当前位置： SCI文献检索 > Nature Communications期刊下所有文献 > Using somatic variant richness to mine signals from rare variants in the cancer genome.

Using somatic variant richness to mine signals from rare variants in the cancer genome.

Abstract：

:To date, the vast preponderance of somatic variants observed in the cancer genome have been rare variants, and it is common in practice to encounter in a new tumor variants that have not been observed previously. Here we focus on probability estimation for encountering such hitherto unseen variants. We draw upon statistical methodology that has been developed in other fields of study, notably in species estimation in ecology, and word frequency estimation in computational linguistics. Analysis of whole-exome and targeted panel sequencing data sets reveal substantial variability in variant "richness" between genes that could be harnessed for clinically relevant problems. We quantify the variant-tissue association and show a strong gene-specific, lineage-dependent pattern of encountering new variants. This variability is largely determined by the proportion of observed variants that are rare. Our findings suggest that variants that occur at very low frequencies can harbor important signals that are clinically consequential.

journal_name

Nat Commun

journal_title

Nature communications

authors

Chakraborty S,Arora A,Begg CB,Shen R

doi

10.1038/s41467-019-13402-z

subject

Has Abstract

pub_date

2019-12-03 00:00:00

pages

5506

issue

1

issn

2041-1723

pii

10.1038/s41467-019-13402-z

journal_volume

10

pub_type

杂志文章

相关文献

Nature Communications文献大全
  • Genome-wide association study identifies variation at 6q25.1 associated with survival in multiple myeloma.

    abstract：:Survival following a diagnosis of multiple myeloma (MM) varies between patients and some of these differences may be a consequence of inherited genetic variation. In this study, to identify genetic markers associated with MM overall survival (MM-OS), we conduct a meta-analysis of four patient series of European ancest...

    journal_title：Nature communications

    pub_type： 杂志文章,meta分析

    doi：10.1038/ncomms10290

    authors： Johnson DC,Weinhold N,Mitchell JS,Chen B,Kaiser M,Begum DB,Hillengass J,Bertsch U,Gregory WA,Cairns D,Jackson GH,Försti A,Nickel J,Hoffmann P,Nöethen MM,Stephens OW,Barlogie B,Davis FE,Hemminki K,Goldschmidt H,Hou

    更新日期：2016-01-08 00:00:00

  • Semaphorin 4C Plexin-B2 signaling in peripheral sensory neurons is pronociceptive in a model of inflammatory pain.

    abstract：:Semaphorins and their transmembrane receptors, Plexins, are key regulators of axon guidance and development of neuronal connectivity. B-type Plexins respond to Class IV semaphorins and mediate a variety of developmental functions. Here we report that the expression of Plexin-B2 and its high-affinity ligand, Sema4C, pe...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/s41467-017-00341-w

    authors： Paldy E,Simonetti M,Worzfeld T,Bali KK,Vicuña L,Offermanns S,Kuner R

    更新日期：2017-08-02 00:00:00

  • Spatiotemporal dynamics of information encoding revealed in orbitofrontal high-gamma.

    abstract：:High-gamma signals mirror the tuning and temporal profiles of neurons near a recording electrode in sensory and motor areas. These frequencies appear to aggregate local neuronal activity, but it is unclear how this relationship affects information encoding in high-gamma activity (HGA) in cortical areas where neurons a...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/s41467-017-01253-5

    authors： Rich EL,Wallis JD

    更新日期：2017-10-26 00:00:00

  • Post-transcriptional 3´-UTR cleavage of mRNA transcripts generates thousands of stable uncapped autonomous RNA fragments.

    abstract：:The majority of mammalian genes contain one or more alternative polyadenylation sites. Choice of polyadenylation sites was suggested as one of the underlying mechanisms for generating longer/shorter transcript isoforms. Here, we demonstrate that mature mRNA transcripts can undergo additional cleavage and polyadenylati...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/s41467-017-02099-7

    authors： Malka Y,Steiman-Shimony A,Rosenthal E,Argaman L,Cohen-Daniel L,Arbib E,Margalit H,Kaplan T,Berger M

    更新日期：2017-12-11 00:00:00

  • A glycoprotein B-neutralizing antibody structure at 2.8 Å uncovers a critical domain for herpesvirus fusion initiation.

    abstract：:Members of the Herpesviridae, including the medically important alphaherpesvirus varicella-zoster virus (VZV), induce fusion of the virion envelope with cell membranes during entry, and between cells to form polykaryocytes in infected tissues. The conserved glycoproteins, gB, gH and gL, are the core functional protein...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/s41467-020-17911-0

    authors： Oliver SL,Xing Y,Chen DH,Roh SH,Pintilie GD,Bushnell DA,Sommer MH,Yang E,Carfi A,Chiu W,Arvin AM

    更新日期：2020-08-18 00:00:00

  • All-optical observation and reconstruction of spin wave dispersion.

    abstract：:To know the properties of a particle or a wave, one should measure how its energy changes with its momentum. The relation between them is called the dispersion relation, which encodes essential information of the kinetics. In a magnet, the wave motion of atomic spins serves as an elementary excitation, called a spin w...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/ncomms15859

    authors： Hashimoto Y,Daimon S,Iguchi R,Oikawa Y,Shen K,Sato K,Bossini D,Tabuchi Y,Satoh T,Hillebrands B,Bauer GEW,Johansen TH,Kirilyuk A,Rasing T,Saitoh E

    更新日期：2017-06-12 00:00:00

  • Frustration-driven C 4 symmetric order in a naturally-heterostructured superconductor Sr2VO3FeAs.

    abstract：:A subtle balance between competing interactions in iron-based superconductors (FeSCs) can be tipped by additional interfacial interactions in a heterostructure, often inducing exotic phases with unprecedented properties. Particularly when the proximity-coupled layer is magnetically active, rich phase diagrams are expe...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/s41467-017-02327-0

    authors： Ok JM,Baek SH,Hoch C,Kremer RK,Park SY,Ji S,Büchner B,Park JH,Hyun SI,Shim JH,Bang Y,Moon EG,Mazin II,Kim JS

    更新日期：2017-12-18 00:00:00

  • Rapid and tunable method to temporally control gene editing based on conditional Cas9 stabilization.

    abstract：:The CRISPR/Cas9 system is a powerful tool for studying gene function. Here, we describe a method that allows temporal control of CRISPR/Cas9 activity based on conditional Cas9 destabilization. We demonstrate that fusing an FKBP12-derived destabilizing domain to Cas9 (DD-Cas9) enables conditional Cas9 expression and te...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/ncomms14370

    authors： Senturk S,Shirole NH,Nowak DG,Corbo V,Pal D,Vaughan A,Tuveson DA,Trotman LC,Kinney JB,Sordella R

    更新日期：2017-02-22 00:00:00

  • Real-time assembly of ribonucleoprotein complexes on nascent RNA transcripts.

    abstract：:Cellular protein-RNA complexes assemble on nascent transcripts, but methods to observe transcription and protein binding in real time and at physiological concentrations are not available. Here, we report a single-molecule approach based on zero-mode waveguides that simultaneously tracks transcription progress and the...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/s41467-018-07423-3

    authors： Duss O,Stepanyuk GA,Grot A,O'Leary SE,Puglisi JD,Williamson JR

    更新日期：2018-11-30 00:00:00

  • An investigation of irreproducibility in maximum likelihood phylogenetic inference.

    abstract：:Phylogenetic trees are essential for studying biology, but their reproducibility under identical parameter settings remains unexplored. Here, we find that 3515 (18.11%) IQ-TREE-inferred and 1813 (9.34%) RAxML-NG-inferred maximum likelihood (ML) gene trees are topologically irreproducible when executing two replicates ...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/s41467-020-20005-6

    authors： Shen XX,Li Y,Hittinger CT,Chen XX,Rokas A

    更新日期：2020-11-30 00:00:00

  • Negative Poisson's ratio in 1T-type crystalline two-dimensional transition metal dichalcogenides.

    abstract：:Materials with a negative Poisson's ratio, also known as auxetic materials, exhibit unusual and counterintuitive mechanical behaviour-becoming fatter in cross-section when stretched. Such behaviour is mostly attributed to some special re-entrant or hinged geometric structures regardless of the chemical composition and...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/ncomms15224

    authors： Yu L,Yan Q,Ruzsinszky A

    更新日期：2017-05-25 00:00:00

  • Pathway engineering in yeast for synthesizing the complex polyketide bikaverin.

    abstract：:Fungal polyketides display remarkable structural diversity and bioactivity, and therefore the biosynthesis and engineering of this large class of molecules is therapeutically significant. Here, we successfully recode, construct and characterize the biosynthetic pathway of bikaverin, a tetracyclic polyketide with antib...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/s41467-020-19984-3

    authors： Zhao M,Zhao Y,Yao M,Iqbal H,Hu Q,Liu H,Qiao B,Li C,Skovbjerg CAS,Nielsen JC,Nielsen J,Frandsen RJN,Yuan Y,Boeke JD

    更新日期：2020-12-03 00:00:00

  • Quantifying electronic band interactions in van der Waals materials using angle-resolved reflected-electron spectroscopy.

    abstract：:High electron mobility is one of graphene's key properties, exploited for applications and fundamental research alike. Highest mobility values are found in heterostructures of graphene and hexagonal boron nitride, which consequently are widely used. However, surprisingly little is known about the interaction between t...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/ncomms13621

    authors： Jobst J,van der Torren AJH,Krasovskii EE,Balgley J,Dean CR,Tromp RM,van der Molen SJ

    更新日期：2016-11-29 00:00:00

  • Ultrafast charge transfer coupled with lattice phonons in two-dimensional covalent organic frameworks.

    abstract：:Covalent organic frameworks (COFs) have emerged as a promising light-harvesting module for artificial photosynthesis and photovoltaics. For efficient generation of free charge carriers, the donor-acceptor (D-A) conjugation has been adopted for two-dimensional (2D) COFs recently. In the 2D D-A COFs, photoexcitation wou...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/s41467-019-09872-w

    authors： Kim TW,Jun S,Ha Y,Yadav RK,Kumar A,Yoo CY,Oh I,Lim HK,Shin JW,Ryoo R,Kim H,Kim J,Baeg JO,Ihee H

    更新日期：2019-04-23 00:00:00

  • Water-dispersible PEG-curcumin/amine-functionalized covalent organic framework nanocomposites as smart carriers for in vivo drug delivery.

    abstract：:Covalent organic frameworks (COFs) as drug-delivery carriers have been mostly evaluated in vitro due to the lack of COFs nanocarriers that are suitable for in vivo studies. Here we develop a series of water-dispersible polymer-COF nanocomposites through the assembly of polyethylene-glycol-modified monofunctional curcu...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/s41467-018-04910-5

    authors： Zhang G,Li X,Liao Q,Liu Y,Xi K,Huang W,Jia X

    更新日期：2018-07-17 00:00:00

  • Islands contribute disproportionately high amounts of evolutionary diversity in passerine birds.

    abstract：:Island systems generally have fewer species than continental areas due to their small size and geographical isolation. Low island diversity reduces the possibility of exportation of island lineages and island systems are not thought to have a major influence on the build-up of continental diversity. However, the view ...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/ncomms9538

    authors： Jønsson KA,Holt BG

    更新日期：2015-10-05 00:00:00

  • BORDER proteins protect expression of neighboring genes by promoting 3' Pol II pausing in plants.

    abstract：:Ensuring that one gene's transcription does not inappropriately affect the expression of its neighbors is a fundamental challenge to gene regulation in a genomic context. In plants, which lack homologs of animal insulator proteins, the mechanisms that prevent transcriptional interference are not well understood. Here ...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/s41467-019-12328-w

    authors： Yu X,Martin PGP,Michaels SD

    更新日期：2019-09-25 00:00:00

  • Probing low-energy hyperbolic polaritons in van der Waals crystals with an electron microscope.

    abstract：:Van der Waals materials exhibit intriguing structural, electronic, and photonic properties. Electron energy loss spectroscopy within scanning transmission electron microscopy allows for nanoscale mapping of such properties. However, its detection is typically limited to energy losses in the eV range-too large for prob...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/s41467-017-00056-y

    authors： Govyadinov AA,Konečná A,Chuvilin A,Vélez S,Dolado I,Nikitin AY,Lopatin S,Casanova F,Hueso LE,Aizpurua J,Hillenbrand R

    更新日期：2017-07-21 00:00:00

  • Arabidopsis calcium-dependent protein kinase 3 regulates actin cytoskeleton organization and immunity.

    abstract：:Pattern-triggered immunity and effector-triggered immunity are two primary forms of innate immunity in land plants. The molecular components and connecting nodes of pattern-triggered immunity and effector-triggered immunity are not fully understood. Here, we report that the Arabidopsis calcium-dependent protein kinase...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/s41467-020-20007-4

    authors： Lu YJ,Li P,Shimono M,Corrion A,Higaki T,He SY,Day B

    更新日期：2020-12-04 00:00:00

  • Observation of photonic anomalous Floquet topological insulators.

    abstract：:Topological insulators are a new class of materials that exhibit robust and scatter-free transport along their edges - independently of the fine details of the system and of the edge - due to topological protection. To classify the topological character of two-dimensional systems without additional symmetries, one com...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/ncomms13756

    authors： Maczewsky LJ,Zeuner JM,Nolte S,Szameit A

    更新日期：2017-01-04 00:00:00

  • Dynamic beam steering with all-dielectric electro-optic III-V multiple-quantum-well metasurfaces.

    abstract：:Tunable metasurfaces enable dynamical control of the key constitutive properties of light at a subwavelength scale. To date, electrically tunable metasurfaces at near-infrared wavelengths have been realized using free carrier modulation, and switching of thermo-optical, liquid crystal and phase change media. However, ...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/s41467-019-11598-8

    authors： Wu PC,Pala RA,Kafaie Shirmanesh G,Cheng WH,Sokhoyan R,Grajower M,Alam MZ,Lee D,Atwater HA

    更新日期：2019-08-13 00:00:00

  • Global patterns of nitrate storage in the vadose zone.

    abstract：:Global-scale nitrogen budgets developed to quantify anthropogenic impacts on the nitrogen cycle do not explicitly consider nitrate stored in the vadose zone. Here we show that the vadose zone is an important store of nitrate that should be considered in future budgets for effective policymaking. Using estimates of gro...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/s41467-017-01321-w

    authors： Ascott MJ,Gooddy DC,Wang L,Stuart ME,Lewis MA,Ward RS,Binley AM

    更新日期：2017-11-10 00:00:00

  • Cytosolic targeting factor AKR2A captures chloroplast outer membrane-localized client proteins at the ribosome during translation.

    abstract：:In eukaryotic cells, organellar proteome biogenesis is pivotal for cellular function. Chloroplasts contain a complex proteome, the biogenesis of which includes post-translational import of nuclear-encoded proteins. However, the mechanisms determining when and how nascent chloroplast-targeted proteins are sorted in the...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/ncomms7843

    authors： Kim DH,Lee JE,Xu ZY,Geem KR,Kwon Y,Park JW,Hwang I

    更新日期：2015-04-16 00:00:00

  • Gingival solitary chemosensory cells are immune sentinels for periodontitis.

    abstract：:Solitary chemosensory cells (SCCs) are epithelial sentinels that utilize bitter Tas2r receptors and coupled taste transduction elements to detect pathogenic bacterial metabolites, triggering host defenses to control the infection. Here we report that SCCs are present in mouse gingival junctional epithelium, where they...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/s41467-019-12505-x

    authors： Zheng X,Tizzano M,Redding K,He J,Peng X,Jiang P,Xu X,Zhou X,Margolskee RF

    更新日期：2019-10-03 00:00:00

  • Early evidence of molariform hypsodonty in a Triassic stem-mammal.

    abstract：:Hypsodonty, the occurrence of high-crowned teeth, is widespread among mammals with diets rich in abrasive material, such as plants or soil, because it increases the durability of dentitions against wear. Hypsodont postcanine teeth evolved independently in multiple mammalian lineages and in the closely related mammalia...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/s41467-019-10719-7

    authors： Melo TP,Ribeiro AM,Martinelli AG,Soares MB

    更新日期：2019-06-28 00:00:00

  • Exceptionally well-preserved Cretaceous microfossils reveal new biomineralization styles.

    abstract：:Calcareous microplankton shells form the dominant components of ancient and modern pelagic sea-floor carbonates and are widely used in palaeoenvironmental reconstructions. The efficacy of these applications, however, is dependent upon minimal geochemical alteration during diagenesis, but these modifying processes are ...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/ncomms3052

    authors： Wendler JE,Bown P

    更新日期：2013-01-01 00:00:00

  • The MerR-like protein BldC binds DNA direct repeats as cooperative multimers to regulate Streptomyces development.

    abstract：:Streptomycetes are notable for their complex life cycle and production of most clinically important antibiotics. A key factor that controls entry into development and the onset of antibiotic production is the 68-residue protein, BldC. BldC is a putative DNA-binding protein related to MerR regulators, but lacks coiled-...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/s41467-018-03576-3

    authors： Schumacher MA,den Hengst CD,Bush MJ,Le TBK,Tran NT,Chandra G,Zeng W,Travis B,Brennan RG,Buttner MJ

    更新日期：2018-03-19 00:00:00

  • Robust microscale superlubricity under high contact pressure enabled by graphene-coated microsphere.

    abstract：:Superlubricity of graphite and graphene has aroused increasing interest in recent years. Yet how to obtain a long-lasting superlubricity between graphene layers, under high applied normal load in ambient atmosphere still remains a challenge but is highly desirable. Here, we report a direct measurement of sliding frict...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/ncomms14029

    authors： Liu SW,Wang HP,Xu Q,Ma TB,Yu G,Zhang C,Geng D,Yu Z,Zhang S,Wang W,Hu YZ,Wang H,Luo J

    更新日期：2017-02-14 00:00:00

  • Drawing a high-resolution functional map of adeno-associated virus capsid by massively parallel sequencing.

    abstract：:Adeno-associated virus (AAV) capsid engineering is an emerging approach to advance gene therapy. However, a systematic analysis on how each capsid amino acid contributes to multiple functions remains challenging. Here we show proof-of-principle and successful application of a novel approach, termed AAV Barcode-Seq, th...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/ncomms4075

    authors： Adachi K,Enoki T,Kawano Y,Veraz M,Nakai H

    更新日期：2014-01-01 00:00:00

  • Rethinking Indian monsoon rainfall prediction in the context of recent global warming.

    abstract：:Prediction of Indian summer monsoon rainfall (ISMR) is at the heart of tropical climate prediction. Despite enormous progress having been made in predicting ISMR since 1886, the operational forecasts during recent decades (1989-2012) have little skill. Here we show, with both dynamical and physical-empirical models, t...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/ncomms8154

    authors： Wang B,Xiang B,Li J,Webster PJ,Rajeevan MN,Liu J,Ha KJ

    更新日期：2015-05-18 00:00:00