Breakpoint analysis of transcriptional and genomic profiles uncovers novel gene fusions spanning multiple human cancer types (Q28486949)

17

object named as

Jonathan R Pollack

0 references

Shirley X. Zhu

13

object named as

Shirley Zhu

0 references

author name string

Craig P Giacomini

1

0 references

Steven Sun

2

0 references

Sushama Varma

3

0 references

A Hunter Shain

4

0 references

Marilyn M Giacomini

5

0 references

Jay Balagtas

6

0 references

Robert T Sweeney

7

0 references

Everett Lai

8

0 references

Catherine A Del Vecchio

9

0 references

Andrew D Forster

10

0 references

Nicole Clarke

11

0 references

Kelli D Montgomery

12

0 references

Albert J Wong

14

0 references

Robert B West

Creative Commons Attribution 4.0 International

16

0 references

language of work or name

English

0 references

publication date

April 2013

0 references

published in

PLOS Genetics

0 references

volume

9

0 references

issue

4

0 references

page(s)

e1003464

0 references

copyright license

start time

25 April 2013

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

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Identification of the transforming EML4-ALK fusion gene in non-small-cell lung cancer

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Identification of four gene variants associated with myocardial infarction

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Determination of stromal signatures in breast carcinoma

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A mitochondrial protein, Bit1, mediates apoptosis regulated by integrins and Groucho/TLE corepressors

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A census of human cancer genes

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The EOL-1 cell line as an in vitro model for the study of FIP1L1-PDGFRA-positive chronic eosinophilic leukemia

19 March 2017

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Fusion of FIG to the receptor tyrosine kinase ROS in a glioblastoma with an interstitial del(6)(q21q21)

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A tyrosine kinase created by fusion of the PDGFRA and FIP1L1 genes as a therapeutic target of imatinib in idiopathic hypereosinophilic syndrome

19 March 2017

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Oncogenic targeting of an activated tyrosine kinase to the Golgi apparatus in a glioblastoma

19 March 2017

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Recurrent rearrangement of the Ewing's sarcoma gene, EWSR1, or its homologue, TAF15, with the transcription factor CIZ/NMP4 in acute leukemia

19 March 2017

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Identification of novel fusion partners of ALK, the anaplastic lymphoma kinase, in anaplastic large-cell lymphoma and inflammatory myofibroblastic tumor

19 March 2017

1 reference

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Panhandle and reverse-panhandle PCR enable cloning of der(11) and der(other) genomic breakpoint junctions of MLL translocations and identify complex translocation of MLL, AF-4, and CDK6.

19 March 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636093

Gene Expression Omnibus: NCBI gene expression and hybridization array data repository

19 March 2017

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Dysregulation of cyclin dependent kinase 6 expression in splenic marginal zone lymphoma through chromosome 7q translocations

19 March 2017

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A novel ETV6-NTRK3 gene fusion in congenital fibrosarcoma

19 March 2017

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Human CREM gene: evolutionary conservation, chromosomal localization, and inducibility of the transcript

19 March 2017

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The PML-RARα fusion mRNA generated by the t(15;17) translocation in acute promyelocytic leukemia encodes a functionally altered RAR

19 March 2017

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Chromosomal translocation t(15;17) in human acute promyelocytic leukemia fuses RARα with a novel putative transcription factor, PML

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636093

Gene fusion with an ETS DNA-binding domain caused by chromosome translocation in human tumours

19 March 2017

1 reference

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Exon array analyses across the NCI-60 reveal potential regulation of TOP1 by transcription pausing at guanosine quartets in the first intron

19 March 2017

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The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity

19 March 2017

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Reorganizing the protein space at the Universal Protein Resource (UniProt)

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636093

The biology of cancer: metabolic reprogramming fuels cell growth and proliferation

7 April 2017

1 reference

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Global survey of phosphotyrosine signaling identifies oncogenic kinases in lung cancer

7 April 2017

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Human epidermal growth factor receptor cDNA sequence and aberrant expression of the amplified gene in A431 epidermoid carcinoma cells

7 April 2017

1 reference

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Letter: A new consistent chromosomal abnormality in chronic myelogenous leukaemia identified by quinacrine fluorescence and Giemsa staining

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636093

EGFRvIII gene rearrangement is an early event in glioblastoma tumorigenesis and expression defines a hierarchy modulated by epigenetic mechanisms.

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636093

Epidermal growth factor receptor variant III contributes to cancer stem cell phenotypes in invasive breast carcinoma

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636093

PARP-1 inhibition as a targeted strategy to treat Ewing's sarcoma

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636093

A transforming KIF5B and RET gene fusion in lung adenocarcinoma revealed from whole-genome and transcriptome sequencing.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636093

Functionally recurrent rearrangements of the MAST kinase and Notch gene families in breast cancer

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636093

Identification of a novel, recurrent HEY1-NCOA2 fusion in mesenchymal chondrosarcoma based on a genome-wide screen of exon-level expression data

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636093

Systematic screen for tyrosine kinase rearrangements identifies a novel C6orf204-PDGFRB fusion in a patient with recurrent T-ALL and an associated myeloproliferative neoplasm

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636093

Genomic sequencing of colorectal adenocarcinomas identifies a recurrent VTI1A-TCF7L2 fusion

29 September 2017

1 reference

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A fused lasso latent feature model for analyzing multi-sample aCGH data

29 September 2017

1 reference

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Detection of recurrent rearrangement breakpoints from copy number data

29 September 2017

1 reference

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CD44-SLC1A2 gene fusions in gastric cancer

29 September 2017

1 reference

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Ras/Raf/MEK/ERK and PI3K/PTEN/Akt/mTOR inhibitors: rationale and importance to inhibiting these pathways in human health

29 September 2017

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Fusion gene microarray reveals cancer type-specificity among fusion genes

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636093

Survey of tyrosine kinase signaling reveals ROS kinase fusions in human cholangiocarcinoma

29 September 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636093

EMT is the dominant program in human colon cancer

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636093

Discovery of non-ETS gene fusions in human prostate cancer using next-generation RNA sequencing

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636093

Rearrangements of the RAF kinase pathway in prostate cancer, gastric cancer and melanoma

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636093

Signatures of mutation and selection in the cancer genome

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636093

Discovery of molecular subtypes in leiomyosarcoma through integrative molecular profiling

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636093

29 September 2017

Emerging Raf inhibitors.

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Chimeric transcript discovery by paired-end transcriptome sequencing

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636093

Molecular genetics of sarcomas: applications to diagnoses and therapy

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636093

A requirement for cyclin-dependent kinase 6 in thymocyte development and tumorigenesis

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636093

A mouse model for EML4-ALK-positive lung cancer

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636093

The multifaceted roles of the receptor tyrosine kinase ROS in development and cancer

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636093

Cloning of genes involved in chromosomal translocations by high-resolution single nucleotide polymorphism genomic microarray

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636093

Genetic factors for ischemic and hemorrhagic stroke in Japanese individuals

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636093

Pancreatic carcinogenesis

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636093

Detection of TMPRSS2-ERG translocations in human prostate cancer by expression profiling using GeneChip Human Exon 1.0 ST arrays

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636093

Alu elements mediate MYB gene tandem duplication in human T-ALL

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636093

Drug transporters as targets for cancer chemotherapy

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636093

Distinct classes of chromosomal rearrangements create oncogenic ETS gene fusions in prostate cancer

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636093

Spatial smoothing and hot spot detection for CGH data using the fused lasso

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636093

The impact of translocations and gene fusions on cancer causation

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636093

A landscape effect in tenosynovial giant-cell tumor from activation of CSF1 expression by a translocation in a minority of tumor cells

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636093

Gene expression profiling identifies clinically relevant subtypes of prostate cancer

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636093

Expression of the ETV6-NTRK3 gene fusion as a primary event in human secretory breast carcinoma

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636093

Advancing the treatment of hematologic malignancies through the development of targeted interventions

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636093

Fusion genes in solid tumors

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636093

Fusion of ETV6 to neurotrophin-3 receptor TRKC in acute myeloid leukemia with t(12;15)(p13;q25).

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636093

Characterization of the genomic breakpoint and chimeric transcripts in the EWS-WT1 gene fusion of desmoplastic small round cell tumor

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636093

CREM gene: use of alternative DNA-binding domains generates multiple antagonists of cAMP-induced transcription

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636093

Inducibility and negative autoregulation of CREM: an alternative promoter directs the expression of ICER, an early response repressor.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636093

Reconstitution of an active surface T3/T-cell antigen receptor by DNA transfer.

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636093

Rearrangement of the human ABL oncogene in a glioblastoma

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636093

Characterization of the epidermal growth factor receptor in human glioma cell lines and xenografts.

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636093

Identification of RET gene fusion by exon array analyses in "pan-negative" lung cancer from never smokers

2 June 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1003464

A novel CLTC-TFE3 gene fusion in pediatric renal adenocarcinoma with t(X;17)(p11.2;q23).

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1003464

ALK-positive diffuse large B-cell lymphoma is associated with Clathrin-ALK rearrangements: report of 6 cases

21 January 2018

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https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1003464

Maintenance of EGFR and EGFRvIII expressions in an in vivo and in vitro model of human glioblastoma multiforme.

21 January 2018

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https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1003464

Chromosomal translocations in human cancer.

21 January 2018

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https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1003464

A cellular oncogene is translocated to the Philadelphia chromosome in chronic myelocytic leukaemia

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1003464

Translocation chromosome 7 of A431 cells contains amplification and rearrangement of EGF receptor gene responsible for production of variant mRNA

21 January 2018

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12 December 2020

Combined microarray analysis of small cell lung cancer reveals altered apoptotic balance and distinct expression signatures of MYC family gene amplification

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12 December 2020

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12 December 2020

Chronic eosinophilic leukaemia with ETV6-NTRK3 fusion transcript in an elderly patient affected with pancreatic carcinoma

1 reference

12 December 2020

In B-cell chronic lymphocytic leukemias, 7q21 translocations lead to overexpression of the CDK6 gene

1 reference

12 December 2020

Fusion genes and rearranged genes as a linear function of chromosome aberrations in cancer

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12 December 2020

10.1371/JOURNAL.PGEN.1003464

Identifiers

DOI

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3530564

3530564

1 reference

1 reference

1 reference