diff --git a/public/ccrcc_wcm_2022/case_lists/cases_all.txt b/public/ccrcc_wcm_2022/case_lists/cases_all.txt new file mode 100644 index 0000000000..15718fdfc6 --- /dev/null +++ b/public/ccrcc_wcm_2022/case_lists/cases_all.txt @@ -0,0 +1,6 @@ +cancer_study_identifier: ccrcc_wcm_2022 +stable_id: ccrcc_wcm_2022_all +case_list_name: All samples +case_list_description: All samples (67 samples) +case_list_category: all_cases_in_study +case_list_ids: WCMC-RCC-036-1 WCMC-RCC-036-2 WCMC-RCC-084-2 WCMC-RCC-048-1 WCMC-RCC-035-1 WCMC-RCC-014-1 WCMC-RCC-057-1 WCMC-RCC-078-1 WCMC-RCC-045-1 WCMC-RCC-060-1 WCMC-RCC-043-1 WCMC-RCC-034-1 WCMC-RCC-032-1 WCMC-RCC-001-1 WCMC-RCC-033-1 WCMC-RCC-058-1 WCMC-RCC-058-2 WCMC-RCC-033-2 WCMC-RCC-015-1 WCMC-RCC-007-1 WCMC-RCC-007-2 WCMC-RCC-015-2 WCMC-RCC-007-4 WCMC-RCC-007-5 WCMC-RCC-006-3 WCMC-RCC-007-7 WCMC-RCC-006-1 WCMC-RCC-069-1 WCMC-RCC-007-6 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-086-1 WCMC-RCC-023-1 WCMC-RCC-015-3 WCMC-RCC-010-1 WCMC-RCC-013-1 WCMC-RCC-041-1 WCMC-RCC-048-2 WCMC-RCC-084-1 WCMC-RCC-050-1 WCMC-RCC-050-2 WCMC-RCC-051-1 WCMC-RCC-085-1 WCMC-RCC-047-1 WCMC-RCC-065-1 WCMC-RCC-065-2 WCMC-RCC-030-2 WCMC-RCC-044-1 WCMC-RCC-030-1 WCMC-RCC-019-1 WCMC-RCC-029-1 WCMC-RCC-029-2 WCMC-RCC-015-4 WCMC-RCC-024-1 WCMC-RCC-026-1 WCMC-RCC-006-2 WCMC-RCC-077-1 WCMC-RCC-003-1 WCMC-RCC-002-1 WCMC-RCC-007-3 WCMC-RCC-039-1 WCMC-RCC-074-2 WCMC-RCC-074-1 diff --git a/public/ccrcc_wcm_2022/case_lists/cases_cna.txt b/public/ccrcc_wcm_2022/case_lists/cases_cna.txt new file mode 100644 index 0000000000..697e491566 --- /dev/null +++ b/public/ccrcc_wcm_2022/case_lists/cases_cna.txt @@ -0,0 +1,6 @@ +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 \ No newline at end of file diff --git a/public/ccrcc_wcm_2022/case_lists/cases_cnaseq.txt b/public/ccrcc_wcm_2022/case_lists/cases_cnaseq.txt new file mode 100644 index 0000000000..85632fc63f --- /dev/null +++ b/public/ccrcc_wcm_2022/case_lists/cases_cnaseq.txt @@ -0,0 +1,6 @@ +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 \ No newline at end of file diff --git a/public/ccrcc_wcm_2022/case_lists/cases_log2CNA.txt b/public/ccrcc_wcm_2022/case_lists/cases_log2CNA.txt new file mode 100644 index 0000000000..54766b9d6c --- /dev/null +++ b/public/ccrcc_wcm_2022/case_lists/cases_log2CNA.txt @@ -0,0 +1,6 @@ +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 diff --git a/public/ccrcc_wcm_2022/case_lists/cases_sequenced.txt b/public/ccrcc_wcm_2022/case_lists/cases_sequenced.txt new file mode 100644 index 0000000000..37f1e79807 --- /dev/null +++ b/public/ccrcc_wcm_2022/case_lists/cases_sequenced.txt @@ -0,0 +1,6 @@ +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 diff --git a/public/ccrcc_wcm_2022/data_clinical_patient.txt b/public/ccrcc_wcm_2022/data_clinical_patient.txt new file mode 100644 index 0000000000..b35c58c38d --- /dev/null +++ b/public/ccrcc_wcm_2022/data_clinical_patient.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:cf0a454e8babbea70b10da2731f58ab18e39f6d490f74ce1642059de188515f0 +size 1633 diff --git a/public/ccrcc_wcm_2022/data_clinical_sample.txt b/public/ccrcc_wcm_2022/data_clinical_sample.txt new file mode 100644 index 0000000000..e0542a999e --- /dev/null +++ b/public/ccrcc_wcm_2022/data_clinical_sample.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:6694e8c658ca37707e7c19b33a1cfa97a05bf9cff84f86dec89b096c905d4f10 +size 9220 diff --git a/public/ccrcc_wcm_2022/data_cna_hg19.seg b/public/ccrcc_wcm_2022/data_cna_hg19.seg new file mode 100644 index 0000000000..0bbc7b37e6 --- /dev/null +++ b/public/ccrcc_wcm_2022/data_cna_hg19.seg @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:308f8542042f32405fcb3f72806afb5dae3ae20aa02970a0c0861f6e9f5e789f +size 281793 diff --git a/public/ccrcc_wcm_2022/data_log2_cna.txt b/public/ccrcc_wcm_2022/data_log2_cna.txt new file mode 100644 index 0000000000..1da70e6ab1 --- /dev/null +++ b/public/ccrcc_wcm_2022/data_log2_cna.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:84e8fd41bfe2b24e44e8f85470dbde6d7deb1cb7fabd6ca4942e3024a8f339e8 +size 16025208 diff --git a/public/ccrcc_wcm_2022/data_mutations.txt b/public/ccrcc_wcm_2022/data_mutations.txt new file mode 100644 index 0000000000..09b68a3df1 --- /dev/null +++ b/public/ccrcc_wcm_2022/data_mutations.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:34f91db7f03dfcc4492e387a54c1fd9df740f8c03afe46dfcd660b94a71a5eac +size 19490246 diff --git a/public/ccrcc_wcm_2022/meta_clinical_patient.txt b/public/ccrcc_wcm_2022/meta_clinical_patient.txt new file mode 100644 index 0000000000..d954c87020 --- /dev/null +++ b/public/ccrcc_wcm_2022/meta_clinical_patient.txt @@ -0,0 +1,4 @@ +cancer_study_identifier: ccrcc_wcm_2022 +genetic_alteration_type: CLINICAL +datatype: PATIENT_ATTRIBUTES +data_filename: data_clinical_patient.txt diff --git a/public/ccrcc_wcm_2022/meta_clinical_sample.txt b/public/ccrcc_wcm_2022/meta_clinical_sample.txt new file mode 100644 index 0000000000..6d72e0c435 --- /dev/null +++ b/public/ccrcc_wcm_2022/meta_clinical_sample.txt @@ -0,0 +1,4 @@ +cancer_study_identifier: ccrcc_wcm_2022 +genetic_alteration_type: CLINICAL +datatype: SAMPLE_ATTRIBUTES +data_filename: data_clinical_sample.txt diff --git a/public/ccrcc_wcm_2022/meta_cna_hg19_seg.txt b/public/ccrcc_wcm_2022/meta_cna_hg19_seg.txt new file mode 100644 index 0000000000..5ad18e0f23 --- /dev/null +++ b/public/ccrcc_wcm_2022/meta_cna_hg19_seg.txt @@ -0,0 +1,6 @@ +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 diff --git a/public/ccrcc_wcm_2022/meta_log2_cna.txt b/public/ccrcc_wcm_2022/meta_log2_cna.txt new file mode 100644 index 0000000000..f52e60145d --- /dev/null +++ b/public/ccrcc_wcm_2022/meta_log2_cna.txt @@ -0,0 +1,8 @@ +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 diff --git a/public/ccrcc_wcm_2022/meta_mutations.txt b/public/ccrcc_wcm_2022/meta_mutations.txt new file mode 100644 index 0000000000..e38353bd5c --- /dev/null +++ b/public/ccrcc_wcm_2022/meta_mutations.txt @@ -0,0 +1,8 @@ +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 diff --git a/public/ccrcc_wcm_2022/meta_study.txt b/public/ccrcc_wcm_2022/meta_study.txt new file mode 100644 index 0000000000..70a86baa0e --- /dev/null +++ b/public/ccrcc_wcm_2022/meta_study.txt @@ -0,0 +1,8 @@ +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