Next-generation DNA sequencing methods.

Recent scientific discoveries that resulted from the application of next-generation DNA sequencing technologies highlight the striking impact of these massively parallel platforms on genetics. These new methods have expanded previously focused readouts from a variety of DNA preparation protocols to a genome-wide scale and have fine-tuned their resolution to single base precision. The sequencing of RNA also has transitioned and now includes full-length cDNA analyses, serial analysis of gene expression (SAGE)-based methods, and noncoding RNA discovery. Next-generation sequencing has also enabled novel applications such as the sequencing of ancient DNA samples, and has substantially widened the scope of metagenomic analysis of environmentally derived samples. Taken together, an astounding potential exists for these technologies to bring enormous change in genetic and biological research and to enhance our fundamental biological knowledge.

[1]  D. Mccormick Sequence the Human Genome , 1986, Bio/Technology.

[2]  Alexander Varshavsky,et al.  Mapping proteinDNA interactions in vivo with formaldehyde: Evidence that histone H4 is retained on a highly transcribed gene , 1988, Cell.

[3]  S. Pääbo,et al.  DNA sequence of the mitochondrial hypervariable region II from the neandertal type specimen. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[4]  John J. Wyrick,et al.  Genome-wide location and function of DNA binding proteins. , 2000, Science.

[5]  W. Goodwin,et al.  Molecular analysis of Neanderthal DNA from the northern Caucasus , 2000, Nature.

[6]  J. Banfield,et al.  An archaeal iron-oxidizing extreme acidophile important in acid mine drainage. , 2000, Science.

[7]  International Human Genome Sequencing Consortium Initial sequencing and analysis of the human genome , 2001, Nature.

[8]  D. Haussler,et al.  A physical map of the human genome , 2001, Nature.

[9]  L. Jermiin,et al.  Mitochondrial DNA sequences in ancient Australians: Implications for modern human origins. , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[10]  Ji Huang,et al.  [Serial analysis of gene expression]. , 2002, Yi chuan = Hereditas.

[11]  O. White,et al.  Environmental Genome Shotgun Sequencing of the Sargasso Sea , 2004, Science.

[12]  Ting Wang,et al.  The gut microbiota as an environmental factor that regulates fat storage. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[13]  J. Banfield,et al.  Community structure and metabolism through reconstruction of microbial genomes from the environment , 2004, Nature.

[14]  F. Bäckhed,et al.  Obesity alters gut microbial ecology. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[15]  F. Bäckhed,et al.  Host-Bacterial Mutualism in the Human Intestine , 2005, Science.

[16]  S. Tringe,et al.  Comparative Metagenomics of Microbial Communities , 2004, Science.

[17]  James R. Knight,et al.  Genome sequencing in microfabricated high-density picolitre reactors , 2005, Nature.

[18]  M. Breitbart,et al.  Using pyrosequencing to shed light on deep mine microbial ecology , 2006, BMC Genomics.

[19]  Edward M. Rubin,et al.  Genomic Sequencing of Pleistocene Cave Bears , 2005, Science.

[20]  Steven J. M. Jones,et al.  BMC Genomics BioMed Central Methodology article , 2006 .

[21]  B. Haas,et al.  Sequencing Medicago truncatula expressed sequenced tags using 454 Life Sciences technology , 2006, BMC Genomics.

[22]  E. Mardis,et al.  An obesity-associated gut microbiome with increased capacity for energy harvest , 2006, Nature.

[23]  Ian Barnes,et al.  Multiplex amplification of the mammoth mitochondrial genome and the evolution of Elephantidae , 2006, Nature.

[24]  Steven M. Johnson,et al.  Flexibility and constraint in the nucleosome core landscape of Caenorhabditis elegans chromatin. , 2006, Genome research.

[25]  Susan M. Huse,et al.  Microbial diversity in the deep sea and the underexplored “rare biosphere” , 2006, Proceedings of the National Academy of Sciences.

[26]  Dmitrij Frishman,et al.  Deciphering the evolution and metabolism of an anammox bacterium from a community genome , 2006, Nature.

[27]  Adrian W. Briggs,et al.  Analysis of one million base pairs of Neanderthal DNA , 2006, Nature.

[28]  Florent E. Angly,et al.  The Marine Viromes of Four Oceanic Regions , 2006, PLoS biology.

[29]  M. Pop,et al.  Metagenomic Analysis of the Human Distal Gut Microbiome , 2006, Science.

[30]  Feng Chen,et al.  Sequencing and Analysis of Neanderthal Genomic DNA , 2006, Science.

[31]  Frank J. Slack,et al.  The Role of MicroRNAs in Cancer , 2006, The Yale journal of biology and medicine.

[32]  Edwin Cuppen,et al.  Diversity of microRNAs in human and chimpanzee brain , 2006, Nature Genetics.

[33]  T. Urich,et al.  Archaea predominate among ammonia-oxidizing prokaryotes in soils , 2006, Nature.

[34]  D. Bentley,et al.  Whole-genome re-sequencing. , 2006, Current opinion in genetics & development.

[35]  Christopher M. Player,et al.  Large-Scale Sequencing Reveals 21U-RNAs and Additional MicroRNAs and Endogenous siRNAs in C. elegans , 2006, Cell.

[36]  Alexander F. Auch,et al.  Metagenomics to Paleogenomics: Large-Scale Sequencing of Mammoth DNA , 2006, Science.

[37]  Stephan C. Schuster,et al.  Whole-Genome Shotgun Sequencing of Mitochondria from Ancient Hair Shafts , 2007, Science.

[38]  B. Meyers,et al.  Construction of small RNA cDNA libraries for deep sequencing. , 2007, Methods.

[39]  Jason S. Cumbie,et al.  Genome-Wide Profiling and Analysis of Arabidopsis siRNAs , 2007, PLoS biology.

[40]  Susan M. Huse,et al.  Microbial Population Structures in the Deep Marine Biosphere , 2007, Science.

[41]  T. Mikkelsen,et al.  Genome-wide maps of chromatin state in pluripotent and lineage-committed cells , 2007, Nature.

[42]  Daniel B. DiGiulio,et al.  Development of the Human Infant Intestinal Microbiota , 2007, PLoS biology.

[43]  Forest Rohwer,et al.  Metagenomic analysis of the microbial community associated with the coral Porites astreoides. , 2007, Environmental microbiology.

[44]  Manolis Kellis,et al.  Discrete Small RNA-Generating Loci as Master Regulators of Transposon Activity in Drosophila , 2007, Cell.

[45]  G. Hannon,et al.  A complex system of small RNAs in the unicellular green alga Chlamydomonas reinhardtii. , 2007, Genes & development.

[46]  Peter Salamon,et al.  Metagenomic and Small-Subunit rRNA Analyses Reveal the Genetic Diversity of Bacteria, Archaea, Fungi, and Viruses in Soil , 2007, Applied and Environmental Microbiology.

[47]  Thomas D. Schmittgen,et al.  Ultraconserved regions encoding ncRNAs are altered in human leukemias and carcinomas. , 2007, Cancer cell.

[48]  Allen D. Delaney,et al.  Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing , 2007, Nature Methods.

[49]  Hiroshi Mori,et al.  Comparative Metagenomics Revealed Commonly Enriched Gene Sets in Human Gut Microbiomes , 2007, DNA research : an international journal for rapid publication of reports on genes and genomes.

[50]  Eugene Berezikov,et al.  A Role for Piwi and piRNAs in Germ Cell Maintenance and Transposon Silencing in Zebrafish , 2007, Cell.

[51]  A. Mortazavi,et al.  Genome-Wide Mapping of in Vivo Protein-DNA Interactions , 2007, Science.

[52]  D. Bartel,et al.  Common Functions for Diverse Small RNAs of Land Plants[W][OA] , 2007, The Plant Cell Online.

[53]  J. Ohlrogge,et al.  Sampling the Arabidopsis Transcriptome with Massively Parallel Pyrosequencing1[W][OA] , 2007, Plant Physiology.

[54]  Mark Leppert,et al.  From linkage maps to quantitative trait loci: the history and science of the Utah genetic reference project. , 2008, Annual review of genomics and human genetics.

[55]  D. Milewicz,et al.  Genetic basis of thoracic aortic aneurysms and dissections: focus on smooth muscle cell contractile dysfunction. , 2008, Annual review of genomics and human genetics.

[56]  S. Tishkoff,et al.  African genetic diversity: implications for human demographic history, modern human origins, and complex disease mapping. , 2008, Annual review of genomics and human genetics.

[57]  Christian Schlötterer,et al.  Gene expression profiling by massively parallel sequencing. , 2007, Genome research.

[58]  Gail Javitt,et al.  The current landscape for direct-to-consumer genetic testing: legal, ethical, and policy issues. , 2008, Annual review of genomics and human genetics.

[59]  M. Ibrahim,et al.  Whole-Genome Resequencing , 2009 .