Third-generation sequencing techniques and applications to drug discovery

Bibliography

• Hall J, Dennler P, Haller S, Genomics drugs in clinical trials. Nat Rev 2010;9(12):988
   Google Scholar
• Beckman RA, Clark J, Chen C. Integrating predictive biomarkers and classifiers into oncology clinical development programmes. Nat Rev 2011;10(10):735-48
   Google Scholar
• Paul SM, Mytelka DS, Dunwiddie CT, How to improve R&D productivity: the pharmaceutical industry's grand challenge. Nat Rev 2010;9(3):203-14
   Google Scholar
• Booth B, Zemmel R. Prospects for productivity. Nat Rev 2004;3(5):451-6
   Google Scholar
• Debouck C, Goodfellow PN. DNA microarrays in drug discovery and development. Nat Genet 1999;21(1 Suppl):48-50
   PubMed Web of Science ®Google Scholar
• Iskar M, Zeller G, Zhao XM, Drug discovery in the age of systems biology: the rise of computational approaches for data integration. Curr Opin biotechnol 2011 [Epub ahead of print]
   PubMed Web of Science ®Google Scholar
• Margulies M, Egholm M, Altman WE, Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005;437(7057):376-80
   PubMed Web of Science ®Google Scholar
• Sanger F, Coulson AR. A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. J Mol Biol 1975;94(3):441-8
   PubMed Web of Science ®Google Scholar
• Bentley DR, Balasubramanian S, Swerdlow HP, Accurate whole human genome sequencing using reversible terminator chemistry. Nature 2008;456(7218):53-9
   PubMed Web of Science ®Google Scholar
• Valouev A, Ichikawa J, Tonthat T, A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. Genome Res 2008;18(7):1051-63
   PubMed Web of Science ®Google Scholar
• Drmanac R, Sparks AB, Callow MJ, Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays. Science (New York, NY) 2010;327(5961):78-81
   Google Scholar
• Rothberg JM, Hinz W, Rearick TM, An integrated semiconductor device enabling non-optical genome sequencing. Nature 2011;475(7356):348-52
   PubMed Web of Science ®Google Scholar
• Metzker ML. Sequencing technologies - the next generation. Nat Rev 2010;11(1):31-46
   Google Scholar
• Ozsolak F, Milos PM. RNA sequencing: advances, challenges and opportunities. Nat Rev 2011;12(2):87-98
   Google Scholar
• Nutiu R, Friedman RC, Luo S, Direct measurement of DNA affinity landscapes on a high-throughput sequencing instrument. Nat Biotechnol 2011;29(7):659-64
   PubMed Web of Science ®Google Scholar
• Mardis ER. The impact of next-generation sequencing technology on genetics. Trends Genet 2008;24(3):133-41
   PubMed Web of Science ®Google Scholar
• Morozova O, Marra MA. Applications of next-generation sequencing technologies in functional genomics. Genomics 2008;92(5):255-64
   PubMed Web of Science ®Google Scholar
• Linsen SE, de Wit E, Janssens G, Limitations and possibilities of small RNA digital gene expression profiling. Nat Methods 2009;6(7):474-6
   PubMed Web of Science ®Google Scholar
• Mamanova L, Andrews RM, James KD, FRT-seq: amplification-free, strand-specific transcriptome sequencing. Nat Methods 2010;7(2):130-2
   PubMed Web of Science ®Google Scholar
• McManus CJ, Duff MO, Eipper-Mains J, Graveley BR. Global analysis of trans-splicing in Drosophila. Proc Natl Acad Sci USA 2010;107(29):12975-9
   PubMed Web of Science ®Google Scholar
• Flaherty P, Natsoulis G, Muralidharan O, Ultrasensitive detection of rare mutations using next-generation targeted resequencing. Nucleic Acids Res 2011;40(1) [Epub ahead of print]
   PubMed Web of Science ®Google Scholar
• Lin MT, Tseng LH, Kamiyama H, Quantifying the relative amount of mouse and human DNA in cancer xenografts using species-specific variation in gene length. Biotechniques 2010;48(3):211-18
   PubMed Web of Science ®Google Scholar
• Donis-Keller H, Maxam AM, Gilbert W. Mapping adenines, guanines, and pyrimidines in RNA. Nucleic Acids Res 1977;4(8):2527-38
   PubMed Web of Science ®Google Scholar
• Harris TD, Buzby PR, Babcock H, Single-molecule DNA sequencing of a viral genome. Science (New York, NY) 2008;320(5872):106-9
   Google Scholar
• Ozsolak F, Kapranov P, Foissac S, Comprehensive polyadenylation site maps in yeast and human reveal pervasive alternative polyadenylation. Cell 2010;143(6):1018-29
   PubMed Web of Science ®Google Scholar
• Ozsolak F, Platt AR, Jones DR, Direct RNA sequencing. Nature 2009;461(7265):814-18
   PubMed Web of Science ®Google Scholar
• Braslavsky I, Hebert B, Kartalov E, Quake SR. Sequence information can be obtained from single DNA molecules. Proc Natl Acad Sci USA 2003;100(7):3960-4
   PubMed Web of Science ®Google Scholar
• Bowers J, Mitchell J, Beer E, Virtual terminator nucleotides for next-generation DNA sequencing. Nat Methods 2009;6(8):593-5
   PubMed Web of Science ®Google Scholar
• Goren A, Ozsolak F, Shoresh N, Chromatin profiling by directly sequencing small quantities of immunoprecipitated DNA. Nat Methods 2010;7(1):47-9
   PubMed Web of Science ®Google Scholar
• Ozsolak F, Ting DT, Wittner BS, Amplification-free digital gene expression profiling from minute cell quantities. Nat Methods 2010;7(8):619-21
   PubMed Web of Science ®Google Scholar
• Orlando L, Ginolhac A, Raghavan M, True single-molecule DNA sequencing of a pleistocene horse bone. Genome Res 2011;21(10):1705-19
   PubMed Web of Science ®Google Scholar
• Thompson JF, Reifenberger JG, Giladi E, Single-step capture and sequencing of natural DNA for detection of BRCA1 mutations. Genome Res 2011 [Epub ahead of print]
   Web of Science ®Google Scholar
• Tessler LA, Reifenberger JG, Mitra RD. Protein quantification in complex mixtures by solid phase single-molecule counting. Anal Chem 2009;81(17):7141-8
   PubMed Web of Science ®Google Scholar
• Levene MJ, Korlach J, Turner SW, Zero-mode waveguides for single-molecule analysis at high concentrations. Science (New York, NY) 2003;299(5607):682-6
   Google Scholar
• Eid J, Fehr A, Gray J, Real-time DNA sequencing from single polymerase molecules. Science (New York, NY) 2009;323(5910):133-8
   Google Scholar
• Chin CS, Sorenson J, Harris JB, The origin of the Haitian cholera outbreak strain. N Engl J Med 2011;364(1):33-42
   PubMed Web of Science ®Google Scholar
• Rasko DA, Webster DR, Sahl JW, Origins of the E. coli strain causing an outbreak of hemolytic-uremic syndrome in Germany. N Engl J Med 2011;365(8):709-17
   PubMed Web of Science ®Google Scholar
• Flusberg BA, Webster DR, Lee JH, Direct detection of DNA methylation during single-molecule, real-time sequencing. Nat Methods 2010;7(6):461-5
   PubMed Web of Science ®Google Scholar
• Uemura S, Aitken CE, Korlach J, Real-time tRNA transit on single translating ribosomes at codon resolution. Nature 2010;464(7291):1012-17
   PubMed Web of Science ®Google Scholar
• Kasianowicz JJ, Brandin E, Branton D, Deamer DW. Characterization of individual polynucleotide molecules using a membrane channel. Proc Natl Acad Sci USA 1996;93(24):13770-3
   PubMed Web of Science ®Google Scholar
• Guan X, Gu LQ, Cheley S, Stochastic sensing of TNT with a genetically engineered pore. ChemBioChem 2005;6(10):1875-81
   PubMed Web of Science ®Google Scholar
• Wu HC, Bayley H. Single-molecule detection of nitrogen mustards by covalent reaction within a protein nanopore. J Am Chem Soc 2008;130(21):6813-19
   PubMed Web of Science ®Google Scholar
• Branton D, Deamer DW, Marziali A, The potential and challenges of nanopore sequencing. Nat Biotechnol 2008;26(10):1146-53
   PubMed Web of Science ®Google Scholar
• Hall AR, Scott A, Rotem D, Hybrid pore formation by directed insertion of alpha-haemolysin into solid-state nanopores. Nat Nanotechnol 2010;5(12):874-7
   PubMed Web of Science ®Google Scholar
• Howorka S, Cheley S, Bayley H. Sequence-specific detection of individual DNA strands using engineered nanopores. Nat Biotechnol 2001;19(7):636-9
   PubMed Web of Science ®Google Scholar
• Dekker C. Solid-state nanopores. Nat Nanotechnol 2007;2(4):209-15
   PubMed Web of Science ®Google Scholar
• Gershow M, Golovchenko JA. Recapturing and trapping single molecules with a solid-state nanopore. Nat Nanotechnol 2007;2(12):775-9
   PubMed Web of Science ®Google Scholar
• Garaj S, Hubbard W, Reina A, Graphene as a subnanometre trans-electrode membrane. Nature 2010;467(7312):190-3
   PubMed Web of Science ®Google Scholar
• Kawano R, Schibel AE, Cauley C, White HS. Controlling the translocation of single-stranded DNA through alpha-hemolysin ion channels using viscosity. Langmuir 2009;25(2):1233-7
   PubMed Web of Science ®Google Scholar
• Lieberman KR, Cherf GM, Doody MJ, Processive replication of single DNA molecules in a nanopore catalyzed by phi29 DNA polymerase. J Am Chem Soc 2010;132(50):17961-72
   PubMed Web of Science ®Google Scholar
• Clarke J, Wu HC, Jayasinghe L, Continuous base identification for single-molecule nanopore DNA sequencing. Nat Nanotechnol 2009;4(4):265-70
   PubMed Web of Science ®Google Scholar
• McNally B, Singer A, Yu Z, Optical recognition of converted DNA nucleotides for single-molecule DNA sequencing using nanopore arrays. Nano Lett 2000;10(6):2237-44
   Google Scholar
• Luan B, Martyna G, Stolovitzky G. Characterizing and controlling the motion of ssDNA in a solid-state nanopore. Biophys J 2011;101(9):2214-22
   PubMed Web of Science ®Google Scholar
• Luan B, Peng H, Polonsky S, Base-by-base ratcheting of single stranded DNA through a solid-state nanopore. Phys Rev Lett 2010;104(23):238103
   PubMedGoogle Scholar
• Greenleaf WJ, Block SM. Single-molecule, motion-based DNA sequencing using RNA polymerase. Science (New York, NY) 2006;313(5788):801
   Google Scholar
• Grutzmann R, Molnar B, Pilarsky C, Sensitive detection of colorectal cancer in peripheral blood by septin 9 DNA methylation assay. PLoS ONE 2008;3(11):e3759
   PubMed Web of Science ®Google Scholar
• Delmore JE, Issa GC, Lemieux ME, BET bromodomain inhibition as a therapeutic strategy to target c-Myc. Cell 2011;146(6):904-17
   PubMed Web of Science ®Google Scholar
• Kaiser J. Epigenetic drugs take on cancer. Science (New York, NY) 2010;330(6004):576-8
   Google Scholar
• Lieberman-Aiden E, van Berkum NL, Williams L, Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science (New York, NY) 2009;326(5950):289-93
   Google Scholar
• Flatz L, Roychoudhuri R, Honda M, Single-cell gene-expression profiling reveals qualitatively distinct CD8 T cells elicited by different gene-based vaccines. Proc Natl Acad Sci USA 2011;108(14):5724-9
   PubMed Web of Science ®Google Scholar
• Navin N, Kendall J, Troge J, Tumour evolution inferred by single-cell sequencing. Nature 2011;472(7341):90-4
   PubMed Web of Science ®Google Scholar
• Tang F, Barbacioru C, Wang Y, mRNA-Seq whole-transcriptome analysis of a single cell. Nat Methods 2009;6(5):377-82
   PubMed Web of Science ®Google Scholar
• Yu M, Stott S, Toner M, Circulating tumor cells: approaches to isolation and characterization. J Cell Biol 2011;192(3):373-82
   PubMed Web of Science ®Google Scholar
• Esteller M. Non-coding RNAs in human disease. Nat Rev 2011;12(12):861-74
   Google Scholar
• Wahlestedt C. Natural antisense and noncoding RNA transcripts as potential drug targets. Drug Discov Today 2006;11(11-12):503-8
   PubMed Web of Science ®Google Scholar
• Zimmermann B, Gesell T, Chen D, Monitoring genomic sequences during SELEX using high-throughput sequencing: neutral SELEX. PLoS One 2010;5(2):e9169
   PubMedGoogle Scholar
• Treangen TJ, Salzberg SL. Repetitive DNA and next-generation sequencing: computational challenges and solutions. Nat Rev 2011;13(1):36-46
   Google Scholar
• Ting DT, Lipson D, Paul S, Aberrant overexpression of satellite repeats in pancreatic and other epithelial cancers. Science (New York, NY) 2011;331(6017):593-6
   Google Scholar
• Li M, Wang B, Zhang M, Symbiotic gut microbes modulate human metabolic phenotypes. Proc Natl Acad Sci USA 2008;105(6):2117-22
   PubMed Web of Science ®Google Scholar
• Backhed F, Ding H, Wang T, The gut microbiota as an environmental factor that regulates fat storage. Proc Natl Acad Sci USA 2004;101(44):15718-23
   PubMed Web of Science ®Google Scholar
• Vijay-Kumar M, Aitken JD, Carvalho FA, Metabolic syndrome and altered gut microbiota in mice lacking Toll-like receptor 5. Science (New York, NY) 2010;328(5975):228-31
   Google Scholar
• Kinross JM, Darzi AW, Nicholson JK. Gut microbiome-host interactions in health and disease. Genome Med 2011;3(3):14
   PubMed Web of Science ®Google Scholar
• Haas BJ, Gevers D, Earl AM, Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res 2011;21(3):494-504
   PubMed Web of Science ®Google Scholar
• Quince C, Lanzen A, Davenport RJ, Turnbaugh PJ. Removing noise from pyrosequenced amplicons. BMC Bioinformatics 2011;12:38
   PubMed Web of Science ®Google Scholar
• Zhang Q, Doak TG, Ye Y. Artificial functional difference between microbial communities caused by length difference of sequencing reads. Pacific Symposium on Biocomputing; 2012. p 259-70
   Google Scholar
• Comas I, Borrell S, Roetzer A, Whole-genome sequencing of rifampicin-resistant Mycobacterium tuberculosis strains identifies compensatory mutations in RNA polymerase genes. Nat Genet 2011
   PubMed Web of Science ®Google Scholar
• Toprak E, Veres A, Michel J, Evolutionary paths to antibiotic resistance under dynamically sustained drug selection. Nat Genet 2011;44(1):101-5
   PubMed Web of Science ®Google Scholar
• Levy S, Sutton G, Ng PC, The diploid genome sequence of an individual human. PLoS Biol 2007;5(10):e254
   PubMed Web of Science ®Google Scholar
• Wheeler DA, Srinivasan M, Egholm M, The complete genome of an individual by massively parallel DNA sequencing. Nature 2008;452(7189):872-6
   PubMed Web of Science ®Google Scholar
• Pushkarev D, Neff NF, Quake SR. Single-molecule sequencing of an individual human genome. Nat Biotechnol 2009;27(9):847-50
   PubMed Web of Science ®Google Scholar
• Kim JI, Ju YS, Park H, A highly annotated whole-genome sequence of a Korean individual. Nature 2009;460(7258):1011-15
   PubMed Web of Science ®Google Scholar
• Ley TJ, Mardis ER, Ding L, DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome. Nature 2008;456(7218):66-72
   PubMed Web of Science ®Google Scholar
• Wang J, Wang W, Li R, The diploid genome sequence of an Asian individual. Nature 2008;456(7218):60-5
   PubMed Web of Science ®Google Scholar
• Li Y, Wang J. Faster human genome sequencing. Nat Biotechnol 2009;27(9):820-1
   PubMed Web of Science ®Google Scholar