Updates to the NF-OSI study (#1760)

* Add mixed_nfosi_2022 * Update citation * Add LICENSE * Update meta * Fix cell line sample file manually * Generate case lists * Update name * Update validation html report * Use v3 of mutations data * Update validation result * Replace bioRxiv citation with better citation * Update study name per review suggestion * Use cleaner citation format per review suggestion * Add pmid field to study meta per review suggestion * Add reference_genome field per review suggestion * Recategorize type_of_cancer per review suggestion * Rename files, no longer use _extended suffix * Rename all case list file to cases_all.txt per review suggestion * Use nst in study id per suggestion * Whoops, propagate study id changes to case list files * update study name, fix clinical, meta data * remove html report * add TMB scores * Add oncotree codes --------- Co-authored-by: Anh Nguyet Vu <[email protected]> Co-authored-by: Anh Nguyet Vu <[email protected]>
cBioPortal · Feb 1, 2023 · aba0099 · aba0099
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diff --git a/public/nst_nfosi_2022/LICENSE b/public/nst_nfosi_2022/LICENSE
diff --git a/public/nst_nfosi_2022/case_lists/cases_all.txt b/public/nst_nfosi_2022/case_lists/cases_all.txt
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+cancer_study_identifier: nst_nfosi_2022
+stable_id: nst_nfosi_2022_all
+case_list_name: All samples
+case_list_description: All samples (19 samples)
+case_list_category: all_cases_in_study
+case_list_ids: 2-010_Neurofibroma	2-026_Neurofibroma	2-013_Plexiform_Neurofibroma	2-004_Plexiform_Neurofibroma	2-012_Neurofibroma	2-031_Cell_Line	2-017_Neurofibroma	2-021_Neurofibroma	2-019_Neurofibroma	2-029_Neurofibroma	2-023_Plexiform_Neurofibroma	2-014_Neurofibroma	2-001_Plexiform_Neurofibroma	2-006_Plexiform_Neurofibroma	2-032_Plexiform_Neurofibroma	2-015_Plexiform_Neurofibroma	2-031_Malignant_Peripheral_Nerve_Sheath_Tumor	2-016_Neurofibroma	2-015_Neurofibroma
diff --git a/public/nst_nfosi_2022/case_lists/cases_sequenced.txt b/public/nst_nfosi_2022/case_lists/cases_sequenced.txt
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+cancer_study_identifier: nst_nfosi_2022
+stable_id: nst_nfosi_2022_sequenced
+case_list_name: Samples with mutation data
+case_list_description: Samples with mutation data (19 samples)
+case_list_category: all_cases_with_mutation_data
+case_list_ids: 2-010_Neurofibroma	2-026_Neurofibroma	2-013_Plexiform_Neurofibroma	2-014_Neurofibroma	2-001_Plexiform_Neurofibroma	2-006_Plexiform_Neurofibroma	2-004_Plexiform_Neurofibroma	2-032_Plexiform_Neurofibroma	2-015_Plexiform_Neurofibroma	2-016_Neurofibroma	2-012_Neurofibroma	2-031_Malignant_Peripheral_Nerve_Sheath_Tumor	2-031_Cell_Line	2-017_Neurofibroma	2-015_Neurofibroma	2-021_Neurofibroma	2-019_Neurofibroma	2-029_Neurofibroma	2-023_Plexiform_Neurofibroma
diff --git a/public/nst_nfosi_2022/data_clinical_patient.txt b/public/nst_nfosi_2022/data_clinical_patient.txt
diff --git a/public/nst_nfosi_2022/data_clinical_sample.txt b/public/nst_nfosi_2022/data_clinical_sample.txt
diff --git a/public/nst_nfosi_2022/data_mutations.txt b/public/nst_nfosi_2022/data_mutations.txt
diff --git a/public/nst_nfosi_2022/meta_clinical_patient.txt b/public/nst_nfosi_2022/meta_clinical_patient.txt
@@ -0,0 +1,4 @@
+cancer_study_identifier: nst_nfosi_2022
+genetic_alteration_type: CLINICAL
+datatype: PATIENT_ATTRIBUTES
+data_filename: data_clinical_patient.txt
diff --git a/public/nst_nfosi_2022/meta_clinical_sample.txt b/public/nst_nfosi_2022/meta_clinical_sample.txt
@@ -0,0 +1,4 @@
+cancer_study_identifier: nst_nfosi_2022
+genetic_alteration_type: CLINICAL
+datatype: SAMPLE_ATTRIBUTES
+data_filename: data_clinical_sample.txt
diff --git a/public/nst_nfosi_2022/meta_mutations.txt b/public/nst_nfosi_2022/meta_mutations.txt
@@ -0,0 +1,8 @@
+cancer_study_identifier: nst_nfosi_2022
+genetic_alteration_type: MUTATION_EXTENDED
+datatype: MAF
+stable_id: mutations
+show_profile_in_analysis_tab: true
+profile_name: Mutations
+profile_description: Mutation data from NF-OSI processing. The data were processed using the "sarek" nf-core pipeline.
+data_filename: data_mutations.txt
diff --git a/public/nst_nfosi_2022/meta_study.txt b/public/nst_nfosi_2022/meta_study.txt
@@ -0,0 +1,8 @@
+cancer_study_identifier: nst_nfosi_2022
+type_of_cancer: nst
+name: Nerve Sheath Tumors (John Hopkins, Sci Data 2020)
+description: Whole-exome sequencing of 18 patients with Nerve Sheath Tumors and their matched normals. The data is contributed by John Hopkins University researchers funded by the Neurofibromatosis Therapeutic Acceleration Program (NTAP). The reprocessing of the raw data is managed by the NF Open Science Initiative (<a href="https://nf.synapse.org/">NF Data Portal</a>).
+citation: Pollard et al. Sci Data 2020
+pmid: 32561749
+reference_genome: hg38
+groups: PUBLIC