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| Status |
Public on Oct 23, 2015 |
| Title |
Genomic DNA damage in oral potentially malignant disorders (OPMDs) and oral squamous cell carcinomas (OSCCs). Early detection of DNA aneuploidy and chromosomal aberrations in non dysplastic OPMDs. |
| Organism |
Homo sapiens |
| Experiment type |
Genome variation profiling by genome tiling array
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| Summary |
Oral potentially malignant disorders (OPMDs) may precede oral squamous cell carcinoma (OSCC). Early detection of OPMDs has a crucial role in OSCC prevention. DNA aneuploidy and chromosomal aberrations are markers of genomic DNA damage and chromosomal instability (CIN), which is involved in cancer development. We explored the relationship among genomic DNA copy number aberrations (CNAs), histological diagnosis and DNA aneuploidy in OPMDs/OSCCs. Samples from OPMDs and OSCCs were processed for high resolution DNA flow cytometry (hr DNA-FCM) to determine the relative DNA content expressed with the DNA index (DI). Additionally, on a subset of these samples, array-Comparative Genomic Hybridization (aCGH) analysis was performed on DNA obtained from diploid nuclei suspension or from aneuploid-enriched nuclei suspensions.
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| Overall design |
DNA copy number aberrations were determined using high resolution arrays on 151 samples (2x105K, n=82 samples, and 4x180K, n=69 samples) (Agilent Technologies, Palo Alto, CA, USA). Labeling, hybridization, scanning and feature extraction were performed as previously described using the cross hybridization method previously described [Castagnola P, Malacarne D, Scaruffi P, Maffei M, Donadini A, et al. (2011) Chromosomal aberrations and aneuploidy in oral potentially malignant lesions: distinctive features for tongue. BMC Cancer 11: 445.].
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| Contributor(s) |
Monticone M, Zoppoli G, Pentenero M, Malacarne D, Cirmena G, Brown D, Aiello C, Marino R, Giaretti W, Castagnola P, Gandolfo S |
| Citation(s) |
26540282, 28877236 |
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| Submission date |
Feb 20, 2015 |
| Last update date |
Aug 02, 2019 |
| Contact name |
Patrizio Castagnola |
| E-mail(s) |
[email protected]
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| Organization name |
IRCCS AOU San Martino - IST
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| Street address |
Largo Rosanna Benzi 10
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| City |
Genova |
| State/province |
GE |
| ZIP/Postal code |
16132 |
| Country |
Italy |
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| Platforms (2) |
| GPL9075 |
Agilent-014698 Human Genome CGH Microarray 105A (G4412A) [Probe Name version] |
| GPL10150 |
Agilent-022060 SurePrint G3 Human CGH Microarray 4x180K (Probe Name version) |
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| Samples (151)
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| Relations |
| BioProject |
PRJNA275946 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE66136_RAW.tar |
3.8 Gb |
(http)(custom) |
TAR (of TXT) |
| Processed data included within Sample table |
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