Browse Gistic Analyses

2014-02-21 stddata__2014_02_15

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:

ParameterValue
core GISTIC version2.0.21
reference genome buildhg19
amplification threshold0.1
deletion threshold0.1
high-level amplification threshold1.0
high-level deletion threshold1.0
broad length cutoff0.70
peak confidence level0.99
cap1.5
gene-GISTICtrue
arm-level peel-offtrue
significance threshold0.25
join segment size4
X chromosome removedfalse
maximum segments/sample2000
minimum samples/disease40

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2013-12-23 stddata__2013_12_10

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:

ParameterValue
core GISTIC version2.0.20
reference genome buildhg19
amplification threshold0.1
deletion threshold0.1
high-level amplification threshold1.0
high-level deletion threshold1.0
broad length cutoff0.70
peak confidence level0.99
cap1.5
gene-GISTICtrue
arm-level peel-offtrue
significance threshold0.25
join segment size4
X chromosome removedfalse
maximum segments/sample2000
minimum samples/disease40

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2013-10-28 stddata__2013_10_10

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:

ParameterValue
core GISTIC version2.0.19
reference genome buildhg19
amplification threshold0.1
deletion threshold0.1
high-level amplification threshold1.0
high-level deletion threshold1.0
broad length cutoff0.70
peak confidence level0.99
cap1.5
gene-GISTICtrue
arm-level peel-offtrue
significance threshold0.25
join segment size4
X chromosome removedfalse
maximum segments/sample2000
minimum samples/disease40

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2013-08-16 TCGA Pan-Cancer data set

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:

ParameterValue
core GISTIC version2.0.18
reference genome buildhg19
amplification threshold0.3
deletion threshold0.3
high-level amplification threshold2.4
high-level deletion threshold1.0
broad length cutoff0.50
peak confidence level0.95
cap1.5
gene-GISTICtrue
arm-level peel-offfor each cancer type, but not for the pooled analysis
significance threshold0.25
join segment size4
X chromosome removedfalse
maximum segments/sample2500
minimum samples/disease40

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2013-07-27 stddata__2013_07_15

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:

ParameterValue
core GISTIC version2.0.18
reference genome buildhg19
amplification threshold0.1
deletion threshold0.1
high-level amplification threshold1.0
high-level deletion threshold1.0
broad length cutoff0.70
peak confidence level0.99
cap1.5
gene-GISTICtrue
arm-level peel-offtrue
significance threshold0.25
join segment size4
X chromosome removedfalse
maximum segments/sample2000
minimum samples/disease40

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2013-07-01 TCGA Pan-Cancer data set

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:

ParameterValue
core GISTIC version2.0.17a
reference genome buildhg19
amplification threshold0.3
deletion threshold0.3
high-level amplification threshold2.4
high-level deletion threshold1.0
broad length cutoff0.70
peak confidence level0.95
cap1.5
gene-GISTICtrue
arm-level peel-offtrue
significance threshold0.25
join segment size4
X chromosome removedfalse
maximum segments/sample2500
minimum samples/disease40

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2013-02-21 stddata__2013_02_03

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:

ParameterValue
core GISTIC version2.0.17a
reference genome buildhg19
amplification threshold0.1
deletion threshold0.1
high-level amplification threshold1.0
high-level deletion threshold1.0
broad length cutoff0.70
peak confidence level0.99
cap1.5
gene-GISTICtrue
arm-level peel-offtrue
significance threshold0.25
join segment size4
X chromosome removedfalse
maximum segments/sample2000
minimum samples/disease40

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2013-01-10 stddata__2012_12_21

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:

ParameterValue
core GISTIC version2.0.17a
reference genome buildhg19
amplification threshold0.1
deletion threshold0.1
high-level amplification threshold1.0
high-level deletion threshold1.0
broad length cutoff0.70
peak confidence level0.99
cap1.5
gene-GISTICtrue
arm-level peel-offtrue
significance threshold0.25
join segment size4
X chromosome removedfalse
maximum segments/sample2000
minimum samples/disease40

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2012-11-20 pipeline 3.0 data

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:

ParameterValue
core GISTIC version2.0.17a
reference genome buildhg19
amplification threshold0.1
deletion threshold0.1
high-level amplification threshold1.0
high-level deletion threshold1.0
broad length cutoff0.50
peak confidence level0.99
cap2.0
gene-GISTICtrue
arm-level peel-offtrue
significance threshold0.25
join segment size10
X chromosome removedfalse
maximum segments/sample1500
minimum samples/disease40

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2012-10-22 SNP pipeline 3.0 data

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:

ParameterValue
core GISTIC version2.0.17a
reference genome buildhg19
amplification threshold0.1
deletion threshold0.1
high-level amplification threshold1.0
high-level deletion threshold1.0
broad length cutoff0.50
peak confidence level0.99
cap2.0
gene-GISTICtrue
arm-level peel-offtrue
significance threshold0.25
join segment size10
X chromosome removedfalse
maximum segments/sample1500
minimum samples/disease40

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2012-04-16 SNP pipeline 2.1 data

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:

ParameterValue
core GISTIC version2.0.17a
reference genome buildhg19
amplification threshold0.3
deletion threshold0.3
high-level amplification threshold1.0
high-level deletion threshold1.0
broad length cutoff0.50
peak confidence level0.99
cap2.0
gene-GISTICtrue
arm-level peel-offtrue
significance threshold0.25
join segment size10
X chromosome removedtrue
maximum segments/sample1500
minimum samples/disease40

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2011-07-13 SNP pipeline 1.0 data

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:

ParameterValue
core GISTIC version2.0.6
reference genome buildhg18
amplification threshold0.3
deletion threshold0.3
high-level amplification threshold1.0
high-level deletion threshold1.0
broad length cutoff0.50
peak confidence level0.99
cap2.0
gene-GISTICtrue
arm-level peel-offtrue
significance threshold0.25
join segment size10
X chromosome removedtrue
maximum segments/sample1500
minimum samples/disease40

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2011-04-27 SNP pipeline 1.0 data

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:

ParameterValue
core GISTIC version2.00.18546
reference genome buildhg18
amplification threshold0.3
deletion threshold0.3
high-level amplification threshold1.0
high-level deletion threshold1.0
broad length cutoff0.50
peak confidence level0.99
cap2.0
gene-GISTICtrue
arm-level peel-offfalse
significance threshold0.25
join segment size10
X chromosome removedtrue
maximum segments/sample1500
minimum samples/disease40

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2011-02-10 SNP pipeline 1.0 data

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:

ParameterValue
core GISTIC version2.00.17554
reference genome buildhg18
amplification threshold0.1
deletion threshold0.1
high-level amplification threshold1.0
high-level deletion threshold1.0
broad length cutoff0.50
peak confidence level0.99
cap2.0
gene-GISTICtrue
arm-level peel-offfalse
significance threshold0.25
join segment size10
X chromosome removedtrue
maximum segments/sample1500
minimum samples/disease40

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2010-11-17 SNP pipeline 1.0 data

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:

ParameterValue
core GISTIC version2.00.14460
reference genome buildhg18
amplification threshold0.1
deletion threshold0.1
high-level amplification threshold1.0
high-level deletion threshold1.0
broad length cutoff0.50
peak confidence level0.99
cap2.0
gene-GISTICtrue
arm-level peel-offfalse
significance threshold0.25
join segment size10
X chromosome removedtrue
maximum segments/sample2600
minimum samples/disease40

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