Development and performance of a targeted whole exome sequencing enrichment kit for the dog (Canis Familiaris Build 3.1).

Abstract:

:Whole exome sequencing is a technique that aims to selectively sequence all exons of protein-coding genes. A canine whole exome sequencing enrichment kit was designed based on the latest canine reference genome (build 3.1.72). Its performance was tested by sequencing 2 exome captures, each consisting of 4 pre-capture pooled, barcoded Illumina libraries on an Illumina HiSeq 2500. At an average sequencing depth of 102x, 83 to 86% of the target regions were completely sequenced with a minimum coverage of five and 90% of the reads mapped on the target regions. Additionally, it is shown that the reproducibility within and between captures is high and that pooling four samples per capture is a valid option. Overall, we have demonstrated the strong performance of this WES enrichment kit and are confident it will be a valuable tool in future disease association studies.

journal_name

Sci Rep

journal_title

Scientific reports

authors

Broeckx BJ,Coopman F,Verhoeven GE,Bavegems V,De Keulenaer S,De Meester E,Van Niewerburgh F,Deforce D

doi

10.1038/srep05597

subject

Has Abstract

pub_date

2014-07-07 00:00:00

pages

5597

issn

2045-2322

pii

srep05597

journal_volume

4

pub_type

杂志文章
  • Establishment of Imaging Spectroscopy of Nuclear Gamma-Rays based on Geometrical Optics.

    abstract::Since the discovery of nuclear gamma-rays, its imaging has been limited to pseudo imaging, such as Compton Camera (CC) and coded mask. Pseudo imaging does not keep physical information (intensity, or brightness in Optics) along a ray, and thus is capable of no more than qualitative imaging of bright objects. To attain...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep41511

    authors: Tanimori T,Mizumura Y,Takada A,Miyamoto S,Takemura T,Kishimoto T,Komura S,Kubo H,Kurosawa S,Matsuoka Y,Miuchi K,Mizumoto T,Nakamasu Y,Nakamura K,Parker JD,Sawano T,Sonoda S,Tomono D,Yoshikawa K

    更新日期:2017-02-03 00:00:00

  • Polychlorinated dibenzo-p-dioxins and dibenzofurans formed from sucralose at high temperatures.

    abstract::Sucralose is a widely-used artificial high-intensity sweetener. Although doubts have been raised about the safety of sucralose by several researchers, it can still be found in a broad range of foods and beverages worldwide, including in baked goods. Sucralose may decompose at high temperatures, and participate in chlo...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep02946

    authors: Dong S,Liu G,Hu J,Zheng M

    更新日期:2013-10-15 00:00:00

  • Prevalence, patterns, and predictors of meditation use among US adults: A nationally representative survey.

    abstract::Emerging evidence suggests substantial health benefits from using meditation. While there are some indications that the popularity of meditation is increasing, little is known about the prevalence, patterns, and predictors of meditation use in the general population. In this secondary analysis of data from the 2012 US...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep36760

    authors: Cramer H,Hall H,Leach M,Frawley J,Zhang Y,Leung B,Adams J,Lauche R

    更新日期:2016-11-10 00:00:00

  • Irregular and suppressed elastic deformation by a structural twist in cellulose nanofibre models.

    abstract::The elastic responsiveness of single cellulose nanofibres is important for advanced analysis of biological tissues and their use in sophisticated functional materials. However, the mechanical responsiveness derived from the twisted structure of cellulose nanofibres (CNFs) has remained unexplored. In this study, finite...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-80890-1

    authors: Uetani K,Uto T,Suzuki N

    更新日期:2021-01-12 00:00:00

  • Electroceutical Treatment of Pseudomonas aeruginosa Biofilms.

    abstract::Electroceutical wound dressings, especially those involving current flow with silver based electrodes, show promise for treating biofilm infections. However, their mechanism of action is poorly understood. We have developed an in vitro agar based model using a bioluminescent strain of Pseudomonas aeruginosa to measure...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-37891-y

    authors: Dusane DH,Lochab V,Jones T,Peters CW,Sindeldecker D,Das A,Roy S,Sen CK,Subramaniam VV,Wozniak DJ,Prakash S,Stoodley P

    更新日期:2019-02-14 00:00:00

  • Visible and UV photo-detection in ZnO nanostructured thin films via simple tuning of solution method.

    abstract::This study demonstrates significant visible light photo-detection capability of pristine ZnO nanostructure thin films possessing substantially high percentage of oxygen vacancies [Formula: see text] and zinc interstitials [Formula: see text], introduced by simple tuning of economical solution method. The demonstrated ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-15125-x

    authors: Khokhra R,Bharti B,Lee HN,Kumar R

    更新日期:2017-11-08 00:00:00

  • Reward and punishment in climate change dilemmas.

    abstract::Mitigating climate change effects involves strategic decisions by individuals that may choose to limit their emissions at a cost. Everyone shares the ensuing benefits and thereby individuals can free ride on the effort of others, which may lead to the tragedy of the commons. For this reason, climate action can be conv...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-52524-8

    authors: Góis AR,Santos FP,Pacheco JM,Santos FC

    更新日期:2019-11-07 00:00:00

  • Global phylogeography suggests extensive eucosmopolitanism in Mesopelagic Fishes (Maurolicus: Sternoptychidae).

    abstract::Fishes in the mesopelagic zone (200-1000 m) have recently been highlighted for potential exploitation. Here we assess global phylogeography in Maurolicus, the Pearlsides, an ecologically important group. We obtained new sequences from mitochondrial COI and nuclear ITS-2 from multiple locations worldwide, representing ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-77528-7

    authors: Rees DJ,Poulsen JY,Sutton TT,Costa PAS,Landaeta MF

    更新日期:2020-11-25 00:00:00

  • RNA-binding protein RBM3 prevents NO-induced apoptosis in human neuroblastoma cells by modulating p38 signaling and miR-143.

    abstract::Nitric oxide (NO)-induced apoptosis in neurons is an important cause of neurodegenerative disease in humans. The cold-inducible protein RBM3 mediates the protective effects of cooling on apoptosis induced by various insults. However, whether RBM3 protects neural cells from NO-induced apoptosis is unclear. This study a...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep41738

    authors: Yang HJ,Ju F,Guo XX,Ma SP,Wang L,Cheng BF,Zhuang RJ,Zhang BB,Shi X,Feng ZW,Wang M

    更新日期:2017-01-30 00:00:00

  • Influence of the human papillomavirus on the radio-responsiveness of cancer stem cells in head and neck cancers.

    abstract::A growing proportion of head and neck cancers (HNC) result from HPV infection. Between HNC aetiological groups (HPV positive and HPV negative) clinical evidence demonstrates significantly better treatment response among HPV positive cancers. Cancer stem cells (CSCs) are identified in HNC tumour populations as agents o...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-59654-4

    authors: Reid P,Staudacher AH,Marcu LG,Olver I,Moghaddasi L,Brown MP,Bezak E

    更新日期:2020-02-17 00:00:00

  • Chimeras and complex cluster states in arrays of spin-torque oscillators.

    abstract::We consider synchronization properties of arrays of spin-torque nano-oscillators coupled via an RC load. We show that while the fully synchronized state of identical oscillators may be locally stable in some parameter range, this synchrony is not globally attracting. Instead, regimes of different levels of composition...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-04918-9

    authors: Zaks M,Pikovsky A

    更新日期:2017-07-05 00:00:00

  • Multidisciplinary approach to COVID-19 risk communication: a framework and tool for individual and regional risk assessment.

    abstract::The COVID-19 pandemic has exceeded over sixty-five million cases globally. Different approaches are followed to mitigate its impact and reduce its spreading in different countries, but limiting mobility and exposure have been de-facto precautions to reduce transmission. However, a full lockdown cannot be sustained for...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-78779-0

    authors: Parajuli RR,Mishra B,Banstola A,Ghimire BR,Poudel S,Sharma K,Dixit SM,Sah SK,Simkhada P,van Teijlingen E

    更新日期:2020-12-10 00:00:00

  • A new genus and two new species of freshwater mussels (Unionidae) from western Indochina.

    abstract::The systematics of Oriental freshwater mussels (Bivalvia: Unionidae) is poorly known. Here, we present an integrative revision of the genus Trapezoideus Simpson, 1900 to further understanding of freshwater mussel diversity in the region. We demonstrate that Trapezoideus as currently circumscribed is non-monophyletic, ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-39365-1

    authors: Konopleva ES,Pfeiffer JM,Vikhrev IV,Kondakov AV,Gofarov MY,Aksenova OV,Lunn Z,Chan N,Bolotov IN

    更新日期:2019-03-11 00:00:00

  • Genetic manipulation of iron biomineralization enhances MR relaxivity in a ferritin-M6A chimeric complex.

    abstract::Ferritin has gained significant attention as a potential reporter gene for in vivo imaging by magnetic resonance imaging (MRI). However, due to the ferritin ferrihydrite core, the relaxivity and sensitivity for detection of native ferritin is relatively low. We report here on a novel chimeric magneto-ferritin reporter...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep26550

    authors: Radoul M,Lewin L,Cohen B,Oren R,Popov S,Davidov G,Vandsburger MH,Harmelin A,Bitton R,Greneche JM,Neeman M,Zarivach R

    更新日期:2016-05-23 00:00:00

  • Characterisation of a flavonoid ligand of the fungal protein Alt a 1.

    abstract::Spores of pathogenic fungi are virtually ubiquitous and cause human disease and severe losses in crops. The endophytic fungi Alternaria species produce host-selective phytotoxins. Alt a 1 is a strongly allergenic protein found in A. alternata that causes severe asthma. Despite the well-established pathogenicity of Alt...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep33468

    authors: Garrido-Arandia M,Silva-Navas J,Ramírez-Castillejo C,Cubells-Baeza N,Gómez-Casado C,Barber D,Pozo JC,Melendi PG,Pacios LF,Díaz-Perales A

    更新日期:2016-09-16 00:00:00

  • Functional characterization of the principal sigma factor RpoD of phytoplasmas via an in vitro transcription assay.

    abstract::Phytoplasmas (class, Mollicutes) are insect-transmissible and plant-pathogenic bacteria that multiply intracellularly in both plants and insects through host switching. Our previous study revealed that phytoplasmal sigma factor rpoD of OY-M strain (rpoDOY) could be a key regulator of host switching, because the expres...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep11893

    authors: Miura C,Komatsu K,Maejima K,Nijo T,Kitazawa Y,Tomomitsu T,Yusa A,Himeno M,Oshima K,Namba S

    更新日期:2015-07-07 00:00:00

  • Proteomics Profiling Reveals Carbohydrate Metabolic Enzymes and 14-3-3 Proteins Play Important Roles for Starch Accumulation during Cassava Root Tuberization.

    abstract::Cassava is one of the most important root crops as a reliable source of food and carbohydrates. Carbohydrate metabolism and starch accumulation in cassava storage root is a cascade process that includes large amounts of proteins and cofactors. Here, comparative proteomics were conducted in cassava root at nine develop...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep19643

    authors: Wang X,Chang L,Tong Z,Wang D,Yin Q,Wang D,Jin X,Yang Q,Wang L,Sun Y,Huang Q,Guo A,Peng M

    更新日期:2016-01-21 00:00:00

  • Accelerating recovery from jet lag: prediction from a multi-oscillator model and its experimental confirmation in model animals.

    abstract::The endogenous circadian clock drives oscillations that are completely synchronized with the environmental day-night rhythms with a period of approximately 24 hours. Temporal misalignment between one's internal circadian clock and the external solar time often occurs in shift workers and long-distance travelers; such ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep46702

    authors: Kori H,Yamaguchi Y,Okamura H

    更新日期:2017-04-26 00:00:00

  • Controlling the Polarity of the Molecular Beam Epitaxy Grown In-Bi Atomic Film on the Si(111) Surface.

    abstract::Synchrotron radiation core-level photoemission spectroscopy, scanning tunneling microscopy (STM), and first-principles calculations have been utilized to explore the growth processes and the atomic structure of the resulting films during the two-step molecular beam epitaxy (MBE) of In and Bi on the Si(111) surface. De...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-37051-2

    authors: Lin CY,Hsu CH,Huang YZ,Hsieh SC,Chen HD,Huang L,Huang ZQ,Chuang FC,Lin DS

    更新日期:2019-01-24 00:00:00

  • miRNA and mRNA expression analysis reveals potential sex-biased miRNA expression.

    abstract::Recent studies suggest that mRNAs may be differentially expressed between males and females. This study aimed to perform expression analysis of mRNA and its main regulatory molecule, microRNA (miRNA), to discuss the potential sex-specific expression patterns using abnormal expression profiles from The Cancer Genome At...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep39812

    authors: Guo L,Zhang Q,Ma X,Wang J,Liang T

    更新日期:2017-01-03 00:00:00

  • Both anti-inflammatory and antiviral properties of novel drug candidate ABX464 are mediated by modulation of RNA splicing.

    abstract::ABX464 is a first-in-class, clinical-stage, small molecule for oral administration that has shown strong anti-inflammatory effects in the DSS-model for inflammatory bowel disease (IBD) and also prevents replication of the HIV virus. ABX464 which binds to cap binding complex (CBC) has demonstrated safety and efficacy i...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-37813-y

    authors: Vautrin A,Manchon L,Garcel A,Campos N,Lapasset L,Laaref AM,Bruno R,Gislard M,Dubois E,Scherrer D,Ehrlich JH,Tazi J

    更新日期:2019-01-28 00:00:00

  • Transcriptome analysis revealed chimeric RNAs, single nucleotide polymorphisms and allele-specific expression in porcine prenatal skeletal muscle.

    abstract::Prenatal skeletal muscle development genetically determines postnatal muscle characteristics such as growth and meat quality in pigs. However, the molecular mechanisms underlying prenatal skeletal muscle development remain unclear. Here, we performed the first genome-wide analysis of chimeric RNAs, single nuclear poly...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep29039

    authors: Yang Y,Tang Z,Fan X,Xu K,Mu Y,Zhou R,Li K

    更新日期:2016-06-29 00:00:00

  • Failure dynamics of the global risk network.

    abstract::Risks threatening modern societies form an intricately interconnected network that often underlies crisis situations. Yet, little is known about how risk materializations in distinct domains influence each other. Here we present an approach in which expert assessments of likelihoods and influence of risks underlie a q...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep10998

    authors: Szymanski BK,Lin X,Asztalos A,Sreenivasan S

    更新日期:2015-06-18 00:00:00

  • Insights into the structure and function of Est3 from the Hansenula polymorpha telomerase.

    abstract::Telomerase is a ribonucleoprotein enzyme, which maintains genome integrity in eukaryotes and ensures continuous cellular proliferation. Telomerase holoenzyme from the thermotolerant yeast Hansenula polymorpha, in addition to the catalytic subunit (TERT) and telomerase RNA (TER), contains accessory proteins Est1 and Es...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-68107-x

    authors: Shepelev NM,Mariasina SS,Mantsyzov AB,Malyavko AN,Efimov SV,Petrova OA,Rodina EV,Zvereva MI,Dontsova OA,Polshakov VI

    更新日期:2020-07-06 00:00:00

  • Specific Y14 domains mediate its nucleo-cytoplasmic shuttling and association with spliced mRNA.

    abstract::Pre-mRNA splicing deposits multi-protein complexes, termed exon junction complexes (EJCs), on mRNAs near exon-exon junctions. The core of EJC consists of four proteins, eIF4AIII, MLN51, Y14 and Magoh. Y14 is a nuclear protein that can shuttle between the nucleus and the cytoplasm, and binds specifically to Magoh. Here...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep00092

    authors: Kataoka N,Diem MD,Yoshida M,Hatai C,Dobashi I,Dreyfuss G,Hagiwara M,Ohno M

    更新日期:2011-01-01 00:00:00

  • The Value of CBCT-based Tumor Density and Volume Variations in Prediction of Early Response to Chemoradiation Therapy in Advanced NSCLC.

    abstract::The correlations between early responses and the variations in physical density and primary tumor volume (TV) according to cone-beam computed tomography (CBCT) during chemoradiotherapy for non-small cell lung cancer (NSCLC) patients were investigated. 54 patients with inoperable and locally advanced NSCLC were include...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-14548-w

    authors: Wen Q,Zhu J,Meng X,Ma C,Bai T,Sun X,Yu J

    更新日期:2017-11-07 00:00:00

  • The evolution of interdisciplinarity in physics research.

    abstract::Science, being a social enterprise, is subject to fragmentation into groups that focus on specialized areas or topics. Often new advances occur through cross-fertilization of ideas between sub-fields that otherwise have little overlap as they study dissimilar phenomena using different techniques. Thus to explore the n...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep00551

    authors: Pan RK,Sinha S,Kaski K,Saramäki J

    更新日期:2012-01-01 00:00:00

  • Selection and validation of miR-1280 as a suitable endogenous normalizer for qRT-PCR Analysis of serum microRNA expression in Hepatocellular Carcinoma.

    abstract::Normalization procedures for the qRT-PCR analysis of miRNA in biological samples are recommended to reduce the variability caused by pre-analytical factors. Since there is no universal standardized normalization strategy for miRNA qRT-PCR studies, we conducted a throughout study to evaluate a panel of small non-coding...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-59682-0

    authors: Pratama MY,Cavalletto L,Tiribelli C,Chemello L,Pascut D

    更新日期:2020-02-21 00:00:00

  • Inhibition of PDGFR signaling prevents muscular fatty infiltration after rotator cuff tear in mice.

    abstract::Fatty infiltration in muscle is often observed in patients with sizable rotator cuff tear (RCT) and is thought to be an irreversible event that significantly compromises muscle plasticity and contraction strength. These changes in the mechanical properties of the affected muscle render surgical repair of RCT highly fo...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep41552

    authors: Shirasawa H,Matsumura N,Shimoda M,Oki S,Yoda M,Tohmonda T,Kanai Y,Matsumoto M,Nakamura M,Horiuchi K

    更新日期:2017-01-31 00:00:00

  • Discordancy Partitioning for Validating Potentially Inconsistent Pharmacogenomic Studies.

    abstract::The Genomics of Drug Sensitivity in Cancer (GDSC) and Cancer Cell Line Encyclopedia (CCLE) are two major studies that can be used to mine for therapeutic biomarkers for cancers of a large variety. Model validation using the two datasets however has proved challenging. Both predictions and signatures do not consistentl...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-15590-4

    authors: Rao JS,Liu H

    更新日期:2017-11-09 00:00:00