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Updated: Aug 29, 2026
Array Comparative Genomic Hybridization (Array CGH) for Detection of Genomic Copy Number Variants
Published on: February 21, 2015
Detection of oncogene amplifications in medulloblastomas by comparative genomic hybridization and array-based
Carol Y K Tong1, Angela B Y Hui, Xiao-Lu Yin
1Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, China.
Object:
Few studies have been conducted to investigate the genomic survey of oncogene amplification in medulloblastoma. Low frequency of N-myc, C-myc, and epidermal grow factor receptor (EGFR) gene amplification (< 10%) has been reported in medulloblastoma. Previous comparative genomic hybridization (CGH) study of primary medulloblastomas has revealed chromosomal amplification on 2p21, 3p, 5p15.3, 7q, 8q24, 11q22.3, and 17q. The aim of this study was to detect common oncogenes involved in medulloblastoma tumorigenesis.
Methods:
The authors studied a series of 14 samples by performing CGH and array-based CGH. The CGH analysis detected nonrandom losses on 8p, 17p, 16q, 8q, and 1p, whereas gains were found on 17q, 12q, 7q, and 1p. Array-based CGH was conducted to investigate amplification of 58 oncogenes throughout the genome of these samples. Gene amplifications identified for the first time included PGY1 at 7q21.1, MDM2 at 12q14.3-q15, and ERBB2 at 17q21.2. The highest frequencies of oncogene gain were detected in D17S1670 (61.5%), PIK3CA (46.2%), PGY1 (38.5%), MET (38.5%), ERBB2 (38.5%), and CSE1L (38.5%). The gain in gene copy numbers was confirmed in 34 additional archival medulloblastoma cases by using fluorescence in situ hybridization analysis.
Conclusions:
This is the first genome-wide survey of multiple oncogene amplifications involved in the development of medulloblastoma. Gains of several candidate oncogenes such as D17S1670, ERBB2, PIK3CA, PGY1, MET, and CSE1L were frequently detected. These genes may be used as molecular markers and therapeutic targets of medulloblastomas.
Insights
This study identified frequent gains of oncogenes like PIK3CA and ERBB2 in medulloblastoma, offering new molecular markers and therapeutic targets for this brain tumor.
Area of Science:
- Genomic analysis of pediatric brain tumors
- Oncogene amplification in cancer development
- Molecular oncology and targeted therapies
Background:
- Medulloblastoma is a common pediatric brain tumor with limited understanding of its genomic landscape.
- Previous studies reported low frequencies of N-myc, C-myc, and EGFR gene amplification.
- Prior CGH studies identified chromosomal amplifications in medulloblastoma, but a comprehensive oncogene survey was lacking.
Purpose of the Study:
- To conduct a genome-wide survey for oncogene amplifications in medulloblastoma.
- To identify common oncogenes driving medulloblastoma tumorigenesis.
- To explore potential molecular markers and therapeutic targets for medulloblastoma.
Main Methods:
- Comparative Genomic Hybridization (CGH) and array-based CGH on 14 primary medulloblastoma samples.
- Investigated amplification of 58 oncogenes across the genome.
- Validated gene copy number gains in 34 additional cases using fluorescence in situ hybridization (FISH).
Main Results:
- Identified novel gene amplifications including PGY1, MDM2, and ERBB2.
- High frequencies of oncogene gains detected in D17S1670 (61.5%), PIK3CA (46.2%), PGY1 (38.5%), MET (38.5%), ERBB2 (38.5%), and CSE1L (38.5%).
- CGH analysis revealed nonrandom chromosomal losses and gains in specific regions.
Conclusions:
- This is the first genome-wide survey of multiple oncogene amplifications in medulloblastoma.
- Frequent gains of candidate oncogenes (D17S1670, ERBB2, PIK3CA, PGY1, MET, CSE1L) were identified.
- These amplified oncogenes represent potential molecular markers and therapeutic targets for medulloblastoma treatment.
