The application of next-generation sequencing technologies to drug discovery and development

Drug Discovery Today

Volumn 16, Issue 11-12, 2011, Pages 512-519

  Woollard, Peter M ^a   Mehta, Nalini A L ^a   Vamathevan, Jessica J ^a   Van Horn, Stephanie ^b   Bonde, Bhushan K ^a   Dow, David J ^a  

^a GLAXOSMITHKLINE   (United Kingdom)

^b GLAXOSMITHKLINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BEDAQUILINE; PHARMACOLOGICAL BIOMARKER;

DRUG DEVELOPMENT; DRUG RESISTANCE; DRUG SCREENING; DRUG TARGETING; EPIGENETICS; GENE SEQUENCE; GENETIC VARIABILITY; HIGH THROUGHPUT SCREENING; HUMAN; NEXT GENERATION SEQUENCING; NONHUMAN; PERSONALIZED MEDICINE; PHARMACOGENETICS; REVIEW; RNA SEQUENCE; SEQUENCE ANALYSIS;

ANIMALS; BIOPHARMACEUTICS; DRUG DISCOVERY; HIGH-THROUGHPUT SCREENING ASSAYS; HUMANS; INDIVIDUALIZED MEDICINE; PHARMACOGENETICS; POLYMORPHISM, GENETIC; SEQUENCE ANALYSIS, DNA; SEQUENCE ANALYSIS, RNA; SOFTWARE;

EID: 79958204656     PISSN: 13596446     EISSN: 18785832     Source Type: Journal    
DOI: 10.1016/j.drudis.2011.03.006     Document Type: Review

References (70)

1. E.S. Lander Initial sequencing and analysis of the human genome Nature 409 2001 860 921 (Pubitemid 32165345)
2. F. Sanger DNA sequencing with chain-terminating inhibitors Proc. Natl. Acad. Sci. U. S. A 74 1977 5463 5467
3. J.C. Venter The sequence of the human genome Science 291 2001 1304 1351
4. J.D. Watson, and F.H. Crick Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid Nature 171 1953 737 738
5. M.L. Metzker Sequencing technologies - the next generation Nat. Rev. Genet. 11 2010 31 46
6. E. Pettersson Generations of sequencing technologies Genomics 93 2009 105 111
7. C. Auffray Systems medicine: the future of medical genomics and healthcare Genome Med. 1 2009 2
8. E. Foot Pharmacogenetics - pivotal to the future of the biopharmaceutical industry Drug Discov. Today 15 2010 325 327
9. J. Shendure The beginning of the end for microarrays? Nat. Methods 5 2008 585 587 (Pubitemid 351911858)
10. N.R. Di Rapid interactome profiling by massive sequencing Nucleic Acids Res. 38 2010 e110
11. H. Matsumura High-throughput SuperSAGE for digital gene expression analysis of multiple samples using next generation sequencing PLoS ONE 5 2010 e12010
12. S. Hashimoto High-resolution analysis of the 5′-end transcriptome using a next generation DNA sequencer PLoS ONE 4 2009 e4108
13. K.V. Voelkerding Next-generation sequencing: from basic research to diagnostics Clin. Chem. 55 2009 641 658
14. J. Eid Real-time DNA sequencing from single polymerase molecules Science 323 2009 133 138
15. I.M. Derrington Nanopore DNA sequencing with MspA Proc. Natl. Acad. Sci. U. S. A 107 2010 16060 16065
16. S.B. Ng Exome sequencing identifies the cause of a Mendelian disorder Nat. Genet. 42 2010 30 35
17. D.W. Bowden Molecular basis of a linkage peak: exome sequencing and family-based analysis identify a rare genetic variant in the ADIPOQ gene in the IRAS Family Study Hum. Mol. Genet. 19 2010 4112 4120
18. M. D'Ascenzo Mutation discovery in the mouse using genetically guided array capture and resequencing Mamm. Genome 20 2009 424 436
19. M.A. Clark Design, synthesis and selection of DNA-encoded small-molecule libraries Nat. Chem. Biol. 5 2009 647 654
20. S.J. Coons The FDA's critical path initiative: a brief introduction Clin. Ther. 31 2009 2572 2573
21. R.J. Leary Development of personalized tumor biomarkers using massively parallel sequencing Sci. Transl. Med. 2 2010 20ra14
22. L.W. Lee Complexity of the microRNA repertoire revealed by next generation sequencing RNA 16 2010 2170 2180
23. C. Auffray Predictive, preventive, personalized and participatory medicine: back to the future Genome Med. 2 2010 57
24. S. Hetherington Genetic variations in HLA-B region and hypersensitivity reactions to abacavir Lancet 359 2002 1121 1122 (Pubitemid 34270738)
25. F. Takeuchi A genome-wide association study confirms VKORC1, CYP2C9, and CYP4F2 as principal genetic determinants of warfarin dose PLoS Genet. 5 2009 e1000433
26. B. Kim Preliminary evidence on the association between XBP1-116C/G polymorphism and response to prophylactic treatment with valproate in bipolar disorders Psychiatry Res. 168 2009 209 212
27. A.M. Leventhal Dopamine D4 receptor gene variation moderates the efficacy of bupropion for smoking cessation Pharmacogenomics J. 2010 DOI: 10.1038/tpj.2010.64.
28. G. Gervasini Pharmacogenetic testing and therapeutic drug monitoring are complementary tools for optimal individualization of drug therapy Eur. J. Clin. Pharmacol. 66 2010 755 774
29. R.M. Durbin A map of human genome variation from population-scale sequencing Nature 467 2010 1061 1073
30. E. Cuyas Errors and reproducibility of DNA array-based detection of allelic variants in ADME genes: PHARMAchip Pharmacogenomics 11 2010 257 266
31. N. Hoppman-Chaney Evaluation of oligonucleotide sequence capture arrays and comparison of next-generation sequencing platforms for use in molecular diagnostics Clin. Chem. 56 2010 1297 1306
32. A. Paruzynski Genome-wide high-throughput integrome analyses by nrLAM-PCR and next-generation sequencing Nat. Protoc. 5 2010 1379 1395
33. R. Bueno Second generation sequencing of the mesothelioma tumor genome PLoS ONE 5 2010 e10612
34. T.J. Ley DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome Nature 456 2008 66 72
35. P.M. Kim Analysis of copy number variants and segmental duplications in the human genome: evidence for a change in the process of formation in recent evolutionary history Genome Res. 18 2008 1865 1874
36. D.J. McBride Use of cancer-specific genomic rearrangements to quantify disease burden in plasma from patients with solid tumors Genes Chromosomes Cancer 49 2010 1062 1069
37. L. Cheng Analysis of chemotherapy response programs in ovarian cancers by the next-generation sequencing technologies Gynecol. Oncol. 117 2010 159 169
38. S.J. Jones Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors Genome Biol. 11 2010 R82
39. J. Beck Next generation sequencing of serum circulating nucleic acids from patients with invasive ductal breast cancer reveals differences to healthy and nonmalignant controls Mol. Cancer Res. 8 2010 335 342
40. G. Ramsingh Complete characterization of the microRNAome in a patient with acute myeloid leukemia Blood 116 2010 5316 5326
41. C.A. Maher Transcriptome sequencing to detect gene fusions in cancer Nature 458 2009 97 101
42. C. Balch Minireview: epigenetic changes in ovarian cancer Endocrinology 150 2009 4003 4011
43. T. Neff, and S.A. Armstrong Chromatin maps, histone modifications and leukemia Leukemia 23 2009 1243 1251
44. C. Popp Genome-wide erasure of DNA methylation in mouse primordial germ cells is affected by AID deficiency Nature 463 2010 1101 1105
45. J.G. Victoria Viral nucleic acids in live-attenuated vaccines: detection of minority variants and an adventitious virus J. Virol. 84 2010 6033 6040
46. D. Onions, and J. Kolman Massively parallel sequencing, a new method for detecting adventitious agents Biologicals 38 2010 377 380
47. J.R. Brown Next generation sequencing for antibacterial drug discovery Int. Drug Discov. 5 2010 18 23
48. T. Le Low-abundance HIV drug-resistant viral variants in treatment-experienced persons correlate with historical antiretroviral use PLoS ONE 4 2009 e6079
49. J. Archer Detection of low-frequency pretherapy chemokine (CXC motif) receptor 4 (CXCR4)-using HIV-1 with ultra-deep pyrosequencing AIDS 23 2009 1209 1218
50. T.A. Davies Infrequent occurrence of single mutations in topoisomerase IV and DNA gyrase genes among US levofloxacin-susceptible clinical isolates of Streptococcus pneumoniae from nine institutions (1999-2003) J. Antimicrob. Chemother. 57 2006 437 442 (Pubitemid 43240195)
51. K. Andries A diarylquinoline drug active on the ATP synthase of Mycobacterium tuberculosis Science 307 2005 223 227 (Pubitemid 40116230)
52. J.S. Towner Newly discovered Ebola virus associated with hemorrhagic fever outbreak in Uganda PLoS Pathog. 4 2008 e1000212
53. E. As-Neto Next-generation phage display: integrating and comparing available molecular tools to enable cost-effective high-throughput analysis PLoS ONE 4 2009 e8338
54. B.G. Richter, and D.P. Sexton Managing and analysing next-generation sequence data PLoS Comput. Biol. 5 2009 e1000369
55. L.D. Stein The case for cloud computing in genome informatics Genome Biol. 11 2010 207
56. N. Palmieri, and C. Schlotterer Mapping accuracy of short reads from massively parallel sequencing and the implications for quantitative expression profiling PLoS ONE 4 2009 e6323
57. B. Langmead Searching for SNPs with cloud computing Genome Biol. 10 2009 R134
58. J.T. Simpson ABySS: a parallel assembler for short read sequence data Genome Res. 19 2009 1117 1123
59. M. Baker Next-generation sequencing: adjusting to data overload Nat. Methods 7 2010 495 499
60. B. Langmead Cloud-scale RNA-sequencing differential expression analysis with Myrna Genome Biol. 11 2010 R83
61. C.W. Fuller The challenges of sequencing by synthesis Nat. Biotechnol. 27 2009 1013 1023
62. L. Shi The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models Nat. Biotechnol. 28 2010 827 838
63. J. Rozowsky PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls Nat. Biotechnol. 27 2009 66 75
64. B.M. Henn Fine-scale population structure and the era of next-generation sequencing Hum. Mol. Genet. 19 2010 R221 R226
65. D.Y. Chiang High-resolution mapping of copy-number alterations with massively parallel sequencing Nat. Methods 6 2009 99 103
66. H.M. Wood Using next-generation sequencing for high resolution multiplex analysis of copy number variation from nanogram quantities of DNA from formalin-fixed paraffin-embedded specimens Nucleic Acids Res. 38 2010 e151
67. N. Cloonan Stem cell transcriptome profiling via massive-scale mRNA sequencing Nat. Methods 5 2008 613 619 (Pubitemid 351911866)
68. S.W. Chi Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps Nature 460 2009 479 486
69. D.R. Morris Ribosomal footprints on a transcriptome landscape Genome Biol. 10 2009 215
70. O. Zagordi Error correction of next-generation sequencing data and reliable estimation of HIV quasispecies Nucleic Acids Res. 38 2010 7400 7409