ccrcc_wcm_2022 study

public/ccrcc_wcm_2022/case_lists/cases_cna.txt

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+cancer_study_identifier: ccrcc_wcm_2022
+stable_id: ccrcc_wcm_2022_cna
+case_list_name: Samples with CNA data
+case_list_description: Samples with mutation data (67 tumor/normal pair samples)
+case_list_category: all_cases_with_cna_data
+case_list_ids: WCMC-RCC-036-1	WCMC-RCC-085-1	WCMC-RCC-084-1	WCMC-RCC-084-2	WCMC-RCC-081-1	WCMC-RCC-078-1	WCMC-RCC-077-1	WCMC-RCC-074-1	WCMC-RCC-074-2	WCMC-RCC-069-1	WCMC-RCC-065-1	WCMC-RCC-065-2	WCMC-RCC-060-1	WCMC-RCC-058-1	WCMC-RCC-058-2	WCMC-RCC-057-1	WCMC-RCC-051-1	WCMC-RCC-050-1	WCMC-RCC-050-2	WCMC-RCC-048-1	WCMC-RCC-048-2	WCMC-RCC-047-1	WCMC-RCC-045-1	WCMC-RCC-044-1	WCMC-RCC-043-1	WCMC-RCC-041-1	WCMC-RCC-039-1	WCMC-RCC-036-2	WCMC-RCC-035-1	WCMC-RCC-034-1	WCMC-RCC-033-1	WCMC-RCC-033-2	WCMC-RCC-032-1	WCMC-RCC-030-1	WCMC-RCC-030-2	WCMC-RCC-029-1	WCMC-RCC-029-2	WCMC-RCC-026-1	WCMC-RCC-024-1	WCMC-RCC-023-1	WCMC-RCC-022-1	WCMC-RCC-008-1	WCMC-RCC-008-2	WCMC-RCC-008-3	WCMC-RCC-008-4	WCMC-RCC-019-1	WCMC-RCC-015-1	WCMC-RCC-015-2	WCMC-RCC-015-3	WCMC-RCC-015-4	WCMC-RCC-014-1	WCMC-RCC-013-1	WCMC-RCC-007-1	WCMC-RCC-007-2	WCMC-RCC-007-3	WCMC-RCC-007-4	WCMC-RCC-007-5	WCMC-RCC-007-6	WCMC-RCC-007-7	WCMC-RCC-086-1	WCMC-RCC-010-1	WCMC-RCC-006-1	WCMC-RCC-006-2	WCMC-RCC-006-3	WCMC-RCC-003-1	WCMC-RCC-002-1	WCMC-RCC-001-1

public/ccrcc_wcm_2022/case_lists/cases_cnaseq.txt

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+cancer_study_identifier: ccrcc_wcm_2022
+stable_id: ccrcc_wcm_2022_cnaseq
+case_list_name: Samples with mutation and CNA data
+case_list_description: Samples with mutation and CNA data (67 tumor/normal pair samples)
+case_list_category: all_cases_with_mutation_and_cna_data
+case_list_ids: WCMC-RCC-036-1	WCMC-RCC-085-1	WCMC-RCC-084-1	WCMC-RCC-084-2	WCMC-RCC-081-1	WCMC-RCC-078-1	WCMC-RCC-077-1	WCMC-RCC-074-1	WCMC-RCC-074-2	WCMC-RCC-069-1	WCMC-RCC-065-1	WCMC-RCC-065-2	WCMC-RCC-060-1	WCMC-RCC-058-1	WCMC-RCC-058-2	WCMC-RCC-057-1	WCMC-RCC-051-1	WCMC-RCC-050-1	WCMC-RCC-050-2	WCMC-RCC-048-1	WCMC-RCC-048-2	WCMC-RCC-047-1	WCMC-RCC-045-1	WCMC-RCC-044-1	WCMC-RCC-043-1	WCMC-RCC-041-1	WCMC-RCC-039-1	WCMC-RCC-036-2	WCMC-RCC-035-1	WCMC-RCC-034-1	WCMC-RCC-033-1	WCMC-RCC-033-2	WCMC-RCC-032-1	WCMC-RCC-030-1	WCMC-RCC-030-2	WCMC-RCC-029-1	WCMC-RCC-029-2	WCMC-RCC-026-1	WCMC-RCC-024-1	WCMC-RCC-023-1	WCMC-RCC-022-1	WCMC-RCC-008-1	WCMC-RCC-008-2	WCMC-RCC-008-3	WCMC-RCC-008-4	WCMC-RCC-019-1	WCMC-RCC-015-1	WCMC-RCC-015-2	WCMC-RCC-015-3	WCMC-RCC-015-4	WCMC-RCC-014-1	WCMC-RCC-013-1	WCMC-RCC-007-1	WCMC-RCC-007-2	WCMC-RCC-007-3	WCMC-RCC-007-4	WCMC-RCC-007-5	WCMC-RCC-007-6	WCMC-RCC-007-7	WCMC-RCC-086-1	WCMC-RCC-010-1	WCMC-RCC-006-1	WCMC-RCC-006-2	WCMC-RCC-006-3	WCMC-RCC-003-1	WCMC-RCC-002-1	WCMC-RCC-001-1

public/ccrcc_wcm_2022/case_lists/cases_log2CNA.txt

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+cancer_study_identifier: ccrcc_wcm_2022
+stable_id: ccrcc_wcm_2022_log2CNA
+case_list_name: Samples with log2 copy-number data
+case_list_description: Samples with log2 copy-number data (67 samples)
+case_list_category: all_cases_with_log2_cna_data
+case_list_ids: WCMC-RCC-084-2	WCMC-RCC-084-1	WCMC-RCC-036-1	WCMC-RCC-036-2	WCMC-RCC-048-2	WCMC-RCC-051-1	WCMC-RCC-033-1	WCMC-RCC-015-3	WCMC-RCC-048-1	WCMC-RCC-035-1	WCMC-RCC-058-1	WCMC-RCC-057-1	WCMC-RCC-078-1	WCMC-RCC-085-1	WCMC-RCC-045-1	WCMC-RCC-047-1	WCMC-RCC-050-1	WCMC-RCC-060-1	WCMC-RCC-065-1	WCMC-RCC-065-2	WCMC-RCC-034-1	WCMC-RCC-030-2	WCMC-RCC-050-2	WCMC-RCC-044-1	WCMC-RCC-007-1	WCMC-RCC-032-1	WCMC-RCC-001-1	WCMC-RCC-019-1	WCMC-RCC-014-1	WCMC-RCC-058-2	WCMC-RCC-033-2	WCMC-RCC-015-1	WCMC-RCC-029-1	WCMC-RCC-007-2	WCMC-RCC-015-2	WCMC-RCC-006-1	WCMC-RCC-069-1	WCMC-RCC-006-3	WCMC-RCC-006-2	WCMC-RCC-007-4	WCMC-RCC-007-5	WCMC-RCC-007-6	WCMC-RCC-043-1	WCMC-RCC-024-1	WCMC-RCC-008-4	WCMC-RCC-008-3	WCMC-RCC-008-2	WCMC-RCC-008-1	WCMC-RCC-022-1	WCMC-RCC-081-1	WCMC-RCC-026-1	WCMC-RCC-010-1	WCMC-RCC-086-1	WCMC-RCC-013-1	WCMC-RCC-015-4	WCMC-RCC-077-1	WCMC-RCC-023-1	WCMC-RCC-007-7	WCMC-RCC-030-1	WCMC-RCC-003-1	WCMC-RCC-002-1	WCMC-RCC-007-3	WCMC-RCC-029-2	WCMC-RCC-039-1	WCMC-RCC-041-1	WCMC-RCC-074-2	WCMC-RCC-074-1

public/ccrcc_wcm_2022/case_lists/cases_sequenced.txt

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+cancer_study_identifier: ccrcc_wcm_2022
+stable_id: ccrcc_wcm_2022_sequenced
+case_list_name: Samples with mutation data
+case_list_description: Samples with mutation data (67 samples)
+case_list_category: all_cases_with_mutation_data
+case_list_ids: WCMC-RCC-048-2	WCMC-RCC-084-1	WCMC-RCC-050-1	WCMC-RCC-050-2	WCMC-RCC-084-2	WCMC-RCC-051-1	WCMC-RCC-033-1	WCMC-RCC-048-1	WCMC-RCC-035-1	WCMC-RCC-058-1	WCMC-RCC-057-1	WCMC-RCC-078-1	WCMC-RCC-085-1	WCMC-RCC-045-1	WCMC-RCC-008-1	WCMC-RCC-047-1	WCMC-RCC-036-1	WCMC-RCC-060-1	WCMC-RCC-065-1	WCMC-RCC-065-2	WCMC-RCC-034-1	WCMC-RCC-030-2	WCMC-RCC-036-2	WCMC-RCC-044-1	WCMC-RCC-030-1	WCMC-RCC-032-1	WCMC-RCC-001-1	WCMC-RCC-019-1	WCMC-RCC-014-1	WCMC-RCC-058-2	WCMC-RCC-033-2	WCMC-RCC-015-1	WCMC-RCC-029-1	WCMC-RCC-029-2	WCMC-RCC-015-2	WCMC-RCC-007-4	WCMC-RCC-007-5	WCMC-RCC-006-3	WCMC-RCC-007-7	WCMC-RCC-007-1	WCMC-RCC-069-1	WCMC-RCC-008-4	WCMC-RCC-007-6	WCMC-RCC-006-1	WCMC-RCC-024-1	WCMC-RCC-006-2	WCMC-RCC-008-3	WCMC-RCC-008-2	WCMC-RCC-015-4	WCMC-RCC-022-1	WCMC-RCC-007-2	WCMC-RCC-026-1	WCMC-RCC-086-1	WCMC-RCC-039-1	WCMC-RCC-077-1	WCMC-RCC-007-3	WCMC-RCC-023-1	WCMC-RCC-015-3	WCMC-RCC-043-1	WCMC-RCC-002-1	WCMC-RCC-010-1	WCMC-RCC-081-1	WCMC-RCC-003-1	WCMC-RCC-013-1	WCMC-RCC-041-1	WCMC-RCC-074-2	WCMC-RCC-074-1

public/ccrcc_wcm_2022/meta_clinical_patient.txt

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+cancer_study_identifier: ccrcc_wcm_2022
+genetic_alteration_type: CLINICAL
+datatype: PATIENT_ATTRIBUTES
+data_filename: data_clinical_patient.txt

public/ccrcc_wcm_2022/meta_clinical_sample.txt

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+cancer_study_identifier: ccrcc_wcm_2022
+genetic_alteration_type: CLINICAL
+datatype: SAMPLE_ATTRIBUTES
+data_filename: data_clinical_sample.txt

public/ccrcc_wcm_2022/meta_cna_hg19_seg.txt

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+cancer_study_identifier: ccrcc_wcm_2022
+genetic_alteration_type: COPY_NUMBER_ALTERATION
+datatype: SEG
+reference_genome_id: hg19
+description: Somatic CNA data(copy number ratio from tumor samples minus ratio from matched normals).
+data_filename: data_cna_hg19.seg

public/ccrcc_wcm_2022/meta_log2_cna.txt

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+cancer_study_identifier: ccrcc_wcm_2022
+genetic_alteration_type: COPY_NUMBER_ALTERATION
+datatype: LOG2-VALUE
+stable_id: log2CNA
+show_profile_in_analysis_tab: false
+profile_name: Log2 copy-number values for each gene.
+profile_description: Log2 copy-number values
+data_filename: data_log2_cna.txt

public/ccrcc_wcm_2022/meta_mutations.txt

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+cancer_study_identifier: ccrcc_wcm_2022
+genetic_alteration_type: MUTATION_EXTENDED
+datatype: MAF
+stable_id: mutations
+show_profile_in_analysis_tab: true
+profile_description: Mutations
+profile_name: Mutation data from whole exome sequencing.
+data_filename: data_mutations.txt

public/ccrcc_wcm_2022/meta_study.txt

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+type_of_cancer: ccrcc
+cancer_study_identifier: ccrcc_wcm_2022
+name: Clear Cell Renal Cell Carcinoma (Cornell, Molecular Oncology 2022)
+description: Whole-exome sequencing of metastatic clear cell renal carcinoma (ccRCC) from 67 tumor/normal pairs from 43 patients. Please note that one sample has been excluded from the original cohort as it didn't meet the quality threshold for Somatic Copy Number Analysis (SCNA).
+citation: van der Mijn et al. Mol Oncol. 2022
+pmid: 35231161
+add_global_case_list: true
+groups: PUBLIC