diff --git a/public/pancan_metaprism_2023/LICENSE b/public/pancan_metaprism_2023/LICENSE new file mode 100644 index 000000000..d5f3c4b53 --- /dev/null +++ b/public/pancan_metaprism_2023/LICENSE @@ -0,0 +1 @@ +The data are available under the ODC Open Database License (ODbL)(http://opendatacommons.org/licenses/odbl/1.0/) (summary available here: http://www.opendatacommons.org/licenses/odbl/1-0/summary/): you are free to share and modify the data so long as you attribute any public use of the database, or works produced from the database; keep the resulting data-sets open; and offer your shared or adapted version of the data-set under the same ODbL license. diff --git a/public/pancan_metaprism_2023/README.md b/public/pancan_metaprism_2023/README.md new file mode 100644 index 000000000..ca78ab172 --- /dev/null +++ b/public/pancan_metaprism_2023/README.md @@ -0,0 +1,72 @@ +# META-PRISM + +**Publication** : The study is now published in Cancer Discovery and is freely available at https://pubmed.ncbi.nlm.nih.gov/36862804/. +**Local Instance** : . +**Local Instance** : . +**Study Id** : pancan_metaprism_2023 +**Reference genome** : GRCh37 + +## Description + +## Clinical data: (data_clinical_patient.txt) (data_clinical_sample.txt) + +- `Supplementary_Table_1.xlsx` Clinical characteristics and samples of the 1,031 patients included in the META-PRISM + cohort. + +**Clinical data remapping**: + +| Original column | Renamed column | Patient/Sample Attribute | +| ---| ---| --- | +| Subject_Id | Patient_Id | Patient | +| Sex | Sex | Patient | +| Age_At_Biopsy | AGE_AT_BIOPSY | Patient | +| Oncotree_Code | Oncotree_Code | Sample | +| Primary_Tumor_Site | Primary Site | Sample | +| Histology | Histology | Sample | +| Metastatic_Sites | Metastatic Site | Sample | +| Treatments_Before_Biopsy | Treatments Before Biopsy | Patient | +| Albumin_At_Biopsy(g/L) | Albumin At Biopsy(g/L) | Patient | +| Lactate_Dehydrogenase_At_Biopsy(UI/L) | Lactate Dehydrogenase At Biopsy(UI/L) | Patient | +| Neutrophils_At_Biopsy(10^9/L) | Neutrophils At Biopsy(10^9/L) | Patient | +| Lymphocytes_At_Biopsy(10^9/L) | Lymphocytes At Biopsy(10^9/L) | Patient | +| GRIM_Score | Gustave Roussy Immune Score | Patient | +| Alcohol | Alcohol History | Patient | +| Smoking_History | Smoking History | Patient | +| Vital_Status | OS status. | Patient | +| Sample_Id_DNA_T | Sample_Id | Sample | + +## Segmented data: (data_cna_hg19.seg) + +- `Data_Table_5.somatic_cna_segments.tsv` Table of all 42,769 curated copy-number segments identified in 569 + WES tumor/normal sample pairs. + +## Mutation data: (data_mutations.txt) + +- `Data_Table_3.somatic_mutations.maf.gz` Table of all 117,747 somatic mutations detected in 569 analyzed + WES tumor/normal sample pairs. Only mutations that pass all filters are included. + +## Zscore Expression data: (data_mrna_seq_tpm_zscores_ref_all_samples.txt) + +- `Data_Table_2.rna_gene_tpm.tsv.gz` Table in 58,288 x 948 format with the expression TPM of 58,288 genes in + the 947 RNAseq tumor samples. + +## SV data: (data_sv.txt) + +- `Data_Table_10.rna_fusions.tsv.gz` Table of all 707,027 fusion calls as identified by Arriba v1.2.0, EricScript v0.5.5, + Pizzly v0.37.3, or StarFusion v1.8.1. + +## Copy number data: (data_cna.txt) + +- `Data_Table_1.rna_gene_counts.tsv.gz` Table in 58,288 x 948 format with the expression raw counts of 58,288 genes in + the 947 RNAseq tumor samples. + +## Mutational Signatures: + +(data_mutational_signatures_counts_SBS.txt) +- `Data_Table_9.sbs_96_signature_counts.tsv` Table in 78 x 451 format with the mutation counts contributed by each of + the 78 signatures from COSMIC SBS v3.2 database in the 450 WES tumor samples . + +(data_mutational_signatures_contribution_SBS.txt) +- `Data_Table_11.rna_ssgsea_immune.tsv` Table in 29 x 948 format with the functional gene expression signatures (ssGSEA + scores) on the 29 gene sets in 947 RNAseq tumor samples. + diff --git a/public/pancan_metaprism_2023/case_lists/cases_all.txt b/public/pancan_metaprism_2023/case_lists/cases_all.txt new file mode 100644 index 000000000..71144fe82 --- /dev/null +++ b/public/pancan_metaprism_2023/case_lists/cases_all.txt @@ -0,0 +1,6 @@ +cancer_study_identifier: pancan_metaprism_2023 +stable_id: pancan_metaprism_2023_all +case_list_name: All samples +case_list_description: All samples (1031 samples) +case_list_category: all_cases_in_study +case_list_ids: MP-0001-R01 MP-0002-D01_R01 MP-0003-R01 MP-0004-D01_R01 MP-0005-D01_R01 MP-0006-D01_R01 MP-0007-D01_R01 MP-0008-R01 MP-0009-R01 MP-0010-D02_R02 MP-0011-D01_R01 MP-0012-R01 MP-0013-D01_R01 MP-0014-D01_R01 MP-0015-D01_R01 MP-0016-R01 MP-0017-R01 MP-0018-R01 MP-0019-R01 MP-0020-R01 MP-0021-R01 MP-0022-R01 MP-0023-R01 MP-0024-R01 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a/public/pancan_metaprism_2023/meta_clinical_sample.txt b/public/pancan_metaprism_2023/meta_clinical_sample.txt new file mode 100755 index 000000000..9588b90ef --- /dev/null +++ b/public/pancan_metaprism_2023/meta_clinical_sample.txt @@ -0,0 +1,4 @@ +cancer_study_identifier: pancan_metaprism_2023 +genetic_alteration_type: CLINICAL +datatype: SAMPLE_ATTRIBUTES +data_filename: data_clinical_sample.txt diff --git a/public/pancan_metaprism_2023/meta_cna.txt b/public/pancan_metaprism_2023/meta_cna.txt new file mode 100644 index 000000000..2e8b18d4a --- /dev/null +++ b/public/pancan_metaprism_2023/meta_cna.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: pancan_metaprism_2023 +stable_id: cna +profile_name: Putative copy-number alterations +profile_description: Putative copy-number calls derived from WES data. Values: -2 = homozygous deletion; -1 = hemizygous deletion; 0 = neutral / no change; 1 = gain; 2 = high level amplification. +genetic_alteration_type: COPY_NUMBER_ALTERATION +datatype: DISCRETE +show_profile_in_analysis_tab: true +data_filename: data_cna.txt diff --git a/public/pancan_metaprism_2023/meta_cna_hg19_seg.txt b/public/pancan_metaprism_2023/meta_cna_hg19_seg.txt new file mode 100644 index 000000000..b212ae75e --- /dev/null +++ b/public/pancan_metaprism_2023/meta_cna_hg19_seg.txt @@ -0,0 +1,6 @@ +cancer_study_identifier: pancan_metaprism_2023 +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/pancan_metaprism_2023/meta_gene_panel_matrix.txt b/public/pancan_metaprism_2023/meta_gene_panel_matrix.txt new file mode 100755 index 000000000..dd04dbf8e --- /dev/null +++ b/public/pancan_metaprism_2023/meta_gene_panel_matrix.txt @@ -0,0 +1,4 @@ +cancer_study_identifier: pancan_metaprism_2023 +genetic_alteration_type: GENE_PANEL_MATRIX +datatype: GENE_PANEL_MATRIX +data_filename: data_gene_panel_matrix.txt diff --git a/public/pancan_metaprism_2023/meta_mrna_seq_tpm.txt b/public/pancan_metaprism_2023/meta_mrna_seq_tpm.txt new file mode 100644 index 000000000..510e57460 --- /dev/null +++ b/public/pancan_metaprism_2023/meta_mrna_seq_tpm.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: pancan_metaprism_2023 +genetic_alteration_type: MRNA_EXPRESSION +datatype: CONTINUOUS +stable_id: rna_seq_mrna +profile_name: mRNA expression +profile_description: Gene expression as quantified by Kallisto v0.44.0 on GENCODE v27 and aggregated to the gene level (58,288 genes) by TxImport v1.16.0. +data_filename: data_mrna_seq_tpm.txt +show_profile_in_analysis_tab: false diff --git a/public/pancan_metaprism_2023/meta_mrna_seq_tpm_zscores_ref_all_samples.txt b/public/pancan_metaprism_2023/meta_mrna_seq_tpm_zscores_ref_all_samples.txt new file mode 100644 index 000000000..3a84ee075 --- /dev/null +++ b/public/pancan_metaprism_2023/meta_mrna_seq_tpm_zscores_ref_all_samples.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: pancan_metaprism_2023 +genetic_alteration_type: MRNA_EXPRESSION +datatype: Z-SCORE +stable_id: mrna_seq_tpm_all_sample_Zscores +show_profile_in_analysis_tab: true +profile_description: Gene expression as quantified by Kallisto v0.44.0 on GENCODE v27 and aggregated to the gene level (58,288 genes) by TxImport v1.16.0. Values are TPMs log-transformed. +profile_name: mRNA expression z-scores relative to all samples (log RNA Seq TPM) +data_filename: data_mrna_seq_tpm_zscores_ref_all_samples.txt \ No newline at end of file diff --git a/public/pancan_metaprism_2023/meta_mutational_signatures_contribution_SBS.txt b/public/pancan_metaprism_2023/meta_mutational_signatures_contribution_SBS.txt new file mode 100644 index 000000000..fcbeb1b51 --- /dev/null +++ b/public/pancan_metaprism_2023/meta_mutational_signatures_contribution_SBS.txt @@ -0,0 +1,12 @@ +cancer_study_identifier: pancan_metaprism_2023 +genetic_alteration_type: GENERIC_ASSAY +generic_assay_type: MUTATIONAL_SIGNATURE +datatype: LIMIT-VALUE +stable_id: mutational_signatures_contribution_SBS +profile_name: Mutational signatures contribution SBS +profile_description: Mutational signature contribution, calculated from PCAWG SBS activity +data_filename: data_mutational_signatures_contribution_SBS.txt +generic_entity_meta_properties: NAME,DESCRIPTION,URL +show_profile_in_analysis_tab: true +value_sort_order: DESC +pivot_threshold_value: 0.0 \ No newline at end of file diff --git a/public/pancan_metaprism_2023/meta_mutational_signatures_counts_SBS.txt b/public/pancan_metaprism_2023/meta_mutational_signatures_counts_SBS.txt new file mode 100644 index 000000000..f1a328bbd --- /dev/null +++ b/public/pancan_metaprism_2023/meta_mutational_signatures_counts_SBS.txt @@ -0,0 +1,10 @@ +cancer_study_identifier: pancan_metaprism_2023 +genetic_alteration_type: GENERIC_ASSAY +generic_assay_type: MUTATIONAL_SIGNATURE +datatype: LIMIT-VALUE +stable_id: mutational_signatures_counts_SBS +profile_name: Mutational signatures counts SBS +profile_description: Mutational count matrix +data_filename: data_mutational_signatures_counts_SBS.txt +show_profile_in_analysis_tab: false +generic_entity_meta_properties: NAME \ No newline at end of file diff --git a/public/pancan_metaprism_2023/meta_mutations.txt b/public/pancan_metaprism_2023/meta_mutations.txt new file mode 100755 index 000000000..e2c87b6c2 --- /dev/null +++ b/public/pancan_metaprism_2023/meta_mutations.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: pancan_metaprism_2023 +genetic_alteration_type: MUTATION_EXTENDED +datatype: MAF +stable_id: mutations +show_profile_in_analysis_tab: true +profile_name: Mutations +profile_description: Whole exome sequencing data analyzed by Mutect2 (GATK v4.1.8.1) and annotated with VEP v104. +data_filename: data_mutations.txt diff --git a/public/pancan_metaprism_2023/meta_study.txt b/public/pancan_metaprism_2023/meta_study.txt new file mode 100644 index 000000000..23a245d7a --- /dev/null +++ b/public/pancan_metaprism_2023/meta_study.txt @@ -0,0 +1,8 @@ +type_of_cancer: mixed +cancer_study_identifier: pancan_metaprism_2023 +name: Refractory Metastatic Solid Tumors (Gustave Roussy, Cancer Discovery 2023) +short_name: META-PRISM (Gustave Roussy, Cancer Discov 2023) +description: Whole exome and transcriptome sequencing of 1031 metastatic and refractory solid tumor and normal pairs. +citation: Pradat et al. Cancer Discovery 2023 +pmid: 36862804 +reference_genome: hg19 \ No newline at end of file diff --git a/public/pancan_metaprism_2023/meta_sv.txt b/public/pancan_metaprism_2023/meta_sv.txt new file mode 100755 index 000000000..6a12478d7 --- /dev/null +++ b/public/pancan_metaprism_2023/meta_sv.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: pancan_metaprism_2023 +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 \ No newline at end of file diff --git a/public/rectal_radiation_msk_2024/case_lists/cases_all.txt b/public/rectal_radiation_msk_2024/case_lists/cases_all.txt new file mode 100644 index 000000000..ed7a9b62e --- /dev/null +++ b/public/rectal_radiation_msk_2024/case_lists/cases_all.txt @@ -0,0 +1,6 @@ +cancer_study_identifier: rectal_radiation_msk_2024 +stable_id: rectal_radiation_msk_2024_all +case_list_name: All samples +case_list_description: All samples (48 samples) +case_list_category: all_cases_in_study +case_list_ids: P-0002902-T01-IM3 P-0010422-T01-IM5 P-0011282-T01-IM5 P-0013159-T01-IM5 P-0015276-T01-IM6 P-0018949-T01-IM6 P-0029141-T01-IM6 P-0032254-T01-IM6 P-0035165-T01-IM6 P-0037948-T01-IM6 P-0038170-T01-IM6 P-0038684-T01-IM6 P-0039051-T01-IM6 P-0045190-T01-IM6 P-0045906-T02-IM6 P-0054770-T01-IM6 P-0063124-T01-IM7 P-0063415-T01-IM7 P-0064170-T01-IM7 P-0065318-T01-IM7 P-0066749-T01-IM7 P-0076840-T01-IM7 P-0079151-T01-IM7 s_C_H35PAE_P001_d01 s_C_CAYX31_P001_d01 s_C_46D50X_P001_d01 s_C_F2AN0K_P001_d01 s_C_M90NHT_P001_d01 s_C_5U25TR_P001_d01 s_C_M4FH1K_M001_d01 s_C_EN5TM0_P001_d01 s_C_33XALX_P002_d02 s_C_5U25TR_P003_d03 s_C_6TKR0Y_P001_d01 s_C_7F0F22_P001_d01 s_C_CAYX31_P003_d03 s_C_CR52MM_P002_d02 s_C_ECM8TT_P002_d02 s_C_F5MTD0_P001_d01 s_C_HR5FRW_P002_d02 s_C_JH5PMJ_P002_d02 s_C_JX9JHM_P001_d01 s_C_K4CY9U_M003_d02 s_C_K99T0C_P002_d02 s_C_M90NHT_P004_d04 s_C_MNLA8T_P001_d01 s_C_P6VVKP_P001_d01 s_C_P74H4L_P002_d02 diff --git a/public/rectal_radiation_msk_2024/case_lists/cases_cna.txt b/public/rectal_radiation_msk_2024/case_lists/cases_cna.txt new file mode 100644 index 000000000..f8ee69894 --- /dev/null +++ b/public/rectal_radiation_msk_2024/case_lists/cases_cna.txt @@ -0,0 +1,6 @@ +cancer_study_identifier: rectal_radiation_msk_2024 +stable_id: rectal_radiation_msk_2024_cna +case_list_name: Samples with CNA data +case_list_description: Samples with CNA data +case_list_category: all_cases_with_cna_data +case_list_ids: P-0038170-T01-IM6 P-0018949-T01-IM6 P-0079151-T01-IM7 P-0032254-T01-IM6 P-0063124-T01-IM7 P-0035165-T01-IM6 P-0002902-T01-IM3 P-0076840-T01-IM7 P-0054770-T01-IM6 P-0011282-T01-IM5 P-0066749-T01-IM7 P-0015276-T01-IM6 P-0045190-T01-IM6 P-0029141-T01-IM6 P-0010422-T01-IM5 P-0039051-T01-IM6 P-0045906-T02-IM6 P-0065318-T01-IM7 P-0037948-T01-IM6 P-0038684-T01-IM6 P-0064170-T01-IM7 P-0063415-T01-IM7 P-0013159-T01-IM5 s_C_46D50X_P001_d01 s_C_5U25TR_P001_d01 s_C_CAYX31_P001_d01 s_C_EN5TM0_P001_d01 s_C_F2AN0K_P001_d01 s_C_H35PAE_P001_d01 s_C_M4FH1K_M001_d01 s_C_M90NHT_P001_d01 diff --git a/public/rectal_radiation_msk_2024/case_lists/cases_cnaseq.txt b/public/rectal_radiation_msk_2024/case_lists/cases_cnaseq.txt new file mode 100644 index 000000000..7cc70f210 --- /dev/null +++ b/public/rectal_radiation_msk_2024/case_lists/cases_cnaseq.txt @@ -0,0 +1,6 @@ +cancer_study_identifier: rectal_radiation_msk_2024 +stable_id: rectal_radiation_msk_2024_cnaseq +case_list_name: Samples with mutation and CNA data +case_list_description: Samples with mutation and CNA data (48 samples) +case_list_category: all_cases_with_mutation_and_cna_data +case_list_ids: P-0002902-T01-IM3 P-0010422-T01-IM5 P-0011282-T01-IM5 P-0013159-T01-IM5 P-0015276-T01-IM6 P-0018949-T01-IM6 P-0029141-T01-IM6 P-0032254-T01-IM6 P-0035165-T01-IM6 P-0037948-T01-IM6 P-0038170-T01-IM6 P-0038684-T01-IM6 P-0039051-T01-IM6 P-0045190-T01-IM6 P-0045906-T02-IM6 P-0054770-T01-IM6 P-0063124-T01-IM7 P-0063415-T01-IM7 P-0064170-T01-IM7 P-0065318-T01-IM7 P-0066749-T01-IM7 P-0076840-T01-IM7 P-0079151-T01-IM7 s_C_H35PAE_P001_d01 s_C_CAYX31_P001_d01 s_C_46D50X_P001_d01 s_C_F2AN0K_P001_d01 s_C_M90NHT_P001_d01 s_C_5U25TR_P001_d01 s_C_M4FH1K_M001_d01 s_C_EN5TM0_P001_d01 s_C_33XALX_P002_d02 s_C_5U25TR_P003_d03 s_C_6TKR0Y_P001_d01 s_C_7F0F22_P001_d01 s_C_CAYX31_P003_d03 s_C_CR52MM_P002_d02 s_C_ECM8TT_P002_d02 s_C_F5MTD0_P001_d01 s_C_HR5FRW_P002_d02 s_C_JH5PMJ_P002_d02 s_C_JX9JHM_P001_d01 s_C_K4CY9U_M003_d02 s_C_K99T0C_P002_d02 s_C_M90NHT_P004_d04 s_C_MNLA8T_P001_d01 s_C_P6VVKP_P001_d01 s_C_P74H4L_P002_d02 diff --git a/public/rectal_radiation_msk_2024/case_lists/cases_sequenced.txt b/public/rectal_radiation_msk_2024/case_lists/cases_sequenced.txt new file mode 100644 index 000000000..90522b5a5 --- /dev/null +++ b/public/rectal_radiation_msk_2024/case_lists/cases_sequenced.txt @@ -0,0 +1,6 @@ +cancer_study_identifier: rectal_radiation_msk_2024 +stable_id: rectal_radiation_msk_2024_sequenced +case_list_name: Samples with mutation data +case_list_description: Samples with mutation data (48 samples) +case_list_category: all_cases_with_mutation_data +case_list_ids: P-0002902-T01-IM3 P-0010422-T01-IM5 P-0011282-T01-IM5 P-0013159-T01-IM5 P-0015276-T01-IM6 P-0018949-T01-IM6 P-0029141-T01-IM6 P-0032254-T01-IM6 P-0035165-T01-IM6 P-0037948-T01-IM6 P-0038170-T01-IM6 P-0038684-T01-IM6 P-0039051-T01-IM6 P-0045190-T01-IM6 P-0045906-T02-IM6 P-0054770-T01-IM6 P-0063124-T01-IM7 P-0063415-T01-IM7 P-0064170-T01-IM7 P-0065318-T01-IM7 P-0066749-T01-IM7 P-0076840-T01-IM7 P-0079151-T01-IM7 s_C_H35PAE_P001_d01 s_C_CAYX31_P001_d01 s_C_46D50X_P001_d01 s_C_F2AN0K_P001_d01 s_C_M90NHT_P001_d01 s_C_5U25TR_P001_d01 s_C_M4FH1K_M001_d01 s_C_EN5TM0_P001_d01 s_C_33XALX_P002_d02 s_C_5U25TR_P003_d03 s_C_6TKR0Y_P001_d01 s_C_7F0F22_P001_d01 s_C_CAYX31_P003_d03 s_C_CR52MM_P002_d02 s_C_ECM8TT_P002_d02 s_C_F5MTD0_P001_d01 s_C_HR5FRW_P002_d02 s_C_JH5PMJ_P002_d02 s_C_JX9JHM_P001_d01 s_C_K4CY9U_M003_d02 s_C_K99T0C_P002_d02 s_C_M90NHT_P004_d04 s_C_MNLA8T_P001_d01 s_C_P6VVKP_P001_d01 s_C_P74H4L_P002_d02 diff --git a/public/rectal_radiation_msk_2024/case_lists/cases_sv.txt b/public/rectal_radiation_msk_2024/case_lists/cases_sv.txt new file mode 100644 index 000000000..454e3cd45 --- /dev/null +++ b/public/rectal_radiation_msk_2024/case_lists/cases_sv.txt @@ -0,0 +1,6 @@ +cancer_study_identifier: rectal_radiation_msk_2024 +stable_id: rectal_radiation_msk_2024_sv +case_list_name: Samples with SV data +case_list_description: All samples with SV data +case_list_category: all_cases_with_sv_data +case_list_ids: P-0038170-T01-IM6 P-0018949-T01-IM6 P-0079151-T01-IM7 P-0032254-T01-IM6 P-0063124-T01-IM7 P-0035165-T01-IM6 P-0002902-T01-IM3 P-0076840-T01-IM7 P-0054770-T01-IM6 P-0011282-T01-IM5 P-0066749-T01-IM7 P-0015276-T01-IM6 P-0045190-T01-IM6 P-0029141-T01-IM6 P-0010422-T01-IM5 P-0039051-T01-IM6 P-0045906-T02-IM6 P-0065318-T01-IM7 P-0037948-T01-IM6 P-0038684-T01-IM6 P-0064170-T01-IM7 P-0063415-T01-IM7 P-0013159-T01-IM5 s_C_46D50X_P001_d01 s_C_5U25TR_P001_d01 s_C_CAYX31_P001_d01 s_C_EN5TM0_P001_d01 s_C_F2AN0K_P001_d01 s_C_H35PAE_P001_d01 s_C_M4FH1K_M001_d01 s_C_M90NHT_P001_d01 diff --git a/public/rectal_radiation_msk_2024/data_clinical_patient.txt b/public/rectal_radiation_msk_2024/data_clinical_patient.txt new file mode 100644 index 000000000..da0b7a959 --- /dev/null +++ b/public/rectal_radiation_msk_2024/data_clinical_patient.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:c17efb2fb1aae6724a1bddad57d57e82db503e91d76072b7399eb4471e0ce24b +size 6083 diff --git a/public/rectal_radiation_msk_2024/data_clinical_sample.txt b/public/rectal_radiation_msk_2024/data_clinical_sample.txt new file mode 100644 index 000000000..ed7506f58 --- /dev/null +++ b/public/rectal_radiation_msk_2024/data_clinical_sample.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:c8cd6cd7ce92185366535f39e7210324f1c18b4c819a2e7f6e099390978fca65 +size 11694 diff --git a/public/rectal_radiation_msk_2024/data_cna.txt b/public/rectal_radiation_msk_2024/data_cna.txt new file mode 100644 index 000000000..881a48488 --- /dev/null +++ b/public/rectal_radiation_msk_2024/data_cna.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:f43a6fa4de50170630f6a529e1235554bc57e23def393b06f3140b7b68e0c5a4 +size 157966 diff --git a/public/rectal_radiation_msk_2024/data_cna_hg19.seg b/public/rectal_radiation_msk_2024/data_cna_hg19.seg new file mode 100644 index 000000000..c65dfec7a --- /dev/null +++ b/public/rectal_radiation_msk_2024/data_cna_hg19.seg @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:4748670b9d70a07a0e42d2cfdcd41510e46caea95ce6db77d63cc20f0599ad0d +size 92660 diff --git a/public/rectal_radiation_msk_2024/data_gene_panel_matrix.txt b/public/rectal_radiation_msk_2024/data_gene_panel_matrix.txt new file mode 100644 index 000000000..90980582b --- /dev/null +++ b/public/rectal_radiation_msk_2024/data_gene_panel_matrix.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:e28b7dd78cc3722daab735a364b5782f8eb702120eb285a4ccdee9a56f66ef8c +size 2105 diff --git a/public/rectal_radiation_msk_2024/data_mutational_signature_pvalue.txt b/public/rectal_radiation_msk_2024/data_mutational_signature_pvalue.txt new file mode 100644 index 000000000..bd826049b --- /dev/null +++ b/public/rectal_radiation_msk_2024/data_mutational_signature_pvalue.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:0a9ff88c7bd409934c6035d18f5c9f004b84397d97ebda2b2a03a2ec3fa99fb9 +size 11212 diff --git a/public/rectal_radiation_msk_2024/data_mutational_signatures_contribution_SBS.txt b/public/rectal_radiation_msk_2024/data_mutational_signatures_contribution_SBS.txt new file mode 100644 index 000000000..702eddde4 --- /dev/null +++ b/public/rectal_radiation_msk_2024/data_mutational_signatures_contribution_SBS.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:4fa937b4e884d326655a9ff5100e660002851a6fe481285e98e63d6dc428f2f2 +size 26186 diff --git a/public/rectal_radiation_msk_2024/data_mutations.txt b/public/rectal_radiation_msk_2024/data_mutations.txt new file mode 100644 index 000000000..0a971ddcd --- /dev/null +++ b/public/rectal_radiation_msk_2024/data_mutations.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:bc9d4924183dd3b7b3fc8b631373b2916e5bd9191e80804381c4bfe969dfe2ca +size 1087410 diff --git a/public/rectal_radiation_msk_2024/data_sv.txt b/public/rectal_radiation_msk_2024/data_sv.txt new file mode 100644 index 000000000..601403e9f --- /dev/null +++ b/public/rectal_radiation_msk_2024/data_sv.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:9a7f9a3d1b8e44642ef23c3d8ebe02385d5e9d2d805e0a0c63293964a82d2402 +size 2417 diff --git a/public/rectal_radiation_msk_2024/meta_clinical_patient.txt b/public/rectal_radiation_msk_2024/meta_clinical_patient.txt new file mode 100644 index 000000000..3618a6bb0 --- /dev/null +++ b/public/rectal_radiation_msk_2024/meta_clinical_patient.txt @@ -0,0 +1,4 @@ +cancer_study_identifier: rectal_radiation_msk_2024 +data_filename: data_clinical_patient.txt +genetic_alteration_type: CLINICAL +datatype: PATIENT_ATTRIBUTES diff --git a/public/rectal_radiation_msk_2024/meta_clinical_sample.txt b/public/rectal_radiation_msk_2024/meta_clinical_sample.txt new file mode 100644 index 000000000..61b23aef7 --- /dev/null +++ b/public/rectal_radiation_msk_2024/meta_clinical_sample.txt @@ -0,0 +1,4 @@ +cancer_study_identifier: rectal_radiation_msk_2024 +data_filename: data_clinical_sample.txt +genetic_alteration_type: CLINICAL +datatype: SAMPLE_ATTRIBUTES diff --git a/public/rectal_radiation_msk_2024/meta_cna.txt b/public/rectal_radiation_msk_2024/meta_cna.txt new file mode 100644 index 000000000..aeaacf7f9 --- /dev/null +++ b/public/rectal_radiation_msk_2024/meta_cna.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: rectal_radiation_msk_2024 +stable_id: cna +profile_name: Putative Copy-Number Alterations +profile_description: Putative copy-number calls. Values: -2 = homozygous deletion; -1 = hemizygous deletion; 0 = neutral / no change; 1 = gain; 2 = high level amplification. +genetic_alteration_type: COPY_NUMBER_ALTERATION +datatype: DISCRETE +data_filename: data_cna.txt +show_profile_in_analysis_tab: true diff --git a/public/rectal_radiation_msk_2024/meta_cna_hg19_seg.txt b/public/rectal_radiation_msk_2024/meta_cna_hg19_seg.txt new file mode 100644 index 000000000..d587441d9 --- /dev/null +++ b/public/rectal_radiation_msk_2024/meta_cna_hg19_seg.txt @@ -0,0 +1,6 @@ +cancer_study_identifier: rectal_radiation_msk_2024 +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/rectal_radiation_msk_2024/meta_gene_panel_matrix.txt b/public/rectal_radiation_msk_2024/meta_gene_panel_matrix.txt new file mode 100644 index 000000000..c4cc86bf9 --- /dev/null +++ b/public/rectal_radiation_msk_2024/meta_gene_panel_matrix.txt @@ -0,0 +1,4 @@ +cancer_study_identifier: rectal_radiation_msk_2024 +genetic_alteration_type: GENE_PANEL_MATRIX +datatype: GENE_PANEL_MATRIX +data_filename: data_gene_panel_matrix.txt diff --git a/public/rectal_radiation_msk_2024/meta_mutational_signature_pvalue.txt b/public/rectal_radiation_msk_2024/meta_mutational_signature_pvalue.txt new file mode 100644 index 000000000..d31b0bb0d --- /dev/null +++ b/public/rectal_radiation_msk_2024/meta_mutational_signature_pvalue.txt @@ -0,0 +1,10 @@ +cancer_study_identifier: rectal_radiation_msk_2024 +genetic_alteration_type: GENERIC_ASSAY +generic_assay_type: MUTATIONAL_SIGNATURE +datatype: LIMIT-VALUE +stable_id: mutational_signature_pvalue +profile_name: Mutational Signature P-Value +profile_description: profile for pvalue of mutational signatures +data_filename: data_mutational_signature_pvalue.txt +show_profile_in_analysis_tab: true +generic_entity_meta_properties: NAME \ No newline at end of file diff --git a/public/rectal_radiation_msk_2024/meta_mutational_signatures_contribution_SBS.txt b/public/rectal_radiation_msk_2024/meta_mutational_signatures_contribution_SBS.txt new file mode 100644 index 000000000..e4596f853 --- /dev/null +++ b/public/rectal_radiation_msk_2024/meta_mutational_signatures_contribution_SBS.txt @@ -0,0 +1,12 @@ +cancer_study_identifier: rectal_radiation_msk_2024 +genetic_alteration_type: GENERIC_ASSAY +generic_assay_type: MUTATIONAL_SIGNATURE +datatype: LIMIT-VALUE +stable_id: mutational_signatures_contribution_SBS +profile_name: Mutational Signatures Contribution SBS +profile_description: Mutational signature contribution, calculated using the algorithm implemented in https://github.com/mskcc/mutation-signatures. +data_filename: data_mutational_signatures_contribution_SBS.txt +show_profile_in_analysis_tab: true +generic_entity_meta_properties: NAME,DESCRIPTION,URL +value_sort_order: DESC +pivot_threshold_value: 0.0 \ No newline at end of file diff --git a/public/rectal_radiation_msk_2024/meta_mutations.txt b/public/rectal_radiation_msk_2024/meta_mutations.txt new file mode 100644 index 000000000..b7fc1d65f --- /dev/null +++ b/public/rectal_radiation_msk_2024/meta_mutations.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: rectal_radiation_msk_2024 +data_filename: data_mutations.txt +stable_id: mutations +genetic_alteration_type: MUTATION_EXTENDED +datatype: MAF +show_profile_in_analysis_tab: TRUE +profile_name: Mutations +profile_description: Mutation data from WES and targeted sequencing. diff --git a/public/rectal_radiation_msk_2024/meta_study.txt b/public/rectal_radiation_msk_2024/meta_study.txt new file mode 100644 index 000000000..9ef019985 --- /dev/null +++ b/public/rectal_radiation_msk_2024/meta_study.txt @@ -0,0 +1,7 @@ +cancer_study_identifier: rectal_radiation_msk_2024 +type_of_cancer: coadread +name: Secondary Rectal Cancers (MSK, JAMA Netw Open 2025) +description: Whole exome and targeted sequencing of 48 secondary rectal adenocarcinoma samples via MSK-IMPACT and their matched normals. +reference_genome: hg19 +citation: Omer DM et al. JAMA Netw Open 2025 +pmid: 40100215 \ No newline at end of file diff --git a/public/rectal_radiation_msk_2024/meta_sv.txt b/public/rectal_radiation_msk_2024/meta_sv.txt new file mode 100644 index 000000000..decdc0886 --- /dev/null +++ b/public/rectal_radiation_msk_2024/meta_sv.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: rectal_radiation_msk_2024 +data_filename: data_sv.txt +stable_id: structural_variants +genetic_alteration_type: STRUCTURAL_VARIANT +datatype: SV +show_profile_in_analysis_tab: TRUE +profile_name: Structural Variants +profile_description: Structural Variant Data