Added study: Luad_mskcc_2023_met_organotropism (#1816)

* init * removed duplicate event
cBioPortal · Jun 21, 2023 · 737d198 · 737d198
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diff --git a/public/luad_mskcc_2023_met_organotropism/LICENSE b/public/luad_mskcc_2023_met_organotropism/LICENSE
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+TCGA data are available under Broad Institute GDAC TCGA Analysis Pipeline License. The Cancer Genome Atlas Consortium is pleased to provide the research community with preliminary data prior to publication. Users are requested to carefully consider that these data are preliminary and have yet to be validated. Researchers are warned that the preliminary data have a significant uncertainty, are likely to change, and should be used with caution.
diff --git a/public/luad_mskcc_2023_met_organotropism/Readme.txt b/public/luad_mskcc_2023_met_organotropism/Readme.txt
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+Gene panels for this study can be found here: https://github.com/cBioPortal/datahub/tree/master/reference_data/gene_panels
diff --git a/public/luad_mskcc_2023_met_organotropism/case_lists/cases_all.txt b/public/luad_mskcc_2023_met_organotropism/case_lists/cases_all.txt
diff --git a/public/luad_mskcc_2023_met_organotropism/case_lists/cases_cna.txt b/public/luad_mskcc_2023_met_organotropism/case_lists/cases_cna.txt
diff --git a/public/luad_mskcc_2023_met_organotropism/case_lists/cases_cnaseq.txt b/public/luad_mskcc_2023_met_organotropism/case_lists/cases_cnaseq.txt
diff --git a/public/luad_mskcc_2023_met_organotropism/case_lists/cases_sequenced.txt b/public/luad_mskcc_2023_met_organotropism/case_lists/cases_sequenced.txt
diff --git a/public/luad_mskcc_2023_met_organotropism/case_lists/cases_sv.txt b/public/luad_mskcc_2023_met_organotropism/case_lists/cases_sv.txt
diff --git a/public/luad_mskcc_2023_met_organotropism/data_clinical_patient.txt b/public/luad_mskcc_2023_met_organotropism/data_clinical_patient.txt
diff --git a/public/luad_mskcc_2023_met_organotropism/data_clinical_sample.txt b/public/luad_mskcc_2023_met_organotropism/data_clinical_sample.txt
diff --git a/public/luad_mskcc_2023_met_organotropism/data_cna.txt b/public/luad_mskcc_2023_met_organotropism/data_cna.txt
diff --git a/public/luad_mskcc_2023_met_organotropism/data_cna_hg19.seg b/public/luad_mskcc_2023_met_organotropism/data_cna_hg19.seg
diff --git a/public/luad_mskcc_2023_met_organotropism/data_gene_panel_matrix.txt b/public/luad_mskcc_2023_met_organotropism/data_gene_panel_matrix.txt
diff --git a/public/luad_mskcc_2023_met_organotropism/data_mutations.txt b/public/luad_mskcc_2023_met_organotropism/data_mutations.txt
diff --git a/public/luad_mskcc_2023_met_organotropism/data_sv.txt b/public/luad_mskcc_2023_met_organotropism/data_sv.txt
diff --git a/public/luad_mskcc_2023_met_organotropism/meta_clinical_patient.txt b/public/luad_mskcc_2023_met_organotropism/meta_clinical_patient.txt
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+cancer_study_identifier: luad_mskcc_2023_met_organotropism
+genetic_alteration_type: CLINICAL
+datatype: PATIENT_ATTRIBUTES
+data_filename: data_clinical_patient.txt
diff --git a/public/luad_mskcc_2023_met_organotropism/meta_clinical_sample.txt b/public/luad_mskcc_2023_met_organotropism/meta_clinical_sample.txt
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+cancer_study_identifier: luad_mskcc_2023_met_organotropism
+genetic_alteration_type: CLINICAL
+datatype: SAMPLE_ATTRIBUTES
+data_filename: data_clinical_sample.txt
diff --git a/public/luad_mskcc_2023_met_organotropism/meta_cna.txt b/public/luad_mskcc_2023_met_organotropism/meta_cna.txt
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+cancer_study_identifier: luad_mskcc_2023_met_organotropism
+genetic_alteration_type: COPY_NUMBER_ALTERATION
+datatype: DISCRETE
+stable_id: cna
+show_profile_in_analysis_tab: true
+profile_name: Putative copy-number alterations from GISTIC
+profile_description: Putative copy-number from GISTIC 2.0. Values: -2 = homozygous deletion; -1 = hemizygous deletion; 0 = neutral / no change; 1 = gain; 2 = high level amplification.
+data_filename: data_cna.txt
diff --git a/public/luad_mskcc_2023_met_organotropism/meta_cna_hg19_seg.txt b/public/luad_mskcc_2023_met_organotropism/meta_cna_hg19_seg.txt
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+cancer_study_identifier: luad_mskcc_2023_met_organotropism
+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/luad_mskcc_2023_met_organotropism/meta_gene_panel_matrix.txt b/public/luad_mskcc_2023_met_organotropism/meta_gene_panel_matrix.txt
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+cancer_study_identifier: luad_mskcc_2023_met_organotropism
+genetic_alteration_type: GENE_PANEL_MATRIX
+datatype: GENE_PANEL_MATRIX
+data_filename: data_gene_panel_matrix.txt
diff --git a/public/luad_mskcc_2023_met_organotropism/meta_mutations.txt b/public/luad_mskcc_2023_met_organotropism/meta_mutations.txt
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+cancer_study_identifier: luad_mskcc_2023_met_organotropism
+genetic_alteration_type: MUTATION_EXTENDED
+datatype: MAF
+stable_id: mutations
+show_profile_in_analysis_tab: true
+profile_description: Somatic mutation data of IMPACT sequencing of 2422 LUAD samples and WES sequencing of 231 LUAD samples.
+profile_name: Mutations
+data_filename: data_mutations.txt
diff --git a/public/luad_mskcc_2023_met_organotropism/meta_study.txt b/public/luad_mskcc_2023_met_organotropism/meta_study.txt
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+type_of_cancer: luad
+cancer_study_identifier: luad_mskcc_2023_met_organotropism
+name: Lung Adenocarcinoma Met Organotropism (MSK, Cancer cell 2023)
+short_name: LUAD Met Organotropism (MSK)
+description: This cohort contains genomic and manually abstracted clinico-pathologic data for 2653 lung adenocarcinoma tumor samples sequenced with a combination of MSK-IMPACT and whole exome sequencing. Analyzed this dataset to identify clinico-pathologic and genomic features associated with metastatic spread to the seven most common sites of metastasis, metastatic burden, and metastasis-free survival.
+pmid: 37084736
+citation: Lengel, Harry B et al. Cancer cell 2023
diff --git a/public/luad_mskcc_2023_met_organotropism/meta_sv.txt b/public/luad_mskcc_2023_met_organotropism/meta_sv.txt
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+cancer_study_identifier: luad_mskcc_2023_met_organotropism
+genetic_alteration_type: STRUCTURAL_VARIANT
+datatype: SV
+stable_id: structural_variants
+show_profile_in_analysis_tab: true
+profile_name: Structural variants
+profile_description: Structural variants data.
+data_filename: data_sv.txt
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		TCGA data are available under Broad Institute GDAC TCGA Analysis Pipeline License. The Cancer Genome Atlas Consortium is pleased to provide the research community with preliminary data prior to publication. Users are requested to carefully consider that these data are preliminary and have yet to be validated. Researchers are warned that the preliminary data have a significant uncertainty, are likely to change, and should be used with caution.
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		Gene panels for this study can be found here: https://github.com/cBioPortal/datahub/tree/master/reference_data/gene_panels