Genetic ancestry data for all TCGA PANCAN studies (#1880)

cBioPortal · Aug 11, 2023 · eff9f47 · eff9f47
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diff --git a/public/gbm_tcga_pan_can_atlas_2018/README.md b/public/gbm_tcga_pan_can_atlas_2018/README.md
@@ -7,4 +7,22 @@
 - File Used: `Merge_Clinical.Level_1.20160128` (clin.merged.txt) for each cancer type.
 
 **Data Transformation** 
-- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597)
+- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597)
+
+### The Genetic Ancestry data:
+
+
+**Data Source**
+- GDAC Firehose: https://gdc.cancer.gov/about-data/publications/CCG-AIM-2020
+- File Used: `Admixture_by_sample.txt` (Admix percent by sample) for each cancer type.
+
+
+### The Methylation data:
+
+**Data Source**
+- GDAC Firehose: https://gdc.cancer.gov/node/977
+- File Used: `jhu-usc.edu_PANCAN_HumanMethylation450.betaValue_whitelisted.tsv` (DNA methylation 450K only beta value data matrix) for each cancer type.
+
+**Data Transformation** 
+ - The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597)
+ - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina.
diff --git a/public/gbm_tcga_pan_can_atlas_2018/data_clinical_patient.txt b/public/gbm_tcga_pan_can_atlas_2018/data_clinical_patient.txt
diff --git a/public/gbm_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt b/public/gbm_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt
diff --git a/public/gbm_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt b/public/gbm_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt
@@ -0,0 +1,11 @@
+cancer_study_identifier: gbm_tcga_pan_can_atlas_2018
+genetic_alteration_type: GENERIC_ASSAY
+generic_assay_type: GENETIC_ANCESTRY
+datatype: LIMIT-VALUE
+stable_id: genetic_ancestry
+profile_name: Genetic Ancestry
+profile_description: Genetic ancestries were determined using five different methods as described in Carrot-Zhang et al (2020). These consensus calls were created based on the ancestral population that received the majority of assignments for each patient. The original data is <a href="https://gdc.cancer.gov/about-data/publications/CCG-AIM-2020">here</a>.
+data_filename: data_genetic_ancestry.txt
+show_profile_in_analysis_tab: true
+generic_entity_meta_properties: NAME
+value_sort_order: ASC
diff --git a/public/hnsc_tcga_pan_can_atlas_2018/README.md b/public/hnsc_tcga_pan_can_atlas_2018/README.md
@@ -7,4 +7,22 @@
 - File Used: `Merge_Clinical.Level_1.20160128` (clin.merged.txt) for each cancer type.
 
 **Data Transformation** 
-- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597)
+- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597)
+
+### The Genetic Ancestry data:
+
+
+**Data Source**
+- GDAC Firehose: https://gdc.cancer.gov/about-data/publications/CCG-AIM-2020
+- File Used: `Admixture_by_sample.txt` (Admix percent by sample) for each cancer type.
+
+
+### The Methylation data:
+
+**Data Source**
+- GDAC Firehose: https://gdc.cancer.gov/node/977
+- File Used: `jhu-usc.edu_PANCAN_HumanMethylation450.betaValue_whitelisted.tsv` (DNA methylation 450K only beta value data matrix) for each cancer type.
+
+**Data Transformation** 
+ - The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597)
+ - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina.
diff --git a/public/hnsc_tcga_pan_can_atlas_2018/data_clinical_patient.txt b/public/hnsc_tcga_pan_can_atlas_2018/data_clinical_patient.txt
diff --git a/public/hnsc_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt b/public/hnsc_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt
diff --git a/public/hnsc_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt b/public/hnsc_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt
@@ -0,0 +1,11 @@
+cancer_study_identifier: hnsc_tcga_pan_can_atlas_2018
+genetic_alteration_type: GENERIC_ASSAY
+generic_assay_type: GENETIC_ANCESTRY
+datatype: LIMIT-VALUE
+stable_id: genetic_ancestry
+profile_name: Genetic Ancestry
+profile_description: Genetic ancestries were determined using five different methods as described in Carrot-Zhang et al (2020). These consensus calls were created based on the ancestral population that received the majority of assignments for each patient. The original data is <a href="https://gdc.cancer.gov/about-data/publications/CCG-AIM-2020">here</a>.
+data_filename: data_genetic_ancestry.txt
+show_profile_in_analysis_tab: true
+generic_entity_meta_properties: NAME
+value_sort_order: ASC
diff --git a/public/kich_tcga_pan_can_atlas_2018/README.md b/public/kich_tcga_pan_can_atlas_2018/README.md
@@ -7,4 +7,22 @@
 - File Used: `Merge_Clinical.Level_1.20160128` (clin.merged.txt) for each cancer type.
 
 **Data Transformation** 
-- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597)
+- The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597)
+
+### The Genetic Ancestry data:
+
+
+**Data Source**
+- GDAC Firehose: https://gdc.cancer.gov/about-data/publications/CCG-AIM-2020
+- File Used: `Admixture_by_sample.txt` (Admix percent by sample) for each cancer type.
+
+
+### The Methylation data:
+
+**Data Source**
+- GDAC Firehose: https://gdc.cancer.gov/node/977
+- File Used: `jhu-usc.edu_PANCAN_HumanMethylation450.betaValue_whitelisted.tsv` (DNA methylation 450K only beta value data matrix) for each cancer type.
+
+**Data Transformation** 
+ - The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597)
+ - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina.
diff --git a/public/kich_tcga_pan_can_atlas_2018/data_clinical_patient.txt b/public/kich_tcga_pan_can_atlas_2018/data_clinical_patient.txt
diff --git a/public/kich_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt b/public/kich_tcga_pan_can_atlas_2018/data_genetic_ancestry.txt
diff --git a/public/kich_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt b/public/kich_tcga_pan_can_atlas_2018/meta_genetic_ancestry.txt
@@ -0,0 +1,11 @@
+cancer_study_identifier: kich_tcga_pan_can_atlas_2018
+genetic_alteration_type: GENERIC_ASSAY
+generic_assay_type: GENETIC_ANCESTRY
+datatype: LIMIT-VALUE
+stable_id: genetic_ancestry
+profile_name: Genetic Ancestry
+profile_description: Genetic ancestries were determined using five different methods as described in Carrot-Zhang et al (2020). These consensus calls were created based on the ancestral population that received the majority of assignments for each patient. The original data is <a href="https://gdc.cancer.gov/about-data/publications/CCG-AIM-2020">here</a>.
+data_filename: data_genetic_ancestry.txt
+show_profile_in_analysis_tab: true
+generic_entity_meta_properties: NAME
+value_sort_order: ASC