What would you do if you could sequence everything? (original) (raw)

• Bentley, D.R. Whole-genome re-sequencing. Curr. Opin. Genet. Dev. 16, 545–552 (2006).
  Article CAS PubMed Google Scholar
• Church, G.M. Genomes for all. Sci. Am. 294, 46–54 (2006).
  Article CAS PubMed Google Scholar
• Zwolak, M. & DiVentra, M. Physical approaches to DNA sequencing and detection. Rev. Mod. Phys. 80, 141–165 (2008).
  Article Google Scholar
• Mardis, E.R. The impact of next-generation sequencing technology on genetics. Trends Genet. 24, 133–141 (2008).
  Article CAS PubMed Google Scholar
• Harris, T.D. et al. Single-Molecule DNA Sequencing of a Viral Genome. Science 320, 106–109 (2008).
  Article CAS PubMed Google Scholar
• International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature 409, 860–921 (2001).
• Drosophila 12 Genomes Consortium. Evolution of genes and genomes on the Drosophila phylogeny. Nature 450, 203–218 (2007).
• Hillier, L.W. et al. Whole-genome sequencing and variant discovery in C. elegans . Nat. Methods 5, 183–188 (2008).
  Article CAS PubMed Google Scholar
• Wheeler, D.A. et al. The complete genome of an individual by massively parallel DNA sequencing. Nature 452, 872–876 (2008).
  Article CAS PubMed Google Scholar
• Millar, C.D., Huynen, L., Subramanian, S., Mohandesan, E. & Lamber, D.M. New developments in ancient genomics. Trends Ecol. Evol. 23, 386–393 (2008).
  Article PubMed Google Scholar
• Ellegren, H. & Sheldon, B.C. Genetic basis of fitness differences in natural populations. Nature 452, 169–175 (2008).
  Article CAS PubMed Google Scholar
• Kruglyak, L. The road to genome-wide association studies. Nat. Rev. Genet. 9, 314–318 (2008).
  Article CAS PubMed Google Scholar
• Sachidanandam, R. et al. A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 409, 928–933 (2001).
  Article CAS PubMed Google Scholar
• International HapMap Consortium. A haplotype map of the human genome. Nature 437, 1299–1320 (2005).
• International HapMap Consortium. A second generation human haplotype map of over 3.1 million SNPs. Nature 449, 851–861 (2007).
• Wellcome Trust Case Control Consortium. Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 447, 661–678 (2007).
• Broadbent, H.M. et al. Susceptibility to coronary artery disease and diabetes is encoded by distinct, tightly linked SNPs in the ANRIL locus on chromosome 9p. Hum. Mol. Genet. 17, 806–814 (2008).
  Article CAS PubMed Google Scholar
• Ke, X., Taylor, M.S. & Cardon, L.R. Singleton SNPs in the human genome and implications for genome-wide association studies. Eur. J. Hum. Genet. 16, 506–515 (2008).
  Article CAS PubMed Google Scholar
• Cohen, J.C. et al. Multiple rare alleles contribute to low plasma levels of HDL cholesterol. Science 305, 869–872 (2004).
  Article CAS PubMed Google Scholar
• McClellan, J.M., Susser, E. & King, M.-C. Schizophrenia: a common disease caused by multiple rare alleles. Br. J. Psychol. 190, 194–199 (2007).
  Article Google Scholar
• Speicher, M.R. & Carter, N.P. The new cytogenetics: blurring the boundaries with molecular biology. Nat. Rev. Genet. 6, 782–792 (2005).
  Article CAS PubMed Google Scholar
• Iafrate, A.J. et al. Detection of large-scale variation in the human genome. Nat. Genet. 36, 949–951 (2004).
  Article CAS PubMed Google Scholar
• Freeman, J.L. et al. Copy number variation: new insights in genome diversity. Genome Res. 16, 949–961 (2006).
  Article CAS PubMed Google Scholar
• Komura, D. et al. Genome-wide detection of human copy number variations using high-density DNA oligonucleotide arrays. Genome Res. 16, 1575–1584 (2006).
  Article CAS PubMed PubMed Central Google Scholar
• Redon, R. et al. Global variation in copy number in the human genome. Nature 444, 444–454 (2006).
  Article CAS PubMed PubMed Central Google Scholar
• Levy, S. et al. The diploid genome sequence of an individual human. PLoS Biol. 5, e254 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• Feuk, L., Marshall, C.R., Wintle, R.F., & Scherer, S.W. Structural variants: changing the landscape of chromosomes and design of disease studies. Hum. Mol. Genet. 15 Spec No 1, R57–R66 (2006).
  Article CAS PubMed Google Scholar
• McCarroll, S.A. & Althshuler, D.M. Copy-number variation and association studies of human disease. Nat. Genet. 39, S37–S42 (2008).
  Article CAS Google Scholar
• Sjoblom, T. et al. The consensus coding sequences of human breast and colorectal cancers. Science 314, 268–274 (2006).
  Article CAS PubMed Google Scholar
• Wood, L.D. et al. The genomic landscapes of human breast and colorectal cancers. Science 318, 1108–1113 (2007).
  Article CAS PubMed Google Scholar
• Chittenden, T. et al. Functional Classification Analysis of Somatically Mutated Genes in Human Breast and Colorectal Cancers. Genomics 91, 508–511 (2008).
  Article CAS PubMed Google Scholar
• Tomlins, S.A. et al. Distinct classes of chromosomal rearrangements create oncogenic ETS gene fusions in prostate cancer. Nature 448, 595–599 (2007).
  Article CAS PubMed Google Scholar
• Nardi, V. et al. Quantitative monitoring by polymerase colony assay of known mutations resistant to ABL kinase inhibitors. Oncogene 27, 775–782 (2008).
  Article CAS PubMed Google Scholar
• Hoffmann, C. et al. DNA bar coding and pyrosequencing to identify rare HIV drug resistance mutations. Nucleic Acids Res. 35, e91 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• Wang, C., Mitsuya, Y., Gharizadeh, B., Ronaghi, M. & Shafer, R.W. Characterization of mutation spectra with ultra-deep pyrosequencing: application to HIV-1 drug resistance. Genome Res. 17, 1195–1201 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• Loman, N.J. & Pallen, M.J. XDR-TB genome sequencing: a glimpse of the microbiology of the future. Future Microbiol. 3, 111–113 (2008).
  Article CAS PubMed Google Scholar
• Holt, K.E. et al. High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi. Nat. Genet. 40, 987–993 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Feng, H., Shuda, M., Chang, Y. & Moore, P.S. Clonal integration of a polyomavirus in human Merkel cell carcinoma. Science 319, 1096–1100 (2007).
  Article CAS Google Scholar
• Palacios, G. et al. A new arenavirus in a cluster of fatal transplant-associated diseases. N. Engl. J. Med. 358, 991–998 (2008).
  Article CAS PubMed Google Scholar
• Cox-Foster, D.L. et al. A metagenomic survey of microbes in honey bee colony collapse disorder. Science 318, 283–287 (2007).
  Article CAS PubMed Google Scholar
• Woyke, T. et al. Symbiosis insights through metagenomic analysis of a microbial consortium. Nature 443, 950–955 (2006).
  Article CAS PubMed Google Scholar
• Marcy, Y. et al. Dissecting biological “dark matter” with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth. Proc. Natl. Acad. Sci. USA 104, 11889–11894 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• Pernthaler, A. et al. Diverse syntrophic partnerships from deep-sea methane vents revealed by direct cell capture and metagenomics. Proc. Natl. Acad. Sci. USA 105, 7052–7057 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Dinsdale, E.A. et al. Functional metagenomic profiling of nine biomes. Nature 452, 629–632 (2008).
  Article CAS PubMed Google Scholar
• Bundy, J.G. et al. 'Systems toxicology' approach identifies coordinated metabolic responses to copper in a terrestrial non-model invertebrate, the earthworm Lumbricus rubellus . BMC Biol. 6, 25 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• van Straalen, N.M. & Roelofs, D. Genomics technology for assessing soil pollution. J. Biol. 7, 19 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Turnbaugh, P.J. et al. The human microbiome project. Nature 449, 804–810 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• Rauch, T.A. et al. High-resolution mapping of DNA hypermethylation and hypomethylation in lung cancer. Proc. Natl. Acad. Sci. USA 105, 252–257 (2007).
  Article PubMed PubMed Central Google Scholar
• Yasui, D.H. et al. Integrated epigenomic analyses of neuronal MeCP2 reveal a role for long-range interaction with active genes. Proc. Natl. Acad. Sci. USA 104, 19416–19421 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• Beck, S. & Rakyan, V.K. The methylome: approaches for global DNA methylation profiling. Trends Genet. 24, 231–237 (2008).
  Article CAS PubMed Google Scholar
• Gitan, R.S., Shi, H., Chen, C.M., Yan, P.S. & Huang, T.H. Methylation-specific oligonucleotide microarray: a new potential for high-throughput methylation analysis. Genome Res. 12, 158–164 (2002).
  Article CAS PubMed PubMed Central Google Scholar
• Hu, M. et al. Distinct epigenetic changes in the stromal cells of breast cancers. Nat. Genet. 37, 899–905 (2005).
  Article CAS PubMed Google Scholar
• Agrelo, R. et al. Epigenetic inactivation of the premature aging Werner syndrome gene in human cancer. Proc. Natl. Acad. Sci. USA 103, 8822–8827 (2006).
  Article CAS PubMed PubMed Central Google Scholar
• Brena, R.M., Huang, T.H. & Plass, C. Quantitative assessment of DNA methylation: potential applications for disease diagnosis, classification, and prognosis in clinical settings. J. Mol. Med. 84, 365–377 (2006).
  Article CAS PubMed Google Scholar
• Fraga, M.F. et al. Epigenetic differences arise during the lifetime of monozygotic twins. Proc. Natl. Acad. Sci. USA 102, 10604–10609 (2005).
  Article CAS PubMed PubMed Central Google Scholar
• Jones, P.A. & Martienssen, R. A blueprint for a Human Epigenome Project: the AACR Human Epigenome Workshop. Cancer Res. 65, 11241–11246 (2005).
  Article CAS PubMed Google Scholar
• Garber, K. Momentum building for human epigenome project. J. Natl. Cancer Inst. 98, 84–86 (2006).
  Article PubMed Google Scholar
• Esteller, M. The necessity of a human epigenome project. Carcinogenesis 27, 1121–1125 (2006).
  Article CAS PubMed Google Scholar
• Eckhardt, F. et al. DNA methylation profiling of human chromosomes 6, 20 and 22. Nat. Genet. 38, 1378–1385 (2006).
  Article CAS PubMed PubMed Central Google Scholar
• Zhang, X. et al. Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis . Cell 126, 1189–1201 (2006).
  Article CAS PubMed Google Scholar
• Mavrich, T.N. et al. Nucleosome organization in the Drosophila genome. Nature 453, 358–362 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Valouev, A. et al. A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. Genome Res. 18, 1051–1063 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Kim, T.H. & Ren, B. Genome-wide analysis of protein-DNA interactions. Annu. Rev. Genomics Hum. Genet. 7, 81–102 (2006).
  Article CAS PubMed Google Scholar
• Massie, C.E. & Mills, I.G. ChIPping away at gene regulation. EMBO Rep. 9, 337–343 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Mendenhall, E.M. & Bernstein, B.E. Chromatin state maps: new technologies, new insights. Curr. Opin. Genet. Dev. 18, 109–115 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Robertson, G. et al. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat. Methods 4, 651–657 (2007).
  Article CAS PubMed Google Scholar
• Euskirchen, G.M. et al. Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologies. Genome Res. 17, 898–909 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• Johnson, D.S., Mortazavi, A., Myers, R.M. & Wold, B. Genome-wide mapping of in vivo protein-DNA interactions. Science 316, 1497–1502 (2007).
  Article CAS PubMed Google Scholar
• Barski, A. et al. High-resolution profiling of histone methylations in the human genome. Cell 129, 823–837 (2007).
  Article CAS PubMed Google Scholar
• Roh, T.Y., Wei, G., Farrell, C.M. & Zhao, K. Genome-wide prediction of conserved and nonconserved enhancers by histone acetylation patterns. Genome Res. 17, 74–81 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• Minsky, N. et al. Monoubiquitinated H2B is associated with the transcribed region of highly expressed genes in human cells. Nat. Cell Biol. 10, 483–488 (2008).
  Article CAS PubMed Google Scholar
• Mikkelsen, T.S. et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448, 553–560 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• Meissner, A. et al. Genome-scale DNA methylation maps of pluirpotent and differentiated cells. Nature 454, 766–770 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Boyer, L.A. et al. Core transcriptional regulatory circuitry in human embryonic stem cells. Cell 122, 947–956 (2005).
  Article CAS PubMed PubMed Central Google Scholar
• Lee, T.I. et al. Control of developmental regulators by Polycomb in human embryonic stem cells. Cell 125, 301–313 (2006).
  Article CAS PubMed PubMed Central Google Scholar
• Gilchrist, M. et al. Systems biology approaches identify ATF3 as a negative regulator of Toll-like receptor 4. Nature 441, 173–178 (2006).
  Article CAS PubMed Google Scholar
• Petersen, D. et al. Three microarray platforms: an analysis of their concordance in profiling gene expression. BMC Genomics 6, 63 (2005).
  Article CAS PubMed PubMed Central Google Scholar
• Encode Project Consortium. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447, 799–816 (2007).
• Kapranov, P. et al. Large-scale transcriptional activity in chromosomes 21 and 22. Science 296, 916–919 (2002).
  Article CAS PubMed Google Scholar
• Cheng, J. et al. Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science 308, 1149–1154 (2005).
  Article CAS PubMed Google Scholar
• Kapranov, P. et al. Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays. Genome Res. 15, 987–997 (2005).
  Article CAS PubMed PubMed Central Google Scholar
• Palatnik, J.F. et al. Control of leaf morphogenesis by microRNAs. Nature 425, 257–263 (2003).
  Article CAS PubMed Google Scholar
• Lu, J. et al. MicroRNA expression profiles classify human cancers. Nature 435, 834–838 (2005).
  Article CAS PubMed Google Scholar
• Abbott, A.L. et al. The let-7 MicroRNA family members mir-48, mir-84, and mir-241 function together to regulate developmental timing in Caenorhabditis elegans . Dev. Cell 9, 403–414 (2005).
  Article CAS PubMed PubMed Central Google Scholar
• Calin, G.A. & Croce, C.M. MicroRNA signatures in human cancers. Nat. Rev. Cancer 6, 857–866 (2006).
  Article CAS PubMed Google Scholar
• Calin, G.A. & Croce, C.M. MicroRNA-cancer connection: the beginning of a new tale. Cancer Res. 66, 7390–7394 (2006).
  Article CAS PubMed Google Scholar
• Huang, Q. et al. The microRNAs miR-373 and miR-520c promote tumour invasion and metastasis. Nat. Cell Biol. 10, 202–210 (2008).
  Article CAS PubMed Google Scholar
• Morin, R.D. et al. Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells. Genome Res. 18, 610–621 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Yu, W. et al. Epigenetic silencing of tumour suppressor gene p15 by its antisense RNA. Nature 451, 202–206 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Lein, E.S. et al. Genome-wide atlas of gene expression in the adult mouse brain. Nature 445, 168–176 (2007).
  Article CAS PubMed Google Scholar
• Liang, W.S. et al. Gene expression profiles in anatomically and functionally distinct regions of the normal aged human brain. Physiol. Genomics 28, 311–322 (2006).
  Article CAS PubMed Google Scholar
• Myers, A.J. et al. A survey of genetic human cortical gene expression. Nat. Genet. 39, 1494–1499 (2007).
  Article CAS PubMed Google Scholar
• Fehlbaum, P., Guihal, C., Bracco, L. & Cochet, O. A microarray configuration to quantify expression levels and relative abundance of splice variants. Nucleic Acids Res. 33, e47 (2005).
  Article PubMed PubMed Central Google Scholar
• Kwan, T. et al. Genome-wide analysis of transcript isoform variation in humans. Nat. Genet. 40, 225–231 (2008).
  Article CAS PubMed Google Scholar
• Blencowe, B.J. Alternative splicing: new insights from global analyses. Cell 126, 37–47 (2006).
  Article CAS PubMed Google Scholar
• Velculescu, V.E., Zhang, L., Vogelstein, B. & Kinzler, K.W. Serial analysis of gene expression. Science 270, 484–487 (1995).
  Article CAS PubMed Google Scholar
• Sun, M. et al. SAGE is far more sensitive than EST for detecting low-abundance transcripts. BMC Genomics 5, 1–4 (2004).
  Article PubMed PubMed Central Google Scholar
• Hirst, M. et al. LongSAGE profiling of nine human embryonic stem cell lines. Genome Biol. 8, R113 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• Mortazavi, A., Williams, B.A., McCue, K., Schaeffer, L. & Wold, B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods 5, 621–628 (2008).
  Article CAS PubMed Google Scholar
• Cloonan, N. et al. Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nat. Methods 5, 613–619 (2008).
  Article CAS PubMed Google Scholar
• Shin, H. et al. Transcriptome analysis for Caenorhabditis elegans based on novel expressed sequence tags. BMC Biol. 6, 30 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Morin, R. et al. Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing. Biotechniques 45, 81–94 (2008).
  Article CAS PubMed Google Scholar
• Nagalakshmi, U. et al. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320, 1344–1349 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Wilhelm, B.T. et al. Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. Nature 453, 1239–1243 (2008).
  Article CAS PubMed Google Scholar
• Rockman, M.V. & Kruglyak, L. Genetics of global gene expression. Nat. Rev. Genet. 7, 862–872 (2006).
  Article CAS PubMed Google Scholar
• Schadt, E.E. et al. Genetics of gene expression surveyed in maize, mouse and man. Nature 422, 297–302 (2003).
  Article CAS PubMed Google Scholar
• Chen, Y. et al. Variations in DNA elucidate molecular networks that cause disease. Nature 452, 429–435 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• De Gobbi, M. et al. A regulatory SNP causes a human genetic disease by creating a new transcriptional promoter. Science 312, 1215–1217 (2006).
  Article CAS PubMed Google Scholar
• Lister, R. et al. Highly integrated single-base resolution maps of the epigenome in Arabidopsis . Cell 133, 523–536 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Chou, C.C., Chen, C.H., Lee, T.T. & Peck, K. Optimization of probe length and the number of probes per gene for optimal microarray analysis of gene expression. Nucleic Acids Res. 32, e99 (2004).
  Article CAS PubMed PubMed Central Google Scholar
• Shendure, J. The beginning of the end for microarrays? Nat. Genet. 5, 585–586 (2008).
  Article CAS Google Scholar
• Pop, M. & Salzburg, S.L. Bioinformatics challenges of new sequencing technology. Trends Genet. 24, 142–149 (2008).
  Article CAS PubMed PubMed Central Google Scholar