|
| Status |
Public on Jul 07, 2013 |
| Title |
FFPE bladder cancer tumor tissue 19 |
| Sample type |
genomic |
| |
|
| Source name |
FFPE bladder cancer tumor tissue
|
| Organism |
Homo sapiens |
| Characteristics |
unique_patient_id: 19
sample_type: tumor
surgery_type: radical cystectomy
summarystage: invasive
tumor stage (t): 3
substage: a
tumor grade (g): 3
node (n): 2
distant mets (m): 1
visceral_metastasis: y
lymphovascular_invasion: 1
ecog_ps (eastern cooperative oncology group performance status): NA
neoadjuvant_chemo: n
adjuvant_chemo: n
metastatic_chemo: y
days_to_tumor_recurrence: 0
recurrence_status: recurrence
days_to_death: 311
vital_status: deceased
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
As per manufacturer (Affymetrix)
|
| Label |
Biotin
|
| Label protocol |
As per manufacturer (Affymetrix)
|
| |
|
| Hybridization protocol |
Hybridization was performed by Affymetrix according to the platform protocol
|
| Scan protocol |
Scanning was performed by Affymetrix
|
| Description |
X0006263_E06
at_array: a520683-00-643559-020512-4128465-91393.CEL
cg_array: a520683-00-912235-050212-4137157-87053.CEL
|
| Data processing |
Data processing was performed by Affymetrix using the NEXUS software (v.6). Tables contain the following columns as provided by Affymetrix.
CopyNumber: The measured copy number value summed over both alleles of the SNP.
Copy_A: The data in this column corresponds to the measured number of copies of the Major_Allele. Values of -1 or -0.5 are an indication of untrustworthy data. -0.5 is used as a minimum value for allelic copy values and -1 is an indication of erroneous data.
Copy_B: The measured number of copies of the Minor_Allele.
AlleleRatio: The allele ratio for the two alleles of the SNP. This ratio corresponds to copy_B/copy_A (minor /major) with the caveat that it is flipped to be copy_A/copy_B (major / minor) in cases where copy_B is significantly larger than copy_A (for the given sample). This flipping (mostly) constrains the allele ratio to the range 0 to 1, so that allele ratios can be smoothed over neighboring SNPs (after excluding homozygous cases). For example, for diploid samples the heterozygous SNPs will smooth to an allele ratio value of 1.0. Or consider another example where a sample has 3 total copies in a given region. This will produce unflipped allele ratios of approximately 0/3, 1/2, 2/1, 3/0. After flipping these values will be normalized to two cases: 0/3 & 1/2. If we then exclude the 0/3 (homozygous) cases and smooth the data across the region the allele ratio will average out to 1/2. A negative allele ratio is due to negative allele copy number. Small negative allele ratios should be treated as zero, while large negative allele ratios are clearly outliers and should be disregarded.
AllelicDifference: The Allelic Difference calculation is based on the formula: (Copy A - Copy B)/(Copy A + Copy B)
Data was segmented using the GLAD algorithm. The 'dfciMIP.glad.txt' are the segmented data (like the Level 3 data in TCGA), calculated with the GLAD algorithm: Sample ID, Chromosome, Start, End, Number of Probes in the segment, log2 copy number ratio of the segment (available on a Series records).
|
| |
|
| Submission date |
Jul 11, 2012 |
| Last update date |
Jul 07, 2013 |
| Contact name |
Markus Riester |
| E-mail(s) |
markus@jimmy.harvard.edu
|
| Organization name |
Dana-Farber Cancer Institute
|
| Department |
Biostatistics & Computational Biology
|
| Lab |
Michor
|
| Street address |
3 Blackfan Circle
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL15793 |
| Series (2) |
| GSE39280 |
DNA copy number gain at 1q23.3 is associated with poor survival in metastatic bladder cancer [Affymetrix] |
| GSE39282 |
DNA copy number gain at 1q23.3 is associated with poor survival in metastatic bladder cancer |
|
