Toward a new era in sequencing

Biotechnology Annual Review

Volumn 13, Issue , 2007, Pages 1-26

  Ziebolz, Burkhard ^a   Droege, Marcus ^a  

^a ROCHE DIAGNOSTICS GMBH   (Germany)

Author keywords

affinity separation; capillary gel electrophoresis; cell lysis; chromatography; cultivation; gene therapy; genetic vaccination; manufacturing; plasmid; recombinant RNase; stability.

Indexed keywords

DNA;

BIOLOGY; DEVICE; DNA SEQUENCE; ELECTROPHORESIS; HUMAN; HUMAN GENOME; HUMAN GENOME PROJECT; MEDICINE; NONHUMAN; REVIEW; SCIENTIST;

ALGORITHMS; CHROMOSOME MAPPING; ELECTROPHORESIS, CAPILLARY; FORECASTING; GENOMICS; SEQUENCE ANALYSIS;

EID: 34548595191     PISSN: 13872656     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S1387-2656(07)13001-5     Document Type: Review

References (45)

1. Hinds D.A., et al. Whole-genome patterns of common DNA variation in three human populations. Science 307 (2005) 1072-1079
2. Hardenbol P., et al. Highly multiplexed molecular inversion probe genotyping: over 10,000 targeted SNPs genotyped in a single tube array. Genome Res. 15 (2005) 269-275
3. Gerhardt M., et al. In-depth, longitudinal analysis of viral quasispecies from an individual triply infected with late-stage human immunodeficiency virus type 1, using a multiple PCR primer approach. J Virol 79 (2005) 8249-8261
4. Kapoor A., et al. Sequencing-based detection of low-frequency human immunodeficiency virus type 1 drug-resistant mutants by an RNA/DNA heteroduplex generator-tracking assay. J Virol 78 (2004) 7112-7123
5. Kwak E.L., et al. Irreversible inhibitors of the EGF receptor may circumvent acquired resistance to gefitinib. Proc Natl Acad Sci USA 102 (2005) 7665-7670
6. Andreis K., et al. A diarylquinoline drug active on the ATP synthase of Mycobacterium tuberculosis. Science 307 (2005) 223-227
7. Emrich C.A., et al. Microfabricated 384-lane capillary array electrophoresis bioanalyzer for ultrahigh-throughput genetic analysis. Anal Chem 74 (2002) 5076-5083
8. Koutny L., et al. Eight hundred-base sequencing in a microfabricated electrophoresis device. Anal Chem 72 (2000) 3388-3391
9. Aborn J.H., et al. A 768-lane microfabricated system for highthroughput DNA sequencing. Lab Chip 5 (2005) 669-674
10. Lagally E.T., and Mathies R.A. Integrated genetic analysis microsystems. J Phys D: Appl Phys 37 (2004) R245-R261
11. Paegel B.M., et al. Microfluidic devices for DNA sequencing: sample preparation and electrophoretic analysis. Curr Opin Biotechnol 14 (2003) 42-50
12. Zwick M.E., et al. Microarray-based resequencing of multiple Bacillus anthracis isolates. Genome Biol 6 (2004) R10
13. Sougakoff W., et al. Use of a high-density DNA probe array for detection mutations involved in rifampicin resistance in Mycobacterium tuberculosis. Clin Microbiol Infect 10 (2004) 289-294
14. Miatra A., et al. The human MitoChip: a high-throughput sequencing microarray for mitochondrial mutation detection. Genome Res 14 (2004) 812-819
15. Gonzalez R., et al. Detection of human immunodeficiency virus type 1 antiretroviral resistance mutations by high-density DNA probe arrays. Clin Microbiol 42 (2004) 2907-2912
16. Read T.D., et al. Comparative genome sequencing for discovery of novel polymorphisms in Bacillus anthracis. Science 296 (2002) 2028-2033
17. Poly F., et al. Genomic diversity in Campylobacter jejuni: identification of C. jejuni 81-176-specific genes. J Clin Microbiol 43 (2005) 2330-2338
18. Deamer D.W., and Akeson M. Nanopores and nucleic acids: prospects for ultrarapid sequencing. Trends Biotechnol 18 (2000) 147-151
19. Meller A., et al. Dynamics of polynucleotide transport through nanometer pores. J Phys Condens Matter 15 (2003) R581-R607
20. Chen P., et al. Atomic layer deposition to fine-tune the surface properties and diameters of fabricated nanopores. NanoLett 4 (2004) 1333-1337
21. Karhanek M., et al. Single molecule detection using nanopipettes and nanoparticles. NanoLett 5 (2004) 403-407
22. Brenner S., et al. Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat Biotechnol 18 (2000) 630-634
23. Margulies M et al. Genome sequencing in open microfabricated high density picoliter reactors. Nature 2005;10.1038/nature03959.
24. Dressman D., et al. Transforming DNA molecules into fluorescent magnetic particles for detection and enumeration of genetic variations. Proc Natl Acad Sci USA 100 (2003) 8817-8822
25. Mitra R.D., and Church G.M. In situ localized amplification and contact replication of many individual DNA molecules. Nucleic Acids Res 27 (1999) e34
26. Mitra R.D., et al. Digital genotyping and haplotyping with polymerase colonies. Proc Natl Acad Sci 100 (2003) 5926-5931
27. Mitra R.D., et al. Fluorescent in situ sequencing on polymerase colonies. Anal Biochem 320 (2003) 55-65
28. Levene M.J., et al. Zero-mode waveguides for single-molecule analysis at high concentrations. Science 299 (2003) 682-685
29. Braslavsky I., et al. Sequence information can be obtained from single DNA molecules. Proc Natl Acad Sci 100 (2003) 3960-3964
30. Simons J et al. Ultra-deep sequencing of HIV from drug resistant patients. XIV International HIV Drug Resistance Workshop, Quebec City, Canada, June 7-11, 2005.
31. http://www.jgi.doe.gov/education/how/index.html
32. http://www.genomesonline.org/
33. Read T.D., et al. Comparative genome sequencing for discovery of novel polymorphisms in Bacillus anthracis. Science 296 (2002) 2028-2033
34. Poinar HN et al. Metagenomics to paleogenomics: large-cale sequencing of mammoth DNA. Science 2006;311:392-439.
35. Päabo S., et al. Genetic analyses from ancient DNA. Annu Rev Genet 38 (2004) 645-679
36. Poinar H.N., et al. Molecular coproscopy: Dung and diet of the extinct ground sloth nothrotheriops shastensis. Science 281 (1998) 02-06
37. Hoess et al. DNA damage and DNA sequence retrieval from ancient tissues. Nucleic Acids Res 1996;24(7):1304-1307.
38. Andries K., et al. A diarylquinoline drug active. On the ATP synthase of Mycobacterium tuberculosis. Science 307 (2005) 223-227
39. Thomas, et al. Sensitive mutation detection in heterogeneous cancer specimens by massively parallel picoliter reactor sequencing. Nat Med 12 7 (2006) 852-855
40. Ng, 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 34 12 (2006)
41. Kim, et al. Methylation and expression of p16INK4 tumor suppressor gene in primary colorectal cancer tissues. Int J Oncol 26 (2001) 1217-1226
42. Herman, et al. Methylation-specific PCR: A novel PCR assay for methylation status of CpG islands. Proc Natl Acad Sci 93 (1996) 9821-9826
43. Girard A, Ravi Sachidanandam R, Hannon GJ and Carmell MA. A germline-specific class of small RNAs binds mammalian Piwi proteins. Nature 2006;4 (June). Advance online publication.
44. Henderson I.R., Zhang X., Lu C., Johnson L., Meyers B.C., Green P.J., and Jacobsen S.E. Dissecting Arabidopsis thaliana DICER function in small RNA processing, gene silencing and DNA methylation patterning. Nat Genet 38 (2006) 721-725
45. Lau NC, Seto AG, Kim J, Kuramochi-Miyagawa S, Nakano T, Bartel DP and Kingston RE. Characterization of the piRNA complex from rat testes. Science 2006;15 (June). Advance online publication.