Broad-spectrum respiratory tract pathogen identification using resequencing DNA microarrays.

Abstract:

:The exponential growth of pathogen nucleic acid sequences available in public domain databases has invited their direct use in pathogen detection, identification, and surveillance strategies. DNA microarray technology has offered the potential for the direct DNA sequence analysis of a broad spectrum of pathogens of interest. However, to achieve the practical attainment of this potential, numerous technical issues, especially nucleic acid amplification, probe specificity, and interpretation strategies of sequence detection, need to be addressed. In this report, we demonstrate an approach that combines the use of a custom-designed Affymetrix resequencing Respiratory Pathogen Microarray (RPM v.1) with methods for microbial nucleic acid enrichment, random nucleic acid amplification, and automated sequence similarity searching for broad-spectrum respiratory pathogen surveillance. Successful proof-of-concept experiments, utilizing clinical samples obtained from patients presenting adenovirus or influenza virus-induced febrile respiratory illness (FRI), demonstrate the ability of this approach for correct species- and strain-level identification with unambiguous statistical interpretation at clinically relevant sensitivity levels. Our results underscore the feasibility of using this approach to expedite the early surveillance of diseases, and provide new information on the incidence of multiple pathogens.

journal_name

Genome Res

journal_title

Genome research

authors

Lin B,Wang Z,Vora GJ,Thornton JA,Schnur JM,Thach DC,Blaney KM,Ligler AG,Malanoski AP,Santiago J,Walter EA,Agan BK,Metzgar D,Seto D,Daum LT,Kruzelock R,Rowley RK,Hanson EH,Tibbetts C,Stenger DA

doi

10.1101/gr.4337206

subject

Has Abstract

pub_date

2006-04-01 00:00:00

pages

527-35

issue

4

eissn

1088-9051

issn

1549-5469

pii

gr.4337206

journal_volume

16

pub_type

杂志文章
  • Next-generation sequencing identifies the natural killer cell microRNA transcriptome.

    abstract::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)...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.107995.110

    authors: Fehniger 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

    更新日期:2010-11-01 00:00:00

  • A positive but complex association between meiotic double-strand break hotspots and open chromatin in Saccharomyces cerevisiae.

    abstract::During meiosis, chromatin undergoes extensive changes to facilitate recombination, homolog pairing, and chromosome segregation. To investigate the relationship between chromatin organization and meiotic processes, we used formaldehyde-assisted isolation of regulatory elements (FAIRE) to map open chromatin during the t...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.096297.109

    authors: Berchowitz LE,Hanlon SE,Lieb JD,Copenhaver GP

    更新日期:2009-12-01 00:00:00

  • The discovery of integrated gene networks for autism and related disorders.

    abstract::Despite considerable genetic heterogeneity underlying neurodevelopmental diseases, there is compelling evidence that many disease genes will map to a much smaller number of biological subnetworks. We developed a computational method, termed MAGI (merging affected genes into integrated networks), that simultaneously in...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.178855.114

    authors: Hormozdiari F,Penn O,Borenstein E,Eichler EE

    更新日期:2015-01-01 00:00:00

  • Transposon expression in the Drosophila brain is driven by neighboring genes and diversifies the neural transcriptome.

    abstract::Somatic transposon expression in neural tissue is commonly considered as a measure of mobilization and has therefore been linked to neuropathology and organismal individuality. We combined genome sequencing data with single-cell mRNA sequencing of the same inbred fly strain to map transposon expression in the Drosophi...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.259200.119

    authors: Treiber CD,Waddell S

    更新日期:2020-11-01 00:00:00

  • A complexity reduction algorithm for analysis and annotation of large genomic sequences.

    abstract::DNA is a universal language encrypted with biological instruction for life. In higher organisms, the genetic information is preserved predominantly in an organized exon/intron structure. When a gene is expressed, the exons are spliced together to form the transcript for protein synthesis. We have developed a complexit...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.313703

    authors: Chuang TJ,Lin WC,Lee HC,Wang CW,Hsiao KL,Wang ZH,Shieh D,Lin SC,Ch'ang LY

    更新日期:2003-02-01 00:00:00

  • Integrated annotations and analyses of small RNA-producing loci from 47 diverse plants.

    abstract::Plant endogenous small RNAs (sRNAs) are important regulators of gene expression. There are two broad categories of plant sRNAs: microRNAs (miRNAs) and endogenous short interfering RNAs (siRNAs). MicroRNA loci are relatively well-annotated but compose only a small minority of the total sRNA pool; siRNA locus annotation...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.256750.119

    authors: Lunardon A,Johnson NR,Hagerott E,Phifer T,Polydore S,Coruh C,Axtell MJ

    更新日期:2020-03-01 00:00:00

  • A periodic pattern of SNPs in the human genome.

    abstract::By surveying a filtered, high-quality set of SNPs in the human genome, we have found that SNPs positioned 1, 2, 4, 6, or 8 bp apart are more frequent than SNPs positioned 3, 5, 7, or 9 bp apart. The observed pattern is not restricted to genomic regions that are known to cause sequencing or alignment errors, for exampl...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.6223207

    authors: Madsen BE,Villesen P,Wiuf C

    更新日期:2007-10-01 00:00:00

  • Massive turnover of functional sequence in human and other mammalian genomes.

    abstract::Despite the availability of dozens of animal genome sequences, two key questions remain unanswered: First, what fraction of any species' genome confers biological function, and second, are apparent differences in organismal complexity reflected in an objective measure of genomic complexity? Here, we address both quest...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.108795.110

    authors: Meader S,Ponting CP,Lunter G

    更新日期:2010-10-01 00:00:00

  • Genome-reconstruction for eukaryotes from complex natural microbial communities.

    abstract::Microbial eukaryotes are integral components of natural microbial communities, and their inclusion is critical for many ecosystem studies, yet the majority of published metagenome analyses ignore eukaryotes. In order to include eukaryotes in environmental studies, we propose a method to recover eukaryotic genomes from...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.228429.117

    authors: West PT,Probst AJ,Grigoriev IV,Thomas BC,Banfield JF

    更新日期:2018-04-01 00:00:00

  • Reconstructing large regions of an ancestral mammalian genome in silico.

    abstract::It is believed that most modern mammalian lineages arose from a series of rapid speciation events near the Cretaceous-Tertiary boundary. It is shown that such a phylogeny makes the common ancestral genome sequence an ideal target for reconstruction. Simulations suggest that with methods currently available, we can exp...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.2800104

    authors: Blanchette M,Green ED,Miller W,Haussler D

    更新日期:2004-12-01 00:00:00

  • The Ensembl automatic gene annotation system.

    abstract::As more genomes are sequenced, there is an increasing need for automated first-pass annotation which allows timely access to important genomic information. The Ensembl gene-building system enables fast automated annotation of eukaryotic genomes. It annotates genes based on evidence derived from known protein, cDNA, an...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.1858004

    authors: Curwen V,Eyras E,Andrews TD,Clarke L,Mongin E,Searle SM,Clamp M

    更新日期:2004-05-01 00:00:00

  • DIG-seq: a genome-wide CRISPR off-target profiling method using chromatin DNA.

    abstract::To investigate whether and how CRISPR-Cas9 on-target and off-target activities are affected by chromatin in eukaryotic cells, we first identified a series of identical endogenous DNA sequences present in both open and closed chromatin regions and then measured mutation frequencies at these sites in human cells using C...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.236620.118

    authors: Kim D,Kim JS

    更新日期:2018-12-01 00:00:00

  • Spotted long oligonucleotide arrays for human gene expression analysis.

    abstract::DNA microarrays produced by deposition (or 'spotting')of a single long oligonucleotide probe for each gene may be an attractive alternative to other types of arrays. We produced spotted oligonucleotide arrays using two large collections of approximately 70-mer probes, and used these arrays to analyze gene expression i...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.1048803

    authors: Barczak A,Rodriguez MW,Hanspers K,Koth LL,Tai YC,Bolstad BM,Speed TP,Erle DJ

    更新日期:2003-07-01 00:00:00

  • Gene expression profiling of single cells from archival tissue with laser-capture microdissection and Smart-3SEQ.

    abstract::RNA sequencing (RNA-seq) is a sensitive and accurate method for quantifying gene expression. Small samples or those whose RNA is degraded, such as formalin-fixed paraffin-embedded (FFPE) tissue, remain challenging to study with nonspecialized RNA-seq protocols. Here, we present a new method, Smart-3SEQ, that accuratel...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.234807.118

    authors: Foley JW,Zhu C,Jolivet P,Zhu SX,Lu P,Meaney MJ,West RB

    更新日期:2019-11-01 00:00:00

  • Identification of complex genomic rearrangements in cancers using CouGaR.

    abstract::The genomic alterations associated with cancers are numerous and varied, involving both isolated and large-scale complex genomic rearrangements (CGRs). Although the underlying mechanisms are not well understood, CGRs have been implicated in tumorigenesis. Here, we introduce CouGaR, a novel method for characterizing th...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.211201.116

    authors: Dzamba M,Ramani AK,Buczkowicz P,Jiang Y,Yu M,Hawkins C,Brudno M

    更新日期:2017-01-01 00:00:00

  • DNA methylation profiling in human B cells reveals immune regulatory elements and epigenetic plasticity at Alu elements during B-cell activation.

    abstract::Memory is a hallmark of adaptive immunity, wherein lymphocytes mount a superior response to a previously encountered antigen. It has been speculated that epigenetic alterations in memory lymphocytes contribute to their functional distinction from their naive counterparts. However, the nature and extent of epigenetic a...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.155473.113

    authors: Lai AY,Mav D,Shah R,Grimm SA,Phadke D,Hatzi K,Melnick A,Geigerman C,Sobol SE,Jaye DL,Wade PA

    更新日期:2013-12-01 00:00:00

  • Nonrandom domain organization of the Arabidopsis genome at the nuclear periphery.

    abstract::The nuclear space is not a homogeneous biochemical environment. Many studies have demonstrated that the transcriptional activity of a gene is linked to its positioning within the nuclear space. Following the discovery of lamin-associated domains (LADs), which are transcriptionally repressed chromatin regions, the nonr...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.215186.116

    authors: Bi X,Cheng YJ,Hu B,Ma X,Wu R,Wang JW,Liu C

    更新日期:2017-07-01 00:00:00

  • Comparative methylome analysis of benign and malignant peripheral nerve sheath tumors.

    abstract::Aberrant DNA methylation (DNAm) was first linked to cancer over 25 yr ago. Since then, many studies have associated hypermethylation of tumor suppressor genes and hypomethylation of oncogenes to the tumorigenic process. However, most of these studies have been limited to the analysis of promoters and CpG islands (CGIs...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.109678.110

    authors: Feber A,Wilson GA,Zhang L,Presneau N,Idowu B,Down TA,Rakyan VK,Noon LA,Lloyd AC,Stupka E,Schiza V,Teschendorff AE,Schroth GP,Flanagan A,Beck S

    更新日期:2011-04-01 00:00:00

  • Murine single-cell RNA-seq reveals cell-identity- and tissue-specific trajectories of aging.

    abstract::Aging is a pleiotropic process affecting many aspects of mammalian physiology. Mammals are composed of distinct cell type identities and tissue environments, but the influence of these cell identities and environments on the trajectory of aging in individual cells remains unclear. Here, we performed single-cell RNA-se...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.253880.119

    authors: Kimmel JC,Penland L,Rubinstein ND,Hendrickson DG,Kelley DR,Rosenthal AZ

    更新日期:2019-12-01 00:00:00

  • Transcription factor binding and modified histones in human bidirectional promoters.

    abstract::Bidirectional promoters have received considerable attention because of their ability to regulate two downstream genes (divergent genes). They are also highly abundant, directing the transcription of approximately 11% of genes in the human genome. We categorized the presence of DNA sequence motifs, binding of transcri...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.5623407

    authors: Lin JM,Collins PJ,Trinklein ND,Fu Y,Xi H,Myers RM,Weng Z

    更新日期:2007-06-01 00:00:00

  • Yeast genetic interaction screen of human genes associated with amyotrophic lateral sclerosis: identification of MAP2K5 kinase as a potential drug target.

    abstract::To understand disease mechanisms, a large-scale analysis of human-yeast genetic interactions was performed. Of 1305 human disease genes assayed, 20 genes exhibited strong toxicity in yeast. Human-yeast genetic interactions were identified by en masse transformation of the human disease genes into a pool of 4653 homozy...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.211649.116

    authors: Jo M,Chung AY,Yachie N,Seo M,Jeon H,Nam Y,Seo Y,Kim E,Zhong Q,Vidal M,Park HC,Roth FP,Suk K

    更新日期:2017-09-01 00:00:00

  • Comparative analysis of gene-expression patterns in human and African great ape cultured fibroblasts.

    abstract::Although much is known about genetic variation in human and African great ape (chimpanzee, bonobo, and gorilla) genomes, substantially less is known about variation in gene-expression profiles within and among these species. This information is necessary for defining transcriptional regulatory networks that contribute...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.1289803

    authors: Karaman MW,Houck ML,Chemnick LG,Nagpal S,Chawannakul D,Sudano D,Pike BL,Ho VV,Ryder OA,Hacia JG

    更新日期:2003-07-01 00:00:00

  • Reprogramming of the human intestinal epigenome by surgical tissue transposition.

    abstract::Extracellular cues play critical roles in the establishment of the epigenome during development and may also contribute to epigenetic perturbations found in disease states. The direct role of the local tissue environment on the post-development human epigenome, however, remains unclear due to limitations in studies of...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.166439.113

    authors: Lay FD,Triche TJ Jr,Tsai YC,Su SF,Martin SE,Daneshmand S,Skinner EC,Liang G,Chihara Y,Jones PA

    更新日期:2014-04-01 00:00:00

  • The marine bacterium Pseudoalteromonas haloplanktis has a complex genome structure composed of two separate genetic units.

    abstract::The genome size of Pseudoalteromonas haloplanktis, a ubiquitous and easily cultured marine bacterium, was measured as a step toward estimating the genome complexity of marine bacterioplankton. To determine total genome size, we digested P. haloplanktis DNA with the restriction endonucleases Notl and Sfil, separated th...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.6.12.1160

    authors: Lanoil BD,Ciuffetti LM,Giovannoni SJ

    更新日期:1996-12-01 00:00:00

  • Large-scale sequencing in human chromosome 12p13: experimental and computational gene structure determination.

    abstract::The detailed genomic organization of a gene-dense region at human chromosome 12p13, spanning 223 kb of contiguous sequence, was determined. This region is composed of 20 genes and several other expressed sequences. Experimental tools including RT-PCR and cDNA sequencing, combined with gene prediction programs, were ut...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.7.3.268

    authors: Ansari-Lari MA,Shen Y,Muzny DM,Lee W,Gibbs RA

    更新日期:1997-03-01 00:00:00

  • Interaction between the X chromosome and an autosome regulates size sexual dimorphism in Portuguese Water Dogs.

    abstract::Size sexual dimorphism occurs in almost all mammals. In Portuguese Water Dogs, much of the difference in skeletal size between females and males is due to the interaction between a Quantitative Trait Locus (QTL) on the X-chromosome and a QTL linked to Insulin-like Growth Factor 1 (IGF-1) on the CFA 15 autosome. In fem...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.3712705

    authors: Chase K,Carrier DR,Adler FR,Ostrander EA,Lark KG

    更新日期:2005-12-01 00:00:00

  • Wolbachia genome integrated in an insect chromosome: evolution and fate of laterally transferred endosymbiont genes.

    abstract::Recent accumulation of microbial genome data has demonstrated that lateral gene transfers constitute an important and universal evolutionary process in prokaryotes, while those in multicellular eukaryotes are still regarded as unusual, except for endosymbiotic gene transfers from mitochondria and plastids. Here we tho...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.7144908

    authors: Nikoh N,Tanaka K,Shibata F,Kondo N,Hizume M,Shimada M,Fukatsu T

    更新日期:2008-02-01 00:00:00

  • A tale of two templates: automatically resolving double traces has many applications, including efficient PCR-based elucidation of alternative splices.

    abstract::Trace Recalling is a novel method for deconvoluting double traces that result from simultaneously sequencing two DNA templates. Trace Recalling identifies up to two bases at each position of such a trace. The resulting ambiguity sequence is aligned to the genome, identifying one template sequence. A second template se...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.5661407

    authors: Tenney AE,Wu JQ,Langton L,Klueh P,Quatrano R,Brent MR

    更新日期:2007-02-01 00:00:00

  • Rapid molecular assays to study human centromere genomics.

    abstract::The centromere is the structural unit responsible for the faithful segregation of chromosomes. Although regulation of centromeric function by epigenetic factors has been well-studied, the contributions of the underlying DNA sequences have been much less well defined, and existing methodologies for studying centromere ...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.219709.116

    authors: Contreras-Galindo R,Fischer S,Saha AK,Lundy JD,Cervantes PW,Mourad M,Wang C,Qian B,Dai M,Meng F,Chinnaiyan A,Omenn GS,Kaplan MH,Markovitz DM

    更新日期:2017-12-01 00:00:00

  • Highly multiplexed molecular inversion probe genotyping: over 10,000 targeted SNPs genotyped in a single tube assay.

    abstract::Large-scale genetic studies are highly dependent on efficient and scalable multiplex SNP assays. In this study, we report the development of Molecular Inversion Probe technology with four-color, single array detection, applied to large-scale genotyping of up to 12,000 SNPs per reaction. While generating 38,429 SNP ass...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.3185605

    authors: Hardenbol P,Yu F,Belmont J,Mackenzie J,Bruckner C,Brundage T,Boudreau A,Chow S,Eberle J,Erbilgin A,Falkowski M,Fitzgerald R,Ghose S,Iartchouk O,Jain M,Karlin-Neumann G,Lu X,Miao X,Moore B,Moorhead M,Namsaraev E,

    更新日期:2005-02-01 00:00:00