2015-06-01 stddata__2015_04_02 regular peel-off
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GISTIC analyses were performed on copy number data from version 3.0 of the SNP pipeline on 29-May-2015. 10844 tumor samples from 33 cancer types were selected for this analysis using the stddata__2015_04_02 TCGA/GDAC tumor sample sets from FireHose. The data set has expanded by 274 patient samples since our analysis of stddata__2014_10_17 and contains two new cancer types, Thymoma (123 patients) and Testicular germ cell tumors (150 patients). Primary tumor samples were used for most cancer types with the exceptions of Cutaneous melanoma which uses metastatic tumor samples, and Acute myeloid leukemia (AML) which uses blood tumor samples. All GISTIC analyses were run using normal peak arbitration (without arm-level peel-off). The minimum number of samples required for a GISTIC analysis was lowered from 40 to 36 to allow an independent analysis of the Cholangiocarcinoma tumor type. These analyses were published to the copy number portal on 2015-Jun-01.
Tumorscape 1.2.1 was run with the following GISTIC parameters:
| Parameter | Value |
|---|
| core GISTIC version | 2.0.22 | | 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 | 0.95 | | cap | 1.5 | | gene-GISTIC | true | | arm-level peel-off | false | | significance threshold | 0.25 | | join segment size | 8 | | X chromosome removed | false | | maximum segments/sample | 2000 | | minimum samples/disease | 35 |
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2015-06-01 stddata__2015_04_02 arm-level peel-off
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GISTIC analyses were performed on copy number data from version 3.0 of the SNP pipeline on 29-May-2015. 10844 tumor samples from 33 cancer types were selected for this analysis using the stddata__2015_04_02 TCGA/GDAC tumor sample sets from FireHose. The data set has expanded by 274 patient samples since our analysis of stddata__2014_10_17 and contains two new cancer types, Thymoma (123 patients) and Testicular germ cell tumors (150 patients). Primary tumor samples were used for most cancer types with the exceptions of Cutaneous melanoma which uses metastatic tumor samples, and Acute myeloid leukemia (AML) which uses blood tumor samples. All GISTIC analyses were run using arm-level peel-off for peak arbitration. The minimum number of samples required for a GISTIC analysis was lowered from 40 to 36 to allow an independent analysis of the Cholangiocarcinoma tumor type. These analyses were published to the copy number portal on 2015-Jun-01.
Tumorscape 1.2.1 was run with the following GISTIC parameters:
| Parameter | Value |
|---|
| core GISTIC version | 2.0.22 | | 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 | 0.95 | | cap | 1.5 | | gene-GISTIC | true | | arm-level peel-off | true | | significance threshold | 0.25 | | join segment size | 8 | | X chromosome removed | false | | maximum segments/sample | 2000 | | minimum samples/disease | 35 |
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2013-08-16 TCGA Pan-Cancer data set
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On 2013-08-16 GISTIC analyses were performed on samples from the Pan-Cancer SNP 6.0 copy number data set ("freeze 4.5") defined by the Pan-Cancer consortium. This data set includes TCGA cancer types whch are represented by a large number of samples. We restricted our analysis to 4934 primary tumor samples which passed level three quality control: bladder cancer (136), breast cancer (880), colorectal adenocarcinomas (585), glioblastoma multiforme (580), head and neck squamous cell cancer (310), kidney clear cell carcinoma (497), acute myeloid leukemia (200), lung adenocarcinoma (357), lung squamous cell carcimoma (344), ovarian serous carcinoma (563), and uterine endometrial carcinoma (496). We used a version of GISTIC that corrects for the dampening of copy number signal by contaminating normal cells using the ABSOLUTE purity estimates for each sample. These results were made available on the TCGA Copy Number Portal 2013-09-05. The differences from the 2013-07-01 TCGA Pan-Cancer results are: (1) broad length cutoff 0.5 (instead of 0.7) was used for all GISTIC analyses; (2) arm-level peel-off was not used for the pooled "all_cancers" analysis.
Tumorscape 1.1.2-tcga was run with the following GISTIC parameters:
| Parameter | Value |
|---|
| core GISTIC version | 2.0.18 | | reference genome build | hg19 | | amplification threshold | 0.3 | | deletion threshold | 0.3 | | high-level amplification threshold | 2.4 | | high-level deletion threshold | 1.0 | | broad length cutoff | 0.50 | | peak confidence level | 0.95 | | cap | 1.5 | | gene-GISTIC | true | | arm-level peel-off | for each cancer type, but not for the pooled analysis | | significance threshold | 0.25 | | join segment size | 4 | | X chromosome removed | false | | maximum segments/sample | 2500 | | minimum samples/disease | 40 |
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2011-02-01 Tumorscape
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We performed GISTIC analyses on processed copy number measurements obtained with the Affymetrix 250K Sty array accross 3,131 cancer samples, including 2,520 tissue specimens, 541 cell lines and 70 melanome short-term cultures. In addition to analyzing the entire data set, we performed individual anaylses on several subsets representing a tissue type or a larger class of cancer.
Tumorscape 0.2 was run with the following GISTIC parameters:
| Parameter | Value |
|---|
| core GISTIC version | 2.0 | | 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 | 0.95 | | cap | 1.5 | | gene-GISTIC | true | | arm-level peel-off | false | | significance threshold | 0.25 | | join segment size | 8 | | X chromosome removed | false | | maximum segments/sample | 2000 | | minimum samples/disease | 40 |
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2014-11-03 stddata__2014_10_17
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GISTIC analyses were performed on copy number data from version 3.0 of the SNP pipeline on 22-Oct-2014. 10570 tumor samples from 31 cancer types were selected for this analysis using the stddata__2014_10_17 TCGA/GDAC tumor sample sets from FireHose. The data set has expanded by 908 patients since our analysis of stddata__2014_09_02 and contains two new cancer types, Cholangiocarcinoma (36 patients) and Uveal melanoma (80 patients). Primary tumor samples were used for most cancer types with the exceptions of Cutaneous melanoma which uses metastatic tumor samples, and Acute myeloid leukemia (AML) which uses blood tumor samples. The pan-cancer "all_cancers" data set was analyzed without using arm-level peel-off in peak arbitration; the cancer type-specific analyses use arm-level peel-off. These analyses were published to the copy number portal on 2014-Nov-03.
Tumorscape 1.2.0 was run with the following GISTIC parameters:
| Parameter | Value |
|---|
| core GISTIC version | 2.0.22 | | 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 | 0.95 | | cap | 1.5 | | gene-GISTIC | true | | arm-level peel-off | true | | significance threshold | 0.25 | | join segment size | 8 | | X chromosome removed | false | | maximum segments/sample | 2000 | | minimum samples/disease | 40 |
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2014-09-08 stddata__2014_09_02
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GISTIC analyses were performed on copy number data from version 3.0 of the SNP pipeline on 04-Sep-2014. 9662 tumor samples from 29 cancer types were selected for this analysis using the stddata__2014_09_02 TCGA/GDAC tumor sample sets from FireHose. The data set has expanded by 441 patients since our analysis of stddata__2014_06_14. Primary tumor samples were used for most cancer types with the exceptions of Cutaneous melanoma which uses metastatic tumor samples, and Acute myeloid leukemia (AML) which uses blood tumor samples. The pan-cancer "all_cancers" data set was analyzed without using arm-level peel-off in peak arbitration; the subsidiary analyses continue to use arm-level peel-off. These analyses were published to the copy number portal on 2014-Sep-09.
Tumorscape 1.2.0 was run with the following GISTIC parameters:
| Parameter | Value |
|---|
| core GISTIC version | 2.0.22 | | 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 | 0.95 | | cap | 1.5 | | gene-GISTIC | true | | arm-level peel-off | true (false for all_cancers) | | significance threshold | 0.25 | | join segment size | 8 | | X chromosome removed | false | | maximum segments/sample | 2000 | | minimum samples/disease | 40 |
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2014-07-08 stddata__2014_06_14
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GISTIC analyses were performed on copy number data from version 3.0 of the SNP pipeline on 30-Jun-2014. 9221 tumor samples from 29 cancer types were selected for this analysis using the stddata__2014_06_14 TCGA/GDAC tumor sample sets from FireHose. The data set has expanded by 180 patients since our analysis of stddata__2014_04_16. Primary tumor samples were used for most cancer types with the exceptions of Cutaneous melanoma which uses metastatic tumor samples, and Acute myeloid leukemia (AML) which uses blood tumor samples. New for this analysis, the pan-cancer "all_cancers" data set was analyzed without using arm-level peel-off in peak arbitration; the subsidiary analyses contunue to use arm-level peel-off. Also introduced in this anaysis is the use of a supplementary germline exclusion CNV list contructed from the analysis of copy number events in 7500 TCGA normals. This strategy, combined with increasing the join segment size from 4 to 8, mitgates the effects of small background events in diseases have fewer SCNAs. These analyses were published to the copy number portal on 2014-Jul-08.
Tumorscape 1.2.0 was run with the following GISTIC parameters:
| Parameter | Value |
|---|
| core GISTIC version | 2.0.21 | | 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 | 0.95 | | cap | 1.5 | | gene-GISTIC | true | | arm-level peel-off | true (except all_cancers) | | significance threshold | 0.25 | | join segment size | 8 | | X chromosome removed | false | | maximum segments/sample | 2000 | | minimum samples/disease | 40 |
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2014-04-28 stddata__2014_04_16
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GISTIC analyses were performed on copy number data from version 3.0 of the SNP pipeline on 19-Apr-2014. 9041 tumor samples from 29 cancer types were selected for this analysis using the stddata__2014_04_16 TCGA/GDAC tumor sample sets from FireHose. The data set has expanded by 378 patients since our analysis of stddata__2014_02_15. We include for the first time the cancer type Pheochromocytoma and Paraganglioma represented by 159 patients. Primary tumor samples were used for most cancer types with the exceptions of Cutaneous melanoma which uses metastatic tumor samples, and Acute myeloid leukemia (AML) which uses blood tumor samples. The GISTIC parameters for this run have been changed: the broad length cut-off is now 0.5 (was 0.7) and the confidence window is now 0.95 (was 0.99) These analyses were published to the copy number portal on 2014-Apr-28.
Tumorscape 1.1.2-tcga was run with the following GISTIC parameters:
| Parameter | Value |
|---|
| core GISTIC version | 2.0.21 | | 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 | 0.95 | | 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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2014-02-21 stddata__2014_02_15
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GISTIC analyses were performed on copy number data from version 3.0 of the SNP pipeline on 20-Feb-2014. 8663 tumor samples from 28 cancer types were selected for this analysis using the stddata__2014_02_15 TCGA/GDAC tumor sample sets from FireHose. The data set has expanded by 486 patients since the analysis of stddata__2013_12_10. Mesothelioma is represented for the first time with samples from 37 patients (not quite enough for an independent GISTIC analysis). Notably, Low-grade glioma has added data from 167 patients bringing its total representation to 463, and Head and neck squamous cell carcinoma has added 57 for a total of 509. Primary tumor samples were used for most cancer types, with the exceptions of Cutaneous melanoma which uses metastatic tumor samples, and Acute myeloid leukemia (AML) which uses blood tumor samples. These data were published to the portal 2014-Feb-21.
Tumorscape 1.1.2-tcga was run with the following GISTIC parameters:
| Parameter | Value |
|---|
| core GISTIC version | 2.0.21 | | 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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2013-12-23 stddata__2013_12_10
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GISTIC analyses were performed on copy number data from version 3.0 of the SNP pipeline on 20-Dec-2013. 8177 tumor samples from 27 cancer types were selected for this analysis using the stddata__2013_12_10 TCGA/GDAC primary tumor sample sets from FireHose, with the exceptions of Cutaneous melanoma which uses a metastatic tumor sample set, and Acute myeloid leukemia (AML) which uses blood tumors. These data were published to the portal 2013-Dec-23.
Tumorscape 1.1.2-tcga was run with the following GISTIC parameters:
| Parameter | Value |
|---|
| core GISTIC version | 2.0.20 | | 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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2013-10-28 stddata__2013_10_10
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GISTIC analyses were performed on copy number data from version 3.0 of the SNP pipeline on 25-Oct-2013. 8055 tumor samples across 27 cancer types were selected for this analysis using the stddata__2013_10_10 TCGA/GDAC primary tumor sample sets from FireHose, with the exceptions of Cutaneous melanoma which uses a metastatic tumor sample set, and Acute myeloid leukemia (AML) which uses blood tumors. Adrenocortical carcinoma (ACC), Cervical squamous cell carcinoma (CESC), Pancreatic adenocarcinoma (PAAD) and Uterine Carcinosarcoma (UCS) are newly added disease types since the last release (stddata__2013__07_15). These data were published to the portal 2013-Oct-28.
Tumorscape 1.1.2-tcga was run with the following GISTIC parameters:
| Parameter | Value |
|---|
| core GISTIC version | 2.0.19 | | 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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2013-07-27 stddata__2013_07_15
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GISTIC analyses were performed on copy number data from version 3.0 of the SNP pipeline on 25-Jul-2013. 7219 tumor samples across 23 cancer types were selected for this analysis using the stddata__2013_07_15 TCGA/GDAC primary tumor sample sets from FireHose, with the exceptions of Cutaneous melanoma which used a metastatic tumor sample set, and Acute myeloid leukemia (AML) which used blood tumors. AML is a newly added disease type since the last release (stddata__2013__02_03). These data were published to the portal 2013-Jul-29.
Tumorscape 1.1.2-tcga was run with the following GISTIC parameters:
| Parameter | Value |
|---|
| core GISTIC version | 2.0.18 | | 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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2013-07-01 TCGA Pan-Cancer data set
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On 2013-03-19 GISTIC analyses were performed on samples from the Pan-Cancer SNP 6.0 copy number data set ("freeze 4.5") defined by the Pan-Cancer consortium. This data set includes TCGA cancer types whch are represented by a large number of samples. We restricted our analysis to 4934 primary tumor samples which passed level three quality control: bladder cancer (136), breast cancer (880), colorectal adenocarcinomas (585), glioblastoma multiforme (580), head and neck squamous cell cancer (310), kidney clear cell carcinoma (497), acute myeloid leukemia (200), lung adenocarcinoma (357), lung squamous cell carcimoma (344), ovarian serous carcinoma (563), and uterine and endometrial carcinoma (496). We used a version of GISTIC that corrects for the dampening of copy number signal by contaminating normal cells using the ABSOLUTE purity estimates for each sample. These data were made available on the TCGA Copy Number Portal 2013-07-31.
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 | 2.4 | | high-level deletion threshold | 1.0 | | broad length cutoff | 0.70 | | peak confidence level | 0.95 | | 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 | 2500 | | minimum samples/disease | 40 |
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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 |
|---|
| 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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