Rapid whole-genome mutational profiling using next-generation sequencing technologies.
AuthorsSmith DR, Quinlan AR, Peckham HE, Makowsky K, Tao W, Woolf B, Shen L, Donahue WF, Tusneem N, Stromberg MP, Stewart DA, Zhang L, Ranade SS, Warner JB, Lee CC, Coleman BE, Zhang Z, McLaughlin SF, Malek JA, Sorenson JM, Blanchard AP, Chapman J, Hillman D, Ch
JournalGenome Res
PubMed ID18775913
Forward genetic mutational studies, adaptive evolution, and phenotypic screening are powerful tools for creating new variant organisms with desirable traits. However, mutations generated in the process cannot be easily identified with traditional genetic tools. We show that new high-throughput, massively parallel sequencing technologies can completely and accurately characterize a ... More
The complete genome sequence of Escherichia coli DH10B: insights into the biology of a laboratory workhorse.
AuthorsDurfee T, Nelson R, Baldwin S, Plunkett G 3rd, Burland V, Mau B, Petrosino JF, Qin X, Muzny DM, Ayele M, Gibbs RA, Csorgo B, Posfai G, Weinstock GM, Blattner FR
JournalJ Bacteriol
PubMed ID18245285
Escherichia coli DH10B was designed for the propagation of large insert DNA library clones. It is used extensively, taking advantage of properties such as high DNA transformation efficiency and maintenance of large plasmids. The strain was constructed by serial genetic recombination steps, but the underlying sequence changes remained unverified. ... More
A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning.
AuthorsValouev A, Ichikawa J, Tonthat T, Stuart J, Ranade S, Peckham H, Zeng K, Malek JA, Costa G, McKernan K, Sidow A, Fire A, Johnson SM
JournalGenome Res
PubMed ID18477713
Using the massively parallel technique of sequencing by oligonucleotide ligation and detection (SOLiD; Applied Biosystems), we have assessed the in vivo positions of more than 44 million putative nucleosome cores in the multicellular genetic model organism Caenorhabditis elegans. These analyses provide a global view of the chromatin architecture of ... More
Full-Malaria/Parasites and Full-Arthropods: databases of full-length cDNAs of parasites and arthropods, update 2009
'Full-Malaria/Parasites is a database for transcriptome studies of apicomplexa and other parasites, which is based on our original full-length cDNA sequences and physical cDNA clone resources. In this update, the database has been expanded to contain the shogun sequencing for the entire sequences of 14 818 non-redundant full-length cDNA clones ... More
Small RNA profiling reveals antisense transcription throughout the KSHV genome and novel small RNAs.
'Kaposi''s sarcoma-associated herpesvirus (KSHV) is a human tumor virus that encodes 12 precursor microRNAs (pre-miRNAs) that give rise to 17 different known approximately 22-nucleotide (nt) effector miRNAs. Like all herpesviruses, KSHV has two modes of infection: (1) a latent mode whereby only a subset of viral genes are expressed and ... More
Exonuclease activity of proofreading DNA polymerases is at the origin of artifacts in molecular profiling studies
AuthorsGury, J; Zinger, L; Gielly, L; Taberlet, P; Geremia, RA
Journal
PubMed ID
'CE fingerprint methods are commonly used in microbial ecology. We have previously noticed that the position and number of peaks in CE-SSCP (single-strand conformation polymorphism) profiles depend on the DNA polymerase used in PCR [1]. Here, we studied the fragments produced by Taq polymerase as well as four commercially available ... More
Complementation of Rickettsia rickettsii RelA/SpoT restores a nonlytic plaque phenotype.
AuthorsClark TR, Ellison DW, Kleba B, Hackstadt T
JournalInfect Immun
PubMed ID21300770
'Spotted fever group rickettsiae are known to produce distinct plaque phenotypes. Strains that cause lytic infections in cell culture form clear plaques, while nonlytic strains form opaque plaques in which the cells remain intact. Clear plaques have historically been associated with more-virulent species or strains of spotted fever group rickettsiae. ... More
A consistency-based consensus algorithm for de novo and reference-guided sequence assembly of short reads.
AuthorsRausch T, Koren S, Denisov G, Weese D, Emde AK, Doring A, Reinert K
JournalBioinformatics
PubMed ID19269990
'MOTIVATION: Novel high-throughput sequencing technologies pose new algorithmic challenges in handling massive amounts of short-read, high-coverage data. A robust and versatile consensus tool is of particular interest for such data since a sound multi-read alignment is a prerequisite for variation analyses, accurate genome assemblies and insert sequencing. RESULTS: A multi-read ... More
De novo sequencing of plant genomes using second-generation technologies.
AuthorsImelfort M, Edwards D
JournalBrief Bioinform
PubMed ID19933209
'The ability to sequence the DNA of an organism has become one of the most important tools in modern biological research. Until recently, the sequencing of even small model genomes required substantial funds and international collaboration. The development of ''second-generation'' sequencing technology has increased the throughput and reduced the ... More
Integrating multiple 'omics' analysis for microbial biology: application and methodologies.
AuthorsZhang W, Li F, Nie L
JournalMicrobiology
PubMed ID19910409
'Recent advances in various ''omics'' technologies enable quantitative monitoring of the abundance of various biological molecules in a high-throughput manner, and thus allow determination of their variation between different biological states on a genomic scale. Several popular ''omics'' platforms that have been used in microbial systems biology include transcriptomics, which ... More
Strand-specific deep sequencing of the transcriptome.
AuthorsVivancos AP, Guell M, Dohm JC, Serrano L, Himmelbauer H
JournalGenome Res
PubMed ID20519413
'Several studies support that antisense-mediated regulation may affect a large proportion of genes. Using the Illumina next-generation sequencing platform, we developed DSSS (direct strand specific sequencing), a strand-specific protocol for transcriptome sequencing. We tested DSSS with RNA from two samples, prokaryotic (Mycoplasma pneumoniae) as well as eukaryotic (Mus musculus), and ... More
Accurate SNP and mutation detection by targeted custom microarray-based genomic enrichment of short-fragment sequencing libraries.
AuthorsMokry M, Feitsma H, Nijman IJ, de Bruijn E, van der Zaag PJ, Guryev V, Cuppen E
JournalNucleic Acids Res
PubMed ID20164091
'Microarray-based enrichment of selected genomic loci is a powerful method for genome complexity reduction for next-generation sequencing. Since the vast majority of exons in vertebrate genomes are smaller than 150 nt, we explored the use of short fragment libraries (85-110 bp) to achieve higher enrichment specificity by reducing carryover ... More
Predictable dynamic program of timing of DNA replication in human cells.
AuthorsDesprat R, Thierry-Mieg D, Lailler N, Lajugie J, Schildkraut C, Thierry-Mieg J, Bouhassira EE
JournalGenome Res
PubMed ID19767418
'The organization of mammalian DNA replication is poorly understood. We have produced high-resolution dynamic maps of the timing of replication in human erythroid, mesenchymal, and embryonic stem (ES) cells using TimEX, a method that relies on gaussian convolution of massive, highly redundant determinations of DNA copy-number variations during S ... More
PerM: efficient mapping of short sequencing reads with periodic full sensitive spaced seeds.
AuthorsChen Y, Souaiaia T, Chen T
JournalBioinformatics
PubMed ID19675096
'MOTIVATION: The explosion of next-generation sequencing data has spawned the design of new algorithms and software tools to provide efficient mapping for different read lengths and sequencing technologies. In particular, ABI''s sequencer (SOLiD system) poses a big computational challenge with its capacity to produce very large amounts of data, and ... More
De novo assembly of human genomes with massively parallel short read sequencing.
AuthorsLi R, Zhu H, Ruan J, Qian W, Fang X, Shi Z, Li Y, Li S, Shan G, Kristiansen K, Li S, Yang H, Wang J, Wang J
JournalGenome Res
PubMed ID20019144
'Next-generation massively parallel DNA sequencing technologies provide ultrahigh throughput at a substantially lower unit data cost; however, the data are very short read length sequences, making de novo assembly extremely challenging. Here, we describe a novel method for de novo assembly of large genomes from short read sequences. ... More
Small silencing RNAs: an expanding universe
AuthorsGhildiyal, M; Zamore, PD
Journal
PubMed ID
'Since the discovery in 1993 of the first small silencing RNA, a dizzying number of small RNA classes have been identified, including microRNAs (miRNAs), small interfering RNAs (siRNAs) and Piwi-interacting RNAs (piRNAs). These classes differ in their biogenesis, their modes of target regulation and in the biological pathways they regulate. ... More
Web-queryable large-scale data sets for hypothesis generation in plant biology.
AuthorsBrady SM, Provart NJ
JournalPlant Cell
PubMed ID19401381
'The approaching end of the 21st century''s first decade marks an exciting time for plant biology. Several National Science Foundation Arabidopsis 2010 Projects will conclude, and whether or not the stated goal of the National Science Foundation 2010 Program-to determine the function of 25,000 Arabidopsis genes by 2010-is reached, these ... More
Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes.
AuthorsHillmer AM, Yao F, Inaki K, Lee WH, Ariyaratne PN, Teo AS, Woo XY, Zhang Z, Zhao H, Ukil L, Chen JP, Zhu F, So JB, Salto-Tellez M, Poh WT, Zawack KF, Nagarajan N, Gao S, Li G, Kumar V, Lim HP, Sia YY, Chan CS, Leong ST, Neo SC, Choi PS, Thoreau H, Tan PB, Shahab A, Ruan X, Bergh J, Hall P, Cacheux-Rataboul V, Wei CL, Yeoh KG, Sung WK, Bourque G, Liu ET, Ruan Y
JournalGenome Res
PubMed ID21467267
'Somatic genome rearrangements are thought to play important roles in cancer development. We optimized a long-span paired-end-tag (PET) sequencing approach using 10-Kb genomic DNA inserts to study human genome structural variations (SVs). The use of a 10-Kb insert size allows the identification of breakpoints within repetitive or homology-containing regions of ... More
BFAST: An Alignment Tool for Large Scale Genome Resequencing
AuthorsHomer, N; Merriman, B; Nelson, SF
Journal
PubMed ID
'Background: The new generation of massively parallel DNA sequencers, combined with the challenge of whole human genome resequencing, result in the need for rapid and accurate alignment of billions of short DNA sequence reads to a large reference genome. Speed is obviously of great importance, but equally important is maintaining ... More
Every genome sequence needs a good map.
AuthorsLewin HA, Larkin DM, Pontius J, O'Brien SJ
JournalGenome Res
PubMed ID19596977
Next Generation Sequencing in Nonmodel Organisms: Has the Future Arrived?
AuthorsJohansson, ML
Journal
PubMed ID
Deep sequencing maps the maize epigenomic landscape.
AuthorsEckardt NA
JournalPlant Cell
PubMed ID19557884
Epigenetic and microRNA-mediated regulation in diabetes.
AuthorsMuhonen P, Holthofer H
JournalNephrol Dial Transplant
PubMed ID19145005
A report on the 2009 SIG on short read sequencing and algorithms (Short-SIG).
AuthorsBrudno M, Medvedev P, Stoye J, De La Vega FM
JournalBioinformatics
PubMed ID19783529
Rise of the Machines
AuthorsGresham, D; Kruglyak, L
Journal
PubMed ID
Efficient mapping of Applied Biosystems SOLiD sequence data to a reference genome for functional genomic applications.
AuthorsOndov BD, Varadarajan A, Passalacqua KD, Bergman NH
JournalBioinformatics
PubMed ID18842598
Here, we report the development of SOCS (short oligonucleotide color space), a program designed for efficient and flexible mapping of Applied Biosystems SOLiD sequence data onto a reference genome. SOCS performs its mapping within the context of 'color space', and it maximizes usable data by allowing a user-specified number of ... More
Population genetic inference from genomic sequence variation.
AuthorsPool JE, Hellmann I, Jensen JD, Nielsen R
JournalGenome Res
PubMed ID20067940
Population genetics has evolved from a theory-driven field with little empirical data into a data-driven discipline in which genome-scale data sets test the limits of available models and computational analysis methods. In humans and a few model organisms, analyses of whole-genome sequence polymorphism data are currently under way. And ... More
Assembly of large genomes using second-generation sequencing.
AuthorsSchatz MC, Delcher AL, Salzberg SL
JournalGenome Res
PubMed ID20508146
Second-generation sequencing technology can now be used to sequence an entire human genome in a matter of days and at low cost. Sequence read lengths, initially very short, have rapidly increased since the technology first appeared, and we now are seeing a growing number of efforts to sequence large genomes ... More
Efficient mapping of Applied Biosystems SOLiD sequence data to a reference genome for functional genomic applications
Here, we report the development of SOCS (short oligonucleotide color space), a program designed for efficient and flexible mapping of Applied Biosystems SOLiD sequence data onto a reference genome. SOCS performs its mapping within the context of color space, and it maximizes usable data by allowing a user-specified number of ... More
The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants.
AuthorsCock PJ, Fields CJ, Goto N, Heuer ML, Rice PM
JournalNucleic Acids Res
PubMed ID20015970
FASTQ has emerged as a common file format for sharing sequencing read data combining both the sequence and an associated per base quality score, despite lacking any formal definition to date, and existing in at least three incompatible variants. This article defines the FASTQ format, covering the original Sanger standard, ... More
Dissection of gene regulatory networks in embryonic stem cells by means of high-throughput sequencing
AuthorsBeisel, C; Paro, R
Journal
PubMed ID
Transcription factor regulation of gene expression and chromatin-controlled epigenetic memory systems are closely cooperating in establishing the pluripotent state of embryonic stem (ES) cells and maintaining cell fate decisions throughout development of an organism. A thorough understanding of the regulatory transcriptional circuitry that rules the underlying plastic yet heritable gene ... More
Slider--maximum use of probability information for alignment of short sequence reads and SNP detection.
AuthorsMalhis N, Butterfield YS, Ester M, Jones SJ
JournalBioinformatics
PubMed ID18974170
MOTIVATION: A plethora of alignment tools have been created that are designed to best fit different types of alignment conditions. While some of these are made for aligning Illumina Sequence Analyzer reads, none of these are fully utilizing its probability (prb) output. In this article, we will introduce ... More
Transcriptional consequences of genomic structural aberrations in breast cancer.
AuthorsInaki K, Hillmer AM, Ukil L, Yao F, Woo XY, Vardy LA, Zawack KF, Lee CW, Ariyaratne PN, Chan YS, Desai KV, Bergh J, Hall P, Putti TC, Ong WL, Shahab A, Cacheux-Rataboul V, Karuturi RK, Sung WK, Ruan X, Bourque G, Ruan Y, Liu ET
JournalGenome Res
PubMed ID21467264
Using a long-span, paired-end deep sequencing strategy, we have comprehensively identified cancer genome rearrangements in eight breast cancer genomes. Herein, we show that 40%-54% of these structural genomic rearrangements result in different forms of fusion transcripts and that 44% are potentially translated. We find that single segmental tandem duplication spanning ... More
Sequence-specific reconstruction from fragmentary databases using seed sequences: implementation and validation on SAGE, proteome and generic sequencing data.
AuthorsSobreira TJ, Gruber A
JournalBioinformatics
PubMed ID18544546
MOTIVATION: DNA assembly programs classically perform an all-against-all comparison of reads to identify overlaps, followed by a multiple sequence alignment and generation of a consensus sequence. If the aim is to assemble a particular segment, instead of a whole genome or transcriptome, a target-specific assembly is a more sensible approach. ... More
A global role for KLF1 in erythropoiesis revealed by ChIP-seq in primary erythroid cells.
AuthorsTallack MR, Whitington T, Yuen WS, Wainwright EN, Keys JR, Gardiner BB, Nourbakhsh E, Cloonan N, Grimmond SM, Bailey TL, Perkins AC
JournalGenome Res
PubMed ID20508144
KLF1 regulates a diverse suite of genes to direct erythroid cell differentiation from bipotent progenitors. To determine the local cis-regulatory contexts and transcription factor networks in which KLF1 operates, we performed KLF1 ChIP-seq in the mouse. We found at least 945 sites in the genome of E14.5 fetal liver erythroid ... More
Bulk Segregation Mapping of Mutations in Closely Related Strains of Mice.
AuthorsXia Y, Won S, Du X, Lin P, Ross C, La Vine D, Wiltshire S, Leiva G, Vidal SM, Whittle B, Goodnow CC, Koziol J, Moresco EM, Beutler B
JournalGenetics
PubMed ID20923982
Phenovariance may be obscured when genetic mapping is performed using highly divergent strains, and closely similar strains are preferred if adequate marker density can be established. We sequenced the C57BL/10J mouse genome using the Applied Biosystems SOLiD platform, and here describe a genome-wide panel of informative markers that permits the ... More
ABySS: a parallel assembler for short read sequence data.
AuthorsSimpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I
JournalGenome Res
PubMed ID19251739
Widespread adoption of massively parallel deoxyribonucleic acid (DNA) sequencing instruments has prompted the recent development of de novo short read assembly algorithms. A common shortcoming of the available tools is their inability to efficiently assemble vast amounts of data generated from large-scale sequencing projects, such as the sequencing of ... More
Genome-wide misexpression of X-linked versus autosomal genes associated with hybrid male sterility.
AuthorsLu X, Shapiro JA, Ting CT, Li Y, Li C, Xu J, Huang H, Cheng YJ, Greenberg AJ, Li SH, Wu ML, Shen Y, Wu CI
JournalGenome Res
PubMed ID20511493
Postmating reproductive isolation is often manifested as hybrid male sterility, for which X-linked genes are overrepresented (the so-called large X effect). In contrast, X-linked genes are significantly under-represented among testis-expressing genes. This seeming contradiction may be germane to the X:autosome imbalance hypothesis on hybrid sterility, in which the X-linked effect ... More
Sequence-specific error profile of Illumina sequencers.
AuthorsNakamura K, Oshima T, Morimoto T, Ikeda S, Yoshikawa H, Shiwa Y, Ishikawa S, Linak MC, Hirai A, Takahashi H, Altaf-Ul-Amin M, Ogasawara N, Kanaya S
JournalNucleic Acids Res
PubMed ID21576222
We identified the sequence-specific starting positions of consecutive miscalls in the mapping of reads obtained from the Illumina Genome Analyser (GA). Detailed analysis of the miscall pattern indicated that the underlying mechanism involves sequence-specific interference of the base elongation process during sequencing. The two major sequence patterns that trigger this ... More
De novo fragment assembly with short mate-paired reads: Does the read length matter?
AuthorsChaisson MJ, Brinza D, Pevzner PA
JournalGenome Res
PubMed ID19056694
Increasing read length is currently viewed as the crucial condition for fragment assembly with next-generation sequencing technologies. However, introducing mate-paired reads (separated by a gap of length, GapLength) opens a possibility to transform short mate-pairs into long mate-reads of length approximately GapLength, and thus raises the question as to ... More
Improvements to services at the European Nucleotide Archive.
AuthorsLeinonen R, Akhtar R, Birney E, Bonfield J, Bower L, Corbett M, Cheng Y, Demiralp F, Faruque N, Goodgame N, Gibson R, Hoad G, Hunter C, Jang M, Leonard S, Lin Q, Lopez R, Maguire M, McWilliam H, Plaister S, Radhakrishnan R, Sobhany S, Slater G, Ten Hoopen
JournalNucleic Acids Res
PubMed ID19906712
The European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena) is Europe's primary nucleotide sequence archival resource, safeguarding open nucleotide data access, engaging in worldwide collaborative data exchange and integrating with the scientific publication process. ENA has made significant contributions to the collaborative nucleotide archival arena as an active proponent of extending the ... More
Chromatin and sequence features that define the fine and gross structure of genomic methylation patterns.
AuthorsEdwards JR, O'Donnell AH, Rollins RA, Peckham HE, Lee C, Milekic MH, Chanrion B, Fu Y, Su T, Hibshoosh H, Gingrich JA, Haghighi F, Nutter R, Bestor TH
JournalGenome Res
PubMed ID20488932
Abnormalities of genomic methylation patterns are lethal or cause disease, but the cues that normally designate CpG dinucleotides for methylation are poorly understood. We have developed a new method of methylation profiling that has single-CpG resolution and can address the methylation status of repeated sequences. We have used this method ... More
Sliced microRNA targets and precise loop-first processing of MIR319 hairpins revealed by analysis of the Physcomitrella patens degradome.
AuthorsAddo-Quaye C, Snyder JA, Park YB, Li YF, Sunkar R, Axtell MJ
JournalRna
PubMed ID19850910
Expression profiling of the 5' ends of uncapped mRNAs (""degradome"""" sequencing) can be used to empirically catalog microRNA (miRNA) targets, to probe patterns of miRNA hairpin processing, to examine mRNA decay, and to analyze accumulation of endogenous short interfering RNA (siRNA) precursors. We sequenced and analyzed the degradome of the ... More
Method for the identification of single mutations in large genomic regions using massive parallel sequencing
Map-based cloning of mutant genes is straightforward if the genome sequence and sufficient molecular markers are available. When a mutated gene in Arabidopsis causes a clear phenotype and is located in a genomic region where sufficient meiotic recombination takes place, the gene can be identified within 6-12 months. However, mutated ... More
Strengths and limitations of laboratory procedures for microRNA detection.
AuthorsKoshiol J, Wang E, Zhao Y, Marincola F, Landi MT
JournalCancer Epidemiol Biomarkers Prev
PubMed ID20332265
BACKGROUND: MicroRNAs (miR) are endogenous, noncoding RNAs involved in many cellular processes and have been associated with the development and progression of cancer. There are many different ways to evaluate miRs. METHODS: We described some of the most commonly used and promising miR detection methods. RESULTS: Each miR detection method ... More
Regulated post-transcriptional RNA cleavage diversifies the eukaryotic transcriptome.
The complexity of the eukaryotic transcriptome is generated by the interplay of transcription initiation, termination, alternative splicing, and other forms of post-transcriptional modification. It was recently shown that RNA transcripts may also undergo cleavage and secondary 5' capping. Here, we show that post-transcriptional cleavage of RNA contributes to the diversification ... More
A pyrosequencing-tailored nucleotide barcode design unveils opportunities for large-scale sample multiplexing.
AuthorsParameswaran P, Jalili R, Tao L, Shokralla S, Gharizadeh B, Ronaghi M, Fire AZ
JournalNucleic Acids Res
PubMed ID17932070
""Multiplexed high-throughput pyrosequencing is currently limited in complexity (number of samples sequenced in parallel), and in capacity (number of sequences obtained per sample). Physical-space segregation of the sequencing platform into a fixed number of channels allows limited multiplexing, but obscures available sequencing space. To overcome these limitations, we have ... More
Evaluation of paired-end sequencing strategies for detection of genome rearrangements in cancer.
AuthorsBashir A, Volik S, Collins C, Bafna V, Raphael BJ
JournalPlos Comput Biol
PubMed ID18404202
Paired-end sequencing is emerging as a key technique for assessing genome rearrangements and structural variation on a genome-wide scale. This technique is particularly useful for detecting copy-neutral rearrangements, such as inversions and translocations, which are common in cancer and can produce novel fusion genes. We address the question of how ... More
Database resources of the National Center for Biotechnology Information.
AuthorsSayers EW, Barrett T, Benson DA, Bolton E, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Federhen S, Feolo M, Fingerman IM, Geer LY, Helmberg W, Kapustin Y, Landsman D, Lipman DJ, Lu Z, Madden TL, Madej T, Maglott DR, Marchler-Bauer A, Miller V, Mizrachi I, Ostell J, Panchenko A, Phan L, Pruitt KD, Schuler GD, Sequeira E, Sherry ST, Shumway M, Sirotkin K, Slotta D, Souvorov A, Starchenko G, Tatusova TA, Wagner L, Wang Y, Wilbur WJ, Yaschenko E, Ye J
JournalNucleic Acids Res
PubMed ID21097890
In addition to maintaining the GenBank(R) 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 ... More
Sequencing and genotypic analysis of the triosephosphate isomerase (TPI1) locus in a large sample of long-lived Germans.
AuthorsRalser M, Nebel A, Kleindorp R, Krobitsch S, Lehrach H, Schreiber S, Reinhardt R, Timmermann B
JournalBmc Genet
PubMed ID18510744
BACKGROUND: Triosephosphate isomerase (TPI) is a central and conserved glycolytic enzyme. In humans, TPI is encoded by a single gene on 12p13, and associated with a rare genetic disorder, TPI deficiency. Reduced TPI activity can increase specific oxidant resistances of model organisms and TPI null-alleles have been hypothesized to ... More
Analysis of HIV-1 Expression Level and Sense of Transcription by High-Throughput Sequencing of the Infected Cell.
AuthorsLefebvre G, Desfarges S, Uyttebroeck F, Munoz M, Beerenwinkel N, Rougemont J, Telenti A, Ciuffi A
JournalJ Virol
PubMed ID21507965
Next-generation sequencing offers an unprecedented opportunity to jointly analyze cellular and viral transcriptional activity without prerequisite knowledge of the nature of the transcripts. SupT1 cells were infected with a vesicular stomatitis virus G envelope protein (VSV-G)-pseudotyped HIV vector. At 24 h postinfection, both cellular and viral transcriptomes were analyzed by ... More
Microarray-based multicycle-enrichment of genomic subsets for targeted next-generation sequencing
The lack of efficient high-throughput methods for enrichment of specific sequences from genomic DNA represents a key bottleneck in exploiting the enormous potential of next-generation sequencers. Such methods would allow for a systematic and targeted analysis of relevant genomic regions. Recent studies reported sequence enrichment using a hybridization step to ... More
PCR-based methods for detecting single-locus DNA methylation biomarkers in cancer diagnostics, prognostics, and response to treatment.
AuthorsKristensen LS, Hansen LL
JournalClin Chem
PubMed ID19520761
BACKGROUND: DNA methylation is a highly characterized epigenetic modification of the human genome that is implicated in cancer. The altered DNA methylation patterns found in cancer cells include not only global hypomethylation but also discrete hypermethylation of specific genes. In particular, numerous tumor suppressor genes undergo epigenetic silencing because ... More
Genome assembly quality: assessment and improvement using the neutral indel model.
AuthorsMeader S, Hillier LW, Locke D, Ponting CP, Lunter G
JournalGenome Res
PubMed ID20305016
We describe a statistical and comparative-genomic approach for quantifying error rates of genome sequence assemblies. The method exploits not substitutions but the pattern of insertions and deletions (indels) in genome-scale alignments for closely related species. Using two- or three-way alignments, the approach estimates the amount of aligned sequence containing clusters ... More
Keeping up with the next generation: massively parallel sequencing in clinical diagnostics.
Authorsten Bosch JR, Grody WW
JournalJ Mol Diagn
PubMed ID18832462
The speed, accuracy, efficiency, and cost-effectiveness of DNA sequencing have been improving continuously since the initial derivation of the technique in the mid-1970s. With the advent of massively parallel sequencing technologies, DNA sequencing costs have been dramatically reduced. No longer is it unthinkable to sequence hundreds or even thousands ... More
Next-generation sequencing: from basic research to diagnostics.
AuthorsVoelkerding KV, Dames SA, Durtschi JD
JournalClin Chem
PubMed ID19246620
BACKGROUND: For the past 30 years, the Sanger method has been the dominant approach and gold standard for DNA sequencing. The commercial launch of the first massively parallel pyrosequencing platform in 2005 ushered in the new era of high-throughput genomic analysis now referred to as next-generation sequencing (NGS). CONTENT: This ... More
Assessing the feasibility of GS FLX Pyrosequencing for sequencing the Atlantic salmon genome.
BACKGROUND: With a whole genome duplication event and wealth of biological data, salmonids are excellent model organisms for studying evolutionary processes, fates of duplicated genes and genetic and physiological processes associated with complex behavioral phenotypes. It is surprising therefore, that no salmonid genome has been sequenced. Atlantic salmon (Salmo ... More
Variation in the large-scale organization of gene expression levels in the hippocampus relates to stable epigenetic variability in behavior.
AuthorsAlter MD, Rubin DB, Ramsey K, Halpern R, Stephan DA, Abbott LF, Hen R
JournalPlos One
PubMed ID18836535
BACKGROUND: Despite sharing the same genes, identical twins demonstrate substantial variability in behavioral traits and in their risk for disease. Epigenetic factors-DNA and chromatin modifications that affect levels of gene expression without affecting the DNA sequence-are thought to be important in establishing this variability. Epigenetically-mediated differences in the levels ... More
Correction of sequencing errors in a mixed set of reads.
AuthorsSalmela L
JournalBioinformatics
PubMed ID20378555
MOTIVATION: High-throughput sequencing technologies produce large sets of short reads that may contain errors. These sequencing errors make de novo assembly challenging. Error correction aims to reduce the error rate prior assembly. Many de novo sequencing projects use reads from several sequencing technologies to get the benefits of all used ... More
Next-generation sequencing identifies the natural killer cell microRNA transcriptome.
AuthorsFehniger TA, Wylie T, Germino E, Leong JW, Magrini VJ, Koul S, Keppel CR, Schneider SE, Koboldt DC, Sullivan RP, Heinz ME, Crosby SD, Nagarajan R, Ramsingh G, Link DC, Ley TJ, Mardis ER
JournalGenome Res
PubMed ID20935160
Natural killer (NK) cells are innate lymphocytes important for early host defense against infectious pathogens and surveillance against malignant transformation. Resting murine NK cells regulate the translation of effector molecule mRNAs (e.g., granzyme B, GzmB) through unclear molecular mechanisms. MicroRNAs (miRNAs) are small noncoding RNAs that post-transcriptionally regulate the translation ... More
Simultaneous high-resolution analysis of vaccinia virus and host cell transcriptomes by deep RNA sequencing.
AuthorsYang Z, Bruno DP, Martens CA, Porcella SF, Moss B
JournalProc Natl Acad Sci U S A
PubMed ID20534518
Deep RNA sequencing was used to simultaneously analyze vaccinia virus (VACV) and HeLa cell transcriptomes at progressive times following infection. VACV, the prototypic member of the poxvirus family, replicates in the cytoplasm and contains a double-stranded DNA genome with approximately 200 closely spaced open reading frames (ORFs). The ... More
Efficient frequency-based de novo short-read clustering for error trimming in next-generation sequencing
AuthorsQu, W; Hashimoto, S; Morishita, S
Journal
PubMed ID
Novel massively parallel sequencing technologies provide highly detailed structures of transcriptomes and genomes by yielding deep coverage of short reads, but their utility is limited by inadequate sequencing quality and short-read lengths. Sequencing-error trimming in short reads is therefore a vital process that could improve the rate of successful reference ... More
Novel Low Abundance and Transient RNAs in Yeast Revealed by Tiling Microarrays and Ultra High-Throughput Sequencing Are Not Conserved Across Closely Related Yeast Species
AuthorsLee, A; Hansen, KD; Bullard, J; Dudoit, S; Sherlock, G
Journal
PubMed ID
A complete description of the transcriptome of an organism is crucial for a comprehensive understanding of how it functions and how its transcriptional networks are controlled, and may provide insights into the organism's evolution. Despite the status of Saccharomyces cerevisiae as arguably the most well-studied model eukaryote, we still do ... More
Genome-Wide Analysis of the 5' and 3' Ends of Vaccinia Virus Early mRNAs Delineates Regulatory Sequences of Annotated and Anomalous Transcripts.
AuthorsYang Z, Bruno DP, Martens CA, Porcella SF, Moss B
JournalJ Virol
PubMed ID21490097
Poxviruses are large DNA viruses that encode a multisubunit RNA polymerase, stage-specific transcription factors, and enzymes that cap and polyadenylate mRNAs within the cytoplasm of infected animal cells. Genome-wide microarray and RNA-seq technologies have been used to profile the transcriptome of vaccinia virus (VACV), the prototype member of the family. ... More
Genome-wide mapping of alternative splicing in Arabidopsis thaliana.
AuthorsFilichkin SA, Priest HD, Givan SA, Shen R, Bryant DW, Fox SE, Wong WK, Mockler TC
JournalGenome Res
PubMed ID19858364
Alternative splicing can enhance transcriptome plasticity and proteome diversity. In plants, alternative splicing can be manifested at different developmental stages, and is frequently associated with specific tissue types or environmental conditions such as abiotic stress. We mapped the Arabidopsis transcriptome at single-base resolution using the Illumina platform for ultrahigh-throughput ... More