Genome wide measurement of DNA copy number changes in neuroblastoma: dissecting amplicons and mapping losses, gains and breakpoints

@article{Michels2006GenomeWM,
  title={Genome wide measurement of DNA copy number changes in neuroblastoma: dissecting amplicons and mapping losses, gains and breakpoints},
  author={Evi Michels and Jo Vandesompele and Jasmien Hoebeeck and Bj{\"o}rn Menten and Katleen De Preter and Genevi{\`e}ve Laureys and Nadine Van Roy and Frank Speleman},
  journal={Cytogenetic and Genome Research},
  year={2006},
  volume={115},
  pages={273 - 282}
}
In the past few years high throughput methods for assessment of DNA copy number alterations have witnessed rapid progress. Both ‘in house’ developed BAC, cDNA, oligonucleotide and commercial arrays are now available and widely applied in the study of the human genome, particularly in the context of disease. Cancer cells are known to exhibit DNA losses, gains and amplifications affecting tumor suppressor genes and proto-oncogenes. Moreover, these patterns of genomic imbalances may be associated… Expand
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References

SHOWING 1-10 OF 104 REFERENCES
High-resolution analysis of chromosomal breakpoints and genomic instability identifies PTPRD as a candidate tumor suppressor gene in neuroblastoma.
Although neuroblastoma is characterized by numerous recurrent, large-scale chromosomal imbalances, the genes targeted by such imbalances have remained elusive. We have applied whole-genomeExpand
Genome-wide detection of chromosomal imbalances in tumors using BAC microarrays
TLDR
A microarray-based CGH method is demonstrated that allows reliable detection of chromosomal deletions and amplifications with high resolution and is an obvious solution to all of the limitations of conventional CGH. Expand
Analysis of chromosome breakpoints in neuroblastoma at sub‐kilobase resolution using fine‐tiling oligonucleotide array CGH
TLDR
It is demonstrated that oligonucleotide array CGH (oaCGH) analysis can routinely map chromosomal imbalance breakpoints at exon‐level resolution, including imbalances that are single copy number genomic alterations. Expand
Comparative genomic hybridization analysis of human neuroblastomas: detection of distal 1p deletions and further molecular genetic characterization of neuroblastoma cell lines.
TLDR
Results show that CGH allows reliable detection of distal 1p deletions, including a small interstitial deletion in cell line SK-N-AS, and also allows the detection of chromosomal imbalance which would otherwise remain undetected, and provides useful information for further molecular characterization of chromosomesomal imbalances. Expand
Sensitive and reliable detection of genomic imbalances in human neuroblastomas using comparative genomic hybridisation analysis.
TLDR
The results show that CGH is a valuable tool for the genetic characterisation of neuroblastomas, both for the detection of frequently occurring genomic imbalances and for the identification of previously unnoticed genetic changes. Expand
Chromosomal localization of DNA amplifications in neuroblastoma tumors using cDNA microarray comparative genomic hybridization.
TLDR
Application of CGH to cDNA microarray targets will help to determine both the variation of amplicon size and help better define amplification-dependent and independent pathways of progression in neuroblastoma. Expand
cDNA array-CGH profiling identifies genomic alterations specific to stage and MYCN-amplification in neuroblastoma
TLDR
It is confirmed that the most frequent specific changes in Stage 4+ tumors were the loss of 1p36 with gain of 2p24-25 and they had fewer genomic alterations compared to either stage 1 or 4-, indicating that for this subgroup of poor risk NB requires a smaller number of genomic changes are required to develop the malignant phenotype. Expand
High‐resolution detection and mapping of genomic DNA alterations in neuroblastoma
We used array‐based comparative genomic hybridization (aCGH) to measure genomic copy number alterations (CNAs) in 42 neuroblastoma cell lines with known 1p36.3, 2p24 (MYCN), 11q23, and 17q23 allelicExpand
Comparative genomic hybridization reveals changes in DNA-copy number in poor-risk neuroblastoma.
TLDR
The applicability of CGH in studies on the genomic changes in pediatric malignancies is demonstrated, adding weight to the argument of multiple elements with oncogenic and/or tumor suppressor potential being involved in the aggressive phenotype of poor-risk neuroblastoma. Expand
COMPARATIVE GENOMIC HYBRIDIZATION (CGH) ANALYSIS OF NEUROBLASTOMAS—AN IMPORTANT METHODOLOGICAL APPROACH IN PAEDIATRIC TUMOUR PATHOLOGY
TLDR
Comparative genomic hybridization was applied to 35 neuroblastomas to obtain a global view of genetic imbalances and shows that CGH is a sensitive method for the detection of all prognostically relevant genetic alterations in neuroblastoma and considerably simplifies the Detection of these alterations. Expand
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