|
| Status |
Public on Sep 24, 2022 |
| Title |
M432 |
| Sample type |
genomic |
| |
|
| Source name |
pediatric liver cancer
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Tumor FFPE
ctnnb1 mutation: p.G34R
tert promoter mutation: WT
age: 1.6
Sex: F
stage (pretext): 3
status: N/A
histology: HB FPA
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
25-50 mg fresh frozen tissue or FFPE tumor blocks cut in 10-20 micron sections (5-10 slides per sample) and one H&E slide are utilized for DNA extraction. These specimens were prepared for genomic DNA extraction from tumor cell-rich areas, which were identified by a surgical pathologist (Dr. Terrada, Dr. Peters). DNA was isolated using the QIAamp DNA FFPE Tissue Kit (Qiagen) or QIAamp DNA Mini Kit for frozen tissue (Qiagen).
|
| Label |
biotin
|
| Label protocol |
standard Affymetrix protocol
|
| |
|
| Hybridization protocol |
The OncoScan platform uses molecular inversion probe (MIP) technology, optimized for FFPE samples, to query over 220,000 SNPs at carefully selected genomic locations, evenly distributed across the genome and with increased density within approximately 900 cancer or cancer related genes. Molecular inversion probes were annealed to the DNA overnight at 58°C. Each sample was then divided into 2 reactions and gap fill and ligation was performed at 58°C with either A and T deoxynucleotides in one reaction or G and C in the second reaction. Circular probe DNA was then linearized by cleavage at site #1 at 37°C, followed by two consecutive PCR amplifications performed on an ABI 9700 Gold-block thermal cycler. Digestion with restriction enzyme HaeIII at cleavage site #2 at 37°C was then performed. The digested products along with biotinylated oligos were loaded onto the arrays and hybridized overnight at 49°C and 60 rpm. The arrays were then washed, stained and scanned.
|
| Scan protocol |
Arrays were scanned using the GeneChip® Scanner 3000 7G (Affymetrix).
|
| Data processing |
CEL files containing the raw array data were analyzed using the OncoScan Console 1.3 software to create OSCHP files containing copy number calls. The data were aligned to the National Center for Biotechnology Information (NCBI) human build GRCh37/hg19 assembly and viewed using the Chromosome Analysis Suite 3.1 (ChAS 3.1) and the OncoScan Nexus Copy Number 7.5 software.
Upon review of the copy number data, if necessary, re-centering of the copy number calls was done using the TuScan algorithm in the ChAS 3.1 software.
|
| |
|
| Submission date |
Sep 23, 2022 |
| Last update date |
Sep 24, 2022 |
| Contact name |
Pavel Sumazin |
| E-mail(s) |
pavel.sumazin@bcm.edu
|
| Phone |
+1 832-824-4539
|
| Organization name |
Baylor College of Medicine
|
| Department |
Pediatric
|
| Lab |
Sumazin Lab
|
| Street address |
1102 Bates St
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL21558 |
| Series (1) |
| GSE214074 |
Hepatoblastomas with carcinoma features represent a biological spectrum of aggressive neoplasms in children and young adults II |
|
