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Novel fusion genes and chimeric transcripts in ependymal tumors

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Harvard

Olsen, TK, Panagopoulos, I, Gorunova, L, Micci, F, Andersen, K, Kilen Andersen, H, Meling, TR, Due-Tønnessen, B, Scheie, D, Heim, S & Brandal, P 2016, 'Novel fusion genes and chimeric transcripts in ependymal tumors' Genes Chromosomes and Cancer, vol. 55, no. 12, pp. 944-953. https://doi.org/10.1002/gcc.22392

APA

Olsen, T. K., Panagopoulos, I., Gorunova, L., Micci, F., Andersen, K., Kilen Andersen, H., ... Brandal, P. (2016). Novel fusion genes and chimeric transcripts in ependymal tumors. Genes Chromosomes and Cancer, 55(12), 944-953. https://doi.org/10.1002/gcc.22392

CBE

Olsen TK, Panagopoulos I, Gorunova L, Micci F, Andersen K, Kilen Andersen H, Meling TR, Due-Tønnessen B, Scheie D, Heim S, Brandal P. 2016. Novel fusion genes and chimeric transcripts in ependymal tumors. Genes Chromosomes and Cancer. 55(12):944-953. https://doi.org/10.1002/gcc.22392

MLA

Vancouver

Olsen TK, Panagopoulos I, Gorunova L, Micci F, Andersen K, Kilen Andersen H et al. Novel fusion genes and chimeric transcripts in ependymal tumors. Genes Chromosomes and Cancer. 2016 Dec;55(12):944-953. https://doi.org/10.1002/gcc.22392

Author

Olsen, Thale Kristin ; Panagopoulos, Ioannis ; Gorunova, Ludmila ; Micci, Francesca ; Andersen, Kristin ; Kilen Andersen, Hege ; Meling, Torstein R ; Due-Tønnessen, Bernt ; Scheie, David ; Heim, Sverre ; Brandal, Petter. / Novel fusion genes and chimeric transcripts in ependymal tumors. In: Genes Chromosomes and Cancer. 2016 ; Vol. 55, No. 12. pp. 944-953.

Bibtex

@article{2e777453045948289d9e1063fea15146,
title = "Novel fusion genes and chimeric transcripts in ependymal tumors",
abstract = "We have previously identified two ALK rearrangements in a subset of ependymal tumors using a combination of cytogenetic data and RNA sequencing. The aim of this study was to perform an unbiased search for fusion transcripts in our entire series of ependymal tumors. Fusion analysis was performed using the FusionCatcher algorithm on 12 RNA-sequenced ependymal tumors. Candidate transcripts were prioritized based on the software's filtering and manual visualization using the BLAST (Basic Local Alignment Search Tool) and BLAT (BLAST-like alignment tool) tools. Genomic and reverse transcriptase PCR with subsequent Sanger sequencing was used to validate the potential fusions. Fluorescent in situ hybridization (FISH) using locus-specific probes was also performed. A total of 841 candidate chimeric transcripts were identified in the 12 tumors, with an average of 49 unique candidate fusions per tumor. After algorithmic and manual filtering, the final list consisted of 24 potential fusion events. Raw RNA-seq read sequences and PCR validation supports two novel fusion genes: a reciprocal fusion gene involving UQCR10 and C1orf194 in an adult spinal ependymoma and a TSPAN4-CD151 fusion gene in a pediatric infratentorial anaplastic ependymoma. Our previously reported ALK rearrangements and the RELA and YAP1 fusions found in supratentorial ependymomas were until now the only known fusion genes present in ependymal tumors. The chimeric transcripts presented here are the first to be reported in infratentorial or spinal ependymomas. Further studies are required to characterize the genomic rearrangements causing these fusion genes, as well as the frequency and functional importance of the fusions. {\circledC} 2016 Wiley Periodicals, Inc.",
author = "Olsen, {Thale Kristin} and Ioannis Panagopoulos and Ludmila Gorunova and Francesca Micci and Kristin Andersen and {Kilen Andersen}, Hege and Meling, {Torstein R} and Bernt Due-T{\o}nnessen and David Scheie and Sverre Heim and Petter Brandal",
note = "{\circledC} 2016 Wiley Periodicals, Inc.",
year = "2016",
month = "12",
doi = "10.1002/gcc.22392",
language = "English",
volume = "55",
pages = "944--953",
journal = "Genes Chromosomes and Cancer",
issn = "1045-2257",
publisher = "John/Wiley & Sons, Inc. John/Wiley & Sons Ltd",
number = "12",

}

RIS

TY - JOUR

T1 - Novel fusion genes and chimeric transcripts in ependymal tumors

AU - Olsen, Thale Kristin

AU - Panagopoulos, Ioannis

AU - Gorunova, Ludmila

AU - Micci, Francesca

AU - Andersen, Kristin

AU - Kilen Andersen, Hege

AU - Meling, Torstein R

AU - Due-Tønnessen, Bernt

AU - Scheie, David

AU - Heim, Sverre

AU - Brandal, Petter

N1 - © 2016 Wiley Periodicals, Inc.

PY - 2016/12

Y1 - 2016/12

N2 - We have previously identified two ALK rearrangements in a subset of ependymal tumors using a combination of cytogenetic data and RNA sequencing. The aim of this study was to perform an unbiased search for fusion transcripts in our entire series of ependymal tumors. Fusion analysis was performed using the FusionCatcher algorithm on 12 RNA-sequenced ependymal tumors. Candidate transcripts were prioritized based on the software's filtering and manual visualization using the BLAST (Basic Local Alignment Search Tool) and BLAT (BLAST-like alignment tool) tools. Genomic and reverse transcriptase PCR with subsequent Sanger sequencing was used to validate the potential fusions. Fluorescent in situ hybridization (FISH) using locus-specific probes was also performed. A total of 841 candidate chimeric transcripts were identified in the 12 tumors, with an average of 49 unique candidate fusions per tumor. After algorithmic and manual filtering, the final list consisted of 24 potential fusion events. Raw RNA-seq read sequences and PCR validation supports two novel fusion genes: a reciprocal fusion gene involving UQCR10 and C1orf194 in an adult spinal ependymoma and a TSPAN4-CD151 fusion gene in a pediatric infratentorial anaplastic ependymoma. Our previously reported ALK rearrangements and the RELA and YAP1 fusions found in supratentorial ependymomas were until now the only known fusion genes present in ependymal tumors. The chimeric transcripts presented here are the first to be reported in infratentorial or spinal ependymomas. Further studies are required to characterize the genomic rearrangements causing these fusion genes, as well as the frequency and functional importance of the fusions. © 2016 Wiley Periodicals, Inc.

AB - We have previously identified two ALK rearrangements in a subset of ependymal tumors using a combination of cytogenetic data and RNA sequencing. The aim of this study was to perform an unbiased search for fusion transcripts in our entire series of ependymal tumors. Fusion analysis was performed using the FusionCatcher algorithm on 12 RNA-sequenced ependymal tumors. Candidate transcripts were prioritized based on the software's filtering and manual visualization using the BLAST (Basic Local Alignment Search Tool) and BLAT (BLAST-like alignment tool) tools. Genomic and reverse transcriptase PCR with subsequent Sanger sequencing was used to validate the potential fusions. Fluorescent in situ hybridization (FISH) using locus-specific probes was also performed. A total of 841 candidate chimeric transcripts were identified in the 12 tumors, with an average of 49 unique candidate fusions per tumor. After algorithmic and manual filtering, the final list consisted of 24 potential fusion events. Raw RNA-seq read sequences and PCR validation supports two novel fusion genes: a reciprocal fusion gene involving UQCR10 and C1orf194 in an adult spinal ependymoma and a TSPAN4-CD151 fusion gene in a pediatric infratentorial anaplastic ependymoma. Our previously reported ALK rearrangements and the RELA and YAP1 fusions found in supratentorial ependymomas were until now the only known fusion genes present in ependymal tumors. The chimeric transcripts presented here are the first to be reported in infratentorial or spinal ependymomas. Further studies are required to characterize the genomic rearrangements causing these fusion genes, as well as the frequency and functional importance of the fusions. © 2016 Wiley Periodicals, Inc.

U2 - 10.1002/gcc.22392

DO - 10.1002/gcc.22392

M3 - Journal article

VL - 55

SP - 944

EP - 953

JO - Genes Chromosomes and Cancer

JF - Genes Chromosomes and Cancer

SN - 1045-2257

IS - 12

ER -

ID: 49285184