PMID addition: CHORD & ctDNA (#2099)

* pmid addtion * Update meta_study.txt * Update meta_study.txt --------- Co-authored-by: RAlhamad <[email protected]> Co-authored-by: Ramya Madupuri <[email protected]>
cBioPortal · Nov 11, 2024 · 1b3c287 · 1b3c287
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diff --git a/public/msk_chord_2024/meta_study.txt b/public/msk_chord_2024/meta_study.txt
@@ -1,4 +1,6 @@
 type_of_cancer: mixed
 cancer_study_identifier: msk_chord_2024
 name: MSK-CHORD (MSK, Nature 2024)
-description: Targeted sequencing of 25040 tumors from 24950 patients and their matched normals via MSK-IMPACT, along with clinical annotations, some of which are derived from natural language processing (denoted NLP). 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>. For commercial use, please contact <a href="mailto: [email protected]">[email protected]</a>
+description: Targeted sequencing of 25040 tumors from 24950 patients and their matched normals via MSK-IMPACT, along with clinical annotations, some of which are derived from natural language processing (denoted NLP). 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>. For commercial use, please contact <a href="mailto: [email protected]">[email protected]</a>
+pmid: 39506116
+citation: Jee, Justin et al. Nature 2024
diff --git a/public/msk_ctdna_vte_2024/case_lists/cases_all.txt b/public/msk_ctdna_vte_2024/case_lists/cases_all.txt
diff --git a/public/msk_ctdna_vte_2024/case_lists/cases_cna.txt b/public/msk_ctdna_vte_2024/case_lists/cases_cna.txt
diff --git a/public/msk_ctdna_vte_2024/case_lists/cases_cnaseq.txt b/public/msk_ctdna_vte_2024/case_lists/cases_cnaseq.txt
diff --git a/public/msk_ctdna_vte_2024/case_lists/cases_sequenced.txt b/public/msk_ctdna_vte_2024/case_lists/cases_sequenced.txt
diff --git a/public/msk_ctdna_vte_2024/case_lists/cases_sv.txt b/public/msk_ctdna_vte_2024/case_lists/cases_sv.txt
diff --git a/public/msk_ctdna_vte_2024/data_clinical_patient.txt b/public/msk_ctdna_vte_2024/data_clinical_patient.txt
diff --git a/public/msk_ctdna_vte_2024/data_clinical_sample.txt b/public/msk_ctdna_vte_2024/data_clinical_sample.txt
diff --git a/public/msk_ctdna_vte_2024/data_cna.txt b/public/msk_ctdna_vte_2024/data_cna.txt
diff --git a/public/msk_ctdna_vte_2024/data_gene_panel_matrix.txt b/public/msk_ctdna_vte_2024/data_gene_panel_matrix.txt
diff --git a/public/msk_ctdna_vte_2024/data_mutations.txt b/public/msk_ctdna_vte_2024/data_mutations.txt
diff --git a/public/msk_ctdna_vte_2024/data_sv.txt b/public/msk_ctdna_vte_2024/data_sv.txt
diff --git a/public/msk_ctdna_vte_2024/meta_clinical_patient.txt b/public/msk_ctdna_vte_2024/meta_clinical_patient.txt
@@ -0,0 +1,4 @@
+cancer_study_identifier: msk_ctdna_vte_2024
+genetic_alteration_type: CLINICAL
+datatype: PATIENT_ATTRIBUTES
+data_filename: data_clinical_patient.txt
diff --git a/public/msk_ctdna_vte_2024/meta_clinical_sample.txt b/public/msk_ctdna_vte_2024/meta_clinical_sample.txt
@@ -0,0 +1,4 @@
+cancer_study_identifier: msk_ctdna_vte_2024
+genetic_alteration_type: CLINICAL
+datatype: SAMPLE_ATTRIBUTES
+data_filename: data_clinical_sample.txt
diff --git a/public/msk_ctdna_vte_2024/meta_cna.txt b/public/msk_ctdna_vte_2024/meta_cna.txt
@@ -0,0 +1,8 @@
+cancer_study_identifier: msk_ctdna_vte_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, HEME on Illumina HiSeq sequencers.
+datatype: DISCRETE
+data_filename: data_cna.txt
+stable_id: gistic
diff --git a/public/msk_ctdna_vte_2024/meta_gene_panel_matrix.txt b/public/msk_ctdna_vte_2024/meta_gene_panel_matrix.txt
@@ -0,0 +1,4 @@
+cancer_study_identifier: msk_ctdna_vte_2024
+data_filename: data_gene_panel_matrix.txt
+genetic_alteration_type: GENE_PANEL_MATRIX
+datatype: GENE_PANEL_MATRIX
diff --git a/public/msk_ctdna_vte_2024/meta_mutations.txt b/public/msk_ctdna_vte_2024/meta_mutations.txt
@@ -0,0 +1,8 @@
+cancer_study_identifier: msk_ctdna_vte_2024
+genetic_alteration_type: MUTATION_EXTENDED
+datatype: MAF
+profile_name: Mutations
+profile_description: Mutation data from MSK-IMPACT, HEME.
+show_profile_in_analysis_tab: true
+data_filename: data_mutations.txt
+stable_id: mutations
diff --git a/public/msk_ctdna_vte_2024/meta_study.txt b/public/msk_ctdna_vte_2024/meta_study.txt
@@ -0,0 +1,6 @@
+type_of_cancer: mixed
+cancer_study_identifier: msk_ctdna_vte_2024
+name: MSK ctDNA Sequencing Cohort (MSK, Nature Medicine 2024)
+description: Targeted sequencing of 5,567 cancer patient ctDNA samples via MSK-ACCESS.
+pmid: 39147831
+citation: Justin et al. Nat Med 2024
diff --git a/public/msk_ctdna_vte_2024/meta_sv.txt b/public/msk_ctdna_vte_2024/meta_sv.txt
@@ -0,0 +1,8 @@
+cancer_study_identifier: msk_ctdna_vte_2024
+genetic_alteration_type: STRUCTURAL_VARIANT
+datatype: SV
+profile_name: Structural Variants
+profile_description: Structural Variants
+show_profile_in_analysis_tab: true
+data_filename: data_sv.txt
+stable_id: structural_variants