|
| Status |
Public on Nov 03, 2013 |
| Title |
Cholangio non-malignant sample 29150572N SNP6 |
| Sample type |
genomic |
| |
|
| Source name |
Cholangio non-malignant sample 29150572N
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: cholangio non-malignant tissue
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from patient specimens using Qiagen Blood and Cell Culture DNA kit (Qiagen, CA). Genomic DNA yield and quality were determined by Nanodrop ND1000 spectrophotometer (Thermo Scientific, MA) and further visually inspected by agarose gel electrophoresis.
|
| Label |
Biotin
|
| Label protocol |
As per manufacturer (Affymetrix)
|
| |
|
| Hybridization protocol |
DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.
|
| Scan protocol |
The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.
|
| Description |
Hybridized to SNP6 array
|
| Data processing |
The data in each tumor raw CEL file was normalized using CRMA-v2 and TumorBoost, and then analyzed with version 2 of the ASCAT algorithm which simultaneously models the aberrant cell fraction, regions of copy number changes and allele counts. The matched non-malignant CEL file is used as a reference in this processing. For each heterozygous position found in the normal tissue, the minor allele frequency (BAF) and the log of the ratio of the total signal intensity in the tumor and matched non-tumor sample (Log R) were calculated for the tumor tissue. ASCAT determined the aberrant cell fraction and mean genomic ploidy that best fits these points.
LRR' = normalized logR value; 'normalized_BAF' = normalized B-allele frequency (after TumorBoost); 'nA' = copy number of allele A; 'nB' = copy number of allele B
**For the non-malignant tissue only the raw BAF value is provided, as this is the only information necessary for processing the tumor using TumorBoost and ASCAT.
|
| |
|
| Submission date |
Aug 08, 2013 |
| Last update date |
Nov 03, 2013 |
| Contact name |
Ioana Cutcutache |
| E-mail(s) |
ioana.cutcutache@duke-nus.edu.sg
|
| Organization name |
Duke-NUS
|
| Department |
Centre for Computational Biology
|
| Lab |
Steve Rozen lab
|
| Street address |
8 College Rd
|
| City |
Singapore |
| State/province |
Singapore |
| ZIP/Postal code |
169857 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL6801 |
| Series (1) |
| GSE49666 |
Distinct Mutational Patterns of Infection and Non-Infection-Related Bile Duct Cancers Revealed by Exome Sequencing |
|
