|
| Status |
Public on Dec 31, 2012 |
| Title |
YP00-13507 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Mucoepidermoid carcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
fusion status: Neg
grade: High Grade
|
| Treatment protocol |
Fresh frozen tumor material from 15 MECs and paraffin embedded tumor material from 13 MECs were retrieved from the department of Pathology at Haartman Institute in Helsinki, the department of pathology at Sahlgrenska University Hospital in Gothenburg and the department of Oral Pathology at Guy's Hospital in London. The tumors were classified as low grade and high grade according to the histologic classification of salivary gland tumours by WHO.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated from FFPE tissue using the standard phenol-chloroform method and from fresh frozen tissue using the QIAamp DNA Mini Kit (Qiagen GmbH, Hilden, Germany) according to the manufacturer instructions.
|
| Label |
Cy5
|
| Label protocol |
3.0 µg of genomic tumor DNA and sex-matched reference DNA (pooled peripheral blood cells from 5 normal female and male genomes) were digested with AluI and Rsa1 (Promega, Madisaon, WI) and labeled with Cy3-dUTP and Cy5-dUTP (Perkin-Elmer Life and Analytical Sciences Inc., Wellesley, MA, USA).
|
| |
|
| Channel 2 |
| Source name |
Normal tissue
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: reference
gender: F
|
| Treatment protocol |
Fresh frozen tumor material from 15 MECs and paraffin embedded tumor material from 13 MECs were retrieved from the department of Pathology at Haartman Institute in Helsinki, the department of pathology at Sahlgrenska University Hospital in Gothenburg and the department of Oral Pathology at Guy's Hospital in London. The tumors were classified as low grade and high grade according to the histologic classification of salivary gland tumours by WHO.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated from FFPE tissue using the standard phenol-chloroform method and from fresh frozen tissue using the QIAamp DNA Mini Kit (Qiagen GmbH, Hilden, Germany) according to the manufacturer instructions.
|
| Label |
Cy3
|
| Label protocol |
3.0 µg of genomic tumor DNA and sex-matched reference DNA (pooled peripheral blood cells from 5 normal female and male genomes) were digested with AluI and Rsa1 (Promega, Madisaon, WI) and labeled with Cy3-dUTP and Cy5-dUTP (Perkin-Elmer Life and Analytical Sciences Inc., Wellesley, MA, USA).
|
| |
|
| |
| Hybridization protocol |
Oligoarray control targets (Cot-1 DNA and Blocking agent) and hybridization buffer (Agilent oligo aCGH/ChIP-on-Chip Hybridization Kit) were added, the samples were denatured and applied to microarrays (Agilent Human Genome CGH Microarray 44K and 244K 60-mer oligonucleotide arrays) as recommended by the manufacturer. The arrays were enclosed in a rotating hybridization oven at 65°C for 40 h. After hybridization, the slides were sequentially washed and dried.
|
| Scan protocol |
The arrays were scanned on an Agilent Microarray Confocal Scanner (G2567AA) and the images were quantified with Agilent Feature Extraction Software (v.7.5) using the intensity-dependent linear normalization method.
|
| Data processing |
Data analysis was carried out using Nexus Copy Number software v.4.1 (BioDiscovery Inc., El Segundo, CA, USA), which uses the Rank segmentation algorithm to define non-random regions of CNAs across the genome. Sex chromosomes were excluded from the analysis. The significance threshold for segmentation was set to p=1.0E-7 and the thresholds of log2 ratio values for gain and loss were 0.4 and −0.3, respectively; the thresholds for high copy number gain/amplification and homozygous deletion were 1.0 and −1.0, respectively.
|
| |
|
| Submission date |
Mar 05, 2012 |
| Last update date |
Dec 31, 2012 |
| Contact name |
Marta Persson |
| E-mail(s) |
[email protected]
|
| Organization name |
Sahlgrenska Cancer Center
|
| Street address |
Box 425
|
| City |
Gotenburg |
| ZIP/Postal code |
405 90 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL2879 |
| Series (1) |
| GSE36282 |
Low- and High-Grade Mucoepidermoid Carcinomas have different genomic profiles and CRTC1-MAML2 Fusion Gene Status |
|
