Transcriptome sequencing to detect gene fusions in cancer View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2009-03

AUTHORS

Christopher A. Maher, Chandan Kumar-Sinha, Xuhong Cao, Shanker Kalyana-Sundaram, Bo Han, Xiaojun Jing, Lee Sam, Terrence Barrette, Nallasivam Palanisamy, Arul M. Chinnaiyan

ABSTRACT

Recurrent gene fusions, typically associated with haematological malignancies and rare bone and soft-tissue tumours, have recently been described in common solid tumours. Here we use an integrative analysis of high-throughput long- and short-read transcriptome sequencing of cancer cells to discover novel gene fusions. As a proof of concept, we successfully used integrative transcriptome sequencing to 're-discover' the BCR-ABL1 (ref. 10) gene fusion in a chronic myelogenous leukaemia cell line and the TMPRSS2-ERG gene fusion in a prostate cancer cell line and tissues. Additionally, we nominated, and experimentally validated, novel gene fusions resulting in chimaeric transcripts in cancer cell lines and tumours. Taken together, this study establishes a robust pipeline for the discovery of novel gene chimaeras using high-throughput sequencing, opening up an important class of cancer-related mutations for comprehensive characterization. More... »

PAGES

97

References to SciGraph publications

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/nature07638

DOI

http://dx.doi.org/10.1038/nature07638

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1009442631

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/19136943


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/2008/1112", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Oncology and Carcinogenesis", 
        "type": "DefinedTerm"
      }, 
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/11", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Medical and Health Sciences", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Base Sequence", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Cell Line, Tumor", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Fusion Proteins, bcr-abl", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Gene Expression Profiling", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Humans", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Leukemia, Myelogenous, Chronic, BCR-ABL Positive", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Male", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Molecular Sequence Data", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Neoplasms", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Oncogene Proteins, Fusion", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Prostatic Neoplasms", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Sequence Analysis, DNA", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "name": [
            "Michigan Center for Translational Pathology,", 
            "Department of Pathology,"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Maher", 
        "givenName": "Christopher A.", 
        "id": "sg:person.01066421566.27", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01066421566.27"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "Michigan Center for Translational Pathology,", 
            "Department of Pathology,"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Kumar-Sinha", 
        "givenName": "Chandan", 
        "id": "sg:person.0754756152.51", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0754756152.51"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Howard Hughes Medical Institute", 
          "id": "https://www.grid.ac/institutes/grid.413575.1", 
          "name": [
            "Michigan Center for Translational Pathology,", 
            "Howard Hughes Medical Institute,"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Cao", 
        "givenName": "Xuhong", 
        "id": "sg:person.01242315247.25", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01242315247.25"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "Michigan Center for Translational Pathology,", 
            "Department of Pathology,"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Kalyana-Sundaram", 
        "givenName": "Shanker", 
        "id": "sg:person.0663717126.40", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0663717126.40"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "Michigan Center for Translational Pathology,", 
            "Department of Pathology,"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Han", 
        "givenName": "Bo", 
        "id": "sg:person.01212655442.84", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01212655442.84"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "Michigan Center for Translational Pathology,", 
            "Department of Pathology,"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Jing", 
        "givenName": "Xiaojun", 
        "id": "sg:person.01304133726.61", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01304133726.61"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "Michigan Center for Translational Pathology,", 
            "Department of Pathology,"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Sam", 
        "givenName": "Lee", 
        "id": "sg:person.0723613341.39", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0723613341.39"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "Michigan Center for Translational Pathology,", 
            "Department of Pathology,"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Barrette", 
        "givenName": "Terrence", 
        "id": "sg:person.01030641561.26", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01030641561.26"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "Michigan Center for Translational Pathology,", 
            "Department of Pathology,"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Palanisamy", 
        "givenName": "Nallasivam", 
        "id": "sg:person.01316020452.03", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01316020452.03"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "University of Michigan\u2013Ann Arbor", 
          "id": "https://www.grid.ac/institutes/grid.214458.e", 
          "name": [
            "Michigan Center for Translational Pathology,", 
            "Howard Hughes Medical Institute,", 
            "Department of Pathology,", 
            "Department of Urology,", 
            "Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Chinnaiyan", 
        "givenName": "Arul M.", 
        "id": "sg:person.01057336674.48", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01057336674.48"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "https://doi.org/10.1056/nejm200412303512724", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1004857680"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gr.229202", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1006260064"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1593/neo.07878", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1007078703"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s1570-8667(03)00065-0", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1013212920"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature05945", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1017221313", 
          "https://doi.org/10.1038/nature05945"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1056/nejmoa062867", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1018371941"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.molcel.2005.03.018", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1018723742"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature06358", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1019681472", 
          "https://doi.org/10.1038/nature06358"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1056/nejmoa020461", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1022255922"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nrc1299", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1022731034", 
          "https://doi.org/10.1038/nrc1299"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nrc1299", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1022731034", 
          "https://doi.org/10.1038/nrc1299"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1002/pros.20499", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1023734418"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1158/1078-0432.ccr-08-0168", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1026339294"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature06024", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1027447235", 
          "https://doi.org/10.1038/nature06024"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/35106108", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1028715647", 
          "https://doi.org/10.1038/35106108"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/35106108", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1028715647", 
          "https://doi.org/10.1038/35106108"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1117679", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1028743308"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.cell.2007.11.025", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1030265584"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1056/nejm200103153441101", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1031768583"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1158/0008-5472.can-07-6158", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1032703495"
        ], 
        "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-2002-3-7-research0034", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1039751959", 
          "https://doi.org/10.1186/gb-2002-3-7-research0034"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gkh103", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1040312195"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1056/nejmoa040938", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1042907590"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1158/0008-5472.can-08-2014", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1045296961"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/315550a0", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1045340731", 
          "https://doi.org/10.1038/315550a0"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/ng1571", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1045470107", 
          "https://doi.org/10.1038/ng1571"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/ng1571", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1045470107", 
          "https://doi.org/10.1038/ng1571"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1074/jbc.m009609200", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1046424473"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s0168-9525(99)01937-x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1048812666"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/ng1335", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1051360590", 
          "https://doi.org/10.1038/ng1335"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/ng1335", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1051360590", 
          "https://doi.org/10.1038/ng1335"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/35057192", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1052791208", 
          "https://doi.org/10.1038/35057192"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/35057192", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1052791208", 
          "https://doi.org/10.1038/35057192"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nrc2402", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1053354178", 
          "https://doi.org/10.1038/nrc2402"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1145720", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1053548183"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://app.dimensions.ai/details/publication/pub.1074613563", 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://app.dimensions.ai/details/publication/pub.1074803062", 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2009-03", 
    "datePublishedReg": "2009-03-01", 
    "description": "Recurrent gene fusions, typically associated with haematological malignancies and rare bone and soft-tissue tumours, have recently been described in common solid tumours. Here we use an integrative analysis of high-throughput long- and short-read transcriptome sequencing of cancer cells to discover novel gene fusions. As a proof of concept, we successfully used integrative transcriptome sequencing to 're-discover' the BCR-ABL1 (ref. 10) gene fusion in a chronic myelogenous leukaemia cell line and the TMPRSS2-ERG gene fusion in a prostate cancer cell line and tissues. Additionally, we nominated, and experimentally validated, novel gene fusions resulting in chimaeric transcripts in cancer cell lines and tumours. Taken together, this study establishes a robust pipeline for the discovery of novel gene chimaeras using high-throughput sequencing, opening up an important class of cancer-related mutations for comprehensive characterization.", 
    "genre": "research_article", 
    "id": "sg:pub.10.1038/nature07638", 
    "inLanguage": [
      "en"
    ], 
    "isAccessibleForFree": true, 
    "isFundedItemOf": [
      {
        "id": "sg:grant.2479789", 
        "type": "MonetaryGrant"
      }, 
      {
        "id": "sg:grant.2699165", 
        "type": "MonetaryGrant"
      }, 
      {
        "id": "sg:grant.2689035", 
        "type": "MonetaryGrant"
      }
    ], 
    "isPartOf": [
      {
        "id": "sg:journal.1018957", 
        "issn": [
          "0090-0028", 
          "1476-4687"
        ], 
        "name": "Nature", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "7234", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "458"
      }
    ], 
    "name": "Transcriptome sequencing to detect gene fusions in cancer", 
    "pagination": "97", 
    "productId": [
      {
        "name": "readcube_id", 
        "type": "PropertyValue", 
        "value": [
          "2cfb54e3e083a466d236e952681ca7f4676653e9ee842d97c648d36e494a2b13"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "19136943"
        ]
      }, 
      {
        "name": "nlm_unique_id", 
        "type": "PropertyValue", 
        "value": [
          "0410462"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1038/nature07638"
        ]
      }, 
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1009442631"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1038/nature07638", 
      "https://app.dimensions.ai/details/publication/pub.1009442631"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2019-04-11T01:14", 
    "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
    "sdPublisher": {
      "name": "Springer Nature - SN SciGraph project", 
      "type": "Organization"
    }, 
    "sdSource": "s3://com-uberresearch-data-dimensions-target-20181106-alternative/cleanup/v134/2549eaecd7973599484d7c17b260dba0a4ecb94b/merge/v9/a6c9fde33151104705d4d7ff012ea9563521a3ce/jats-lookup/v90/0000000001_0000000264/records_8697_00000549.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "https://www.nature.com/articles/nature07638"
  }
]
 

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.10.1038/nature07638'

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

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1038/nature07638'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/nature07638'

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

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1038/nature07638'


 

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

327 TRIPLES      21 PREDICATES      74 URIs      33 LITERALS      21 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1038/nature07638 schema:about N12b963f8c856465facc24dc121ee179f
2 N1407ac6c9d6b4aa29b9ad2a395a98d0b
3 N3446bbc100e3430280d5466ac1f85495
4 N3da64f92d11a494cbdf6dccef1a0fbc0
5 N4a866e6f8b0c4fb8a3710ebb8b12f781
6 N80d002fa47634e92a25ed1427c1802b1
7 N867fe13124fc4bd48b3d14205384b884
8 N87db959536d442678eb423247babc914
9 Nd2b919940594465bb3d829efeb882867
10 Nde98994dbd704250b04b05c06b8768b0
11 Ndf4d3229fb574b8e895f207033f0ceb1
12 Nf06015f43da941b6888fcdbed268ed04
13 anzsrc-for:11
14 anzsrc-for:1112
15 schema:author N88c8d0a96e704a5fae337d20d55d44ab
16 schema:citation sg:pub.10.1038/315550a0
17 sg:pub.10.1038/35057192
18 sg:pub.10.1038/35106108
19 sg:pub.10.1038/nature05610
20 sg:pub.10.1038/nature05945
21 sg:pub.10.1038/nature06024
22 sg:pub.10.1038/nature06358
23 sg:pub.10.1038/ng1335
24 sg:pub.10.1038/ng1571
25 sg:pub.10.1038/nrc1299
26 sg:pub.10.1038/nrc2402
27 sg:pub.10.1186/gb-2002-3-7-research0034
28 https://app.dimensions.ai/details/publication/pub.1074613563
29 https://app.dimensions.ai/details/publication/pub.1074803062
30 https://doi.org/10.1002/pros.20499
31 https://doi.org/10.1016/j.cell.2007.11.025
32 https://doi.org/10.1016/j.molcel.2005.03.018
33 https://doi.org/10.1016/s0168-9525(99)01937-x
34 https://doi.org/10.1016/s1570-8667(03)00065-0
35 https://doi.org/10.1056/nejm200103153441101
36 https://doi.org/10.1056/nejm200412303512724
37 https://doi.org/10.1056/nejmoa020461
38 https://doi.org/10.1056/nejmoa040938
39 https://doi.org/10.1056/nejmoa062867
40 https://doi.org/10.1074/jbc.m009609200
41 https://doi.org/10.1093/nar/gkh103
42 https://doi.org/10.1101/gr.229202
43 https://doi.org/10.1126/science.1117679
44 https://doi.org/10.1126/science.1145720
45 https://doi.org/10.1158/0008-5472.can-07-6158
46 https://doi.org/10.1158/0008-5472.can-08-2014
47 https://doi.org/10.1158/1078-0432.ccr-08-0168
48 https://doi.org/10.1593/neo.07878
49 schema:datePublished 2009-03
50 schema:datePublishedReg 2009-03-01
51 schema:description Recurrent gene fusions, typically associated with haematological malignancies and rare bone and soft-tissue tumours, have recently been described in common solid tumours. Here we use an integrative analysis of high-throughput long- and short-read transcriptome sequencing of cancer cells to discover novel gene fusions. As a proof of concept, we successfully used integrative transcriptome sequencing to 're-discover' the BCR-ABL1 (ref. 10) gene fusion in a chronic myelogenous leukaemia cell line and the TMPRSS2-ERG gene fusion in a prostate cancer cell line and tissues. Additionally, we nominated, and experimentally validated, novel gene fusions resulting in chimaeric transcripts in cancer cell lines and tumours. Taken together, this study establishes a robust pipeline for the discovery of novel gene chimaeras using high-throughput sequencing, opening up an important class of cancer-related mutations for comprehensive characterization.
52 schema:genre research_article
53 schema:inLanguage en
54 schema:isAccessibleForFree true
55 schema:isPartOf N968d530f28764a89b3c45aa2dd76b0cf
56 Nd84f329008dc495b93937f8c8a73bcbb
57 sg:journal.1018957
58 schema:name Transcriptome sequencing to detect gene fusions in cancer
59 schema:pagination 97
60 schema:productId N14b7668df4e64dcdba7dfe6400418b73
61 N5dd952dbcb3a4710876241fd885a7578
62 N6958888f24b144348b145657293d6cb6
63 Nac6d446f62bb4993bc4a34acbed0ac12
64 Nc3b2915eb22747e294023a9595c57a94
65 schema:sameAs https://app.dimensions.ai/details/publication/pub.1009442631
66 https://doi.org/10.1038/nature07638
67 schema:sdDatePublished 2019-04-11T01:14
68 schema:sdLicense https://scigraph.springernature.com/explorer/license/
69 schema:sdPublisher N24b8e59340be421bab62057176000acb
70 schema:url https://www.nature.com/articles/nature07638
71 sgo:license sg:explorer/license/
72 sgo:sdDataset articles
73 rdf:type schema:ScholarlyArticle
74 N109e8c25f58e48b3bc7cd93416390c9c schema:name Department of Pathology,
75 Michigan Center for Translational Pathology,
76 rdf:type schema:Organization
77 N11942caa4bea48b8aaef8f06dfc70489 schema:name Department of Pathology,
78 Michigan Center for Translational Pathology,
79 rdf:type schema:Organization
80 N12b963f8c856465facc24dc121ee179f schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
81 schema:name Gene Expression Profiling
82 rdf:type schema:DefinedTerm
83 N1407ac6c9d6b4aa29b9ad2a395a98d0b schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
84 schema:name Prostatic Neoplasms
85 rdf:type schema:DefinedTerm
86 N14b7668df4e64dcdba7dfe6400418b73 schema:name pubmed_id
87 schema:value 19136943
88 rdf:type schema:PropertyValue
89 N24b8e59340be421bab62057176000acb schema:name Springer Nature - SN SciGraph project
90 rdf:type schema:Organization
91 N3446bbc100e3430280d5466ac1f85495 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
92 schema:name Neoplasms
93 rdf:type schema:DefinedTerm
94 N38eef478c1044fe9978ef9a9e509c577 rdf:first sg:person.01304133726.61
95 rdf:rest Nbbeaf3bd5b304218b43f0c82a3fa917b
96 N3da64f92d11a494cbdf6dccef1a0fbc0 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
97 schema:name Cell Line, Tumor
98 rdf:type schema:DefinedTerm
99 N412fa2f8f7e74d86ab741da20d0d300b rdf:first sg:person.01057336674.48
100 rdf:rest rdf:nil
101 N4a866e6f8b0c4fb8a3710ebb8b12f781 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
102 schema:name Leukemia, Myelogenous, Chronic, BCR-ABL Positive
103 rdf:type schema:DefinedTerm
104 N54dc98eb35c6403483a426f39991cd2b schema:name Department of Pathology,
105 Michigan Center for Translational Pathology,
106 rdf:type schema:Organization
107 N5b3929fc0ced42bdbc50e482b479b712 rdf:first sg:person.01030641561.26
108 rdf:rest Nfd23dd555673408aae1a20031f6c091f
109 N5dd952dbcb3a4710876241fd885a7578 schema:name readcube_id
110 schema:value 2cfb54e3e083a466d236e952681ca7f4676653e9ee842d97c648d36e494a2b13
111 rdf:type schema:PropertyValue
112 N5fc0e2c455064029bb2f99287fcd6c4d schema:name Department of Pathology,
113 Michigan Center for Translational Pathology,
114 rdf:type schema:Organization
115 N626531ba27d64837b9fe2c88aefd9970 rdf:first sg:person.0663717126.40
116 rdf:rest Nf5af7c429e45443eb3faebb68a232c13
117 N6958888f24b144348b145657293d6cb6 schema:name nlm_unique_id
118 schema:value 0410462
119 rdf:type schema:PropertyValue
120 N80d002fa47634e92a25ed1427c1802b1 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
121 schema:name Male
122 rdf:type schema:DefinedTerm
123 N867fe13124fc4bd48b3d14205384b884 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
124 schema:name Molecular Sequence Data
125 rdf:type schema:DefinedTerm
126 N87db959536d442678eb423247babc914 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
127 schema:name Humans
128 rdf:type schema:DefinedTerm
129 N88c8d0a96e704a5fae337d20d55d44ab rdf:first sg:person.01066421566.27
130 rdf:rest Na3948e14eba34d1e911fe07040a2bcba
131 N968d530f28764a89b3c45aa2dd76b0cf schema:volumeNumber 458
132 rdf:type schema:PublicationVolume
133 N977e9869a0ce44ab922704109223cdd7 rdf:first sg:person.01242315247.25
134 rdf:rest N626531ba27d64837b9fe2c88aefd9970
135 Na3948e14eba34d1e911fe07040a2bcba rdf:first sg:person.0754756152.51
136 rdf:rest N977e9869a0ce44ab922704109223cdd7
137 Nac6d446f62bb4993bc4a34acbed0ac12 schema:name doi
138 schema:value 10.1038/nature07638
139 rdf:type schema:PropertyValue
140 Nb7028285819b469e8f323449545d7201 schema:name Department of Pathology,
141 Michigan Center for Translational Pathology,
142 rdf:type schema:Organization
143 Nbbeaf3bd5b304218b43f0c82a3fa917b rdf:first sg:person.0723613341.39
144 rdf:rest N5b3929fc0ced42bdbc50e482b479b712
145 Nc308f27b71a3434fb4846866b14aaae4 schema:name Department of Pathology,
146 Michigan Center for Translational Pathology,
147 rdf:type schema:Organization
148 Nc3b2915eb22747e294023a9595c57a94 schema:name dimensions_id
149 schema:value pub.1009442631
150 rdf:type schema:PropertyValue
151 Nd2b919940594465bb3d829efeb882867 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
152 schema:name Sequence Analysis, DNA
153 rdf:type schema:DefinedTerm
154 Nd84f329008dc495b93937f8c8a73bcbb schema:issueNumber 7234
155 rdf:type schema:PublicationIssue
156 Nde98994dbd704250b04b05c06b8768b0 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
157 schema:name Base Sequence
158 rdf:type schema:DefinedTerm
159 Ndf4d3229fb574b8e895f207033f0ceb1 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
160 schema:name Fusion Proteins, bcr-abl
161 rdf:type schema:DefinedTerm
162 Ne620598d930d461fac6a85f84ec1230f schema:name Department of Pathology,
163 Michigan Center for Translational Pathology,
164 rdf:type schema:Organization
165 Nee360d407dfc44d3bbc46c3f59439aaf schema:name Department of Pathology,
166 Michigan Center for Translational Pathology,
167 rdf:type schema:Organization
168 Nf06015f43da941b6888fcdbed268ed04 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
169 schema:name Oncogene Proteins, Fusion
170 rdf:type schema:DefinedTerm
171 Nf5af7c429e45443eb3faebb68a232c13 rdf:first sg:person.01212655442.84
172 rdf:rest N38eef478c1044fe9978ef9a9e509c577
173 Nfd23dd555673408aae1a20031f6c091f rdf:first sg:person.01316020452.03
174 rdf:rest N412fa2f8f7e74d86ab741da20d0d300b
175 anzsrc-for:11 schema:inDefinedTermSet anzsrc-for:
176 schema:name Medical and Health Sciences
177 rdf:type schema:DefinedTerm
178 anzsrc-for:1112 schema:inDefinedTermSet anzsrc-for:
179 schema:name Oncology and Carcinogenesis
180 rdf:type schema:DefinedTerm
181 sg:grant.2479789 http://pending.schema.org/fundedItem sg:pub.10.1038/nature07638
182 rdf:type schema:MonetaryGrant
183 sg:grant.2689035 http://pending.schema.org/fundedItem sg:pub.10.1038/nature07638
184 rdf:type schema:MonetaryGrant
185 sg:grant.2699165 http://pending.schema.org/fundedItem sg:pub.10.1038/nature07638
186 rdf:type schema:MonetaryGrant
187 sg:journal.1018957 schema:issn 0090-0028
188 1476-4687
189 schema:name Nature
190 rdf:type schema:Periodical
191 sg:person.01030641561.26 schema:affiliation Nc308f27b71a3434fb4846866b14aaae4
192 schema:familyName Barrette
193 schema:givenName Terrence
194 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01030641561.26
195 rdf:type schema:Person
196 sg:person.01057336674.48 schema:affiliation https://www.grid.ac/institutes/grid.214458.e
197 schema:familyName Chinnaiyan
198 schema:givenName Arul M.
199 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01057336674.48
200 rdf:type schema:Person
201 sg:person.01066421566.27 schema:affiliation Nee360d407dfc44d3bbc46c3f59439aaf
202 schema:familyName Maher
203 schema:givenName Christopher A.
204 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01066421566.27
205 rdf:type schema:Person
206 sg:person.01212655442.84 schema:affiliation N5fc0e2c455064029bb2f99287fcd6c4d
207 schema:familyName Han
208 schema:givenName Bo
209 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01212655442.84
210 rdf:type schema:Person
211 sg:person.01242315247.25 schema:affiliation https://www.grid.ac/institutes/grid.413575.1
212 schema:familyName Cao
213 schema:givenName Xuhong
214 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01242315247.25
215 rdf:type schema:Person
216 sg:person.01304133726.61 schema:affiliation Ne620598d930d461fac6a85f84ec1230f
217 schema:familyName Jing
218 schema:givenName Xiaojun
219 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01304133726.61
220 rdf:type schema:Person
221 sg:person.01316020452.03 schema:affiliation N109e8c25f58e48b3bc7cd93416390c9c
222 schema:familyName Palanisamy
223 schema:givenName Nallasivam
224 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01316020452.03
225 rdf:type schema:Person
226 sg:person.0663717126.40 schema:affiliation N54dc98eb35c6403483a426f39991cd2b
227 schema:familyName Kalyana-Sundaram
228 schema:givenName Shanker
229 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0663717126.40
230 rdf:type schema:Person
231 sg:person.0723613341.39 schema:affiliation Nb7028285819b469e8f323449545d7201
232 schema:familyName Sam
233 schema:givenName Lee
234 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0723613341.39
235 rdf:type schema:Person
236 sg:person.0754756152.51 schema:affiliation N11942caa4bea48b8aaef8f06dfc70489
237 schema:familyName Kumar-Sinha
238 schema:givenName Chandan
239 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0754756152.51
240 rdf:type schema:Person
241 sg:pub.10.1038/315550a0 schema:sameAs https://app.dimensions.ai/details/publication/pub.1045340731
242 https://doi.org/10.1038/315550a0
243 rdf:type schema:CreativeWork
244 sg:pub.10.1038/35057192 schema:sameAs https://app.dimensions.ai/details/publication/pub.1052791208
245 https://doi.org/10.1038/35057192
246 rdf:type schema:CreativeWork
247 sg:pub.10.1038/35106108 schema:sameAs https://app.dimensions.ai/details/publication/pub.1028715647
248 https://doi.org/10.1038/35106108
249 rdf:type schema:CreativeWork
250 sg:pub.10.1038/nature05610 schema:sameAs https://app.dimensions.ai/details/publication/pub.1033482125
251 https://doi.org/10.1038/nature05610
252 rdf:type schema:CreativeWork
253 sg:pub.10.1038/nature05945 schema:sameAs https://app.dimensions.ai/details/publication/pub.1017221313
254 https://doi.org/10.1038/nature05945
255 rdf:type schema:CreativeWork
256 sg:pub.10.1038/nature06024 schema:sameAs https://app.dimensions.ai/details/publication/pub.1027447235
257 https://doi.org/10.1038/nature06024
258 rdf:type schema:CreativeWork
259 sg:pub.10.1038/nature06358 schema:sameAs https://app.dimensions.ai/details/publication/pub.1019681472
260 https://doi.org/10.1038/nature06358
261 rdf:type schema:CreativeWork
262 sg:pub.10.1038/ng1335 schema:sameAs https://app.dimensions.ai/details/publication/pub.1051360590
263 https://doi.org/10.1038/ng1335
264 rdf:type schema:CreativeWork
265 sg:pub.10.1038/ng1571 schema:sameAs https://app.dimensions.ai/details/publication/pub.1045470107
266 https://doi.org/10.1038/ng1571
267 rdf:type schema:CreativeWork
268 sg:pub.10.1038/nrc1299 schema:sameAs https://app.dimensions.ai/details/publication/pub.1022731034
269 https://doi.org/10.1038/nrc1299
270 rdf:type schema:CreativeWork
271 sg:pub.10.1038/nrc2402 schema:sameAs https://app.dimensions.ai/details/publication/pub.1053354178
272 https://doi.org/10.1038/nrc2402
273 rdf:type schema:CreativeWork
274 sg:pub.10.1186/gb-2002-3-7-research0034 schema:sameAs https://app.dimensions.ai/details/publication/pub.1039751959
275 https://doi.org/10.1186/gb-2002-3-7-research0034
276 rdf:type schema:CreativeWork
277 https://app.dimensions.ai/details/publication/pub.1074613563 schema:CreativeWork
278 https://app.dimensions.ai/details/publication/pub.1074803062 schema:CreativeWork
279 https://doi.org/10.1002/pros.20499 schema:sameAs https://app.dimensions.ai/details/publication/pub.1023734418
280 rdf:type schema:CreativeWork
281 https://doi.org/10.1016/j.cell.2007.11.025 schema:sameAs https://app.dimensions.ai/details/publication/pub.1030265584
282 rdf:type schema:CreativeWork
283 https://doi.org/10.1016/j.molcel.2005.03.018 schema:sameAs https://app.dimensions.ai/details/publication/pub.1018723742
284 rdf:type schema:CreativeWork
285 https://doi.org/10.1016/s0168-9525(99)01937-x schema:sameAs https://app.dimensions.ai/details/publication/pub.1048812666
286 rdf:type schema:CreativeWork
287 https://doi.org/10.1016/s1570-8667(03)00065-0 schema:sameAs https://app.dimensions.ai/details/publication/pub.1013212920
288 rdf:type schema:CreativeWork
289 https://doi.org/10.1056/nejm200103153441101 schema:sameAs https://app.dimensions.ai/details/publication/pub.1031768583
290 rdf:type schema:CreativeWork
291 https://doi.org/10.1056/nejm200412303512724 schema:sameAs https://app.dimensions.ai/details/publication/pub.1004857680
292 rdf:type schema:CreativeWork
293 https://doi.org/10.1056/nejmoa020461 schema:sameAs https://app.dimensions.ai/details/publication/pub.1022255922
294 rdf:type schema:CreativeWork
295 https://doi.org/10.1056/nejmoa040938 schema:sameAs https://app.dimensions.ai/details/publication/pub.1042907590
296 rdf:type schema:CreativeWork
297 https://doi.org/10.1056/nejmoa062867 schema:sameAs https://app.dimensions.ai/details/publication/pub.1018371941
298 rdf:type schema:CreativeWork
299 https://doi.org/10.1074/jbc.m009609200 schema:sameAs https://app.dimensions.ai/details/publication/pub.1046424473
300 rdf:type schema:CreativeWork
301 https://doi.org/10.1093/nar/gkh103 schema:sameAs https://app.dimensions.ai/details/publication/pub.1040312195
302 rdf:type schema:CreativeWork
303 https://doi.org/10.1101/gr.229202 schema:sameAs https://app.dimensions.ai/details/publication/pub.1006260064
304 rdf:type schema:CreativeWork
305 https://doi.org/10.1126/science.1117679 schema:sameAs https://app.dimensions.ai/details/publication/pub.1028743308
306 rdf:type schema:CreativeWork
307 https://doi.org/10.1126/science.1145720 schema:sameAs https://app.dimensions.ai/details/publication/pub.1053548183
308 rdf:type schema:CreativeWork
309 https://doi.org/10.1158/0008-5472.can-07-6158 schema:sameAs https://app.dimensions.ai/details/publication/pub.1032703495
310 rdf:type schema:CreativeWork
311 https://doi.org/10.1158/0008-5472.can-08-2014 schema:sameAs https://app.dimensions.ai/details/publication/pub.1045296961
312 rdf:type schema:CreativeWork
313 https://doi.org/10.1158/1078-0432.ccr-08-0168 schema:sameAs https://app.dimensions.ai/details/publication/pub.1026339294
314 rdf:type schema:CreativeWork
315 https://doi.org/10.1593/neo.07878 schema:sameAs https://app.dimensions.ai/details/publication/pub.1007078703
316 rdf:type schema:CreativeWork
317 https://www.grid.ac/institutes/grid.214458.e schema:alternateName University of Michigan–Ann Arbor
318 schema:name Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
319 Department of Pathology,
320 Department of Urology,
321 Howard Hughes Medical Institute,
322 Michigan Center for Translational Pathology,
323 rdf:type schema:Organization
324 https://www.grid.ac/institutes/grid.413575.1 schema:alternateName Howard Hughes Medical Institute
325 schema:name Howard Hughes Medical Institute,
326 Michigan Center for Translational Pathology,
327 rdf:type schema:Organization
 




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


...