Transcriptomics,Genomics

Dataset Information

42

Frequent miRNA-convergent fusion gene events in breast cancer


ABSTRACT: Studies of fusion genes have mainly focused on the formation of fusions that result in the production of hybrid proteins or, alternatively, on promoter-switching events that put a gene under the control of aberrant signals. However, gene fusions may also disrupt the transcriptional control of genes that are encoded in introns downstream of the breakpoint. By ignoring structural constraints of the transcribed fusions, we highlight the importance of a largely unexplored function of fusion genes. Using breast cancer as an example, we show that miRNA host genes are specifically enriched in fusion genes and that many different, low-frequency, 5' partners may deregulate the same miRNA irrespective of the coding potential of the fusion transcript. These results indicate that the concept of recurrence, defined by the rate of functionally important aberrations, needs to be revised to encompass convergent fusions that affect a miRNA independently of transcript structure and protein-coding potential. Overall design: Illumina paired-end RNA-sequencing was performed on 1600 sequencing libraries (49 technical replicates, 1552 tumour samples) for fusion gene detection analysis. miRNA sequencing was performed on a subset of the fusion detection samples, 191 sequence libraries (5 technical replicates, 186 tumour samples), for miRNA transcript expression estimation. ------------------------------------ This represents the miRNA sequencing component of 191 libraries only. -------------------------------------- The authors state "due to Swedish law, the patient consent, and the risk that the sequencing data contains personally-identifiable information andhereditary mutations, we cannot deposit the short sequencing read data in a repository". Thus, this submission is incomplete.

INSTRUMENT(S): Illumina NextSeq 500 (Homo sapiens)

SUBMITTER: Carlos Rovira 

PROVIDER: GSE100769 | GEO | 2017-10-31

SECONDARY ACCESSION(S): PRJNA392938

REPOSITORIES: GEO

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Publications


Studies of fusion genes have mainly focused on the formation of fusions that result in the production of hybrid proteins or, alternatively, on promoter-switching events that put a gene under the control of aberrant signals. However, gene fusions may also disrupt the transcriptional control of genes that are encoded in introns downstream of the breakpoint. By ignoring structural constraints of the transcribed fusions, we highlight the importance of a largely unexplored function of fusion genes. H  ...[more]

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