2013-02-21 stddata__2013_02_03
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GISTIC analyses were performed on copy number data from version 3.0 of the SNP pipeline on 04-Jan-2013. 6547 tumor samples across 22 cancer types were selected for this analysis using the stddata__2013_02_03 TCGA/GDAC primary tumor sample sets from FireHose, with the exception of Cutaneous melanoma which used a metastatic tumor sample set. Pancreatic adenocarcinoma samples were omitted from this update. These data were published to the portal 2013-Feb-21.
Tumorscape 1.1.2-tcga was run with the following GISTIC parameters:
| Parameter | Value |
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| core GISTIC version | 2.0.17a | | reference genome build | hg19 | | amplification threshold | 0.1 | | deletion threshold | 0.1 | | high-level amplification threshold | 1.0 | | high-level deletion threshold | 1.0 | | broad length cutoff | 0.70 | | peak confidence level | 0.99 | | cap | 1.5 | | gene-GISTIC | true | | arm-level peel-off | true | | significance threshold | 0.25 | | join segment size | 4 | | X chromosome removed | false | | maximum segments/sample | 2000 | | minimum samples/disease | 40 |
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2013-01-10 stddata__2012_12_21
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GISTIC analyses were performed on copy number data from version 3.0 of the SNP pipeline on 04-Jan-2013. 6327 tumor samples across 22 cancer types were selected for this analysis using the stddata__2012_12_21 TCGA/GDAC primary tumor sample sets from FireHose, with the exception of Cutaneous melanoma which used a metastatic tumor sample set. Pancreatic adenocarcinoma samples were omitted from this update. The parameters used for the GISTIC analyses were modified to match those used for FireHose GISTIC analyses; specifically the broad length cutoff was raised from 0.5 to 0.7, the cap was lowered from 2.0 to 1.5, and the join segment size was lowered from 10 to 4. These data were published to the portal 2013-Jan-10.
Tumorscape 1.1.2-tcga was run with the following GISTIC parameters:
| Parameter | Value |
|---|
| core GISTIC version | 2.0.17a | | reference genome build | hg19 | | amplification threshold | 0.1 | | deletion threshold | 0.1 | | high-level amplification threshold | 1.0 | | high-level deletion threshold | 1.0 | | broad length cutoff | 0.70 | | peak confidence level | 0.99 | | cap | 1.5 | | gene-GISTIC | true | | arm-level peel-off | true | | significance threshold | 0.25 | | join segment size | 4 | | X chromosome removed | false | | maximum segments/sample | 2000 | | minimum samples/disease | 40 |
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2012-11-20 pipeline 3.0 data
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These analyses were performed on copy number data from version 3.0 of the SNP pipeline on 19-Nov-2012. 6161 tumor samples across 23 cancer types were selected for this analysis using the stddata__2012_10_04 TCGA/GDAC individual set from FireHose. The data published here on 2012-11-20 were reanalyzed on 2012-12-07 with tumorscape version 1.1.1-tcga to make a correction to the gene deletion frequencies.
Tumorscape 1.1.2-tcga was run with the following GISTIC parameters:
| Parameter | Value |
|---|
| core GISTIC version | 2.0.17a | | reference genome build | hg19 | | amplification threshold | 0.1 | | deletion threshold | 0.1 | | high-level amplification threshold | 1.0 | | high-level deletion threshold | 1.0 | | broad length cutoff | 0.50 | | peak confidence level | 0.99 | | cap | 2.0 | | gene-GISTIC | true | | arm-level peel-off | true | | significance threshold | 0.25 | | join segment size | 10 | | X chromosome removed | false | | maximum segments/sample | 1500 | | minimum samples/disease | 40 |
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2012-10-22 SNP pipeline 3.0 data
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These analyses were performed on copy number data from version 3.0 of the SNP pipeline on 12-Oct-2012. 5793 tumor samples across 22 cancer types were selected for this analysis using the stddata__2012_08_27 TCGA/GDAC individual set from FireHose. This was the first analysis on the TCGA Copy Number Portal to include the X chromosome. The data published here on 2012-10-22 were reanalyzed on 2012-12-07 with tumorscape version 1.1.1-tcga to make a correction to the gene deletion frequencies.
Tumorscape 1.1.2-tcga was run with the following GISTIC parameters:
| Parameter | Value |
|---|
| core GISTIC version | 2.0.17a | | reference genome build | hg19 | | amplification threshold | 0.1 | | deletion threshold | 0.1 | | high-level amplification threshold | 1.0 | | high-level deletion threshold | 1.0 | | broad length cutoff | 0.50 | | peak confidence level | 0.99 | | cap | 2.0 | | gene-GISTIC | true | | arm-level peel-off | true | | significance threshold | 0.25 | | join segment size | 10 | | X chromosome removed | false | | maximum segments/sample | 1500 | | minimum samples/disease | 40 |
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2012-04-16 SNP pipeline 2.1 data
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These data were processed using version 2.1 of the SNP pipeline on 15-April-2012. 4404 samples were selected using the stddata__2012_03_21 PANCANCER individual set. This was the first Tumorscape run to use the hg19 reference genome. The data published here on 2012-06-16 were reanalyzed on 2012-12-07 with tumorscape version 1.1.1-tcga to make a correction to the gene deletion frequencies.
Tumorscape 1.1.2-tcga was run with the following GISTIC parameters:
| Parameter | Value |
|---|
| core GISTIC version | 2.0.17a | | reference genome build | hg19 | | amplification threshold | 0.3 | | deletion threshold | 0.3 | | high-level amplification threshold | 1.0 | | high-level deletion threshold | 1.0 | | broad length cutoff | 0.50 | | peak confidence level | 0.99 | | cap | 2.0 | | gene-GISTIC | true | | arm-level peel-off | true | | significance threshold | 0.25 | | join segment size | 10 | | X chromosome removed | true | | maximum segments/sample | 1500 | | minimum samples/disease | 40 |
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2011-07-13 SNP pipeline 1.0 data
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These data were processed using version 1.0 of the SNP pipeline on 13-Jul-2011. 2886 samples from 18 different cancer types were selected using the prod__2011_05_25__pancancer individual set from TCGA/GDAC FireHose (excluding 30 low-grade glioma samples). This is the first data set to use the arm-level peel-off feature of GISTIC, which helps reduce the fragmentation of amplification or deletion peaks due to chromothripsis or noise.
Tumorscape 1.0.6-tcga was run with the following GISTIC parameters:
| Parameter | Value |
|---|
| core GISTIC version | 2.0.6 | | reference genome build | hg18 | | amplification threshold | 0.3 | | deletion threshold | 0.3 | | high-level amplification threshold | 1.0 | | high-level deletion threshold | 1.0 | | broad length cutoff | 0.50 | | peak confidence level | 0.99 | | cap | 2.0 | | gene-GISTIC | true | | arm-level peel-off | true | | significance threshold | 0.25 | | join segment size | 10 | | X chromosome removed | true | | maximum segments/sample | 1500 | | minimum samples/disease | 40 |
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2011-04-27 SNP pipeline 1.0 data
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These data were processed using version 1.0 of the SNP pipeline on 14-Feb-2011. The lung, colorectal and endometrial samples were taken from the prod__2010_12_23 TCGA/GDAC individual sets in FireHose. The balance were taken from the prod__2011_01_14 TCGA/GDAC individual sets. These 1955 samples spanning 11 cancer types in this data set are identical to those of the previous data set (2011-02-10), however, the analysis and presentaton were improved. The noise thresholds for the GISTIC analysis were raised from 0.1 to 0.3 to accomodate background noise observed in the data. Several errors in the event frequency analyses, counts of cancer types, and the order of peak presentation in the 2011-02-11 data set were corrected.
Tumorscape 1.0.3-tcga was run with the following GISTIC parameters:
| Parameter | Value |
|---|
| core GISTIC version | 2.00.18546 | | reference genome build | hg18 | | amplification threshold | 0.3 | | deletion threshold | 0.3 | | high-level amplification threshold | 1.0 | | high-level deletion threshold | 1.0 | | broad length cutoff | 0.50 | | peak confidence level | 0.99 | | cap | 2.0 | | gene-GISTIC | true | | arm-level peel-off | false | | significance threshold | 0.25 | | join segment size | 10 | | X chromosome removed | true | | maximum segments/sample | 1500 | | minimum samples/disease | 40 |
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2011-02-10 SNP pipeline 1.0 data
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These data were processed using version 1.0 of the SNP pipeline on 27-Jan-2011. These 1955 samples span 11 cancer types. The lung, colorectal and endometrial samples were taken from the prod__2010_12_23 TCGA/GDAC individual sets in FireHose. The balance (ovary, breast, kidney, stomach, GBM cancer types) were taken from the prod__2011_01_14 TCGA/GDAC individual sets. The germline CNV removal list was changed from a composite drawn from several studies to a list created from variations detected within the TCGA copy number data for blood normals.
Tumorscape 1.0.1-tcga was run with the following GISTIC parameters:
| Parameter | Value |
|---|
| core GISTIC version | 2.00.17554 | | reference genome build | hg18 | | amplification threshold | 0.1 | | deletion threshold | 0.1 | | high-level amplification threshold | 1.0 | | high-level deletion threshold | 1.0 | | broad length cutoff | 0.50 | | peak confidence level | 0.99 | | cap | 2.0 | | gene-GISTIC | true | | arm-level peel-off | false | | significance threshold | 0.25 | | join segment size | 10 | | X chromosome removed | true | | maximum segments/sample | 1500 | | minimum samples/disease | 40 |
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2010-11-17 SNP pipeline 1.0 data
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The data for this pilot run of the TCGA Copy Number Portal were processed using version 1.0 of the SNP pipeline on 17-Nov-2010. The data set was created by combining the prod__2010_11_05 TCGA/GDAC individual sets for breast cancer, colon cancer, ovarian cancer and glioblastoma multiforme.
Tumorscape 1.0.0-tcga was run with the following GISTIC parameters:
| Parameter | Value |
|---|
| core GISTIC version | 2.00.14460 | | reference genome build | hg18 | | amplification threshold | 0.1 | | deletion threshold | 0.1 | | high-level amplification threshold | 1.0 | | high-level deletion threshold | 1.0 | | broad length cutoff | 0.50 | | peak confidence level | 0.99 | | cap | 2.0 | | gene-GISTIC | true | | arm-level peel-off | false | | significance threshold | 0.25 | | join segment size | 10 | | X chromosome removed | true | | maximum segments/sample | 2600 | | minimum samples/disease | 40 |
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