 680-685
40. Zhou Z.Y., et al. Pyrosequencing, a high-throughput method for detecting single nucleotide polymorphisms in the dihydrofolate reductase and dihydropteroate synthetase genes of Plasmodium falciparum. J. Clin. Microbiol. 44 (2006) 3900-3910
41. Zhou Z., et al. Pyrosequencing - a high-throughput method for detecting single nucleotide polymorphisms (SNPS) in the dihydrofolate reductase and dihydropteroate synthetase genes of Plasmodium falciparum. Am. J. Trop. Med. Hygiene 75 (2006) 56
42. Swaminathan K., et al. Global repeat discovery and estimation of genomic copy number in a large, complex genome using a high-throughput 454 sequence survey. BMC Genomics 8 (2007) 132
43. Korbel J.O., et al. Paired-end mapping reveals extensive structural variation in the human genome. Science 318 (2007) 420-426
44. Rodriguez-Canales J., et al. Identification of a unique epigenetic sub-microenvironment in prostate cancer. J. Pathol. 211 (2007) 410-419
45. Bollati V., et al. Changes in DNA methylation patterns in subjects exposed to low-dose benzene. Cancer Res. 67 (2007) 876-880
46. Liu T., et al. Regulation of Cdx2 expression by promoter methylation, and effects of Cdx2 transfection on morphology and gene expression of human esophageal epithelial cells. Carcinogenesis 28 (2007) 488-496
47. Beier V., et al. Monitoring methylation changes in cancer. Analytics of Protein-DNA Interactions vol. 104 (2007), Springer-Verlag, Berlin 1-11
48. Chelbi S.T., et al. Expressional and epigenetic alterations of placental serine protease inhibitors - SERPINA3 is a potential marker of preeclampsia. Hypertension 49 (2007) 76-83
49. Goldberg S.M., et al. A sanger/pyrosequencing hybrid approach for the generation of high-quality draft assemblies of marine microbial genomes. Proc. Natl. Acad. Sci. U. S. A. 103 (2006) 11240-11245
50. Bainbridge M.N., et al. Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach. BMC Genomics 7 (2006) 11
51. Cheung F., et al. Sequencing Medicago truncatula expressed sequenced tags using 454 Life Sciences technology. BMC Genomics 7 (2006) 272
52. Chetverina H.V., and Chetverin A.B. Cloning of RNA molecules in vitro. Nucleic Acids Res. 21 (1993) 2348-2353
53. Mikkelsen T.S., et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448 (2007) 553-560
54. Barski A., et al. High-resolution profiling of histone methylations in the human genome. Cell 129 (2007) 823-837
55. Wakaguri H., et al. DBTSS: database of transcription start sites, progress report 2008. Nucleic Acids Res. 36 (2007) D97-D101
56. Robertson G., et al. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat. Methods 4 (2007) 651-657
57. Fields S. Molecular biology. Site-seeing by sequencing. Science 316 (2007) 1441-1442
58. Johnson D.S., et al. Genome-wide mapping of in vivo protein-DNA interactions. Science 316 (2007) 1497-1502
59. Warren R.L., et al. Assembling millions of short DNA sequences using SSAKE. Bioinformatics 23 (2007) 500-501
60. Jeck W.R., et al. Extending assembly of short DNA sequences to handle error. Bioinformatics 23 (2007) 2942-2944
61. Mitra R.D., et al. Fluorescent in situ sequencing on polymerase colonies. Anal. Biochem. 320 (2003) 55-65
62. Porreca G.J., et al. Multiplex amplification of large sets of human exons. Nat. Methods 4 (2007) 931-936
63. Kim J.B., et al. Polony multiplex analysis of gene expression (PMAGE) in mouse hypertrophic cardiomyopathy. Science 316 (2007) 1481-1484
64. Zhang K., et al. Long-range polony haplotyping of individual human chromosome molecules. Nat. Genet. 38 (2006) 382-387
65. Nardi V., et al. Quantitative monitoring by polymerase colony assay of known mutations resistant to ABL kinase inhibitors. Oncogene 27 (2008) 775-782
66. Levene M.J., et al. Zero-mode waveguides for single-molecule analysis at high concentrations. Science 299 (2003) 682-686
67. Rich A. The rise of single-molecule DNA biochemistry. Proc. Natl. Acad. Sci. U. S. A. 95 (1998) 13999-14000
68. Blazej R.G., et al. Microfabricated bioprocessor for integrated nanoliter-scale Sanger DNA sequencing. Proc. Natl. Acad. Sci. U. S. A. 103 (2006) 7240-7245
69. Deamer D.W., and Akeson M. Nanopores and nucleic acids: prospects for ultrarapid sequencing. Trends Biotechnol. 18 (2000) 147-151
70. Wheeler D.A., et al. The complete genome of an individual by massively parallel DNA sequencing. Nature 452 (2008) 872-876