GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2011-04-28

AUTHORS

Craig H Mermel, Steven E Schumacher, Barbara Hill, Matthew L Meyerson, Rameen Beroukhim, Gad Getz

ABSTRACT

We describe methods with enhanced power and specificity to identify genes targeted by somatic copy-number alterations (SCNAs) that drive cancer growth. By separating SCNA profiles into underlying arm-level and focal alterations, we improve the estimation of background rates for each category. We additionally describe a probabilistic method for defining the boundaries of selected-for SCNA regions with user-defined confidence. Here we detail this revised computational approach, GISTIC2.0, and validate its performance in real and simulated datasets. More... »

PAGES

r41

References to SciGraph publications

  • 2009-12-08. Sequencing technologies — the next generation in NATURE REVIEWS GENETICS
  • 2007-10-02. Assessment of algorithms for high throughput detection of genomic copy number variation in oligonucleotide microarray data in BMC BIOINFORMATICS
  • 2001-08-03. Model-based analysis of oligonucleotide arrays: model validation, design issues and standard error application in GENOME BIOLOGY
  • 2009-04. The cancer genome in NATURE
  • 2009-12-16. A comprehensive catalogue of somatic mutations from a human cancer genome in NATURE
  • 2008-11-30. High-resolution mapping of copy-number alterations with massively parallel sequencing in NATURE METHODS
  • 2008-09-14. CDK8 is a colorectal cancer oncogene that regulates β-catenin activity in NATURE
  • 2009-07. Boveri revisited: chromosomal instability, aneuploidy and tumorigenesis in NATURE REVIEWS MOLECULAR CELL BIOLOGY
  • 2007-11-04. Characterizing the cancer genome in lung adenocarcinoma in NATURE
  • 2007-03. Patterns of somatic mutation in human cancer genomes in NATURE
  • 2010-02. The landscape of somatic copy-number alteration across human cancers in NATURE
  • 2009-10-04. SOX2 is an amplified lineage-survival oncogene in lung and esophageal squamous cell carcinomas in NATURE GENETICS
  • 2009-12. Complex landscapes of somatic rearrangement in human breast cancer genomes in NATURE
  • 2010-02. Signatures of mutation and selection in the cancer genome in NATURE
  • 2008-09-07. Integrated detection and population-genetic analysis of SNPs and copy number variation in NATURE GENETICS
  • 2008-09-04. Comprehensive genomic characterization defines human glioblastoma genes and core pathways in NATURE
  • 2010-04-14. JISTIC: Identification of Significant Targets in Cancer in BMC BIOINFORMATICS
  • 2009-03-08. Multiple recurrent genetic events converge on control of histone lysine methylation in medulloblastoma in NATURE GENETICS
  • 2006-11-16. Cancer as an evolutionary and ecological process in NATURE REVIEWS CANCER
  • 2001-09-12. Arrays of DNA-binding sites in GENOME BIOLOGY
  • 2009-12-16. A small-cell lung cancer genome with complex signatures of tobacco exposure in NATURE
  • 2010-01. A census of amplified and overexpressed human cancer genes in NATURE REVIEWS CANCER
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1186/gb-2011-12-4-r41

    DOI

    http://dx.doi.org/10.1186/gb-2011-12-4-r41

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1036416165

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/21527027


    Indexing Status Check whether this publication has been indexed by Scopus and Web Of Science using the SN Indexing Status Tool
    Incoming Citations Browse incoming citations for this publication using opencitations.net

    JSON-LD is the canonical representation for SciGraph data.

    TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT

    [
      {
        "@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json", 
        "about": [
          {
            "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/05", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Environmental Sciences", 
            "type": "DefinedTerm"
          }, 
          {
            "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/06", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Biological Sciences", 
            "type": "DefinedTerm"
          }, 
          {
            "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/08", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Information and Computing Sciences", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Algorithms", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Computational Biology", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Computer Simulation", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Gene Dosage", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Humans", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Models, Theoretical", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Neoplasms", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Software", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Tumor Suppressor Proteins", 
            "type": "DefinedTerm"
          }
        ], 
        "author": [
          {
            "affiliation": {
              "alternateName": "The Center for Cancer Genome Discovery, Dana Farber Cancer Institute, 44 Binney Street, 02115, Boston, MA, USA", 
              "id": "http://www.grid.ac/institutes/grid.65499.37", 
              "name": [
                "Cancer Program, The Broad Institute of MIT and Harvard, 7 Cambridge Center, 02142, Cambridge, MA, USA", 
                "Department of Medical Oncology, Dana Farber Cancer Institute, 44 Binney Street, 02115, Boston, MA, USA", 
                "Department of Cancer Biology, Dana Farber Cancer Institute, 44 Binney Street, 02115, Boston, MA, USA", 
                "The Center for Cancer Genome Discovery, Dana Farber Cancer Institute, 44 Binney Street, 02115, Boston, MA, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Mermel", 
            "givenName": "Craig H", 
            "id": "sg:person.01066471003.08", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01066471003.08"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "The Center for Cancer Genome Discovery, Dana Farber Cancer Institute, 44 Binney Street, 02115, Boston, MA, USA", 
              "id": "http://www.grid.ac/institutes/grid.65499.37", 
              "name": [
                "Cancer Program, The Broad Institute of MIT and Harvard, 7 Cambridge Center, 02142, Cambridge, MA, USA", 
                "Department of Medical Oncology, Dana Farber Cancer Institute, 44 Binney Street, 02115, Boston, MA, USA", 
                "Department of Cancer Biology, Dana Farber Cancer Institute, 44 Binney Street, 02115, Boston, MA, USA", 
                "The Center for Cancer Genome Discovery, Dana Farber Cancer Institute, 44 Binney Street, 02115, Boston, MA, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Schumacher", 
            "givenName": "Steven E", 
            "id": "sg:person.01055166050.55", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01055166050.55"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Cancer Program, The Broad Institute of MIT and Harvard, 7 Cambridge Center, 02142, Cambridge, MA, USA", 
              "id": "http://www.grid.ac/institutes/grid.66859.34", 
              "name": [
                "Cancer Program, The Broad Institute of MIT and Harvard, 7 Cambridge Center, 02142, Cambridge, MA, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Hill", 
            "givenName": "Barbara", 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "The Center for Cancer Genome Discovery, Dana Farber Cancer Institute, 44 Binney Street, 02115, Boston, MA, USA", 
              "id": "http://www.grid.ac/institutes/grid.65499.37", 
              "name": [
                "Cancer Program, The Broad Institute of MIT and Harvard, 7 Cambridge Center, 02142, Cambridge, MA, USA", 
                "Department of Medical Oncology, Dana Farber Cancer Institute, 44 Binney Street, 02115, Boston, MA, USA", 
                "Department of Cancer Biology, Dana Farber Cancer Institute, 44 Binney Street, 02115, Boston, MA, USA", 
                "The Center for Cancer Genome Discovery, Dana Farber Cancer Institute, 44 Binney Street, 02115, Boston, MA, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Meyerson", 
            "givenName": "Matthew L", 
            "id": "sg:person.016012142422.14", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.016012142422.14"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "The Center for Cancer Genome Discovery, Dana Farber Cancer Institute, 44 Binney Street, 02115, Boston, MA, USA", 
              "id": "http://www.grid.ac/institutes/grid.65499.37", 
              "name": [
                "Cancer Program, The Broad Institute of MIT and Harvard, 7 Cambridge Center, 02142, Cambridge, MA, USA", 
                "Department of Medical Oncology, Dana Farber Cancer Institute, 44 Binney Street, 02115, Boston, MA, USA", 
                "Department of Cancer Biology, Dana Farber Cancer Institute, 44 Binney Street, 02115, Boston, MA, USA", 
                "The Center for Cancer Genome Discovery, Dana Farber Cancer Institute, 44 Binney Street, 02115, Boston, MA, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Beroukhim", 
            "givenName": "Rameen", 
            "id": "sg:person.01310170137.53", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01310170137.53"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Cancer Program, The Broad Institute of MIT and Harvard, 7 Cambridge Center, 02142, Cambridge, MA, USA", 
              "id": "http://www.grid.ac/institutes/grid.66859.34", 
              "name": [
                "Cancer Program, The Broad Institute of MIT and Harvard, 7 Cambridge Center, 02142, Cambridge, MA, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Getz", 
            "givenName": "Gad", 
            "id": "sg:person.01316313531.32", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01316313531.32"
            ], 
            "type": "Person"
          }
        ], 
        "citation": [
          {
            "id": "sg:pub.10.1038/nature06358", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1019681472", 
              "https://doi.org/10.1038/nature06358"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nmeth.1276", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1025333243", 
              "https://doi.org/10.1038/nmeth.1276"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/1471-2105-11-189", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1011737467", 
              "https://doi.org/10.1186/1471-2105-11-189"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nrm2718", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1024297992", 
              "https://doi.org/10.1038/nrm2718"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature08822", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1010635813", 
              "https://doi.org/10.1038/nature08822"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature07385", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1039570773", 
              "https://doi.org/10.1038/nature07385"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature08645", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1050729897", 
              "https://doi.org/10.1038/nature08645"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/gb-2001-2-8-research0032", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1015228558", 
              "https://doi.org/10.1186/gb-2001-2-8-research0032"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature07179", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1010877750", 
              "https://doi.org/10.1038/nature07179"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ng.238", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1047420273", 
              "https://doi.org/10.1038/ng.238"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature08658", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1014288207", 
              "https://doi.org/10.1038/nature08658"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature05610", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1033482125", 
              "https://doi.org/10.1038/nature05610"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/gb-2001-2-10-reports0032", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1085169177", 
              "https://doi.org/10.1186/gb-2001-2-10-reports0032"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ng.336", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1035880217", 
              "https://doi.org/10.1038/ng.336"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nrg2626", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1023911485", 
              "https://doi.org/10.1038/nrg2626"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ng.465", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1025808150", 
              "https://doi.org/10.1038/ng.465"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/1471-2105-8-368", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1007193249", 
              "https://doi.org/10.1186/1471-2105-8-368"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nrc2771", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1029567400", 
              "https://doi.org/10.1038/nrc2771"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature08629", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1041012667", 
              "https://doi.org/10.1038/nature08629"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature08768", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1002735811", 
              "https://doi.org/10.1038/nature08768"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature07943", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1004829095", 
              "https://doi.org/10.1038/nature07943"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nrc2013", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1023245275", 
              "https://doi.org/10.1038/nrc2013"
            ], 
            "type": "CreativeWork"
          }
        ], 
        "datePublished": "2011-04-28", 
        "datePublishedReg": "2011-04-28", 
        "description": "We describe methods with enhanced power and specificity to identify genes targeted by somatic copy-number alterations (SCNAs) that drive cancer growth. By separating SCNA profiles into underlying arm-level and focal alterations, we improve the estimation of background rates for each category. We additionally describe a probabilistic method for defining the boundaries of selected-for SCNA regions with user-defined confidence. Here we detail this revised computational approach, GISTIC2.0, and validate its performance in real and simulated datasets.", 
        "genre": "article", 
        "id": "sg:pub.10.1186/gb-2011-12-4-r41", 
        "isAccessibleForFree": true, 
        "isFundedItemOf": [
          {
            "id": "sg:grant.2411168", 
            "type": "MonetaryGrant"
          }, 
          {
            "id": "sg:grant.2683815", 
            "type": "MonetaryGrant"
          }, 
          {
            "id": "sg:grant.2696338", 
            "type": "MonetaryGrant"
          }
        ], 
        "isPartOf": [
          {
            "id": "sg:journal.1023439", 
            "issn": [
              "1474-760X", 
              "1465-6906"
            ], 
            "name": "Genome Biology", 
            "publisher": "Springer Nature", 
            "type": "Periodical"
          }, 
          {
            "issueNumber": "4", 
            "type": "PublicationIssue"
          }, 
          {
            "type": "PublicationVolume", 
            "volumeNumber": "12"
          }
        ], 
        "keywords": [
          "user-defined confidence", 
          "probabilistic method", 
          "computational approach", 
          "somatic copy number alterations", 
          "dataset", 
          "copy number alterations", 
          "method", 
          "performance", 
          "focal somatic copy number alterations", 
          "SCNA profiles", 
          "estimation", 
          "SCNA regions", 
          "facilitates", 
          "human cancers", 
          "enhanced power", 
          "cancer growth", 
          "confidence", 
          "power", 
          "confident localization", 
          "localization", 
          "categories", 
          "genes", 
          "alterations", 
          "boundaries", 
          "focal alterations", 
          "growth", 
          "target", 
          "specificity", 
          "background rate", 
          "region", 
          "rate", 
          "GISTIC2.0", 
          "cancer", 
          "profile", 
          "approach"
        ], 
        "name": "GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers", 
        "pagination": "r41", 
        "productId": [
          {
            "name": "dimensions_id", 
            "type": "PropertyValue", 
            "value": [
              "pub.1036416165"
            ]
          }, 
          {
            "name": "doi", 
            "type": "PropertyValue", 
            "value": [
              "10.1186/gb-2011-12-4-r41"
            ]
          }, 
          {
            "name": "pubmed_id", 
            "type": "PropertyValue", 
            "value": [
              "21527027"
            ]
          }
        ], 
        "sameAs": [
          "https://doi.org/10.1186/gb-2011-12-4-r41", 
          "https://app.dimensions.ai/details/publication/pub.1036416165"
        ], 
        "sdDataset": "articles", 
        "sdDatePublished": "2022-09-02T15:54", 
        "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
        "sdPublisher": {
          "name": "Springer Nature - SN SciGraph project", 
          "type": "Organization"
        }, 
        "sdSource": "s3://com-springernature-scigraph/baseset/20220902/entities/gbq_results/article/article_549.jsonl", 
        "type": "ScholarlyArticle", 
        "url": "https://doi.org/10.1186/gb-2011-12-4-r41"
      }
    ]
     

    Download the RDF metadata as:  json-ld nt turtle xml License info

    HOW TO GET THIS DATA PROGRAMMATICALLY:

    JSON-LD is a popular format for linked data which is fully compatible with JSON.

    curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1186/gb-2011-12-4-r41'

    N-Triples is a line-based linked data format ideal for batch operations.

    curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1186/gb-2011-12-4-r41'

    Turtle is a human-readable linked data format.

    curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/gb-2011-12-4-r41'

    RDF/XML is a standard XML format for linked data.

    curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/gb-2011-12-4-r41'


     

    This table displays all metadata directly associated to this object as RDF triples.

    270 TRIPLES      21 PREDICATES      92 URIs      61 LITERALS      16 BLANK NODES

    Subject Predicate Object
    1 sg:pub.10.1186/gb-2011-12-4-r41 schema:about N03cbf1b7b71542848b5704dc695d76df
    2 N2c1610c6026a457b8b9be28e5af7ba4d
    3 N48e77626c1074ec9957fd3bee5e05527
    4 N65f0e8c97a57431ba82e378bf3b5cdc4
    5 N8b903f1e4fef4a4a85faaabdb9a97af1
    6 Na782b523e72446a1be5ee79fd1de5cb7
    7 Ne8555a35da3c470d82f2d27d4a7b73f0
    8 Nf7c83dc61fb0486ea03d7aa8eb20355f
    9 Nfb4302f9dac34e779eb83a7bd04799ac
    10 anzsrc-for:05
    11 anzsrc-for:06
    12 anzsrc-for:08
    13 schema:author N39ac195f50094229990785a33f19d02a
    14 schema:citation sg:pub.10.1038/nature05610
    15 sg:pub.10.1038/nature06358
    16 sg:pub.10.1038/nature07179
    17 sg:pub.10.1038/nature07385
    18 sg:pub.10.1038/nature07943
    19 sg:pub.10.1038/nature08629
    20 sg:pub.10.1038/nature08645
    21 sg:pub.10.1038/nature08658
    22 sg:pub.10.1038/nature08768
    23 sg:pub.10.1038/nature08822
    24 sg:pub.10.1038/ng.238
    25 sg:pub.10.1038/ng.336
    26 sg:pub.10.1038/ng.465
    27 sg:pub.10.1038/nmeth.1276
    28 sg:pub.10.1038/nrc2013
    29 sg:pub.10.1038/nrc2771
    30 sg:pub.10.1038/nrg2626
    31 sg:pub.10.1038/nrm2718
    32 sg:pub.10.1186/1471-2105-11-189
    33 sg:pub.10.1186/1471-2105-8-368
    34 sg:pub.10.1186/gb-2001-2-10-reports0032
    35 sg:pub.10.1186/gb-2001-2-8-research0032
    36 schema:datePublished 2011-04-28
    37 schema:datePublishedReg 2011-04-28
    38 schema:description We describe methods with enhanced power and specificity to identify genes targeted by somatic copy-number alterations (SCNAs) that drive cancer growth. By separating SCNA profiles into underlying arm-level and focal alterations, we improve the estimation of background rates for each category. We additionally describe a probabilistic method for defining the boundaries of selected-for SCNA regions with user-defined confidence. Here we detail this revised computational approach, GISTIC2.0, and validate its performance in real and simulated datasets.
    39 schema:genre article
    40 schema:isAccessibleForFree true
    41 schema:isPartOf N05c00aeee1b94f5e82d918c9998537d2
    42 Nd1ae5dbcd902427da2f7aaf154075597
    43 sg:journal.1023439
    44 schema:keywords GISTIC2.0
    45 SCNA profiles
    46 SCNA regions
    47 alterations
    48 approach
    49 background rate
    50 boundaries
    51 cancer
    52 cancer growth
    53 categories
    54 computational approach
    55 confidence
    56 confident localization
    57 copy number alterations
    58 dataset
    59 enhanced power
    60 estimation
    61 facilitates
    62 focal alterations
    63 focal somatic copy number alterations
    64 genes
    65 growth
    66 human cancers
    67 localization
    68 method
    69 performance
    70 power
    71 probabilistic method
    72 profile
    73 rate
    74 region
    75 somatic copy number alterations
    76 specificity
    77 target
    78 user-defined confidence
    79 schema:name GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers
    80 schema:pagination r41
    81 schema:productId N5de05adcdbd14f85ba030af02d3e0835
    82 N7c5d8f7994294d42b1d288f0aa687c14
    83 Nde52dd6f62474e3cb015301396e77ccb
    84 schema:sameAs https://app.dimensions.ai/details/publication/pub.1036416165
    85 https://doi.org/10.1186/gb-2011-12-4-r41
    86 schema:sdDatePublished 2022-09-02T15:54
    87 schema:sdLicense https://scigraph.springernature.com/explorer/license/
    88 schema:sdPublisher N93df0069ef9f4ba8831bb88fa2424f57
    89 schema:url https://doi.org/10.1186/gb-2011-12-4-r41
    90 sgo:license sg:explorer/license/
    91 sgo:sdDataset articles
    92 rdf:type schema:ScholarlyArticle
    93 N03cbf1b7b71542848b5704dc695d76df schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    94 schema:name Models, Theoretical
    95 rdf:type schema:DefinedTerm
    96 N05c00aeee1b94f5e82d918c9998537d2 schema:issueNumber 4
    97 rdf:type schema:PublicationIssue
    98 N2c1610c6026a457b8b9be28e5af7ba4d schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    99 schema:name Computational Biology
    100 rdf:type schema:DefinedTerm
    101 N39ac195f50094229990785a33f19d02a rdf:first sg:person.01066471003.08
    102 rdf:rest N4080c73940c44007a478178b4bf00d4f
    103 N4080c73940c44007a478178b4bf00d4f rdf:first sg:person.01055166050.55
    104 rdf:rest N6237ce95efcc4103b99b7d722bf3a6fc
    105 N48e77626c1074ec9957fd3bee5e05527 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    106 schema:name Algorithms
    107 rdf:type schema:DefinedTerm
    108 N4fbb4bb07d874fe3a08cec97c13c1662 rdf:first sg:person.01310170137.53
    109 rdf:rest Nd480a3b29089445c98616d96df2f650e
    110 N5de05adcdbd14f85ba030af02d3e0835 schema:name dimensions_id
    111 schema:value pub.1036416165
    112 rdf:type schema:PropertyValue
    113 N6237ce95efcc4103b99b7d722bf3a6fc rdf:first N9d1de288ec52428cb8e282ac95470aca
    114 rdf:rest N62d37f795e5e4af7bb91864f824bd041
    115 N62d37f795e5e4af7bb91864f824bd041 rdf:first sg:person.016012142422.14
    116 rdf:rest N4fbb4bb07d874fe3a08cec97c13c1662
    117 N65f0e8c97a57431ba82e378bf3b5cdc4 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    118 schema:name Computer Simulation
    119 rdf:type schema:DefinedTerm
    120 N7c5d8f7994294d42b1d288f0aa687c14 schema:name pubmed_id
    121 schema:value 21527027
    122 rdf:type schema:PropertyValue
    123 N8b903f1e4fef4a4a85faaabdb9a97af1 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    124 schema:name Software
    125 rdf:type schema:DefinedTerm
    126 N93df0069ef9f4ba8831bb88fa2424f57 schema:name Springer Nature - SN SciGraph project
    127 rdf:type schema:Organization
    128 N9d1de288ec52428cb8e282ac95470aca schema:affiliation grid-institutes:grid.66859.34
    129 schema:familyName Hill
    130 schema:givenName Barbara
    131 rdf:type schema:Person
    132 Na782b523e72446a1be5ee79fd1de5cb7 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    133 schema:name Tumor Suppressor Proteins
    134 rdf:type schema:DefinedTerm
    135 Nd1ae5dbcd902427da2f7aaf154075597 schema:volumeNumber 12
    136 rdf:type schema:PublicationVolume
    137 Nd480a3b29089445c98616d96df2f650e rdf:first sg:person.01316313531.32
    138 rdf:rest rdf:nil
    139 Nde52dd6f62474e3cb015301396e77ccb schema:name doi
    140 schema:value 10.1186/gb-2011-12-4-r41
    141 rdf:type schema:PropertyValue
    142 Ne8555a35da3c470d82f2d27d4a7b73f0 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    143 schema:name Gene Dosage
    144 rdf:type schema:DefinedTerm
    145 Nf7c83dc61fb0486ea03d7aa8eb20355f schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    146 schema:name Neoplasms
    147 rdf:type schema:DefinedTerm
    148 Nfb4302f9dac34e779eb83a7bd04799ac schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    149 schema:name Humans
    150 rdf:type schema:DefinedTerm
    151 anzsrc-for:05 schema:inDefinedTermSet anzsrc-for:
    152 schema:name Environmental Sciences
    153 rdf:type schema:DefinedTerm
    154 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
    155 schema:name Biological Sciences
    156 rdf:type schema:DefinedTerm
    157 anzsrc-for:08 schema:inDefinedTermSet anzsrc-for:
    158 schema:name Information and Computing Sciences
    159 rdf:type schema:DefinedTerm
    160 sg:grant.2411168 http://pending.schema.org/fundedItem sg:pub.10.1186/gb-2011-12-4-r41
    161 rdf:type schema:MonetaryGrant
    162 sg:grant.2683815 http://pending.schema.org/fundedItem sg:pub.10.1186/gb-2011-12-4-r41
    163 rdf:type schema:MonetaryGrant
    164 sg:grant.2696338 http://pending.schema.org/fundedItem sg:pub.10.1186/gb-2011-12-4-r41
    165 rdf:type schema:MonetaryGrant
    166 sg:journal.1023439 schema:issn 1465-6906
    167 1474-760X
    168 schema:name Genome Biology
    169 schema:publisher Springer Nature
    170 rdf:type schema:Periodical
    171 sg:person.01055166050.55 schema:affiliation grid-institutes:grid.65499.37
    172 schema:familyName Schumacher
    173 schema:givenName Steven E
    174 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01055166050.55
    175 rdf:type schema:Person
    176 sg:person.01066471003.08 schema:affiliation grid-institutes:grid.65499.37
    177 schema:familyName Mermel
    178 schema:givenName Craig H
    179 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01066471003.08
    180 rdf:type schema:Person
    181 sg:person.01310170137.53 schema:affiliation grid-institutes:grid.65499.37
    182 schema:familyName Beroukhim
    183 schema:givenName Rameen
    184 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01310170137.53
    185 rdf:type schema:Person
    186 sg:person.01316313531.32 schema:affiliation grid-institutes:grid.66859.34
    187 schema:familyName Getz
    188 schema:givenName Gad
    189 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01316313531.32
    190 rdf:type schema:Person
    191 sg:person.016012142422.14 schema:affiliation grid-institutes:grid.65499.37
    192 schema:familyName Meyerson
    193 schema:givenName Matthew L
    194 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.016012142422.14
    195 rdf:type schema:Person
    196 sg:pub.10.1038/nature05610 schema:sameAs https://app.dimensions.ai/details/publication/pub.1033482125
    197 https://doi.org/10.1038/nature05610
    198 rdf:type schema:CreativeWork
    199 sg:pub.10.1038/nature06358 schema:sameAs https://app.dimensions.ai/details/publication/pub.1019681472
    200 https://doi.org/10.1038/nature06358
    201 rdf:type schema:CreativeWork
    202 sg:pub.10.1038/nature07179 schema:sameAs https://app.dimensions.ai/details/publication/pub.1010877750
    203 https://doi.org/10.1038/nature07179
    204 rdf:type schema:CreativeWork
    205 sg:pub.10.1038/nature07385 schema:sameAs https://app.dimensions.ai/details/publication/pub.1039570773
    206 https://doi.org/10.1038/nature07385
    207 rdf:type schema:CreativeWork
    208 sg:pub.10.1038/nature07943 schema:sameAs https://app.dimensions.ai/details/publication/pub.1004829095
    209 https://doi.org/10.1038/nature07943
    210 rdf:type schema:CreativeWork
    211 sg:pub.10.1038/nature08629 schema:sameAs https://app.dimensions.ai/details/publication/pub.1041012667
    212 https://doi.org/10.1038/nature08629
    213 rdf:type schema:CreativeWork
    214 sg:pub.10.1038/nature08645 schema:sameAs https://app.dimensions.ai/details/publication/pub.1050729897
    215 https://doi.org/10.1038/nature08645
    216 rdf:type schema:CreativeWork
    217 sg:pub.10.1038/nature08658 schema:sameAs https://app.dimensions.ai/details/publication/pub.1014288207
    218 https://doi.org/10.1038/nature08658
    219 rdf:type schema:CreativeWork
    220 sg:pub.10.1038/nature08768 schema:sameAs https://app.dimensions.ai/details/publication/pub.1002735811
    221 https://doi.org/10.1038/nature08768
    222 rdf:type schema:CreativeWork
    223 sg:pub.10.1038/nature08822 schema:sameAs https://app.dimensions.ai/details/publication/pub.1010635813
    224 https://doi.org/10.1038/nature08822
    225 rdf:type schema:CreativeWork
    226 sg:pub.10.1038/ng.238 schema:sameAs https://app.dimensions.ai/details/publication/pub.1047420273
    227 https://doi.org/10.1038/ng.238
    228 rdf:type schema:CreativeWork
    229 sg:pub.10.1038/ng.336 schema:sameAs https://app.dimensions.ai/details/publication/pub.1035880217
    230 https://doi.org/10.1038/ng.336
    231 rdf:type schema:CreativeWork
    232 sg:pub.10.1038/ng.465 schema:sameAs https://app.dimensions.ai/details/publication/pub.1025808150
    233 https://doi.org/10.1038/ng.465
    234 rdf:type schema:CreativeWork
    235 sg:pub.10.1038/nmeth.1276 schema:sameAs https://app.dimensions.ai/details/publication/pub.1025333243
    236 https://doi.org/10.1038/nmeth.1276
    237 rdf:type schema:CreativeWork
    238 sg:pub.10.1038/nrc2013 schema:sameAs https://app.dimensions.ai/details/publication/pub.1023245275
    239 https://doi.org/10.1038/nrc2013
    240 rdf:type schema:CreativeWork
    241 sg:pub.10.1038/nrc2771 schema:sameAs https://app.dimensions.ai/details/publication/pub.1029567400
    242 https://doi.org/10.1038/nrc2771
    243 rdf:type schema:CreativeWork
    244 sg:pub.10.1038/nrg2626 schema:sameAs https://app.dimensions.ai/details/publication/pub.1023911485
    245 https://doi.org/10.1038/nrg2626
    246 rdf:type schema:CreativeWork
    247 sg:pub.10.1038/nrm2718 schema:sameAs https://app.dimensions.ai/details/publication/pub.1024297992
    248 https://doi.org/10.1038/nrm2718
    249 rdf:type schema:CreativeWork
    250 sg:pub.10.1186/1471-2105-11-189 schema:sameAs https://app.dimensions.ai/details/publication/pub.1011737467
    251 https://doi.org/10.1186/1471-2105-11-189
    252 rdf:type schema:CreativeWork
    253 sg:pub.10.1186/1471-2105-8-368 schema:sameAs https://app.dimensions.ai/details/publication/pub.1007193249
    254 https://doi.org/10.1186/1471-2105-8-368
    255 rdf:type schema:CreativeWork
    256 sg:pub.10.1186/gb-2001-2-10-reports0032 schema:sameAs https://app.dimensions.ai/details/publication/pub.1085169177
    257 https://doi.org/10.1186/gb-2001-2-10-reports0032
    258 rdf:type schema:CreativeWork
    259 sg:pub.10.1186/gb-2001-2-8-research0032 schema:sameAs https://app.dimensions.ai/details/publication/pub.1015228558
    260 https://doi.org/10.1186/gb-2001-2-8-research0032
    261 rdf:type schema:CreativeWork
    262 grid-institutes:grid.65499.37 schema:alternateName The Center for Cancer Genome Discovery, Dana Farber Cancer Institute, 44 Binney Street, 02115, Boston, MA, USA
    263 schema:name Cancer Program, The Broad Institute of MIT and Harvard, 7 Cambridge Center, 02142, Cambridge, MA, USA
    264 Department of Cancer Biology, Dana Farber Cancer Institute, 44 Binney Street, 02115, Boston, MA, USA
    265 Department of Medical Oncology, Dana Farber Cancer Institute, 44 Binney Street, 02115, Boston, MA, USA
    266 The Center for Cancer Genome Discovery, Dana Farber Cancer Institute, 44 Binney Street, 02115, Boston, MA, USA
    267 rdf:type schema:Organization
    268 grid-institutes:grid.66859.34 schema:alternateName Cancer Program, The Broad Institute of MIT and Harvard, 7 Cambridge Center, 02142, Cambridge, MA, USA
    269 schema:name Cancer Program, The Broad Institute of MIT and Harvard, 7 Cambridge Center, 02142, Cambridge, MA, USA
    270 rdf:type schema:Organization
     




    Preview window. Press ESC to close (or click here)


    ...