December Public Release Studies (#2097)

* december release studies * review fixes * error fix * error fix * error fix * updated the journal * updates * review updates * update * Update meta_study.txt * Update meta_study.txt * Update meta_study.txt * Update meta_study.txt * Update meta_study.txt * Update meta_study.txt * removed treat * remove study * fix error * Update meta_study.txt * Update meta_study.txt * Update meta_study.txt * Update meta_study.txt * Update meta_study.txt --------- Co-authored-by: RAlhamad <[email protected]> Co-authored-by: sbabyanusha <[email protected]> Co-authored-by: sbabyanusha <[email protected]>
cBioPortal · Dec 18, 2024 · 854c4a4 · 854c4a4
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diff --git a/public/asclc_msk_2024/case_lists/cases_all.txt b/public/asclc_msk_2024/case_lists/cases_all.txt
@@ -0,0 +1,6 @@
+cancer_study_identifier: asclc_msk_2024
+stable_id: asclc_msk_2024_all
+case_list_name: All samples
+case_list_description: All samples (31 samples)
+case_list_category: all_cases_in_study
+case_list_ids: P-0020333-T01-IM6	P-0039631-T04-IM6	P-0039208-T02-IM6	P-0013002-T01-IM5	P-0046178-T03-IM6	P-0038280-T02-IM6	P-0010928-T01-IM5	P-0004452-T02-IM7	P-0070307-T02-IM7	P-0026198-T01-IM6	P-0060626-T01-IM7	P-0002797-T01-IM3	P-0079554-T02-IM7	P-0045246-T01-IM6	P-0010928-T02-IM6	P-0039631-T05-IM6	P-0038280-T01-IM6	P-0046178-T02-IM6	P-0038280-T03-IM6	P-0026198-T02-IM6	P-0079554-T01-IM7	P-0038280-T05-IM7	P-0020429-T01-IM6	P-0004452-T01-IM5	P-0039208-T01-IM6	P-0070901-T01-IM7	P-0039631-T01-IM6	P-0044597-T01-IM6	P-0012905-T01-IM5	P-0004394-T01-IM5	P-0073997-T01-IM7
diff --git a/public/asclc_msk_2024/case_lists/cases_cna.txt b/public/asclc_msk_2024/case_lists/cases_cna.txt
@@ -0,0 +1,6 @@
+cancer_study_identifier: asclc_msk_2024
+stable_id: asclc_msk_2024_cna
+case_list_name: Samples with CNA data
+case_list_description: Samples with CNA data (31 samples)
+case_list_category: all_cases_with_cna_data
+case_list_ids: P-0020333-T01-IM6	P-0039631-T04-IM6	P-0039208-T02-IM6	P-0013002-T01-IM5	P-0046178-T03-IM6	P-0038280-T02-IM6	P-0010928-T01-IM5	P-0004452-T02-IM7	P-0070307-T02-IM7	P-0026198-T01-IM6	P-0060626-T01-IM7	P-0002797-T01-IM3	P-0079554-T02-IM7	P-0045246-T01-IM6	P-0010928-T02-IM6	P-0039631-T05-IM6	P-0038280-T01-IM6	P-0046178-T02-IM6	P-0038280-T03-IM6	P-0026198-T02-IM6	P-0079554-T01-IM7	P-0038280-T05-IM7	P-0020429-T01-IM6	P-0004452-T01-IM5	P-0039208-T01-IM6	P-0070901-T01-IM7	P-0039631-T01-IM6	P-0044597-T01-IM6	P-0012905-T01-IM5	P-0004394-T01-IM5	P-0073997-T01-IM7
diff --git a/public/asclc_msk_2024/case_lists/cases_cnaseq.txt b/public/asclc_msk_2024/case_lists/cases_cnaseq.txt
@@ -0,0 +1,6 @@
+cancer_study_identifier: asclc_msk_2024
+stable_id: asclc_msk_2024_cnaseq
+case_list_name: Samples with mutation and CNA data
+case_list_description: Samples with mutation and CNA data (31 samples)
+case_list_category: all_cases_with_mutation_and_cna_data
+case_list_ids: P-0020333-T01-IM6	P-0039631-T04-IM6	P-0039208-T02-IM6	P-0013002-T01-IM5	P-0046178-T03-IM6	P-0038280-T02-IM6	P-0010928-T01-IM5	P-0004452-T02-IM7	P-0070307-T02-IM7	P-0026198-T01-IM6	P-0060626-T01-IM7	P-0002797-T01-IM3	P-0079554-T02-IM7	P-0045246-T01-IM6	P-0010928-T02-IM6	P-0039631-T05-IM6	P-0038280-T01-IM6	P-0046178-T02-IM6	P-0038280-T03-IM6	P-0026198-T02-IM6	P-0079554-T01-IM7	P-0038280-T05-IM7	P-0020429-T01-IM6	P-0004452-T01-IM5	P-0039208-T01-IM6	P-0070901-T01-IM7	P-0039631-T01-IM6	P-0044597-T01-IM6	P-0012905-T01-IM5	P-0004394-T01-IM5	P-0073997-T01-IM7
diff --git a/public/asclc_msk_2024/case_lists/cases_mrna_seq_tpm.txt b/public/asclc_msk_2024/case_lists/cases_mrna_seq_tpm.txt
@@ -0,0 +1,6 @@
+cancer_study_identifier: asclc_msk_2024
+stable_id: asclc_msk_2024_rna_seq_mrna
+case_list_name: Samples with mRNA data (RNA Seq TPM)
+case_list_description: Samples with mRNA expression data (31 samples)
+case_list_category: all_cases_with_mrna_rnaseq_data
+case_list_ids: P-0020333-T01-IM6	P-0039631-T04-IM6	P-0039208-T02-IM6	P-0013002-T01-IM5	P-0046178-T03-IM6	P-0038280-T02-IM6	P-0010928-T01-IM5	P-0004452-T02-IM7	P-0070307-T02-IM7	P-0026198-T01-IM6	P-0060626-T01-IM7	P-0002797-T01-IM3	P-0079554-T02-IM7	P-0045246-T01-IM6	P-0010928-T02-IM6	P-0039631-T05-IM6	P-0038280-T01-IM6	P-0046178-T02-IM6	P-0038280-T03-IM6	P-0026198-T02-IM6	P-0079554-T01-IM7	P-0038280-T05-IM7	P-0020429-T01-IM6	P-0004452-T01-IM5	P-0039208-T01-IM6	P-0070901-T01-IM7	P-0039631-T01-IM6	P-0044597-T01-IM6	P-0012905-T01-IM5	P-0004394-T01-IM5	P-0073997-T01-IM7
diff --git a/public/asclc_msk_2024/case_lists/cases_sequenced.txt b/public/asclc_msk_2024/case_lists/cases_sequenced.txt
@@ -0,0 +1,6 @@
+cancer_study_identifier: asclc_msk_2024
+stable_id: asclc_msk_2024_sequenced
+case_list_name: Samples with mutation data
+case_list_description: Samples with mutation data (31 samples)
+case_list_category: all_cases_with_mutation_data
+case_list_ids: P-0020333-T01-IM6	P-0039631-T04-IM6	P-0039208-T02-IM6	P-0013002-T01-IM5	P-0046178-T03-IM6	P-0038280-T02-IM6	P-0010928-T01-IM5	P-0004452-T02-IM7	P-0070307-T02-IM7	P-0026198-T01-IM6	P-0060626-T01-IM7	P-0002797-T01-IM3	P-0079554-T02-IM7	P-0045246-T01-IM6	P-0010928-T02-IM6	P-0039631-T05-IM6	P-0038280-T01-IM6	P-0046178-T02-IM6	P-0038280-T03-IM6	P-0026198-T02-IM6	P-0079554-T01-IM7	P-0038280-T05-IM7	P-0020429-T01-IM6	P-0004452-T01-IM5	P-0039208-T01-IM6	P-0070901-T01-IM7	P-0039631-T01-IM6	P-0044597-T01-IM6	P-0012905-T01-IM5	P-0004394-T01-IM5	P-0073997-T01-IM7
diff --git a/public/asclc_msk_2024/case_lists/cases_sv.txt b/public/asclc_msk_2024/case_lists/cases_sv.txt
@@ -0,0 +1,6 @@
+cancer_study_identifier: asclc_msk_2024
+stable_id: asclc_msk_2024_sv
+case_list_name: Samples with SV data
+case_list_description: All samples with SV data (31 samples)
+case_list_category: all_cases_with_sv_data
+case_list_ids: P-0020333-T01-IM6	P-0039631-T04-IM6	P-0039208-T02-IM6	P-0013002-T01-IM5	P-0046178-T03-IM6	P-0038280-T02-IM6	P-0010928-T01-IM5	P-0004452-T02-IM7	P-0070307-T02-IM7	P-0026198-T01-IM6	P-0060626-T01-IM7	P-0002797-T01-IM3	P-0079554-T02-IM7	P-0045246-T01-IM6	P-0010928-T02-IM6	P-0039631-T05-IM6	P-0038280-T01-IM6	P-0046178-T02-IM6	P-0038280-T03-IM6	P-0026198-T02-IM6	P-0079554-T01-IM7	P-0038280-T05-IM7	P-0020429-T01-IM6	P-0004452-T01-IM5	P-0039208-T01-IM6	P-0070901-T01-IM7	P-0039631-T01-IM6	P-0044597-T01-IM6	P-0012905-T01-IM5	P-0004394-T01-IM5	P-0073997-T01-IM7
diff --git a/public/asclc_msk_2024/data_clinical_patient.txt b/public/asclc_msk_2024/data_clinical_patient.txt
diff --git a/public/asclc_msk_2024/data_clinical_sample.txt b/public/asclc_msk_2024/data_clinical_sample.txt
diff --git a/public/asclc_msk_2024/data_cna.txt b/public/asclc_msk_2024/data_cna.txt
diff --git a/public/asclc_msk_2024/data_cna_hg19.seg b/public/asclc_msk_2024/data_cna_hg19.seg
diff --git a/public/asclc_msk_2024/data_gene_panel_matrix.txt b/public/asclc_msk_2024/data_gene_panel_matrix.txt
diff --git a/public/asclc_msk_2024/data_mrna_seq_tpm.txt b/public/asclc_msk_2024/data_mrna_seq_tpm.txt
diff --git a/public/asclc_msk_2024/data_mrna_seq_tpm_zscores_ref_all_samples.txt b/public/asclc_msk_2024/data_mrna_seq_tpm_zscores_ref_all_samples.txt
diff --git a/public/asclc_msk_2024/data_mutations.txt b/public/asclc_msk_2024/data_mutations.txt
diff --git a/public/asclc_msk_2024/data_sv.txt b/public/asclc_msk_2024/data_sv.txt
diff --git a/public/asclc_msk_2024/data_timeline_diagnosis.txt b/public/asclc_msk_2024/data_timeline_diagnosis.txt
diff --git a/public/asclc_msk_2024/data_timeline_pdl1.txt b/public/asclc_msk_2024/data_timeline_pdl1.txt
diff --git a/public/asclc_msk_2024/data_timeline_prior_meds.txt b/public/asclc_msk_2024/data_timeline_prior_meds.txt
diff --git a/public/asclc_msk_2024/data_timeline_radiation.txt b/public/asclc_msk_2024/data_timeline_radiation.txt
diff --git a/public/asclc_msk_2024/data_timeline_specimen.txt b/public/asclc_msk_2024/data_timeline_specimen.txt
diff --git a/public/asclc_msk_2024/data_timeline_specimen_surgery.txt b/public/asclc_msk_2024/data_timeline_specimen_surgery.txt
diff --git a/public/asclc_msk_2024/data_timeline_surgery.txt b/public/asclc_msk_2024/data_timeline_surgery.txt
diff --git a/public/asclc_msk_2024/data_timeline_timeline_follow_up.txt b/public/asclc_msk_2024/data_timeline_timeline_follow_up.txt
diff --git a/public/asclc_msk_2024/data_timeline_treatment.txt b/public/asclc_msk_2024/data_timeline_treatment.txt
diff --git a/public/asclc_msk_2024/data_timeline_tumor_sites.txt b/public/asclc_msk_2024/data_timeline_tumor_sites.txt
diff --git a/public/asclc_msk_2024/meta_clinical_patient.txt b/public/asclc_msk_2024/meta_clinical_patient.txt
@@ -0,0 +1,4 @@
+cancer_study_identifier: asclc_msk_2024
+data_filename: data_clinical_patient.txt
+genetic_alteration_type: CLINICAL
+datatype: PATIENT_ATTRIBUTES
diff --git a/public/asclc_msk_2024/meta_clinical_sample.txt b/public/asclc_msk_2024/meta_clinical_sample.txt
@@ -0,0 +1,4 @@
+cancer_study_identifier: asclc_msk_2024
+data_filename: data_clinical_sample.txt
+genetic_alteration_type: CLINICAL
+datatype: SAMPLE_ATTRIBUTES
diff --git a/public/asclc_msk_2024/meta_cna.txt b/public/asclc_msk_2024/meta_cna.txt
@@ -0,0 +1,8 @@
+cancer_study_identifier: asclc_msk_2024
+genetic_alteration_type: COPY_NUMBER_ALTERATION
+show_profile_in_analysis_tab: true
+profile_name: Copy Number Alterations (MSK-IMPACT, HEME)
+profile_description: Copy number alterations from targeted sequencing via MK-IMPACT on Illumina HiSeq sequencers.
+datatype: DISCRETE
+data_filename: data_cna.txt
+stable_id: cna
diff --git a/public/asclc_msk_2024/meta_cna_hg19_seg.txt b/public/asclc_msk_2024/meta_cna_hg19_seg.txt
@@ -0,0 +1,9 @@
+cancer_study_identifier: asclc_msk_2024
+data_filename: data_cna_hg19.seg
+genetic_alteration_type: COPY_NUMBER_ALTERATION
+datatype: SEG
+show_profile_in_analysis_tab: FALSE
+profile_name: Segment data values
+profile_description: Somatic CNA data (copy number ratio from tumor samples minus ratio from matched normals) 
+reference_genome_id: hg19
+description: segment data for asclc_msk_2024 study
diff --git a/public/asclc_msk_2024/meta_gene_panel_matrix.txt b/public/asclc_msk_2024/meta_gene_panel_matrix.txt
@@ -0,0 +1,4 @@
+cancer_study_identifier: asclc_msk_2024
+genetic_alteration_type: GENE_PANEL_MATRIX
+datatype: GENE_PANEL_MATRIX
+data_filename: data_gene_panel_matrix.txt
diff --git a/public/asclc_msk_2024/meta_mrna_seq_tpm.txt b/public/asclc_msk_2024/meta_mrna_seq_tpm.txt
@@ -0,0 +1,9 @@
+cancer_study_identifier: asclc_msk_2024
+genetic_alteration_type: MRNA_EXPRESSION
+datatype: CONTINUOUS
+data_filename: data_mrna_seq_tpm.txt
+stable_id: mrna_seq_tpm
+show_profile_in_analysis_tab: FALSE
+profile_description: mRNA Expression (TPM)
+profile_name: mRNA expression normalized counts (TPM)
+source_stable_id: rna_seq_mrna
diff --git a/public/asclc_msk_2024/meta_mrna_seq_tpm_zscores_ref_all_samples.txt b/public/asclc_msk_2024/meta_mrna_seq_tpm_zscores_ref_all_samples.txt
@@ -0,0 +1,8 @@
+cancer_study_identifier: asclc_msk_2024
+genetic_alteration_type: MRNA_EXPRESSION
+datatype: Z-SCORE
+stable_id: mrna_seq_tpm_all_sample_Zscores
+show_profile_in_analysis_tab: true
+profile_name: mRNA expression z-scores (TPM)
+profile_description: Expression levels z-scores (TPM)
+data_filename: data_mrna_seq_tpm_zscores_ref_all_samples.txt
diff --git a/public/asclc_msk_2024/meta_mutations.txt b/public/asclc_msk_2024/meta_mutations.txt
@@ -0,0 +1,8 @@
+cancer_study_identifier: asclc_msk_2024
+genetic_alteration_type: MUTATION_EXTENDED
+datatype: MAF
+stable_id: mutations
+show_profile_in_analysis_tab: true
+profile_description: Somatic mutation data from targeted sequencing of 31 lung cancer samples
+profile_name: Mutations
+data_filename: data_mutations.txt
diff --git a/public/asclc_msk_2024/meta_study.txt b/public/asclc_msk_2024/meta_study.txt
@@ -0,0 +1,6 @@
+cancer_study_identifier: asclc_msk_2024
+type_of_cancer: lung
+name: Atypical Small Cell Lung Cancer (MSK, Cancer Discov 2024)
+description: Targeted sequencing of 31 atypical small cell lung cancers lacking RB1 and TP53 co-inactivation and their matched normals via MSK-IMPACT, including structural variant analysis via whole-genome sequencing. This data is available under the <a href="https://creativecommons.org/licenses/by-nc-nd/4.0/deed.en">Creative Commons BY-NC-ND 4.0 license</a>.
+pmid: 39185963
+citation: Rekhtman N et al. Cancer Discov 2024
diff --git a/public/asclc_msk_2024/meta_sv.txt b/public/asclc_msk_2024/meta_sv.txt
@@ -0,0 +1,8 @@
+cancer_study_identifier: asclc_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 (WGS)
+profile_description: Structural variant data through whole-genome sequencing. 
diff --git a/public/asclc_msk_2024/meta_timeline_diagnosistxt.txt b/public/asclc_msk_2024/meta_timeline_diagnosistxt.txt
@@ -0,0 +1,4 @@
+cancer_study_identifier: asclc_msk_2024
+data_filename: data_timeline_diagnosis.txt
+genetic_alteration_type: CLINICAL
+datatype: TIMELINE
diff --git a/public/asclc_msk_2024/meta_timeline_pdl1.txt b/public/asclc_msk_2024/meta_timeline_pdl1.txt
@@ -0,0 +1,4 @@
+cancer_study_identifier: asclc_msk_2024
+data_filename: data_timeline_pdl1.txt
+genetic_alteration_type: CLINICAL
+datatype: TIMELINE
diff --git a/public/asclc_msk_2024/meta_timeline_prior_meds.txt b/public/asclc_msk_2024/meta_timeline_prior_meds.txt
@@ -0,0 +1,4 @@
+cancer_study_identifier: asclc_msk_2024
+data_filename: data_timeline_prior_meds.txt
+genetic_alteration_type: CLINICAL
+datatype: TIMELINE
diff --git a/public/asclc_msk_2024/meta_timeline_radiation.txt b/public/asclc_msk_2024/meta_timeline_radiation.txt
@@ -0,0 +1,4 @@
+cancer_study_identifier: asclc_msk_2024
+data_filename: data_timeline_radiation.txt
+genetic_alteration_type: CLINICAL
+datatype: TIMELINE
diff --git a/public/asclc_msk_2024/meta_timeline_specimen.txt b/public/asclc_msk_2024/meta_timeline_specimen.txt
@@ -0,0 +1,4 @@
+cancer_study_identifier: asclc_msk_2024
+data_filename: data_timeline_specimen.txt
+genetic_alteration_type: CLINICAL
+datatype: TIMELINE
diff --git a/public/asclc_msk_2024/meta_timeline_specimen_surgery.txt b/public/asclc_msk_2024/meta_timeline_specimen_surgery.txt
@@ -0,0 +1,4 @@
+cancer_study_identifier: asclc_msk_2024
+data_filename: data_timeline_specimen_surgery.txt
+genetic_alteration_type: CLINICAL
+datatype: TIMELINE
diff --git a/public/asclc_msk_2024/meta_timeline_surgery.txt b/public/asclc_msk_2024/meta_timeline_surgery.txt
@@ -0,0 +1,4 @@
+cancer_study_identifier: asclc_msk_2024
+data_filename: data_timeline_surgery.txt
+genetic_alteration_type: CLINICAL
+datatype: TIMELINE
diff --git a/public/asclc_msk_2024/meta_timeline_timeline_follow_up.txt b/public/asclc_msk_2024/meta_timeline_timeline_follow_up.txt
@@ -0,0 +1,4 @@
+cancer_study_identifier: asclc_msk_2024
+data_filename: data_timeline_timeline_follow_up.txt
+genetic_alteration_type: CLINICAL
+datatype: TIMELINE
diff --git a/public/asclc_msk_2024/meta_timeline_treatment.txt b/public/asclc_msk_2024/meta_timeline_treatment.txt
@@ -0,0 +1,4 @@
+cancer_study_identifier: asclc_msk_2024
+data_filename: data_timeline_treatment.txt
+genetic_alteration_type: CLINICAL
+datatype: TIMELINE
diff --git a/public/asclc_msk_2024/meta_timeline_tumor_sites.txt b/public/asclc_msk_2024/meta_timeline_tumor_sites.txt
@@ -0,0 +1,4 @@
+cancer_study_identifier: asclc_msk_2024
+data_filename: data_timeline_tumor_sites.txt
+genetic_alteration_type: CLINICAL
+datatype: TIMELINE
diff --git a/public/brca_dfci_2020/README.md b/public/brca_dfci_2020/README.md
@@ -0,0 +1,28 @@
+Study Curation and Transformation README 
+
+General information
+
+Curator name: Chizobam Ugboaja (Georgetown University 2024)
+Reference publication: 32404308
+Reference genome used: GRCh37
+
+Clinical Data
+
+Supplementary file: (Supplementary Table S1)
+Supplementary table title: (Clinical Samples Included in Landscape Analysis) Sample size: (59 samples and 58 patients)
+
+Timeline Data
+Supplementary file: (Supplementary Table S1)
+Prescription/treatment data obtained from clinical file
+
+Mutation Data
+
+Supplementary file: (Supplementary Table S3, Sheet 1) 
+Supplementary table title : (Exome and mutational information) 
+Reference genome: (GRCh37)
+
+Segmented Data
+Supplementary file: (Supplementary Table S3, Sheet 2)
+Supplementary table title : (CNVs - segment level)
+
+* NOTE: data pending from author include CNA, enrichment, and survival analysis*
diff --git a/public/brca_dfci_2020/case_lists/cases_all.txt b/public/brca_dfci_2020/case_lists/cases_all.txt
@@ -0,0 +1,6 @@
+cancer_study_identifier: brca_dfci_2020																																																											
+stable_id: brca_dfci_2020_all																																																											
+case_list_name: All samples																																																											
+case_list_description: All samples (59 samples)																																																											
+case_list_category: all_cases_in_study																																																											
+case_list_ids: 177_Prospective1	185_T1	191_T1	195_T1	260_T1	290_T2	292_T1	294_T2	295_T1	299_T1	303_T1	306_T1	307_T1	314_T1	315_T1	327_T1	329_T1	330_T1	331_T1	333_T1	338_T1	346_T1	349_T1	350_T1	357_T1	358_T1	361_T1	366_T2	372_T1	376_T2	381_T1	383_T1	385_T1	386_T1	387_T1	391_T1	394_T2	397_T1	398_T1	401_T1	408_T1A	408_T1B	430_T1	434_T1	452_T2	459_Archival1	473_T1	496_T1	509_T1	515_T1	516_T1	532_T1	535_T1	538_T1	552_T1	567_T1	568_T1	606_T1	614_T1
diff --git a/public/brca_dfci_2020/case_lists/cases_sequenced.txt b/public/brca_dfci_2020/case_lists/cases_sequenced.txt
@@ -0,0 +1,6 @@
+cancer_study_identifier: brca_dfci_2020
+stable_id: brca_dfci_2020_sequenced
+case_list_name: Samples with mutation data
+case_list_description: Samples with mutation data (59 samples)
+case_list_category: all_cases_with_mutation_data
+case_list_ids: 177_Prospective1	185_T1	191_T1	195_T1	260_T1	290_T2	292_T1	294_T2	295_T1	299_T1	303_T1	306_T1	307_T1	314_T1	315_T1	327_T1	329_T1	330_T1	331_T1	333_T1	338_T1	346_T1	349_T1	350_T1	357_T1	358_T1	361_T1	366_T2	372_T1	376_T2	381_T1	383_T1	385_T1	386_T1	387_T1	391_T1	394_T2	397_T1	398_T1	401_T1	408_T1A	408_T1B	430_T1	434_T1	452_T2	459_Archival1	473_T1	496_T1	509_T1	515_T1	516_T1	532_T1	535_T1	538_T1	552_T1	567_T1	568_T1	606_T1	614_T1
diff --git a/public/brca_dfci_2020/data_clinical_patient.txt b/public/brca_dfci_2020/data_clinical_patient.txt
diff --git a/public/brca_dfci_2020/data_clinical_sample.txt b/public/brca_dfci_2020/data_clinical_sample.txt
diff --git a/public/brca_dfci_2020/data_mutations.txt b/public/brca_dfci_2020/data_mutations.txt
diff --git a/public/brca_dfci_2020/meta_clinical_patient.txt b/public/brca_dfci_2020/meta_clinical_patient.txt
@@ -0,0 +1 @@
+cancer_study_identifier: brca_dfci_2020genetic_alteration_type: CLINICALdatatype: PATIENT_ATTRIBUTESdata_filename: data_clinical_patient.txt

diff --git a/public/brca_dfci_2020/meta_clinical_sample.txt b/public/brca_dfci_2020/meta_clinical_sample.txt
@@ -0,0 +1 @@
+cancer_study_identifier: brca_dfci_2020genetic_alteration_type: CLINICALdatatype: SAMPLE_ATTRIBUTESdata_filename: data_clinical_sample.txt

diff --git a/public/brca_dfci_2020/meta_mutations.txt b/public/brca_dfci_2020/meta_mutations.txt
@@ -0,0 +1 @@
+cancer_study_identifier: brca_dfci_2020data_filename: data_mutations.txtstable_id: mutationsgenetic_alteration_type: MUTATION_EXTENDEDdatatype: MAFshow_profile_in_analysis_tab: TRUEprofile_name: Mutationsprofile_description: Mutation data from whole exome sequencing.

diff --git a/public/brca_dfci_2020/meta_study.txt b/public/brca_dfci_2020/meta_study.txt
@@ -0,0 +1 @@
+type_of_cancer: brcacancer_study_identifier: brca_dfci_2020name: Metastatic Breast Cancer (DFCI, Cancer Discov 2020)description: Whole-exome sequencing of 59 CDK4/6i exposed metastatic breast cancer tumors and their matched normals.citation: Wander, Seth A et al. Cancer Discov 2020pmid: 32404308

diff --git a/public/hcc_msk_2024/case_lists/cases_all.txt b/public/hcc_msk_2024/case_lists/cases_all.txt
diff --git a/public/hcc_msk_2024/case_lists/cases_cna.txt b/public/hcc_msk_2024/case_lists/cases_cna.txt
diff --git a/public/hcc_msk_2024/case_lists/cases_cnaseq.txt b/public/hcc_msk_2024/case_lists/cases_cnaseq.txt
diff --git a/public/hcc_msk_2024/case_lists/cases_sequenced.txt b/public/hcc_msk_2024/case_lists/cases_sequenced.txt
diff --git a/public/hcc_msk_2024/case_lists/cases_sv.txt b/public/hcc_msk_2024/case_lists/cases_sv.txt
diff --git a/public/hcc_msk_2024/data_clinical_patient.txt b/public/hcc_msk_2024/data_clinical_patient.txt
diff --git a/public/hcc_msk_2024/data_clinical_sample.txt b/public/hcc_msk_2024/data_clinical_sample.txt
diff --git a/public/hcc_msk_2024/data_cna.txt b/public/hcc_msk_2024/data_cna.txt
diff --git a/public/hcc_msk_2024/data_cna_hg19.seg b/public/hcc_msk_2024/data_cna_hg19.seg
diff --git a/public/hcc_msk_2024/data_gene_panel_matrix.txt b/public/hcc_msk_2024/data_gene_panel_matrix.txt
diff --git a/public/hcc_msk_2024/data_mutations.txt b/public/hcc_msk_2024/data_mutations.txt
diff --git a/public/hcc_msk_2024/data_sv.txt b/public/hcc_msk_2024/data_sv.txt
diff --git a/public/hcc_msk_2024/meta_clinical_patient.txt b/public/hcc_msk_2024/meta_clinical_patient.txt
@@ -0,0 +1,4 @@
+cancer_study_identifier: hcc_msk_2024
+data_filename: data_clinical_patient.txt
+genetic_alteration_type: CLINICAL
+datatype: PATIENT_ATTRIBUTES
diff --git a/public/hcc_msk_2024/meta_clinical_sample.txt b/public/hcc_msk_2024/meta_clinical_sample.txt
@@ -0,0 +1,4 @@
+cancer_study_identifier: hcc_msk_2024
+data_filename: data_clinical_sample.txt
+genetic_alteration_type: CLINICAL
+datatype: SAMPLE_ATTRIBUTES
diff --git a/public/hcc_msk_2024/meta_cna.txt b/public/hcc_msk_2024/meta_cna.txt
@@ -0,0 +1,8 @@
+cancer_study_identifier: hcc_msk_2024
+genetic_alteration_type: COPY_NUMBER_ALTERATION
+show_profile_in_analysis_tab: true
+profile_name: Copy Number Alterations (MSK-IMPACT, HEME)
+profile_description: Copy number alterations from targeted sequencing via MK-IMPACT on Illumina HiSeq sequencers.
+datatype: DISCRETE
+data_filename: data_cna.txt
+stable_id: cna
diff --git a/public/hcc_msk_2024/meta_cna_hg19_seg.txt b/public/hcc_msk_2024/meta_cna_hg19_seg.txt
@@ -0,0 +1,9 @@
+cancer_study_identifier: hcc_msk_2024
+data_filename: data_cna_hg19.seg
+genetic_alteration_type: COPY_NUMBER_ALTERATION
+datatype: SEG
+show_profile_in_analysis_tab: FALSE
+profile_name: Segment data values
+profile_description: Somatic CNA data (copy number ratio from tumor samples minus ratio from matched normals) 
+reference_genome_id: hg19
+description: segment data for asclc_msk_2024 study
diff --git a/public/hcc_msk_2024/meta_gene_panel_matrix.txt b/public/hcc_msk_2024/meta_gene_panel_matrix.txt
@@ -0,0 +1,4 @@
+cancer_study_identifier: hcc_msk_2024
+genetic_alteration_type: GENE_PANEL_MATRIX
+datatype: GENE_PANEL_MATRIX
+data_filename: data_gene_panel_matrix.txt
diff --git a/public/hcc_msk_2024/meta_mutations.txt b/public/hcc_msk_2024/meta_mutations.txt
@@ -0,0 +1,8 @@
+cancer_study_identifier: hcc_msk_2024
+genetic_alteration_type: MUTATION_EXTENDED
+datatype: MAF
+stable_id: mutations
+show_profile_in_analysis_tab: true
+profile_description: Somatic mutation data from targeted sequencing samples.
+profile_name: Mutations
+data_filename: data_mutations.txt
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		@@ -0,0 +1 @@
		cancer_study_identifier: brca_dfci_2020genetic_alteration_type: CLINICALdatatype: PATIENT_ATTRIBUTESdata_filename: data_clinical_patient.txt
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		cancer_study_identifier: brca_dfci_2020data_filename: data_mutations.txtstable_id: mutationsgenetic_alteration_type: MUTATION_EXTENDEDdatatype: MAFshow_profile_in_analysis_tab: TRUEprofile_name: Mutationsprofile_description: Mutation data from whole exome sequencing.
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Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		type_of_cancer: brcacancer_study_identifier: brca_dfci_2020name: Metastatic Breast Cancer (DFCI, Cancer Discov 2020)description: Whole-exome sequencing of 59 CDK4/6i exposed metastatic breast cancer tumors and their matched normals.citation: Wander, Seth A et al. Cancer Discov 2020pmid: 32404308
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