Christmas is coming. I want to share some interesting things with you. Christmas Tree DNA: Complex Conifer Genome Begins To Yield To Research Efforts http://www.huffingtonpost.com/2012/12/13/christmas-tree-genome-new-dna-study-conifers_n_2294265.html ; (Again, genome sequencing, we really have rich resources for genome sequences. Understanding the functions will a changllege). A Functional and Structural Mongolian Scots Pine (Pinus sylvestris var. mongolica) Model Integrating Architecture, Biomass and Effects of Precipitation http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0043531 ; (If you want to go green and don't buy Christmas tree year by year. You could generated one by modelling. Don't forget to put some lights on your Christmas Tree.) Merry Christmas!
MolBioLib: a C++11 framework for rapid development and deployment of bioinformatics tasks Authors:Toshiro K. Ohsumi and Mark L. Borowsky MolBioLib is developed to address the need for adaptable next-generation sequencing analysis tools. The result is a compact, portable and extensively tested C++11 software framework and set of applications tailored to the demands of next-generation sequencing data and applicable to many other applications. MolBioLib is designed to work with common file formats and data types used both in genomic analysis and general data analysis. A central relational-database-like Table class is a flexible and powerful object to intuitively represent and work with a wide variety of tabular datasets, ranging from alignment data to annotations. MolBioLib has been used to identify causative single-nucleotide polymorphisms in whole genome sequencing, detect balanced chromosomal rearrangements and compute enrichment of messenger RNAs (mRNAs) on microtubules, typically requiring applications of under 200 lines of code. MolBioLib includes programs to perform a wide variety of analysis tasks, such as computing read coverage, annotating genomic intervals and novel peak calling with a wavelet algorithm. Availability: MolBioLib is available for download at:http://sourceforge.net/projects/molbiolib More details about MolBioLib can be found at http://bioinformatics.oxfordjournals.org/content/28/19/2412.full#ref-22
Provider: Quertle (www.quertle.info) Content: text/plain; charset=UTF-8 TY- JOUR TI- Genome of a songbird unveiled AU- Pinaud, Raphael PY- 2011 T2- Journal of Biology J2- J Biol UR- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2871510/ VL- 9 IS- 3 SP- 19-19 DO- 10.1186/jbiol222 C2- 2871510 N2- An international collaborative effort has recently uncovered the genome of the zebra finch, a songbird model that has provided unique insights into an array of biological phenomena. See research articles , ,and N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- Reprogramming of the non-coding transcriptome during brain development AU- Valadkhan, Saba AU- Nilsen, Timothy W PY- 2011 T2- Journal of Biology J2- J Biol UR- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2871522/ VL- 9 IS- 1 SP- 5-5 DO- 10.1186/jbiol197 C2- 2871522 N2- A recent global analysis of gene expression during the differentiation of neuronal stem cells to neurons and oligodendrocytes indicates a complex pattern of changes in the expression of both protein-coding transcripts and long non-protein-coding RNAs. See research article . N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- LINE-1 Retrotransposition Activity in Human Genomes AU- Beck, Christine R AU- Collier, Pamela AU- Macfarlane, Catriona AU- Malig, Maika AU- Kidd, Jeffrey M AU- Eichler, Evan E AU- Badge, Richard M AU- Moran, John V PY- 2011 T2- Cell J2- Cell UR- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013285/ VL- 141 IS- 7 SP- 1159-1170 DO- 10.1016/j.cell.2010.05.021 C2- 3013285 N2- Summary: Long Interspersed Element-1 (LINE-1 or L1) sequences comprise the bulk of retrotransposition activity in the human genome; however, the abundance of highly active or hot L1s in the human population remains largely unexplored. Here, we used a fosmid-based, paired-end DNA sequencing strategy to identify 68 full-length L1s which are differentially present among individuals but are absent from the human genome reference sequence. The majority of these L1s were highly active in a cultured cell retrotransposition assay. Genotyping 26 elements revealed that two L1s are only found in Africa and that two more are absent from the H952 subset of the Human Genome Diversity Panel. Therefore, these results suggest that hot L1s are more abundant in the human population than previously appreciated, and that ongoing L1 retrotransposition continues to be a major source of inter-individual genetic variation. N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- Lrp12/Mig13a Reveals Changing Patterns of Preplate Neuronal Polarity during Corticogenesis that Are Absent in Reeler Mutant Mice AU- Schneider, Stephanie AU- Gulacsi, Alexandra AU- Hatten, Mary E PY- 2011 T2- Cerebral Cortex (New York, NY) J2- Cereb Cortex UR- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3000567/ VL- 21 IS- 1 SP- 134-144 DO- 10.1093/cercor/bhq070 C2- 3000567 N2- During corticogenesis, the earliest generated neurons form the preplate, which evolves into the marginal zone and subplate. Lrp12/Mig13a, a mammalian gene related to the Caenorhabditis elegans neuroblast migration gene mig-13, is expressed in a subpopulation of preplate neurons that undergo ventrally directed tangential migrations in the preplate layer and pioneer axon projections to the anterior commissure. As the preplate separates, Lrp12/Mig13a-positive neurons polarize in the radial plane and form a pseudocolumnar pattern, prior to moving to a deeper position within the emerging subplate layer. These changes in neuronal polarity do not occur in reeler mutant mice, revealing the earliest known defect in reeler cortical patterning and suggesting that the alignment of preplate neurons into a pseudolayer facilitates the movement of later-born radially migrating neurons into the emerging cortical plate. N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- ENCODE whole-genome data in the UCSC genome browser (2011 update) AU- Raney, Brian J AU- Cline, Melissa S AU- Rosenbloom, Kate R AU- Dreszer, Timothy R AU- Learned, Katrina AU- Barber, Galt P AU- Meyer, Laurence R AU- Sloan, Cricket A AU- Malladi, Venkat S AU- Roskin, Krishna M AU- Suh, Bernard B AU- Hinrichs, Angie S AU- Clawson, Hiram AU- Zweig, Ann S AU- Kirkup, Vanessa AU- Fujita, Pauline A AU- Rhead, Brooke AU- Smith, Kayla E AU- Pohl, Andy AU- Kuhn, Robert M AU- Karolchik, Donna AU- Haussler, David AU- Kent, W James PY- 2011 T2- Nucleic Acids Research J2- Nucleic Acids Res UR- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013645/ VL- 39 IS- Database issue SP- D871-D875 DO- 10.1093/nar/gkq1017 C2- 3013645 N2- The ENCODE project is an international consortium with a goal of cataloguing all the functional elements in the human genome. The ENCODE Data Coordination Center (DCC) at the University of California, Santa Cruz serves as the central repository for ENCODE data. In this role, the DCC offers a collection of high-throughput, genome-wide data generated with technologies such as ChIP-Seq, RNA-Seq, DNA digestion and others. This data helps illuminate transcription factor-binding sites, histone marks, chromatin accessibility, DNA methylation, RNA expression, RNA binding and other cell-state indicators. It includes sequences with quality scores, alignments, signals calculated from the alignments, and in most cases, element or peak calls calculated from the signal data. Each data set is available for visualization and download via the UCSC Genome Browser (). ENCODE data can also be retrieved using a metadata system that captures the experimental parameters of each assay. The ENCODE web portal at UCSC () provides information about the ENCODE data and links for access. N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- BACs as Tools for the Study of Genomic Imprinting AU- Tunster, S J AU- Van De Pette, M AU- John, R M PY- 2011 T2- Journal of Biomedicine and Biotechnology J2- J Biomed Biotechnol UR- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3010669/ VL- 2011 DO- 10.1155/2011/283013 C2- 3010669 N2- Genomic imprinting in mammals results in the expression of genes from only one parental allele. Imprinting occurs as a consequence of epigenetic marks set down either in the father's or the mother's germ line and affects a very specific category of mammalian gene. A greater understanding of this distinctive phenomenon can be gained from studies using large genomic clones, called bacterial artificial chromosomes (BACs). Here, we review the important applications of BACs to imprinting research, covering physical mapping studies and the use of BACs as transgenes in mice to study gene expression patterns, to identify imprinting centres, and to isolate the consequences of altered gene dosage. We also highlight the significant and unique advantages that rapid BAC engineering brings to genomic imprinting research. N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- Hymenoptera Genome Database: integrated community resources for insect species of the order Hymenoptera AU- Munoz-Torres, Monica C AU- Reese, Justin T AU- Childers, Christopher P AU- Bennett, Anna K AU- Sundaram, Jaideep P AU- Childs, Kevin L AU- Anzola, Juan M AU- Milshina, Natalia AU- Elsik, Christine G PY- 2011 T2- Nucleic Acids Research J2- Nucleic Acids Res UR- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013718/ VL- 39 IS- Database issue SP- D658-D662 DO- 10.1093/nar/gkq1145 C2- 3013718 N2- The Hymenoptera Genome Database (HGD) is a comprehensive model organism database that caters to the needs of scientists working on insect species of the order Hymenoptera. This system implements open-source software and relational databases providing access to curated data contributed by an extensive, active research community. HGD contains data from 9 different species across 200 million years in the phylogeny of Hymenoptera, allowing researchers to leverage genetic, genome sequence and gene expression data, as well as the biological knowledge of related model organisms. The availability of resources across an order greatly facilitates comparative genomics and enhances our understanding of the biology of agriculturally important Hymenoptera species through genomics. Curated data at HGD includes predicted and annotated gene sets supported with evidence tracks such as ESTs/cDNAs, small RNA sequences and GC composition domains. Data at HGD can be queried using genome browsers and/or BLAST/PSI-BLAST servers, and it may also be downloaded to perform local searches. We encourage the public to access and contribute data to HGD at: . N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing AU- Martelli, Pier L AU- D'Antonio, Mattia AU- Bonizzoni, Paola AU- Castrignan, Tiziana AU- D'Erchia, Anna M AU- D'Onorio De Meo, Paolo AU- Fariselli, Piero AU- Finelli, Michele AU- Licciulli, Flavio AU- Mangiulli, Marina AU- Mignone, Flavio AU- Pavesi, Giulio AU- Picardi, Ernesto AU- Rizzi, Raffaella AU- Rossi, Ivan AU- Valletti, Alessio AU- Zauli, Andrea AU- Zambelli, Federico AU- Casadio, Rita AU- Pesole, Graziano PY- 2011 T2- Nucleic Acids Research J2- Nucleic Acids Res UR- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013677/ VL- 39 IS- Database issue SP- D80-D85 DO- 10.1093/nar/gkq1073 C2- 3013677 N2- Alternative splicing is emerging as a major mechanism for the expansion of the transcriptome and proteome diversity, particularly in human and other vertebrates. However, the proportion of alternative transcripts and proteins actually endowed with functional activity is currently highly debated. We present here a new release of ASPicDB which now provides a unique annotation resource of human protein variants generated by alternative splicing. A total of 256939 protein variants from 17191 multi-exon genes have been extensively annotated through state of the art machine learning tools providing information of the protein type (globular and transmembrane), localization, presence of PFAM domains, signal peptides, GPI-anchor propeptides, transmembrane and coiled-coil segments. Furthermore, full-length variants can be now specifically selected based on the annotation of CAGE-tags and polyA signal and/or polyA sites, marking transcription initiation and termination sites, respectively. The retrieval can be carried out at gene, transcript, exon, protein or splice site level allowing the selection of data sets fulfilling one or more features settled by the user. The retrieval interface also enables the selection of protein variants showing specific differences in the annotated features. ASPicDB is available at . N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- TIARA: a database for accurate analysis of multiple personal genomes based on cross-technology AU- Hong, Dongwan AU- Park, Sung-Soo AU- Ju, Young Seok AU- Kim, Sheehyun AU- Shin, Jong-Yeon AU- Kim, Sujung AU- Yu, Saet-Byeol AU- Lee, Won-Chul AU- Lee, Seungbok AU- Park, Hansoo AU- Kim, Jong-Il AU- Seo, Jeong-Sun PY- 2011 T2- Nucleic Acids Research J2- Nucleic Acids Res UR- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013693/ VL- 39 IS- Database issue SP- D883-D888 DO- 10.1093/nar/gkq1101 C2- 3013693 N2- High-throughput genomic technologies have been used to explore personal human genomes for the past few years. Although the integration of technologies is important for high-accuracy detection of personal genomic variations, no databases have been prepared to systematically archive genomes and to facilitate the comparison of personal genomic data sets prepared using a variety of experimental platforms. We describe here the Total Integrated Archive of Short-Read and Array (TIARA; ) database, which contains personal genomic information obtained from next generation sequencing (NGS) techniques and ultra-high-resolution comparative genomic hybridization (CGH) arrays. This database improves the accuracy of detecting personal genomic variations, such as SNPs, short indels and structural variants (SVs). At present, 36 individual genomes have been archived and may be displayed in the database. TIARA supports a user-friendly genome browser, which retrieves read-depths (RDs) and log2 ratios from NGS and CGH arrays, respectively. In addition, this database provides information on all genomic variants and the raw data, including short reads and feature-level CGH data, through anonymous file transfer protocol. More personal genomes will be archived as more individuals are analyzed by NGS or CGH array. TIARA provides a new approach to the accurate interpretation of personal genomes for genome research. N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- Primate and Rodent Specific Intron Gains and the Origin of Retrogenes with Splice Variants AU- Szcze?niak, Micha? W AU- Ciomborowska, Joanna AU- Nowak, Witold AU- Rogozin, Igor B AU- Maka?owska, Izabela PY- 2011 T2- Molecular biology and evolution J2- Mol Biol Evol UR- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3002245/ VL- 28 IS- 1 SP- 33-37 DO- 10.1093/molbev/msq260 C2- 3002245 N2- Retroposition, a leading mechanism for gene duplication, is an important process shaping the evolution of genomes. Retrogenes are also involved in the gene structure evolution as a major player in the process of intron deletion. Here, we demonstrate the role of retrogenes in intron gain in mammals. We identified one case of intronization, the transformation of exonic sequences into an intron, in the primate specific retrogene RNF113B and two independent intronization events in the retrogene DCAF12L2, one in the common ancestor of primates and rodents and another one in the rodent lineage. Intron gain resulted from the origin of new splice variants, and both genes have two transcript forms, one with retained intron and one with the intron spliced out. Evolution of these genes, especially RNF113B, has been very dynamic and has been accompanied by several additional events including parental gene loss, secondary retroposition, and exaptation of transposable elements. N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- Structural insights and ab initio sequencing within the DING proteins family AU- Elias, Mikael AU- Liebschner, Dorothee AU- Gotthard, Guillaume AU- Chabriere, Eric PY- 2011 T2- Journal of Synchrotron Radiation J2- J Synchrotron Radiat UR- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3004253/ VL- 18 IS- Pt 1 SP- 45-49 DO- 10.1107/S0909049510036009 C2- 3004253 N2- DING proteins constitute an intriguing family of phosphate-binding proteins that was identified in a wide range of organisms, from prokaryotes and archae to eukaryotes. Despite their seemingly ubiquitous occurrence in eukaryotes, their encoding genes are missing from sequenced genomes. Such a lack has considerably hampered functional studies. In humans, these proteins have been related to several diseases, like atherosclerosis, kidney stones, inflammation processes and HIV inhibition. The human phosphate binding protein is a human representative of the DING family that was serendipitously discovered from human plasma. An original approach was developed to determine ab initio the complete and exact sequence of this 38?kDa protein by utilizing mass spectrometry and X-ray data in tandem. Taking advantage of this first complete eukaryotic DING sequence, a immunohistochemistry study was undertaken to check the presence of DING proteins in various mice tissues, revealing that these proteins are widely expressed. Finally, the structure of a bacterial representative from Pseudomonas fluorescens was solved at sub-angstrom resolution, allowing the molecular mechanism of the phosphate binding in these high-affinity proteins to be elucidated. N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- dbDNV: a resource of duplicated gene nucleotide variants in human genome AU- Ho, Meng-Ru AU- Tsai, Kuo-Wang AU- Chen, Chun-Houh AU- Lin, Wen-Chang PY- 2011 T2- Nucleic Acids Research J2- Nucleic Acids Res UR- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013738/ VL- 39 IS- Database issue SP- D920-D925 DO- 10.1093/nar/gkq1197 C2- 3013738 N2- Gene duplications are scattered widely throughout the human genome. A single-base difference located in nearly identical duplicated segments may be misjudged as a single nucleotide polymorphism (SNP) from individuals. This imperfection is undistinguishable in current genotyping methods. As the next-generation sequencing technologies become more popular for sequence-based association studies, numerous ambiguous SNPs are rapidly accumulated. Thus, analyzing duplication variations in the reference genome to assist in preventing false positive SNPs is imperative. We have identified 10% of human genes associated with duplicated gene loci (DGL). Through meticulous sequence alignments of DGL, we systematically designated 1236956 variations as duplicated gene nucleotide variants (DNVs). The DNV database (dbDNV) () has been established to promote more accurate variation annotation. Aside from the flat file download, users can explore the gene-related duplications and the associated DNVs by DGL and DNV searches, respectively. In addition, the dbDNV contains 304110 DNV-coupled SNPs. From DNV-coupled SNP search, users observe which SNP records are also variants among duplicates. This is useful while 58% of exonic SNPs in DGL are DNV-coupled. Because of high accumulation of ambiguous SNPs, we suggest that annotating SNPs with DNVs possibilities should improve association studies of these variants with human diseases. N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- Database resources of the National Center for Biotechnology Information AU- Sayers, Eric W AU- Barrett, Tanya AU- Benson, Dennis A AU- Bolton, Evan AU- Bryant, Stephen H AU- Canese, Kathi AU- Chetvernin, Vyacheslav AU- Church, Deanna M AU- Dicuccio, Michael AU- Federhen, Scott AU- Feolo, Michael AU- Fingerman, Ian M AU- Geer, Lewis Y AU- Helmberg, Wolfgang AU- Kapustin, Yuri AU- Landsman, David AU- Lipman, David J AU- Lu, Zhiyong AU- Madden, Thomas L AU- Madej, Tom AU- Maglott, Donna R AU- Marchler-Bauer, Aron AU- Miller, Vadim AU- Mizrachi, Ilene AU- Ostell, James AU- Panchenko, Anna AU- Phan, Lon AU- Pruitt, Kim D AU- Schuler, Gregory D AU- Sequeira, Edwin AU- Sherry, Stephen T AU- Shumway, Martin AU- Sirotkin, Karl AU- Slotta, Douglas AU- Souvorov, Alexandre AU- Starchenko, Grigory AU- Tatusova, Tatiana A AU- Wagner, Lukas AU- Wang, Yanli AU- Wilbur, W John AU- Yaschenko, Eugene AU- Ye, Jian PY- 2011 T2- Nucleic Acids Research J2- Nucleic Acids Res UR- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013733/ VL- 39 IS- Database issue SP- D38-D51 DO- 10.1093/nar/gkq1172 C2- 3013733 N2- In addition to maintaining the GenBank nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI Web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central (PMC), Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Primer-BLAST, COBALT, Electronic PCR, OrfFinder, Splign, ProSplign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, dbVar, Epigenomics, Cancer Chromosomes, Entrez Genomes and related tools, the Map Viewer, Model Maker, Evidence Viewer, Trace Archive, Sequence Read Archive, Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus (GEO), Entrez Probe, GENSAT, Online Mendelian Inheritance in Man (OMIM), Online Mendelian Inheritance in Animals (OMIA), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART), IBIS, Biosystems, Peptidome, OMSSA, Protein Clusters and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page at . N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- Isolation of Specific Clones from Nonarrayed BAC Libraries through Homologous Recombination AU- Nefedov, Mikhail AU- Carbone, Lucia AU- Field, Matthew AU- Schein, Jacquie AU- de Jong, Pieter J PY- 2011 T2- Journal of Biomedicine and Biotechnology J2- J Biomed Biotechnol UR- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2957146/ VL- 2011 DO- 10.1155/2011/560124 C2- 2957146 N2- We have developed a new approach to screen bacterial artificial chromosome (BAC) libraries by recombination selection. To test this method, we constructed an orangutan BAC library using an E. coli strain (DY380) with temperature inducible homologous recombination (HR) capability. We amplified one library segment, induced HR at 42C to make it recombination proficient, and prepared electrocompetent cells for transformation with a kanamycin cassette to target sequences in the orangutan genome through terminal recombineering homologies. Kanamycin-resistant colonies were tested for the presence of BACs containing the targeted genes by the use of a PCR-assay to confirm the presence of the kanamycin insertion. The results indicate that this is an effective approach for screening clones. The advantage of recombination screening is that it avoids the high costs associated with the preparation, screening, and archival storage of arrayed BAC libraries. In addition, the screening can be conceivably combined with genetic engineering to create knockout and reporter constructs for functional studies. N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- DBASS3 and DBASS5: databases of aberrant 3- and 5-splice sites AU- Buratti, Emanuele AU- Chivers, Martin AU- Hwang, Gyulin AU- Vorechovsky, Igor PY- 2011 T2- Nucleic Acids Research J2- Nucleic Acids Res UR- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013770/ VL- 39 IS- Database issue SP- D86-D91 DO- 10.1093/nar/gkq887 C2- 3013770 N2- DBASS3 and DBASS5 provide comprehensive repositories of new exon boundaries that were induced by pathogenic mutations in human disease genes. Aberrant 5- and 3-splice sites were activated either by mutations in the consensus sequences of natural exonintron junctions (cryptic sites) or elsewhere (de novo sites). DBASS3 and DBASS5 currently contain approximately 900 records of cryptic and de novo 3- and 5-splice sites that were produced by over a thousand different mutations in approximately 360 genes. DBASS3 and DBASS5 data can be searched by disease phenotype, gene, mutation, location of aberrant splice sites in introns and exons and their distance from authentic counterparts, by bibliographic references and by the splice-site strength estimated with several prediction algorithms. The user can also retrieve reference sequences of both aberrant and authentic splice sites with the underlying mutation. These data will facilitate identification of introns or exons frequently involved in aberrant splicing, mutation analysis of human disease genes and study of germline or somatic mutations that impair RNA processing. Finally, this resource will be useful for fine-tuning splice-site prediction algorithms, better definition of auxiliary splicing signals and design of new reporter assays. DBASS3 and DBASS5 are freely available at . N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- Identification of causal sequence variants of disease in the next generation sequencing era. AU- Kingsley, Christopher B PY- 2011 T2- Methods in molecular biology (Clifton, N.J.) J2- Methods Mol Biol UR- http://www.ncbi.nlm.nih.gov/pubmed/21204025 VL- 700 SP- 37-46 N2- Over the last decade, genetic studies have identified numerous associations between single nucleotide polymorphism (SNP) alleles in the human genome and important human diseases. Unfortunately, extending these initial associative findings to identification of the true causal variants that underlie disease susceptibility is usually not a straightforward task. Causal variant identification typically involves searching through sizable regions of genomic DNA in the vicinity of disease-associated SNPs for sequence variants in functional elements including protein coding, regulatory, and structural sequences. Prioritization of these searches is greatly aided by knowledge of the location of functional sequences in the human genome. This chapter briefly reviews several of the common approaches used to functionally annotate the human genome and discusses how this information can be used in concert with the emerging technology of next generation high-throughput sequencing to identify causal variants of human disease. N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- Cell-Based Co-transfection Microarrays for Use with HEK293T Cells on a Poly D: -Lysine-Coated Polystyrene Microplate. AU- Soni, Meenal AU- Lai, Fang PY- 2011 T2- Methods in molecular biology (Clifton, N.J.) J2- Methods Mol Biol UR- http://www.ncbi.nlm.nih.gov/pubmed/21104051 VL- 706 SP- 13-25 N2- Analysis of the human genome sequence has identified thousands of putative genes with unknown function; therefore, a new tool allowing for rapid identification of gene functions is needed. Reverse transfection microarray technology, which turns a DNA microarray into a cell-based microarray, has emerged for simultaneously studying the function of many genes. Since the initial demonstration in 2001, many variations have surfaced, making the technology more versatile for a broad range of applications. We have developed a protocol to make ready-to-transfect DNA microarrays in a 96-well microplate for co-transfection of two plasmids into HEK293T cells. This cell-based microarray in a microplate may be used for screening hundreds of analytes against multiple protein targets in parallel, providing a powerful tool for functional genomics and drug discovery. N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- Bovine Genome Database: integrated tools for genome annotation and discovery AU- Childers, Christopher P AU- Reese, Justin T AU- Sundaram, Jaideep P AU- Vile, Donald C AU- Dickens, C Michael AU- Childs, Kevin L AU- Salih, Hanni AU- Bennett, Anna K AU- Hagen, Darren E AU- Adelson, David L AU- Elsik, Christine G PY- 2011 T2- Nucleic Acids Research J2- Nucleic Acids Res UR- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013744/ VL- 39 IS- Database issue SP- D830-D834 DO- 10.1093/nar/gkq1235 C2- 3013744 N2- The Bovine Genome Database (BGD; ) strives to improve annotation of the bovine genome and to integrate the genome sequence with other genomics data. BGD includes GBrowse genome browsers, the Apollo Annotation Editor, a quantitative trait loci (QTL) viewer, BLAST databases and gene pages. Genome browsers, available for both scaffold and chromosome coordinate systems, display the bovine Official Gene Set (OGS), RefSeq and Ensembl gene models, non-coding RNA, repeats, pseudogenes, single-nucleotide polymorphism, markers, QTL and alignments to complementary DNAs, ESTs and protein homologs. The Bovine QTL viewer is connected to the BGD Chromosome GBrowse, allowing for the identification of candidate genes underlying QTL. The Apollo Annotation Editor connects directly to the BGD Chado database to provide researchers with remote access to gene evidence in a graphical interface that allows editing and creating new gene models. Researchers may upload their annotations to the BGD server for review and integration into the subsequent release of the OGS. Gene pages display information for individual OGS gene models, including gene structure, transcript variants, functional descriptions, gene symbols, Gene Ontology terms, annotator comments and links to National Center for Biotechnology Information and Ensembl. Each gene page is linked to a wiki page to allow input from the research community. N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- Characterization of New Otic Enhancers of the Pou3f4 Gene Reveal Distinct Signaling Pathway Regulation and Spatio-Temporal Patterns AU- Robert-Moreno, lex AU- Naranjo, Silvia AU- de la Calle-Mustienes, Elisa AU- Gmez-Skarmeta, Jos Luis AU- Alsina, Berta PY- 2010 T2- PLoS ONE J2- PLoS One UR- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013142/ VL- 5 IS- 12 DO- 10.1371/journal.pone.0015907 C2- 3013142 N2- POU3F4 is a member of the POU-homedomain transcription factor family with a prominent role in inner ear development. Mutations in the human POU3F4 coding unit leads to X-linked deafness type 3 (DFN3), characterized by conductive hearing loss and progressive sensorineural deafness. Microdeletions found 1 Mb 5 upstream of the coding region also displayed the same phenotype, suggesting that cis-regulatory elements might be present in that region. Indeed, we and others have recently identified several enhancers at the 1 Mb 5 upstream interval of the pou3f4 locus. Here we characterize the spatio-temporal patterns of these regulatory elements in zebrafish transgenic lines. We show that the most distal enhancer (HCNR 81675) is activated earlier and drives GFP reporter expression initially to a broad ear domain to progressively restrict to the sensory patches. The proximal enhancer (HCNR 82478) is switched later during development and promotes expression, among in other tissues, in sensory patches from its onset. The third enhancer (HCNR 81728) is also active at later stages in the otic mesenchyme and in the otic epithelium. We also characterize the signaling pathways regulating these enhancers. While HCNR 81675 is regulated by very early signals of retinoic acid, HCNR 82478 is regulated by Fgf activity at a later stage and the HCNR 81728 enhancer is under the control of Hh signaling. Finally, we show that Sox2 and Pax2 transcription factors are bound to HCNR 81675 genomic region during otic development and specific mutations to these transcription factor binding sites abrogates HCNR 81675 enhancer activity. Altogether, our results suggest that pou3f4 expression in inner ear might be under the control of distinct regulatory elements that fine-tune the spatio-temporal activity of this gene and provides novel data on the signaling mechanisms controlling pou3f4 function. N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- Activation of Pluripotency Genes in Human Fibroblast Cells by a Novel mRNA Based Approach AU- Plews, Jordan R. AU- Li, JianLiang AU- Jones, Mark AU- Moore, Harry D. AU- Mason, Chris AU- Andrews, Peter W. AU- Na, Jie PY- 2010 T2 - PLoS ONE J2- PLoS One UR- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3012685/ VL- 5 IS- 12 DO- 10.1371/journal.pone.0014397 C2- 3012685 N2- Background: Several methods have been used to induce somatic cells to re-enter the pluripotent state. Viral transduction of reprogramming genes yields higher efficiency but involves random insertions of viral sequences into the human genome. Although induced pluripotent stem (iPS) cells can be obtained with the removable PiggyBac transposon system or an episomal system, both approaches still use DNA constructs so that resulting cell lines need to be thoroughly analyzed to confirm they are free of harmful genetic modification. Thus a method to change cell fate without using DNA will be very useful in regenerative medicine. Methodology/Principal Findings: In this study, we synthesized mRNAs encoding OCT4, SOX2, cMYC, KLF4 and SV40 large T (LT) and electroporated them into human fibroblast cells. Upon transfection, fibroblasts expressed these factors at levels comparable to, or higher than those in human embryonic stem (ES) cells. Ectopically expressed OCT4 localized to the cell nucleus within 4 hours after mRNA introduction. Transfecting fibroblasts with a mixture of mRNAs encoding all five factors significantly increased the expression of endogenous OCT4, NANOG, DNMT3, REX1 and SALL4. When such transfected fibroblasts were also exposed to several small molecules (valproic acid, BIX01294 and 5-aza-2-deoxycytidine) and cultured in human embryonic stem cell (ES) medium they formed small aggregates positive for alkaline phosphatase activity and OCT4 protein within 30 days. Conclusion/Significance: Our results demonstrate that mRNA transfection can be a useful approach to precisely control the protein expression level and short-term expression of reprogramming factors is sufficient to activate pluripotency genes in differentiated cells. N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- The complete genome sequence of Corynebacterium pseudotuberculosis FRC41 isolated from a 12-year-old girl with necrotizing lymphadenitis reveals insights into gene-regulatory networks contributing to virulence. AU- Trost, Eva AU- Ott, Lisa AU- Schneider, Jessica AU- Schroder, Jasmin AU- Jaenicke, Sebastian AU- Goesmann, Alexander AU- Husemann, Peter AU- Stoye, Jens AU- Alves Dorella, Fernanda AU- Souza Rocha, Flavia AU- de Castro Soares, Siomar AU- D'Afonseca, Vivian AU- Miyoshi, Anderson AU- Ruiz, Jeronimo AU- Silva, Artur AU- Azevedo, Vasco AU- Burkovski, Andreas AU- Guiso, Nicole AU- Join-Lambert, Olivier F AU- Kayal, Samer AU- Tauch, Andreas PY- 2010 T2- BMC genomics J2- BMC Genomics UR- http://www.ncbi.nlm.nih.gov/pubmed/21192786 VL- 11 IS- 1 SP- 728 N2- ABSTRACT: BACKGROUND: Corynebacterium pseudotuberculosis is generally regarded as an important animal pathogen that rarely infects humans. Clinical strains are occasionally recovered from human cases of lymphadenitis, such as C. pseudotuberculosis FRC41 that was isolated from the inguinal lymph node of a 12-year-old girl with necrotizing lymphadenitis. To detect potential virulence factors and corresponding gene-regulatory networks in this human isolate, the genome sequence of C. pseudotuberculosis FCR41 was determined by pyrosequencing and functionally annotated. RESULTS: Sequencing and assembly of the C. pseudotuberculosis FRC41 genome yielded a circular chromosome with a size of 2,337,913 bp and a mean G+C content of 52.2%. Specific gene sets associated with iron and zinc homeostasis were detected among the 2,110 predicted protein-coding regions and integrated into a gene-regulatory network that is linked with both the central metabolism and the oxidative stress response of FRC41. Two gene clusters encode proteins involved in the sortase-mediated polymerization of adhesive pili that can probably mediate the adherence to host tissue to facilitate additional ligand-receptor interactions and the delivery of virulence factors. The prominent virulence factors phospholipase D (Pld) and corynebacterial protease CP40 are encoded in the genome of this human isolate. The genome annotation revealed additional serine proteases, neuraminidase H, nitric oxide reductase, an invasion-associated protein, and acyl-CoA carboxylase subunits involved in mycolic acid biosynthesis as potential virulence factors. The cAMP-sensing transcription regulator GlxR plays a key role in controlling the expression of several genes contributing to virulence. CONCLUSION: The functional data deduced from the genome sequencing and the extended knowledge of virulence factors indicate that the human isolate C. pseudotuberculosis FRC41 is equipped with a distinct gene set promoting its survival under unfavorable environmental conditions encountered in the mammalian host. N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- Analysis of MicroRNA Expression in the Prepubertal Testis AU- Buchold, Gregory M AU- Coarfa, Cristian AU- Kim, Jong AU- Milosavljevic, Aleksandar AU- Gunaratne, Preethi H AU- Matzuk, Martin M PY- 2010 T2- PLoS ONE J2- PLoS One UR- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3012074/ VL- 5 IS- 12 DO- 10.1371/journal.pone.0015317 C2- 3012074 N2- Only thirteen microRNAs are conserved between D. melanogaster and the mouse; however, conditional loss of miRNA function through mutation of Dicer causes defects in proliferation of premeiotic germ cells in both species. This highlights the potentially important, but uncharacterized, role of miRNAs during early spermatogenesis. The goal of this study was to characterize on postnatal day 7, 10, and 14 the content and editing of murine testicular miRNAs, which predominantly arise from spermatogonia and spermatocytes, in contrast to prior descriptions of miRNAs in the adult mouse testis which largely reflects the content of spermatids. Previous studies have shown miRNAs to be abundant in the mouse testis by postnatal day 14; however, through Next Generation Sequencing of testes from a B6;129 background we found abundant earlier expression of miRNAs and describe shifts in the miRNA signature during this period. We detected robust expression of miRNAs encoded on the X chromosome in postnatal day 14 testes, consistent with prior studies showing their resistance to meiotic sex chromosome inactivation. Unexpectedly, we also found a similar positional enrichment for most miRNAs on chromosome 2 at postnatal day 14 and for those on chromosome 12 at postnatal day 7. We quantified in vivo developmental changes in three types of miRNA variation including 5 heterogeneity, editing, and 3 nucleotide addition. We identified eleven putative novel pubertal testis miRNAs whose developmental expression suggests a possible role in early male germ cell development. These studies provide a foundation for interpretation of miRNA changes associated with testicular pathology and identification of novel components of the miRNA editing machinery in the testis. N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- Primate-specific evolution of noncoding element insertion into PLA2G4C and human preterm birth AU- Plunkett, Jevon AU- Doniger, Scott AU- Morgan, Thomas AU- Haataja, Ritva AU- Hallman, Mikko AU- Puttonen, Hilkka AU- Menon, Ramkumar AU- Kuczynski, Edward AU- Norwitz, Errol AU- Snegovskikh, Victoria AU- Palotie, Aarno AU- Peltonen, Leena AU- Fellman, Vineta AU- Defranco, Emily A AU- Chaudhari, Bimal P AU- Oates, John AU- Boutaud, Olivier AU- McGregor, Tracy L AU- McElroy, Jude J AU- Teramo, Kari AU- Borecki, Ingrid AU- Fay, Justin C AU- Muglia, Louis J PY- 2010 T2- BMC Medical Genomics J2- BMC Medical Genomics UR- http://www.biomedcentral.com/1755-8794/3/62 VL- 3 IS- 1 SP- 62 DO- 10.1186/1755-8794-3-62 N2- Abstract Background: The onset of birth in humans, like other apes, differs from non-primate mammals in its endocrine physiology. We hypothesize that higher primate-specific gene evolution may lead to these differences and target genes involved in human preterm birth, an area of global health significance. Methods: We performed a comparative genomics screen of highly conserved noncoding elements and identified PLA2G4C, a phospholipase A isoform involved in prostaglandin biosynthesis as human accelerated. To examine whether this gene demonstrating primate-specific evolution was associated with birth timing, we genotyped and analyzed 8 common single nucleotide polymorphisms (SNPs) in PLA2G4C in US Hispanic (n = 73 preterm, 292 control), US White (n = 147 preterm, 157 control) and US Black (n = 79 preterm, 166 control) mothers. Results: Detailed structural and phylogenic analysis of PLA2G4C suggested a short genomic element within the gene duplicated from a paralogous highly conserved element on chromosome 1 specifically in primates. SNPs rs8110925 and rs2307276 in US Hispanics and rs11564620 in US Whites were significant after correcting for multiple tests (p 0.006). Additionally, rs11564620 (Thr360Pro) was associated with increased metabolite levels of the prostaglandin thromboxane in healthy individuals (p = 0.02), suggesting this variant may affect PLA2G4C activity. Conclusions: Our findings suggest that variation in PLA2G4C may influence preterm birth risk by increasing levels of prostaglandins, which are known to regulate labor. N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- Complete genome sequence of the zoonotic pathogen Chlamydophila psittaci. AU- Seth-Smith, Helena M B AU- Harris, Simon R AU- Rance, Richard AU- West, Anthony P AU- Severin, Juliette A AU- Ossewaarde, Jacobus M AU- Cutcliffe, Lesley T AU- Skilton, Rachel J AU- Marsh, Pete AU- Parkhill, Julian AU- Clarke, Ian N AU- Thomson, Nicholas R PY- 2010 T2- Journal of bacteriology J2- J Bacteriol UR- http://www.ncbi.nlm.nih.gov/pubmed/21183672 N2- We present the first genome sequence of Chlamydophila psittaci, an intracellular pathogen of birds, and a human zoonotic pathogen. A comparison with previously sequenced Chlamydophila genomes shows that, like other chlamydiae, most of the genome diversity is restricted to the plasticity zone. The Cp. psittaci plasmid was also sequenced. N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- Cancer and Neurodegeneration: Between the Devil and the Deep Blue Sea AU- Plun-Favreau, Hlne AU- Lewis, Patrick A AU- Hardy, John AU- Martins, L Miguel AU- Wood, Nicholas W PY- 2010 T2- PLoS Genetics J2- PLoS Genet UR- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3009676/ VL- 6 IS- 12 DO- 10.1371/journal.pgen.1001257 C2- 3009676 N2- Cancer and neurodegeneration are often thought of as disease mechanisms at opposite ends of a spectrum; one due to enhanced resistance to cell death and the other due to premature cell death. There is now accumulating evidence to link these two disparate processes. An increasing number of genetic studies add weight to epidemiological evidence suggesting that sufferers of a neurodegenerative disorder have a reduced incidence for most cancers, but an increased risk for other cancers. Many of the genes associated with either cancer and/or neurodegeneration play a central role in cell cycle control, DNA repair, and kinase signalling. However, the links between these two families of diseases remain to be proven. In this review, we discuss recent and sometimes as yet incomplete genetic discoveries that highlight the overlap of molecular pathways implicated in cancer and neurodegeneration. N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- A Novel HMM-Based Method for Detecting Enriched Transcription Factor Binding Sites Reveals RUNX3 as a Potential Target in Pancreatic Cancer Biology AU- Levkovitz, Liron AU- Yosef, Nir AU- Gershengorn, Marvin C AU- Ruppin, Eytan AU- Sharan, Roded AU- Oron, Yoram PY- 2010 T2- PLoS ONE J2- PLoS One UR- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3008686/ VL- 5 IS- 12 DO- 10.1371/journal.pone.0014423 C2- 3008686 N2- Background: Pancreatic adenocarcinoma (PAC) is one of the most intractable malignancies. In order to search for potential new therapeutic targets, we relied on computational methods aimed at identifying transcription factor binding sites (TFBSs) over-represented in the promoter regions of genes differentially expressed in PAC. Though many computational methods have been implemented to accomplish this, none has gained overall acceptance or produced proven novel targets in PAC. To this end we have developed DEMON, a novel method for motif detection. Methodology: DEMON relies on a hidden Markov model to score the appearance of sequence motifs, taking into account all potential sites in a promoter of potentially varying binding affinities. We demonstrate DEMON's accuracy on simulated and real data sets. Applying DEMON to PAC-related data sets identifies the RUNX family as highly enriched in PAC-related genes. Using a novel experimental paradigm to distinguish between normal and PAC cells, we find that RUNX3 mRNA (but not RUNX1 or RUNX2 mRNAs) exhibits time-dependent increases in normal but not in PAC cells. These increases are accompanied by changes in mRNA levels of putative RUNX gene targets. Conclusions: The integrated application of DEMON and a novel differentiation system led to the identification of a single family member, RUNX3, which together with four of its putative targets showed a robust response to a differentiation stimulus in healthy cells, whereas this regulatory mechanism was absent in PAC cells, emphasizing RUNX3 as a promising target for further studies. N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- Nicotinic Receptor Gene CHRNA4 Interacts with Processing Load in Attention AU- Espeseth, Thomas AU- Sneve, Markus Handal AU- Rootwelt, Helge AU- Laeng, Bruno PY- 2010 T2- PLoS ONE J2- PLoS One UR- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3008676/ VL- 5 IS- 12 DO- 10.1371/journal.pone.0014407 C2- 3008676 N2- Background: Pharmacological studies suggest that cholinergic neurotransmission mediates increases in attentional effort in response to high processing load during attention demanding tasks . Methodology/Principal Findings: In the present study we tested whether individual variation in CHRNA4, a gene coding for a subcomponent in 42 nicotinic receptors in the human brain, interacted with processing load in multiple-object tracking (MOT) and visual search (VS). We hypothesized that the impact of genotype would increase with greater processing load in the MOT task. Similarly, we predicted that genotype would influence performance under high but not low load in the VS task. Two hundred and two healthy persons (age range?=?39 77, Mean ?=?57.5, SD?=?9.4) performed the MOT task in which twelve identical circular objects moved about the display in an independent and unpredictable manner. Two to six objects were designated as targets and the remaining objects were distracters. The same observers also performed a visual search for a target letter (i.e. X or Z) presented together with five non-targets while ignoring centrally presented distracters (i.e. X, Z, or L). Targets differed from non-targets by a unique feature in the low load condition, whereas they shared features in the high load condition. CHRNA4 genotype interacted with processing load in both tasks. Homozygotes for the T allele (N?=?62) had better tracking capacity in the MOT task and identified targets faster in the high load trials of the VS task. Conclusion: The results support the hypothesis that the cholinergic system modulates attentional effort, and that common genetic variation can be used to study the molecular biology of cognition. N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- Somatic Mutation Profiles of MSI and MSS Colorectal Cancer Identified by Whole Exome Next Generation Sequencing and Bioinformatics Analysis AU- Timmermann, Bernd AU- Kerick, Martin AU- Roehr, Christina AU- Fischer, Axel AU- Isau, Melanie AU- Boerno, Stefan T AU- Wunderlich, Andrea AU- Barmeyer, Christian AU- Seemann, Petra AU- Koenig, Jana AU- Lappe, Michael AU- Kuss, Andreas W AU- Garshasbi, Masoud AU- Bertram, Lars AU- Trappe, Kathrin AU- Werber, Martin AU- Herrmann, Bernhard G AU- Zatloukal, Kurt AU- Lehrach, Hans AU- Schweiger, Michal R PY- 2010 T2- PLoS ONE J2- PLoS One UR- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3008745/ VL- 5 IS- 12 DO- 10.1371/journal.pone.0015661 C2- 3008745 N2- Background: Colorectal cancer (CRC) is with approximately 1 million cases the third most common cancer worldwide. Extensive research is ongoing to decipher the underlying genetic patterns with the hope to improve early cancer diagnosis and treatment. In this direction, the recent progress in next generation sequencing technologies has revolutionized the field of cancer genomics. However, one caveat of these studies remains the large amount of genetic variations identified and their interpretation. Methodology/Principal Findings: Here we present the first work on whole exome NGS of primary colon cancers. We performed 454 whole exome pyrosequencing of tumor as well as adjacent not affected normal colonic tissue from microsatellite stable (MSS) and microsatellite instable (MSI) colon cancer patients and identified more than 50,000 small nucleotide variations for each tissue. According to predictions based on MSS and MSI pathomechanisms we identified eight times more somatic non-synonymous variations in MSI cancers than in MSS and we were able to reproduce the result in four additional CRCs. Our bioinformatics filtering approach narrowed down the rate of most significant mutations to 359 for MSI and 45 for MSS CRCs with predicted altered protein functions. In both CRCs, MSI and MSS, we found somatic mutations in the intracellular kinase domain of bone morphogenetic protein receptor 1A, BMPR1A, a gene where so far germline mutations are associated with juvenile polyposis syndrome, and show that the mutations functionally impair the protein function. Conclusions/Significance: We conclude that with deep sequencing of tumor exomes one may be able to predict the microsatellite status of CRC and in addition identify potentially clinically relevant mutations. N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- High-Definition Mapping of Retroviral Integration Sites Defines the Fate of Allogeneic T Cells After Donor Lymphocyte Infusion AU- Cattoglio, Claudia AU- Maruggi, Giulietta AU- Bartholomae, Cynthia AU- Malani, Nirav AU- Pellin, Danilo AU- Cocchiarella, Fabienne AU- Magnani, Zulma AU- Ciceri, Fabio AU- Ambrosi, Alessandro AU- von Kalle, Christof AU- Bushman, Frederic D AU- Bonini, Chiara AU- Schmidt, Manfred AU- Mavilio, Fulvio AU- Recchia, Alessandra PY- 2010 T2- PLoS ONE J2- PLoS One UR- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3008730/ VL- 5 IS- 12 DO- 10.1371/journal.pone.0015688 C2- 3008730 N2- The infusion of donor lymphocytes transduced with a retroviral vector expressing the HSV-TK suicide gene in patients undergoing hematopoietic stem cell transplantation for leukemia/lymphoma promotes immune reconstitution and prevents infections and graft-versus-host disease. Analysis of the clonal dynamics of genetically modified lymphocytes in vivo is of crucial importance to understand the potential genotoxic risk of this therapeutic approach. We used linear amplification-mediated PCR and pyrosequencing to build a genome-wide, high-definition map of retroviral integration sites in the genome of peripheral blood T cells from two different donors and used gene expression profiling and bioinformatics to associate integration clusters to transcriptional activity and to genetic and epigenetic features of the T cell genome. Comparison with matched random controls and with integrations obtained from CD34+ hematopoietic stem/progenitor cells showed that integration clusters occur within chromatin regions bearing epigenetic marks associated with active promoters and regulatory elements in a cell-specific fashion. Analysis of integration sites in T cells obtained ex vivo two months after infusion showed no evidence of integration-related clonal expansion or dominance, but rather loss of cells harboring integration events interfering with RNA post-transcriptional processing. The study shows that high-definition maps of retroviral integration sites are a powerful tool to analyze the fate of genetically modified T cells in patients and the biological consequences of retroviral transduction. N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- In silico prediction of drug targets in Vibrio cholerae. AU- Katara, Pramod AU- Grover, Atul AU- Kuntal, Himani AU- Sharma, Vinay PY- 2010 T2- Protoplasma J2- Protoplasma UR- http://www.ncbi.nlm.nih.gov/pubmed/21174131 N2- Identification of potential drug targets is the first step in the process of modern drug discovery, subjected to their validation and drug development. Whole genome sequences of a number of organisms allow prediction of potential drug targets using sequence comparison approaches. Here, we present a subtractive approach exploiting the knowledge of global gene expression along with sequence comparisons to predict the potential drug targets more efficiently. Based on the knowledge of 155 known virulence and their coexpressed genes mined from microarray database in the public domain, 357 coexpressed probable virulence genes for Vibrio cholerae were predicted. Based on screening of Database of Essential Genes using blastn, a total of 102 genes out of these 357 were enlisted as vitally essential genes, and hence good putative drug targets. As the effective drug target is a protein which is only present in the pathogen, similarity search of these 102 essential genes against human genome sequence led to subtraction of 66 genes, thus leaving behind a subset of 36 genes whose products have been called as potential drug targets. The gene ontology analysis using Blast2GO of these 36 genes revealed their roles in important metabolic pathways of V. cholerae or on the surface of the pathogen. Thus, we propose that the products of these genes be evaluated as target sites of drugs against V. cholerae in future investigations. N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- Gene processing control loops suggested by sequencing, splicing, and RNA folding AU- Jeffries, Clark D AU- Perkins, Diana O AU- Guan, Xiaojun PY- 2010 T2- BMC bioinformatics J2- BMC Bioinformatics UR- http://www.biomedcentral.com/1471-2105/11/602 VL- 11 IS- 1 SP- 602 DO- 10.1186/1471-2105-11-602 N2- Abstract Background: Small RNAs are known to regulate diverse gene expression processes including translation, transcription, and splicing. Among small RNAs, the microRNAs (miRNAs) of 17 to 27 nucleotides (nts) undergo biogeneses including primary transcription, RNA excision and folding, nuclear export, cytoplasmic processing, and then bioactivity as regulatory agents. We propose that analogous hairpins from RNA molecules that function as part of the spliceosome might also be the source of small, regulatory RNAs (somewhat smaller than miRNAs). Results: Deep sequencing technology has enabled discovery of a novel 16-nt RNA sequence in total RNA from human brain that we propose is derived from RNU1, an RNA component of spliceosome assembly. Bioinformatic alignments compel inquiring whether the novel 16-nt sequence or its precursor have a regulatory function as well as determining aspects of how processing intersects with the miRNA biogenesis pathway. Specifically, our preliminary in silico investigations reveal the sequence could regulate splicing factor Arg/Ser rich 1 (SFRS1), a gene coding an essential protein component of the spliceosome. All 16-base source sequences in the UCSC Human Genome Browser are within the 14 instances of RNU1 genes listed in wgEncodeGencodeAutoV3. Furthermore, 10 of the 14 instances of the sequence are also within a common 28-nt hairpin-forming subsequence of RNU1. Conclusions: An abundant 16-nt RNA sequence is sourced from a spliceosomal RNA, lies in a stem of a predicted RNA hairpin, and includes reverse complements of subsequences of the 3'UTR of a gene coding for a spliceosome protein. Thus RNU1 could function both as a component of spliceosome assembly and as inhibitor of production of the essential, spliceosome protein coded by SFRS1. Beyond this example, a general procedure is needed for systematic discovery of multiple alignments of sequencing, splicing, and RNA folding data. N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- Aromatase Is a Direct Target of FOXL2: C134W in Granulosa Cell Tumors via a Single Highly Conserved Binding Site in the Ovarian Specific Promoter AU- Fleming, Nicholas I AU- Knower, Kevin C AU- Lazarus, Kyren A AU- Fuller, Peter J AU- Simpson, Evan R AU- Clyne, Colin D PY- 2010 T2- PLoS ONE J2- PLoS One UR- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3004790/ VL- 5 IS- 12 DO- 10.1371/journal.pone.0014389 C2- 3004790 N2- Background: Granulosa cell tumors (GCT) of the ovary often express aromatase and synthesize estrogen, which in turn may influence their progression. Recently a specific point mutation (C134W) in the FOXL2 protein was identified in 94% of adult-type GCT and it is likely to contribute to their development. A number of genes are known to be regulated by FOXL2, including aromatase/CYP19A1, but it is unclear which are direct targets and whether the C134W mutation alters their regulation. Recently, it has been reported that FOXL2 forms a complex with steroidogenic factor 1 (SF-1) which is a known regulator of aromatase in granulosa cells. Methodology/Principal Findings: In this work, the human GCT-derived cell lines KGN and COV434 were heterozygous and wildtype for the FOXL2:C134W mutation, respectively. KGN had abundant FOXL2 mRNA expression but it was not expressed in COV434. Expression of exogenous FOXL2:C134W in COV434 cells induced higher expression of a luciferase reporter for the ovarian specific aromatase promoter, promoter II (PII) (516bp) than expression of wildtype FOXL2, but did not alter induction of a similar reporter for the steroidogenic acute regulatory protein (StAR) promoter (1300bp). Co-immunoprecipitation confirmed that FOXL2 bound SF-1 and that it also bound its homologue, liver receptor homologue 1 (LRH-1), however, the C134W mutation did not alter these interactions or induce a selective binding of the proteins. A highly conserved putative binding site for FOXL2 was identified in PII. FOXL2 was demonstrated to bind the site by electrophoretic mobility shift assays (EMSA) and site-directed mutagenesis of this element blocked its differential induction by wildtype FOXL2 and FOXL2:C134W. Conclusions/Significance: These findings suggest that aromatase is a direct target of FOXL2:C134W in adult-type GCT via a single distinctive and highly conserved binding site in PII and therefore provide insight into the pathogenic mechanism of this mutation. N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- Evidences showing wide presence of small genomic aberrations in chronic lymphocytic leukemia AU- Kim, Yeong C AU- Jung, Yong-Chul AU- Chen, Jun AU- Alhasan, Ali H AU- Kaewsaard, Parawee AU- Zhang, Yanming AU- Ma, Shuo AU- Rosen, Steve AU- Wang, San Ming PY- 2010 T2- BMC research notes J2- BMC Res Notes UR- http://www.biomedcentral.com/1756-0500/3/341 VL- 3 IS- 1 SP- 341 DO- 10.1186/1756-0500-3-341 C2- 3016268 N2- Abstract Background: Chronic lymphocytic leukemia (CLL) is the most common adult leukemia in the western population. Although genetic factors are considered to contribute to CLL etiology, at present genomic aberrations identified in CLL are limited compared with those identified in other types of leukemia, which raises the question of the degree of genetic influence on CLL. We performed a high-resolution genome scanning study to address this issue. Findings: Using the restriction paired-end-based Ditag Genome Scanning technique, we analyzed three primary CLL samples at a kilobase resolution, and further validated the results in eight primary CLL samples including the two used for ditag collection. From 51,632 paired-end tags commonly detected in the three CLL samples representing 5% of the HindIII restriction fragments in the genomes, we identified 230 paired-end tags that were present in all three CLL genomes but not in multiple normal human genome reference sequences. Mapping the full-length sequences of the fragments detected by these unmapped tags in seven additional CLL samples confirmed that these are the genomic aberrations caused by small insertions and deletions, and base changes spreading across coding and non-coding regions. Conclusions: Our study identified hundreds of loci with insertion, deletion, base change, and restriction site polymorphism present in both coding and non-coding regions in CLL genomes, indicating the wide presence of small genomic aberrations in chronic lymphocytic leukemia. Our study supports the use of a whole genome sequencing approach for comprehensively decoding the CLL genome for better understanding of the genetic defects in CLL. N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- A Rare Myelin Protein Zero (MPZ) Variant Alters Enhancer Activity In Vitro and In Vivo AU- Antonellis, Anthony AU- Dennis, Megan Y AU- Burzynski, Grzegorz AU- Huynh, Jimmy AU- Maduro, Valerie AU- Hodonsky, Chani J AU- Khajavi, Mehrdad AU- Szigeti, Kinga AU- Mukkamala, Sandeep AU- Bessling, Seneca L AU- NISC Comparative Sequencing Program AU- Pavan, William J AU- McCallion, Andrew S AU- Lupski, James R AU- Green, Eric D PY- 2010 T2- PLoS ONE J2- PLoS One UR- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3002941/ VL- 5 IS- 12 DO- 10.1371/journal.pone.0014346 C2- 3002941 N2- Background: Myelin protein zero (MPZ) is a critical structural component of myelin in the peripheral nervous system. The MPZ gene is regulated, in part, by the transcription factors SOX10 and EGR2. Mutations in MPZ, SOX10, and EGR2 have been implicated in demyelinating peripheral neuropathies, suggesting that components of this transcriptional network are candidates for harboring disease-causing mutations (or otherwise functional variants) that affect MPZ expression. Methodology: We utilized a combination of multi-species sequence comparisons, transcription factor-binding site predictions, targeted human DNA re-sequencing, and in vitro and in vivo enhancer assays to study human non-coding MPZ variants. Principal Findings: Our efforts revealed a variant within the first intron of MPZ that resides within a previously described SOX10 binding site is associated with decreased enhancer activity, and alters binding of nuclear proteins. Additionally, the genomic segment harboring this variant directs tissue-relevant reporter gene expression in zebrafish. Conclusions: This is the first reported MPZ variant within a cis-acting transcriptional regulatory element. While we were unable to implicate this variant in disease onset, our data suggests that similar non-coding sequences should be screened for mutations in patients with neurological disease. Furthermore, our multi-faceted approach for examining the functional significance of non-coding variants can be readily generalized to study other loci important for myelin structure and function. N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- Recombinant expression, purification and copper-binding characteristics of the amino terminus of a Plasmodium falciparum copper transport protein AU- Choveaux, David AU- Goldring, JP Dean PY- 2010 T2- Malaria journal J2- Malar J UR- http://www.malariajournal.com/content/9/S2/-P62 VL- 9 IS- Suppl 2 SP- P62 DO- 10.1186/1475-2875-9-S2-P62 N2- N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- Concurrent genetic alterations in DNA polymerase proofreading and mismatch repair in human colorectal cancer. AU- Yoshida, Rintaro AU- Miyashita, Kaname AU- Inoue, Mayuko AU- Shimamoto, Akiyoshi AU- Yan, Zhao AU- Egashira, Akinori AU- Oki, Eiji AU- Kakeji, Yoshishiro AU- Oda, Shinya AU- Maehara, Yoshihiko PY- 2010 T2- European journal of human genetics : EJHG J2- Eur J Hum Genet UR- http://www.ncbi.nlm.nih.gov/pubmed/21157497 N2- Genomic sequences encoding the 3' exonuclease (proofreading) domains of both replicative DNA polymerases, pol delta and pol epsilon, were explored simultaneously in human colorectal carcinomas including six established cell lines. Three unequivocal sequence alterations, including one previously reported, were found, and all these were considered as dysfunctional mutations in light of the local amino-acid sequences. In particular, the F367S mutation found in the POLE gene encoding the pol epsilon catalytic subunit, which includes the proofreading domain, is the first found in human diseases. Surprisingly, the tumours carrying these proofreading domain mutations were all defective in DNA mismatch repair (MMR). In addition to the two cell lines with acknowledged MMR gene mutations, the third tumour was also demonstrated to harbour a distinct mutation in MLH1, and indeed exhibited a microsatellite-unstable phenotype. These findings suggest that, in concert with MMR deficiency, defective polymerase proofreading may also contribute to the mutator phenotype observed in human colorectal cancer. Our observations may suggest previously unrecognised complexities in the molecular abnormalities underlying the mutator phenotype in human neoplasms.European Journal of Human Genetics advance online publication, 15 December 2010; doi:10.1038/ejhg.2010.216. N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- Evolution of MicroRNAs and the Diversification of Species. AU- Loh, Yong-Hwee E AU- Yi, Soojin V AU- Streelman, J Todd PY- 2010 T2- Genome Biology and Evolution J2- Genome Biol Evol UR- http://www.ncbi.nlm.nih.gov/pubmed/21169229 N2- MicroRNAs (miRNAs) are ancient, short, non-coding RNA molecules that regulate the transcriptome through post-transcriptional mechanisms. miRNA riboregulation is involved in a diverse range of biological processes and mis-regulation is implicated in disease. It is generally thought that miRNAs function to canalize cellular outputs, for instance as 'fail-safe' repressors of gene mis-expression. Genomic surveys in humans have revealed reduced genetic polymorphism and the signature of negative selection for both miRNAs themselves and the target sequences to which they are predicted to bind. We investigated the evolution of miRNAs and their binding sites across cichlid fishes from Lake Malawi (East Africa), where hundreds of diverse species have evolved in the last million years. Using low-coverage genome sequence data, we identified 100 cichlid miRNA genes with mature regions that are highly conserved in other animal species. We computationally predicted target sites on the 3'-UTRs of cichlid genes to which miRNAs may bind, and found that these sites possessed elevated single nucleotide polymorphism (SNP) densities. Furthermore, polymorphic sites in predicted miRNA targets showed higher minor allele frequencies on average and greater genetic differentiation between Malawi lineages when compared to a neutral expectation and non-target 3' UTR SNPs. Our data suggest that divergent selection on miRNA riboregulation may have contributed to the diversification of cichlid species, and may similarly play a role in rapid phenotypic evolution of other natural systems. N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- A unique chromatin signature uncovers early developmental enhancers in humans. AU- Rada-Iglesias, Alvaro AU- Bajpai, Ruchi AU- Swigut, Tomek AU- Brugmann, Samantha A AU- Flynn, Ryan A AU- Wysocka, Joanna PY- 2010 T2- Nature J2- Nature UR- http://www.ncbi.nlm.nih.gov/pubmed/21160473 N2- Cell-fate transitions involve the integration of genomic information encoded by regulatory elements, such as enhancers, with the cellular environment. However, identification of genomic sequences that control human embryonic development represents a formidable challenge. Here we show that in human embryonic stem cells (hESCs), unique chromatin signatures identify two distinct classes of genomic elements, both of which are marked by the presence of chromatin regulators p300 and BRG1, monomethylation of histone H3 at lysine 4 (H3K4me1), and low nucleosomal density. In addition, elements of the first class are distinguished by the acetylation of histone H3 at lysine 27 (H3K27ac), overlap with previously characterized hESC enhancers, and are located proximally to genes expressed in hESCs and the epiblast. In contrast, elements of the second class, which we term 'poised enhancers', are distinguished by the absence of H3K27ac, enrichment of histone H3 lysine 27 trimethylation (H3K27me3), and are linked to genes inactive in hESCs and instead are involved in orchestrating early steps in embryogenesis, such as gastrulation, mesoderm formation and neurulation. Consistent with the poised identity, during differentiation of hESCs to neuroepithelium, a neuroectoderm-specific subset of poised enhancers acquires a chromatin signature associated with active enhancers. When assayed in zebrafish embryos, poised enhancers are able to direct cell-type and stage-specific expression characteristic of their proximal developmental gene, even in the absence of sequence conservation in the fish genome. Our data demonstrate that early developmental enhancers are epigenetically pre-marked in hESCs and indicate an unappreciated role of H3K27me3 at distal regulatory elements. Moreover, the wealth of new regulatory sequences identified here provides an invaluable resource for studies and isolation of transient, rare cell populations representing early stages of human embryogenesis. N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- Next generation sequencing and analysis of a conserved transcriptome of New Zealand's kiwi AU- Subramanian, Sankar AU- Huynen, Leon AU- Millar, Craig D AU- Lambert, David M PY- 2010 T2- BMC evolutionary biology J2- BMC Evol Biol UR- http://www.biomedcentral.com/1471-2148/10/387 VL- 10 IS- 1 SP- 387 DO- 10.1186/1471-2148-10-387 C2- 3009673 N2- Abstract Background: Kiwi is a highly distinctive, flightless and endangered ratite bird endemic to New Zealand. To understand the patterns of molecular evolution of the nuclear protein-coding genes in brown kiwi (Apteryx australis mantelli) and to determine the timescale of avian history we sequenced a transcriptome obtained from a kiwi embryo using next generation sequencing methods. We then assembled the conserved protein-coding regions using the chicken proteome as a scaffold. Results: Using 1,543 conserved protein coding genes we estimated the neutral evolutionary divergence between the kiwi and chicken to be ~45%, which is approximately equal to the divergence computed for the human-mouse pair using the same set of genes. A large fraction of genes was found to be under high selective constraint, as most of the expressed genes appeared to be involved in developmental gene regulation. Our study suggests a significant relationship between gene expression levels and protein evolution. Using sequences from over 700 nuclear genes we estimated the divergence between the two basal avian groups, Palaeognathae and Neognathae to be 132 million years, which is consistent with previous studies using mitochondrial genes. Conclusions: The results of this investigation revealed patterns of mutation and purifying selection in conserved protein coding regions in birds. Furthermore this study suggests a relatively cost-effective way of obtaining a glimpse into the fundamental molecular evolutionary attributes of a genome, particularly when no closely related genomic sequence is available. N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- Transcriptional Activation of REST by Sp1 in Huntington's Disease Models AU- Ravache, Myriam AU- Weber, Chantal AU- Mrienne, Karine AU- Trottier, Yvon PY- 2010 T2- PLoS ONE J2- PLoS One UR- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3001865/ VL- 5 IS- 12 DO- 10.1371/journal.pone.0014311 C2- 3001865 N2- In Huntington's disease (HD), mutant huntingtin (mHtt) disrupts the normal transcriptional program of disease neurons by altering the function of several gene expression regulators such as Sp1. REST (Repressor Element-1 Silencing Transcription Factor), a key regulator of neuronal differentiation, is also aberrantly activated in HD by a mechanism that remains unclear. Here, we show that the level of REST mRNA is increased in HD mice and in NG108 cells differentiated into neuronal-like cells and expressing a toxic mHtt fragment. Using luciferase reporter gene assay, we delimited the REST promoter regions essential for mHtt-mediated REST upregulation and found that they contain Sp factor binding sites. We provide evidence that Sp1 and Sp3 bind REST promoter and interplay to fine-tune REST transcription. In undifferentiated NG108 cells, Sp1 and Sp3 have antagonistic effect, Sp1 acting as an activator and Sp3 as a repressor. Upon neuronal differentiation, we show that the amount and ratio of Sp1/Sp3 proteins decline, as does REST expression, and that the transcriptional role of Sp3 shifts toward a weak activator. Therefore, our results provide new molecular information to the transcriptional regulation of REST during neuronal differentiation. Importantly, specific knockdown of Sp1 abolishes REST upregulation in NG108 neuronal-like cells expressing mHtt. Our data together with earlier reports suggest that mHtt triggers a pathogenic cascade involving Sp1 activation, which leads to REST upregulation and repression of neuronal genes. N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- Personalized medicine - The promised land are we there yet? AU- Li, Chumei PY- 2010 T2- Clinical genetics J2- Clin Genet UR- http://www.ncbi.nlm.nih.gov/pubmed/21204795 N2- The delivery of personalized genomic medicine (see box1 for a comparison of genomic vs. genetic medicine and box2 for glossary) hinges on obtaining personal genomic data through genome-wide association studies (GWAS) or whole genome sequencing. After the completion of the human genome project (see box 3 for human genome projects and its derivative projects) in 2003, there appeared to be a period of euphoric optimism that as soon as the cost of sequencing the whole human genome could be brought down to an affordable range, the promise of personalized medicine would become a reality. However, inasmuch as the miraculous technological advancements are making whole genome data acquisition an inexpensive reality, we are also starting to appreciate that making sense of the enormous amount of genomic data is a far bigger hurdle. Issues, both scientific and ethico-legal, will have to be addressed as genomic data are been pushed for clinical and direct-to-consumer utilization. N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER- TY- JOUR TI- Mining human genome for novel purinergic P2Y receptors: a sequence analysis and molecular modeling approach. AU- Bhatnagar, Sonika AU- Mishra, Shubhi AU- Pathak, Ravi PY- 2010 T2- Journal of receptor and signal transduction research J2- J Recept Signal Transduct Res UR- http://www.ncbi.nlm.nih.gov/pubmed/21142848 N2- The purinergic P2Y receptors are G-protein coupled receptors (GPCRs) that control many physiological processes by mediating cellular responses to purines, pyrimidines and their analogues. They can be used as potential therapeutic targets in a variety of disease conditions. Therefore, it is critical to identify new members of this family of receptors from the human genome and characterize them for their role in health and disease. In the present work, molecular modeling was carried out for the 21 known P2Y receptors. Binding site analysis was done on the basis of docking and site-directed mutagenesis data. Thus, conserved features of P2Y receptors could be formulated. These features can be used to determine the purinergic nature of potential P2Y receptors in the human genome. We applied this knowledge to human genome GPCR sequences found by sensitive sequence search techniques and identified two orphan receptors, namely GPR34 and GP171 that have all the necessary conserved features of P2Y receptors. N1- Exported from www.Quertle.info. Search query: Genome-sequencing . ER-
Genome Project Standards in a New Era of Sequencing 9 OCTOBER 2009 VOL 326 SCIENCE Standard Draft : minimally or unfiltered data, from any number of different sequencing platforms, that are assembled into contigs. This is the minimum standard for a submission to the public databases. Sequence of this quality will likely harbor many regions of poor quality and can be relatively incomplete. It may not always be possible to remove contaminating sequence data. Despite its shortcomings, Standard Draft is the least expensive to produce and still possesses useful information. High-Quality Draft : overall coverage representing at least 90% of the genome or target region. Efforts should be made to exclude contaminating sequences. This is still a draft assembly with little or no manual review of the product. Sequence errors and misassem- blies are possible, with no implied order and orientation to contigs. This is appropriate for general assessment of gene content. Improved High-Quality Draft : additional work has been performed beyond the initial shotgun sequencing and High-Quality Draft assembly, by using either manual or automated methods. This should contain no discernable misassemblies and should have undergone some form of gap resolution to reduce the number of contigs and supercontigs (or scaffolds). Undetectable misassemblies are still possible, particularly in repetitive regions. Low-quality regions and potential base errors may also be present. This standard is normally adequate for comparison with other genomes. Annotation-Directed Improvement : may overlap with the previous standards, but the term emphasizes the verifi cation and correction of anomalies within coding regions, such as frameshifts, and stop codons. It will most often be used in cases involving complex genomes where improvement beyond this category fails to outweigh the associated costs. Gene models (gene calls, including intronexon determination for eukaryotes) and annotation of the genomic content should fully support the biology of the organism and the scientifi c questions being investigated. Exceptions to this gene-specifi c fi nishing standard should be noted in the submission. Repeat regions at this level are not resolved, so errors in those regions are much more likely. This standard is useful for gene comparisons, alternative splicing analysis, and pathway reconstruction. Noncontiguous Finished : describes highquality assemblies that have been subject to automated and manual improvement, and where closure approaches have been successful for almost all gaps, misassemblies, and low-quality regions. Attempts have been made to resolve all gap and sequence uncertainties, and only those recalcitrant to resolution remain (with notations in the genome submission as to the nature of the uncertainty). This product is thus of Finished quality with the only exception being repetitive or intractable gaps, along with heterochromatic sequence for eukaryotic applications. Thus, it is appropriate for most analyses. For nearly all higher organisms, this is the grade previously called Finished. Finished : refers to the current gold standard; genome sequences with less than 1 error per 100,000 base pairs and where each replicon is assembled into a single contiguous sequence with a minimal number of possible exceptions commented in the submission record. All sequences are complete and have been reviewed and edited, all known misassemblies have been resolved, and repetitive sequences have been ordered and correctly assembled. Remaining exceptions to highly accurate sequence within the euchromatin are commented in the submission. The Finished product is appropriate for all types of detailed analyses and acts as a high-quality reference genome for comparative purposes. Some microbial genome sequences where multiple platforms have been used for the same genome have exceeded this standard, and it is believed that no bases are incorrect except for natural, low-level biological variation. 全文下载： Genome Project Standards in a New Era of Sequencin
标签: Sequencing
