Adding crc study with updates (#1866)

* Adding crc study with updates * Study edits * Patient file edit --------- Co-authored-by: RAlhamad <[email protected]> Co-authored-by: Ramya Madupuri <[email protected]>
cBioPortal · Aug 1, 2023 · 4d8cef4 · 4d8cef4
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diff --git a/public/crc_eo_2020/case_lists/cases_all.txt b/public/crc_eo_2020/case_lists/cases_all.txt
diff --git a/public/crc_eo_2020/case_lists/cases_cna.txt b/public/crc_eo_2020/case_lists/cases_cna.txt
diff --git a/public/crc_eo_2020/case_lists/cases_cnaseq.txt b/public/crc_eo_2020/case_lists/cases_cnaseq.txt
diff --git a/public/crc_eo_2020/case_lists/cases_sequenced.txt b/public/crc_eo_2020/case_lists/cases_sequenced.txt
diff --git a/public/crc_eo_2020/case_lists/cases_sv.txt b/public/crc_eo_2020/case_lists/cases_sv.txt
diff --git a/public/crc_eo_2020/data_clinical_patient.txt b/public/crc_eo_2020/data_clinical_patient.txt
diff --git a/public/crc_eo_2020/data_clinical_sample.txt b/public/crc_eo_2020/data_clinical_sample.txt
diff --git a/public/crc_eo_2020/data_cna.txt b/public/crc_eo_2020/data_cna.txt
diff --git a/public/crc_eo_2020/data_cna_hg19.seg b/public/crc_eo_2020/data_cna_hg19.seg
diff --git a/public/crc_eo_2020/data_gene_panel_matrix.txt b/public/crc_eo_2020/data_gene_panel_matrix.txt
diff --git a/public/crc_eo_2020/data_mutations.txt b/public/crc_eo_2020/data_mutations.txt
diff --git a/public/crc_eo_2020/data_sv.txt b/public/crc_eo_2020/data_sv.txt
diff --git a/public/crc_eo_2020/meta_clinical_patient.txt b/public/crc_eo_2020/meta_clinical_patient.txt
@@ -0,0 +1,4 @@
+cancer_study_identifier: crc_eo_2020
+genetic_alteration_type: CLINICAL
+datatype: PATIENT_ATTRIBUTES
+data_filename: data_clinical_patient.txt
diff --git a/public/crc_eo_2020/meta_clinical_sample.txt b/public/crc_eo_2020/meta_clinical_sample.txt
@@ -0,0 +1,4 @@
+cancer_study_identifier: crc_eo_2020
+genetic_alteration_type: CLINICAL
+datatype: SAMPLE_ATTRIBUTES
+data_filename: data_clinical_sample.txt
diff --git a/public/crc_eo_2020/meta_cna.txt b/public/crc_eo_2020/meta_cna.txt
@@ -0,0 +1,8 @@
+cancer_study_identifier: crc_eo_2020
+genetic_alteration_type: COPY_NUMBER_ALTERATION
+stable_id: cna
+show_profile_in_analysis_tab: true
+profile_name: Copy Number Alterations
+profile_description: Copy number alterations from targeted sequencing via MK-IMPACT on Illumina HiSeq sequencers.
+datatype: DISCRETE
+data_filename: data_cna.txt
diff --git a/public/crc_eo_2020/meta_cna_hg19_seg.txt b/public/crc_eo_2020/meta_cna_hg19_seg.txt
@@ -0,0 +1,6 @@
+cancer_study_identifier: crc_eo_2020
+reference_genome_id: hg19
+genetic_alteration_type: COPY_NUMBER_ALTERATION
+datatype: SEG
+description: Somatic CNA data (copy number ratio from tumor samples minus ratio from matched normals).
+data_filename: data_cna_hg19.seg
diff --git a/public/crc_eo_2020/meta_gene_panel_matrix.txt b/public/crc_eo_2020/meta_gene_panel_matrix.txt
@@ -0,0 +1,4 @@
+cancer_study_identifier: crc_eo_2020
+data_filename: data_gene_panel_matrix.txt
+genetic_alteration_type: GENE_PANEL_MATRIX
+datatype: GENE_PANEL_MATRIX
diff --git a/public/crc_eo_2020/meta_mutations.txt b/public/crc_eo_2020/meta_mutations.txt
@@ -0,0 +1,8 @@
+cancer_study_identifier: crc_eo_2020
+stable_id: mutations
+profile_name: Mutations
+profile_description: Targeted sequencing of early and average onset colorectal cancer via MSK-IMPACT on Illumina HiSeq sequencers. 
+genetic_alteration_type: MUTATION_EXTENDED
+datatype: MAF
+show_profile_in_analysis_tab: true
+data_filename: data_mutations.txt
diff --git a/public/crc_eo_2020/meta_study.txt b/public/crc_eo_2020/meta_study.txt
@@ -0,0 +1,7 @@
+type_of_cancer: bowel
+cancer_study_identifier: crc_eo_2020
+name: Colorectal Cancer (MSK, JNCI 2021)
+short_name: CRC (MSK, 2021)
+description: Targeted sequencing of 1,516 samples from 818 patients with early onset and 698 patients with average onset colorectal cancer and their matched normals.
+citation: Cercek et al. JNCI 2021
+pmid: 34405229
diff --git a/public/crc_eo_2020/meta_sv.txt b/public/crc_eo_2020/meta_sv.txt
@@ -0,0 +1,8 @@
+cancer_study_identifier: crc_eo_2020
+genetic_alteration_type: STRUCTURAL_VARIANT
+datatype: SV
+stable_id: structural_variants
+show_profile_in_analysis_tab: true
+profile_name: Structural variants
+profile_description: Structural Variant Data.
+data_filename: data_sv.txt