Next-generation DNA sequencing methods

Annual Review of Genomics and Human Genetics

Volumn 9, Issue , 2008, Pages 387-402

  Mardis, Elaine R ^a  

^a WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Massively parallel sequencing; Resequencing; Sequencing by synthesis

Indexed keywords

COMPLEMENTARY DNA; DEOXYRIBONUCLEOPROTEIN; MICRORNA; POLYDEOXYRIBONUCLEOTIDE SYNTHASE; TRANSCRIPTOME; UNTRANSLATED RNA;

CHEMISTRY; CHROMATIN IMMUNOPRECIPITATION; COMPUTER PROGRAM; DNA LIBRARY; DNA SEQUENCE; ENZYMOLOGY; EPIGENETICS; GENE AMPLIFICATION; GENETIC SCREENING; GENETICS; GENOMICS; HUMAN; POLYMERASE CHAIN REACTION; PROTEIN INTERACTION; REVIEW; RNA SEQUENCE; SERIAL ANALYSIS OF GENE EXPRESSION;

CHROMATIN IMMUNOPRECIPITATION; FOSSILS; GENE EXPRESSION PROFILING; GENOME, HUMAN; GENOMICS; HUMANS; RNA, UNTRANSLATED; SEQUENCE ANALYSIS, DNA;

EID: 52949096084     PISSN: 15278204     EISSN: None     Source Type: Book Series    
DOI: 10.1146/annurev.genom.9.081307.164359     Document Type: Review

References (55)

1. Adcock GJ, Dennis ES, Easteal S, Huttley GA, Jermiin LS, et al. 2001. Mitochondrial DNA sequences in ancient Australians: implications for modern human origins. Proc. Natl. Acad. Sci. USA 98:537-42
2. Angly FE, Felts B, Breitbart M, Salamon P, Edwards RA, et al. 2006. The marine viromes of four oceanic regions. PLoS Biol. 4:e368
3. Axtell MJ, Snyder JA, Bartel DP. 2007. Common functions for diverse small RNAs of land plants. Plant Cell 19:1750-69
4. Bäckhed F, Ding H, Wang T, Hooper LV, Koh GY, et al. 2004. The gut microbiota as an environmental factor that regulates fat storage. Proc. Natl. Acad. Sci. USA 101:15718-23
5. Bäckhed F, Ley RE, Sonnenburg JL, Peterson DA, Gordon JI. 2005. Host-bacterial mutualism in the human intestine. Science 307:1915-20
6. Bainbridge MN, Warren RL, Hirst M, Romanuik T, Zeng T, et al. 2006. Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach. BMC Genomics 7:246
7. Bentley DR. 2006. Whole-genome resequencing. Curr. Opin. Genet. Dev. 16:545-52
8. Berezikov E, Thuemmler F, van Laake LW, Kondova I, Bontrop R, et al. 2006. Diversity of microRNAs in human and chimpanzee brain. Nat. Genet. 38:1375-77
9. Brennecke J, Aravin AA, Stark A, Dus M, Kellis M, et al. 2007. Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila. Cell 128:1089-103
10. Calin GA, Liu CG, Ferracin M, Hyslop T, Spizzo R, et al. 2007. Ultraconserved regions encoding ncRNAs are altered in human leukemias and carcinomas. Cancer Cell 12:215-29
11. Cheung F, Haas BJ, Goldberg SM, May GD, Xiao Y, Town CD. 2006. Sequencing Medicago truncatula expressed sequenced tags using 454 Life Sciences technology. BMC Genomics 7:272
12. Edwards KJ, Bond PL, Gihring TM, Banfield JF. 2000. An archaeal iron-oxidizing extreme acidophile important in acid mine drainage. Science 287:1796-99
13. Edwards RA, Rodriguez-Brito B, Wegley L, Haynes M, Breitbart M, et al. 2006. Using pyrosequencing to shed light on deep mine microbial ecology. BMC Genomics 7:57
14. Fierer N, Breitbart M, Nulton J, Salamon P, Lozupone C, et al. 2007. Metagenomic and small-subunit rRNA analyses of the genetic diversity of bacteria, archaea, fungi, and viruses in soil. Appl. Environ. Microbiol. 73:7059-66
15. Gilbert MT, Tomsho LP, Rendulic S, Packard M, Drautz DI, et al. 2007. Whole-genome shotgun sequencing of mitochondria from ancient hair shafts. Science 317:1927-30
16. Gill SR, Pop M, Deboy RT, Eckburg PB, Turnbaugh PJ, et al. 2006. Metagenomic analysis of the human distal gut microbiome. Science 312:1355-59
17. Green RE, Krause J, Ptak SF,, Briggs AW, Ronan MT, et al. 2006. Analysis of one million base pairs of Neanderthal DNA. Nature 444:330-36
18. Houwing S, Kamminga LM, Berezikov E, Cronembold D, Girard A, et al. 2007. A role for Piwi and piRNAs in germ cell maintenance and transposon silencing in zebrafish. Cell 129:69-82
19. Huber JA, Mark Welch DB, Morrison HG, Huse SM, Neal PR, et al. 2007. Microbial population structures in the deep marine biosphere. Science 318:97-100
20. Johnson DS, Mortazavi A, Myers RM, Wold B. 2007. Genome-wide mapping of in vivo protein-DNA interactions. Science 316:1497-502
21. Johnson SM, Tan FJ, McCullough HL, Riordan DP, Fire AZ. 2006. Flexibility and constraint in the nucleosome core landscape of Caenorhabditis elegans chromatin. Genome Res. 16:1505-16
22. Kasschau KD, Fahlgren N, Chapman EJ, Sullivan CM, Cumbie JS, et al. 2007. Genome-wide profiling and analysis of Arabidopsis siRNAs. PLoS Biol. 5:e57
23. Krause J, Dear PH, Pollack JL, Slatkin M, Spriggs H, et al. 2006. Multiplex amplification of the mammoth mitochondrial genome and the evolution of Elephantidae. Nature 439:724-27
24. Krings M, Geisert H, Schmitz RW, Krainitzki H, Paabo S. 1999. DNA sequence of the mitochondrial hypervariable region II from the Neandertal type specimen. Proc. Natl. Acad. Sci. USA 96:5581-85
25. Kurokawa K, Itoh T, Kuwahara T, Oshima K, Toh H, et al. 2007. Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. DNA Res. 14:169-81
26. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, et al. 2001. Initial sequencing and analysis of the human genome. Nature 409:860-921
27. Leininger S, Urich T, Schloter M, Schwark L, Qi J, et al. 2006. Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature 442:806-9
28. Ley RE, Bäckhed F, Turnbaugh P, Lozupone CA, Knight RD, Gordon JI. 2005. Obesity alters gut microbial ecology. Proc. Natl. Acad. Sci. USA 102:11070-75
29. Lu C, Meyers BC, Green PJ. 2007. Construction of small RNA cDNA libraries for deep sequencing. Methods 43:110-17
30. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, et al. 2005. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376-80
31. McPherson JD, Marra M, Hillier L, Waterston RH, Chinwalla A, et al. 2001. A physical map of the human genome. Nature 409:934-41
32. Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, et al. 2007. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448:553-60
33. Noonan JP, Coop G, Kudaravalli S, Smith D, Krause J, et al. 2006. Sequencing and analysis of Neanderthal genomic DNA. Science 314:1113-18
34. Noonan JP, Hofreiter M, Smith D, Priest JR, Rohland N, et al. 2005. Genomic sequencing of Pleistocene cave bears. Science 309:597-99
35. Ovchinnikov IV, Gotherstrom A, Romanova GP, Kharitonov VM, Liden K, Goodwin W. 2000. Molecular analysis of Neanderthal DNA from the northern Caucasus. Nature 404:490-93
36. Palmer C, Bik EM, Digiulio DB, Relman DA, Brown PO. 2007. Development of the human infant intestinal microbiota. PLoS Biol. 5:e177
37. Poinar HN, Schwarz C, Qi J, Shapiro B, Macphee RD, et al. 2006. Metagenomics to paleogenomics: large-scale sequencing of mammoth DNA. Science 311:392-94
38. Ren B, Robert F, Wyrick JJ, Aparicio O, Jennings EG, et al. 2000. Genome-wide location and function of DNA binding proteins. Science 290:2306-9
39. Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, et al. 2007. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat. Methods 4:651-57
40. Rogaev EI, Moliaka YK, Malyarchuk BA, Kondrashov FA, Derenko MV, et al. 2006. Complete mitochondrial genome and phylogeny of Pleistocene mammoth Mammuthus primigenius. PLoS Biol. 4:e73
41. Ruby JG, Jan C, Player C, Axtell MJ, Lee W, et al. 2006. Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans. Cell 127:1193-207
42. Sogin ML, Morrison HG, Huber JA, Welch DM, Huse SM, et al. 2006. Microbial diversity in the deep sea and the underexplored "rare biosphere". Proc. Natl. Acad. Sci. USA 103:12115-20
43. Solomon MJ, Larsen PL, Varshavsky A. 1988. Mapping protein-DNA interactions in vivo with formaldehyde: evidence that histone H4 is retained on a highly transcribed gene. Cell 53:937-47
44. Stahlhut Espinosa CE, Slack FJ. 2006. The role of microRNAs in cancer. Yale J. Biol. Med. 79:131-40
45. Strous M, Pelletier E, Mangenot S, Rattei T, Lehner A, et al. 2006. Deciphering the evolution and metabolism of an anammox bacterium from a community genome. Nature 440:790-94
46. Torres TT, Metta M, Ottenwälder B, Schlötterer C. 2007. Gene expression profiling by massively parallel sequencing. Genome Res. 18:172-77
47. Tringe SG, von Mering C, Kobayashi A, Salamov AA, Chen K, et al. 2005. Comparative metagenomics of microbial communities. Science 308:554-57
48. Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, Gordon JI. 2006. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444:1027-31
49. Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, et al. 2004. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428:37-43
50. Velculescu VE, Zhang L, Vogelstein B, Kinzler KW. 1995. Serial analysis of gene expression. Science 270:484-87
51. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, et al. 2001. The sequence of the human genome. Science 291:1304-51
52. Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, et al. 2004. Environmental genome shotgun sequencing of the Sargasso Sea. Science 304:66-74
53. Weber AP, Weber KL, Carr K, Wilkerson C, Ohlrogge JB. 2007. Sampling the Arabidopsis transcriptome with massively parallel pyrosequencing. Plant Physiol. 144:32-42
54. Wegley L, Edwards R, Rodriguez-Brito B, Liu H, Rohwer F. 2007. Metagenomic analysis of the microbial community associated with the coral Porites astreoides. Environ. Microbiol. 9:2707-19
55. Zhao T, Li G, Mi S, Li S, Hannon GJ, et al. 2007. A complex system of small RNAs in the unicellular green alga Chlamydomonas reinhardtii. Genes Dev. 21:1190-203