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Identification of a novel recurrent 1q42.2-1qter deletion in high risk MYCN single copy 11q deleted neuroblastomas

Annelies Fieuw UGent, Candy Kumps UGent, Alexander Schramm, Filip Pattyn UGent, Björn Menten UGent, Francesca Antonacci, Peter Sudmant, Johannes H Schulte, Nadine Van Roy UGent and Sarah Vergult UGent, et al. (2012) INTERNATIONAL JOURNAL OF CANCER. 130(11). p.2599-2606
abstract
Neuroblastoma is an aggressive embryonal tumor that accounts for ~15% of childhood cancer deaths. Hitherto, despite the availability of comprehensive genomic data on DNA copy number changes in neuroblastoma, relatively little is known about the genes driving neuroblastoma tumorigenesis. In this study, high resolution array comparative genome hybridization (CGH) was performed on 188 primary neuroblastoma tumors and 33 neuroblastoma cell lines to search for previously undetected recurrent DNA copy number gains and losses. A new recurrent distal chromosome 1q deletion (del(1)(q42.2qter)) was detected in seven cases. Further analysis of available array CGH datasets revealed 13 additional similar distal 1q deletions. The majority of all detected 1q deletions was found in high risk 11q deleted tumors without MYCN amplification (Fisher exact test p 5 5.61 3 1025). Using ultra-high resolution (~115 bp resolution) custom arrays covering the breakpoints on 1q for 11 samples, clustering of nine breakpoints was observed within a 12.5-kb region, of which eight were found in a 7-kb copy number variable region, whereas the remaining two breakpoints were colocated 1.4-Mb proximal. The commonly deleted region contains one miRNA (hsa-mir-1537), four transcribed ultra conserved region elements (uc.43-uc.46) and 130 protein coding genes including at least two bona fide tumor suppressor genes, EGLN1 (or PHD2) and FH. This finding further contributes to the delineation of the genomic profile of aggressive neuroblastoma, offers perspectives for the identification of genes contributing to the disease phenotype and may be relevant in the light of assessment of response to new molecular treatments.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
array CGH, neuroblastoma, chromosome 1, deletion, EXPRESSION, SUBGROUPS, NUMBER, GENES, CLASSIFICATION, MUTATIONS, PHENOTYPE, PROFILES, BREAST, TUMORS
journal title
INTERNATIONAL JOURNAL OF CANCER
Int. J. Cancer
volume
130
issue
11
pages
2599 - 2606
Web of Science type
Article
Web of Science id
000302013200013
JCR category
ONCOLOGY
JCR impact factor
6.198 (2012)
JCR rank
23/196 (2012)
JCR quartile
1 (2012)
ISSN
0020-7136
DOI
10.1002/ijc.26317
language
English
UGent publication?
yes
classification
A1
copyright statement
I have transferred the copyright for this publication to the publisher
id
1986993
handle
http://hdl.handle.net/1854/LU-1986993
date created
2012-01-16 11:41:53
date last changed
2012-09-19 12:59:42
@article{1986993,
  abstract     = {Neuroblastoma is an aggressive embryonal tumor that accounts for {\texttildelow}15\% of childhood cancer deaths. Hitherto, despite the availability of comprehensive genomic data on DNA copy number changes in neuroblastoma, relatively little is known about the genes driving neuroblastoma tumorigenesis. In this study, high resolution array comparative genome hybridization (CGH) was performed on 188 primary neuroblastoma tumors and 33 neuroblastoma cell lines to search for previously undetected recurrent DNA copy number gains and losses. A new recurrent distal chromosome 1q deletion (del(1)(q42.2qter)) was detected in seven cases. Further analysis of available array CGH datasets revealed 13 additional similar distal 1q deletions. The majority of all detected 1q deletions was found in high risk 11q deleted tumors without MYCN amplification (Fisher exact test p 5 5.61 3 1025). Using ultra-high resolution ({\texttildelow}115 bp resolution) custom arrays covering the breakpoints on 1q for 11 samples, clustering of nine breakpoints was observed within a 12.5-kb region, of which eight were found in a 7-kb copy number variable region, whereas the remaining two breakpoints were colocated 1.4-Mb proximal. The commonly deleted region contains one miRNA (hsa-mir-1537), four transcribed ultra conserved region elements (uc.43-uc.46) and 130 protein coding genes including at least two bona fide tumor suppressor genes, EGLN1 (or PHD2) and FH. This finding further contributes to the delineation of the genomic profile of aggressive neuroblastoma, offers perspectives for the identification of genes contributing to the disease phenotype and may be relevant in the light of assessment of response to new molecular treatments.},
  author       = {Fieuw, Annelies and Kumps, Candy and Schramm, Alexander and Pattyn, Filip and Menten, Bj{\"o}rn and Antonacci, Francesca and Sudmant, Peter and Schulte, Johannes H and Van Roy, Nadine and Vergult, Sarah and Buckley, Patrick G and De Paepe, Anne and Noguera, Rosa and Versteeg, Rogier and Stallings, Raymond and Eggert, Angelika  and Vandesompele, Jo and De Preter, Katleen and Speleman, Franki},
  issn         = {0020-7136},
  journal      = {INTERNATIONAL JOURNAL OF CANCER},
  keyword      = {array CGH,neuroblastoma,chromosome 1,deletion,EXPRESSION,SUBGROUPS,NUMBER,GENES,CLASSIFICATION,MUTATIONS,PHENOTYPE,PROFILES,BREAST,TUMORS},
  language     = {eng},
  number       = {11},
  pages        = {2599--2606},
  title        = {Identification of a novel recurrent 1q42.2-1qter deletion in high risk MYCN single copy 11q deleted neuroblastomas},
  url          = {http://dx.doi.org/10.1002/ijc.26317},
  volume       = {130},
  year         = {2012},
}

Chicago
Fieuw, Annelies, Candy Kumps, Alexander Schramm, Filip Pattyn, Björn Menten, Francesca Antonacci, Peter Sudmant, et al. 2012. “Identification of a Novel Recurrent 1q42.2-1qter Deletion in High Risk MYCN Single Copy 11q Deleted Neuroblastomas.” International Journal of Cancer 130 (11): 2599–2606.
APA
Fieuw, A., Kumps, C., Schramm, A., Pattyn, F., Menten, B., Antonacci, F., Sudmant, P., et al. (2012). Identification of a novel recurrent 1q42.2-1qter deletion in high risk MYCN single copy 11q deleted neuroblastomas. INTERNATIONAL JOURNAL OF CANCER, 130(11), 2599–2606.
Vancouver
1.
Fieuw A, Kumps C, Schramm A, Pattyn F, Menten B, Antonacci F, et al. Identification of a novel recurrent 1q42.2-1qter deletion in high risk MYCN single copy 11q deleted neuroblastomas. INTERNATIONAL JOURNAL OF CANCER. 2012;130(11):2599–606.
MLA
Fieuw, Annelies, Candy Kumps, Alexander Schramm, et al. “Identification of a Novel Recurrent 1q42.2-1qter Deletion in High Risk MYCN Single Copy 11q Deleted Neuroblastomas.” INTERNATIONAL JOURNAL OF CANCER 130.11 (2012): 2599–2606. Print.