USP42--RUNX1

Hyperlinks to databases below
COSMIC CHIMERKB CHIMERPUB CHIMERSEQ CHITARS
FARE-CAFE TICDB TUMOR_FUSION_GDPFusionCancerConjoinG
1000Genome18CancersBodymap2HPANon_Tumor_Cells
Babiceanu_DatasetBanned_DatasetKnown_FusionsONGene DatabaseBushman Cancer Gene Database
Tumor Gene Set By UniprotOesophagus_DatasetGliomas_DatasetProstate_DatasetPancreases_Dataset
GTExKlijn_DatasetFimereli_Dataset Literature Cortex_Dataset
ChromothripsisDB

Link to Genecards:

USP42 RUNX1

COSMIC

The fusion gene pair USP42--RUNX1 information is not available in COSMIC database.

ChimerKB

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The fusion gene pair USP42--RUNX1 information is not available in CHIMERKB (CHIMERDB 3.0) database.

ChimerPUB

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The fusion gene pair USP42--RUNX1 information is available in CHIMERPUB (CHIMERDB 3.0) database.

Fusion_pairTranslocationPMIDDiseaseValidationGene TypeSentence_highlight
USP42_RUNX1t(7;21) / t(7;21)(p22;q22) / t(7;21) / 20064152myelodysplastic syndrome FISH;PCR;RT-PCR - Thus, our studies have identified t(7;21)(p22;q22) as a rare but recurrent abnormality in MDS/AML, with the existence of alternative spliced forms of the RUNX1-USP42 transcript in different patients. /// Molecular analysis of 100 MDS and AML marrow specimens by RT-PCR did not reveal new cases with the RUNX1-USP42 fusion.
USP42_RUNX1t(7;21) / t(7;21)(p22;q22) / 22867997acute myeloid leukemia;myeloid leukemia;leukemia FISH - Three cases of the recently described translocation, t(7;21)(p22;q22), were identified, which expressed RUNX1-USP42 (ubiquitin-specific protease 42) fusion transcripts, associated with 5q abnormalities and hyperploidy.
USP42_RUNX1t(7;21)(p22;q22) / t(7;21) / 23877199acute myeloid leukemia;myeloid leukemia;leukemia PCR - The rare but recurrent RUNX1-USP42 fusion gene is the result of a t(7;21)(p22;q22) chromosomal translocation and has been described in 6 cases of acute myeloid leukemia (AML) and one case of refractory anemia with excess of blast. /// "The bone marrow cells in the present case also had a 5q deletion, and it was revealed that 5 out of the 8 reported cases (including the present case) with t(7;21)(p22;q22)/RUNX1-USP42 also had cytogenetic abnormalities of 5q. " /// PCR amplified two RUNX1-USP42 cDNA fragments but no reciprocal USP42-RUNX1 fragment indicating that the RUNX1-USP42 is the leukemogenic fusion gene. /// "The predicted RUNX1-USP42 fusion protein would contain the Runt homology domain (RHD), which is responsible for heterodimerization with CBFB and for DNA binding, and the catalytic UCH (ubiquitin carboxyl terminal hydroxylase) domain of the USP42 protein. "
USP42_RUNX1del(5q) / 24673627- - - Whole transcriptome sequencing of a paediatric case of de novo acute myeloid leukaemia with del(5q) reveals RUNX1-USP42 and PRDM16-SKI fusion transcripts..
USP42_RUNX1t(7;21)(p22;q22) / t(7;21) / 21319259acute myeloid leukemia;myeloid leukemia;leukemia PCR;ISH - Sequence analysis of the reverse transcription-polymerase chain reaction products confirmed the presence of two in-frame RUNX1-USP42 and one reciprocal in-frame USP42-RUNX1 fusion transcripts.

ChimerSEQ

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The fusion gene pair USP42--RUNX1 information is available in CHIMERSEQ (CHIMERDB 3.0) database.

Fusion_pair5'Gene Junction (Chr/Position/Strand)3'Gene Junction (Chr/Position/Strand)5'Gene_locus3'Gene_locusBreakpoint_TypeGenome_BuildFrameChr_infoCancertype_or_diseaseBarcodeIDGene TypeSource
USP42_RUNX1chr7/6151080/ chr21/36167216/ 7p22.1 21q22.12 Exonic hg19 - Inter-chr NA FR727327 Transcription_Factor ChiTaRs

ChiTaRS 2.1

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The fusion gene pair USP42--RUNX1 information is available in CHITARS database.

OrganismChimeraIDFusion genepairHead geneTail gene
GeneChromosomeGenomic_startGenomic_stopStrandFusiongene_startposFusiongene_endpos%IdentGeneChromosomeGenomic_startGenomic_stopStrandFusiongene_startposFusiongene_endpos%Ident
Human FR727327USP42--RUNX1 USP427 6150846 6151080 + 1 235 100 RUNX121 36167216 36167584 - 233 601 100

FARE-CAFE

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The fusion gene pair USP42--RUNX1 information is not available in FARE-CAFE.

TicDB

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The fusion gene pair USP42--RUNX1 information is not available in TicDB.

TUMOR FUSION Gene Data Portal

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The fusion gene pair USP42--RUNX1 information is not available in TUMOR FUSION Gene Data Portal.

FusionCancer

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The fusion gene pair USP42--RUNX1 information is not available in FusionCancer Database.

ConjoinG

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The fusion gene pair USP42--RUNX1 information is not available in ConjoinG Database.

1000Genome

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Fusion gene USP42--RUNX1 has not been seen in a healthy sample (RNA-seq data from some samples from 1000 genomes project: Greger et al., Tandem RNA Chimeras Contribute to Transcriptome Diversity in Human Population and Are Associated with Intronic Genetic Variants, Plos One, Aug 2014 ). Therefore this candidate fusion gene has a low probability of being a false positive. [Fusion gene List compiled from FusionCatcher]

18Cancers

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Fusion gene USP42--RUNX1 is not found in a RNA-seq dataset of 18 types of cancers from 600 tumor samples (B. Alaei-Mahabadia et al., Global analysis of somatic structural genomic alterations and their impact on gene expression in diverse human cancers, PNAS, Nov. 2016 )

Bodymap2

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Fusion gene USP42--RUNX1 is not found in the list of known false positive fusion genes. The list has been generated from healthy human samples collected from 16 organs from Illumina BodyMap2 RNA-seq database. A candidate fusion gene found in this list has a very high probability of being a false positive. [Fusion gene List compiled from FusionCatcher]

HPA

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Fusion gene USP42--RUNX1 is not found in a healthy sample (RNA-seq database of 27 healthy tissues from 95 human individuals). A candidate fusion gene found in this dataset has a very high probability of being a false positive. [Fusion gene List compiled from FusionCatcher]

Non_Tumor_Cells

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Fusion gene USP42--RUNX1 was not found among the fusion genes which have been previously reported/found in non-tumor cell lines, like for example HEK293. The genes which are observed in those list can be considered as non-somatic mutation. [Fusion gene List compiled from FusionCatcher]

Babiceanu_Dataset

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The fusion gene pair USP42--RUNX1 information is not available in Babiceanu_Dataset.

Banned_Dataset

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Fusion gene USP42--RUNX1 is not found in the list of known false positive fusion genes. A candidate fusion gene found in this list has a very high probability of being a false positive. [Fusion gene List compiled from FusionCatcher]

Known_Fusions

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Fusion gene USP42--RUNX1 has not been found in the list of fusions previously reported or published in scientific articles/reports/books/abstracts/databases, indexed by Google, Google Scholar, PubMed, etc. The list has been manually curated by FusionCatcher software. This label has only the role to answer with YES or NO the question "has ever before a given (candidate) fusion gene been published or reported?". This label does not have in anyway the role to provide the original references to the original scientific articles/reports/books/abstracts/databases for a given fusion gene.[Fusion gene List compiled from FusionCatcher]

ONGene Database

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The head gene USP42 is not a known oncogene according to ONGENE database.


The tail gene RUNX1 is a known oncogene according to ONGENE database.

Bushman Cancer Gene Database

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The head gene USP42 is not cancer associated according to Bushman Cancer Gene database.


The tail gene RUNX1 is cancer associated according to Bushman Cancer Gene database.

Tumor Gene Set By Uniprot

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The head gene USP42 is not a proto-oncogene or tumor suppresor gene according to Uniprot database.


The tail gene RUNX1 is proto-oncogene or tumor suppresor gene according to Uniprot database.

Oesophagus_Dataset

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Fusion gene USP42--RUNX1 is not found in oesophageal tumors from TCGA samples, which are published here.

Gliomas_Dataset

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Fusion gene USP42--RUNX1 is not found in the RNA-seq dataset of 272 glioblastomas, published here.

Prostate_Dataset

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The fusion gene pair USP42--RUNX1 information is not available in Prostate Dataset (150 prostate tumor RNAs, Robison et al, Integrative Clinical Genomics of Advanced Prostate Cancer, Cell, Vol. 161, May 2015, http://dx.doi.org/10.1016/j.cell.2015.05.001).

Pancreases_Dataset

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Fusion gene USP42--RUNX1 is not found in pancreatic tumor dataset, published here.

GTEx

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Fusion gene USP42--RUNX1 has not been found in a healthy sample (GTEx database of healthy tissues (thru FusionAnnotator)). A candidate fusion gene found in this set has a very high probability of being a false positive. [Fusion gene List compiled from FusionCatcher]

Klijin_Dataset

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The fusion gene pair USP42--RUNX1 information is not available in Klijn Dataset.

Fimereli_Dataset

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The fusion gene pair USP42--RUNX1 information is not found in Fimereli_Dataset.

Literature

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The fusion gene pair USP42--RUNX1 information is not found in known fusion genelist compiled from literature.

Cortex_Dataset

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Fusion gene USP42--RUNX1 is not found in Cortex_Dataset (Fusion genes found in healthy human brains (BA9 prefrontal cortex)) . A candidate fusion gene found in this dataset has a very high probability of being a false positive.

ChromothripsisDB

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The fusion gene pair USP42--RUNX1 information is not available in ChromothripsisDB database.