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| Status |
Public on Mar 09, 2019 |
| Title |
FUSCCTNBC102_FrozenPrimaryTumorTissue |
| Sample type |
genomic |
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| Source name |
Patient FUSCCTNBC102 fresh frozen primary tumor tissue
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| Organism |
Homo sapiens |
| Characteristics |
patient id: FUSCCTNBC102
tissue: Primary triple negative breast cancer
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Tumor tissues were macrodissected to avoid the influence of stromal tissues (< 10% stromal). The percentage of tumor cells was confirmed to be 50% or more in all the breast cancer specimens. Total DNA was isolated from 485 fresh frozen TNBC samples using TGuide M24 (Tiangen, Beijing, China). The purity and quantity of total DNA were estimated by measuring absorbance at 260 nm (A260) and 280 nm (A280) using a NanoDrop 2000 spectrophotometer (Thermo Scientific, Wilmington, DE, USA). The extracted DNA was considered pure and suitable for future experiments when the A260/A280 ratio was within 1.6-1.9
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| Label |
biotin
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| Label protocol |
As per manufacturer (Affymetrix)
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| Hybridization protocol |
Genome-wide copy number analysis was performed using an OncoScan CNV Assay Kit (Affymetrix, Santa Clara, CA, USA) according to the manufacturer’s recommendations. Briefly, a total of 80 ng of DNA from each tumor sample was processed. Molecular inversion probes (MIPs) were added to the sample DNA and annealed at 58°C overnight. The annealed DNA was divided into two equal parts and incubated with AT or GC gap-fill master mixes for ligation. Then, the unincorporated, non-circularized MIPs and the remains of the genomic template were removed through exonuclease treatment. The circularized MIPs were linearized with a cleavage enzyme, and the first PCR amplification was performed, followed by a second amplification. The amplified products were digested with HaeIII, and the small fragments containing the specific SNP genotype were hybridized onto arrays.
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| Scan protocol |
The arrays were washed and stained using GeneChip Fluidics Station 450 (Affymetrix, Inc.) and scanned in GeneChip Scanner 3000 7G (Affymetrix, Inc.). The fluorescence of clusters was measured to generate a DAT file. Cluster intensity values were automatically calculated using a built-in algorithm from DAT files using GeneChip Command Console software (Affymetrix, Inc.), and a CEL file was generated.
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| Description |
Copy number profiling of patient FUSCCTNBC102, fresh frozen primary tumor tissue
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| Data processing |
An analysis of Affymetrix OncoScan CNV SNP probe assays was performed with OncoScan Console (v1.3) software (Affymetrix, Inc.). BioDiscovery Nexus ExpressTM for OncoScan 3 software was used to assess recurrent germline/potential false-positive calls by using a reference cohort of DNA from 23 white blood cell samples (regions altered in 12 or more patients were defined as recurrent germline/potential false-positive calls which would be removed later). Probe-level output from OncoScan Console were analyzed using ASCAT (v2.4.2)(Van Loo et al., 2010) to obtain segmented copy number calls, estimated tumor ploidy as well as estimated tumor purity.
Primary data description: Output (probe level) of OncoScan Console (v1.3): Log2Ratio, WeightedLog2Ratio, AllelicDifference, NormalDiploid, BAF (B allele frequency)
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| Submission date |
Aug 14, 2018 |
| Last update date |
Mar 09, 2019 |
| Contact name |
Zhi-Ming Shao |
| E-mail(s) |
09301010134@fudan.edu.cn
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| Organization name |
Fudan University Shanghai Cancer Center
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| Street address |
270 Dong An Road, Build 7, RM304
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| City |
Shanghai |
| ZIP/Postal code |
200032 |
| Country |
China |
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| Platform ID |
GPL21558 |
| Series (1) |
| GSE118527 |
Affymetrix SNP array data (Oncoscan CNV) for Fudan University Shanghai Cancer Center Triple Negative Breast Cancer (FUSCCTNBC) project |
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| Supplementary file |
Size |
Download |
File type/resource |
| GSM3331684_FUSCCTNBC102_A.CEL.gz |
4.6 Mb |
(ftp)(http) |
CEL |
| GSM3331684_FUSCCTNBC102_C.CEL.gz |
4.7 Mb |
(ftp)(http) |
CEL |
| GSM3331684_Processed_FUSCCTNBC102_OncoScan.ProbeLevel.txt.gz |
5.4 Mb |
(ftp)(http) |
TXT |
| Processed data provided as supplementary file |
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