Merge pull request #2270 from cBioPortal/update_data

Rima-Waleed · web-flow · commit ba7fbd3828e7 · 2026-03-09T14:35:41.000-04:00
lgg_ctf_synodos: update study for public release
diff --git a/public/lgg_ctf_synodos_2025/case_lists/case-list.txt b/public/lgg_ctf_synodos_2025/case_lists/case-list.txt
diff --git a/public/lgg_ctf_synodos_2025/case_lists/cases_all.txt b/public/lgg_ctf_synodos_2025/case_lists/cases_all.txt
@@ -0,0 +1,6 @@
+cancer_study_identifier: lgg_ctf_synodos_2025
+stable_id: lgg_ctf_synodos_2025_all
+case_list_name: All samples
+case_list_description: All samples (31 samples)
+case_list_category: all_cases_in_study
+case_list_ids: SYN_NF_045	SYN_NF_004	SYN_NF_047	SYN_NF_037	SYN_NF_031	SYN_NF_003	SYN_NF_040	SYN_NF_033	SYN_NF_001	SYN_NF_007	SYN_NF_060	SYN_NF_015	SYN_NF_062	SYN_NF_057	SYN_NF_058	SYN_NF_055	SYN_NF_030	SYN_NF_044	SYN_NF_009	SYN_NF_042	SYN_NF_036	SYN_NF_035	SYN_NF_034	SYN_NF_011	SYN_NF_010	SYN_NF_013	SYN_NF_012	SYN_NF_059	SYN_NF_014	SYN_NF_017	SYN_NF_043
diff --git a/public/lgg_ctf_synodos_2025/case_lists/cases_sequenced.txt b/public/lgg_ctf_synodos_2025/case_lists/cases_sequenced.txt
@@ -0,0 +1,6 @@
+cancer_study_identifier: lgg_ctf_synodos_2025
+stable_id: lgg_ctf_synodos_2025_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: SYN_NF_045	SYN_NF_004	SYN_NF_047	SYN_NF_037	SYN_NF_031	SYN_NF_003	SYN_NF_040	SYN_NF_033	SYN_NF_001	SYN_NF_007	SYN_NF_060	SYN_NF_015	SYN_NF_062	SYN_NF_057	SYN_NF_058	SYN_NF_055	SYN_NF_030	SYN_NF_044	SYN_NF_009	SYN_NF_042	SYN_NF_036	SYN_NF_035	SYN_NF_034	SYN_NF_011	SYN_NF_010	SYN_NF_013	SYN_NF_012	SYN_NF_059	SYN_NF_014	SYN_NF_017	SYN_NF_043
diff --git a/public/lgg_ctf_synodos_2025/data_clinical_patient.txt b/public/lgg_ctf_synodos_2025/data_clinical_patient.txt
@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:ed3e7c6f317d79097d95cc43e427c50d8148ddaec984340ad5f7464fc5018c46
-size 5256
+oid sha256:feb5e6198c5ad22ec777d10dcf3d2b15ffd71d91aa0107d0c34f630c10618841
+size 5349
diff --git a/public/lgg_ctf_synodos_2025/data_clinical_sample.txt b/public/lgg_ctf_synodos_2025/data_clinical_sample.txt
@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:a0a33a7f0d32093069676863829500916445f4a6f104229b0d68319b03d6a521
-size 2919
+oid sha256:1c7947352fdb63c72d205766b8f89707d5d4f559811c5c631ecb42b1c680c651
+size 4243
diff --git a/public/lgg_ctf_synodos_2025/data_gene_panel_matrix.txt b/public/lgg_ctf_synodos_2025/data_gene_panel_matrix.txt
@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:e7e469e68634e6dbaf8f4e876adf327b14d90a621def2aeb0240e70097fe8d27
-size 475
+oid sha256:928236150f69c2b0ea55d0178bac41e0569b159f721eb1713633bf626c44493b
+size 484
diff --git a/public/lgg_ctf_synodos_2025/data_mrna_seq_tpm.txt b/public/lgg_ctf_synodos_2025/data_mrna_seq_tpm.txt
diff --git a/public/lgg_ctf_synodos_2025/data_mrna_seq_tpm_zscores_ref_all_samples.txt b/public/lgg_ctf_synodos_2025/data_mrna_seq_tpm_zscores_ref_all_samples.txt
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:68e0d9aebad94efa0af95b987457e88b1b30ba25a2b9704fd24ab5f72c787913
+size 4664567
diff --git a/public/lgg_ctf_synodos_2025/data_mutations.txt b/public/lgg_ctf_synodos_2025/data_mutations.txt
@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:fd30ed55a01c937916d0b39aea56746e3b1396ebc1244137042fcc4bfec34acf
-size 36502411
+oid sha256:0291aff9b58b1c657d3c74a679e00d4e6e79284877d5b1c1af4efe79dd56d3d6
+size 37522528
diff --git a/public/lgg_ctf_synodos_2025/meta_gene_panel_matrix.txt b/public/lgg_ctf_synodos_2025/meta_gene_panel_matrix.txt
@@ -0,0 +1,4 @@
+cancer_study_identifier: lgg_ctf_synodos_2025
+genetic_alteration_type: GENE_PANEL_MATRIX
+datatype: GENE_PANEL_MATRIX
+data_filename: data_gene_panel_matrix.txt
diff --git a/public/lgg_ctf_synodos_2025/meta_mrna_seq_tpm.txt b/public/lgg_ctf_synodos_2025/meta_mrna_seq_tpm.txt
@@ -3,6 +3,6 @@ genetic_alteration_type: MRNA_EXPRESSION
 datatype: CONTINUOUS
 stable_id: mrna_seq_tpm
 show_profile_in_analysis_tab: true
-profile_name: Normalized gene expression
+profile_name: TPM normalized gene expression
 profile_description: Normalized gene expression levels (TPM)
-data_filename: data_expression_tpm.txt
+data_filename: data_mrna_seq_tpm.txt
diff --git a/public/lgg_ctf_synodos_2025/meta_mrna_seq_tpm_zscores_ref_all_samples.txt b/public/lgg_ctf_synodos_2025/meta_mrna_seq_tpm_zscores_ref_all_samples.txt
@@ -0,0 +1,8 @@
+cancer_study_identifier: lgg_ctf_synodos_2025
+genetic_alteration_type: MRNA_EXPRESSION
+datatype: Z-SCORE
+stable_id: mrna_seq_tpm_all_sample_Zscores
+show_profile_in_analysis_tab: true
+profile_name: Gene expression z-scores
+profile_description: Z-score normalized gene expression levels (TPM)
+data_filename: data_mrna_seq_tpm_zscores_ref_all_samples.txt
diff --git a/public/lgg_ctf_synodos_2025/meta_study.txt b/public/lgg_ctf_synodos_2025/meta_study.txt
@@ -1,7 +1,8 @@
 cancer_study_identifier: lgg_ctf_synodos_2025
 type_of_cancer: lggnos
-name: "Data from Synodos for NF1 LGG Project (Children's Tumor Foundation)"
-description: The data are contributed by researchers funded by the Neurofibromatosis Therapeutic Acceleration Program (NTAP). The reprocessing of the raw data is managed by the NF Open Science Initiative (https://nf.synapse.org/).
-citation: 'Fisher, M. J. et al. Integrated molecular and clinical analysis of low-grade gliomas in children with neurofibromatosis type 1. Acta Neuropathol (2021). https://doi.org/10.1007/s00401-021-02276-5'
+name: Pediatric Low-Grade Glioma (CTF, Acta Neuropathol 2021)
+description: Whole genome sequencing of pediatric low-grade gliomas with neurofibromatosis. The data are contributed by researchers funded by the Children's Tumor Foundation (CTF). The reprocessing of the raw data is managed by <a href=https://nf.synapse.org/">NF Open Science Initiative</a>.
+citation: Fisher, M. J. et al. Acta neuropathologica 2021
+pmid: 33585982
 groups: PUBLIC
 reference_genome: hg38

Original file line number	Diff line number	Diff line change
`@@ -0,0 +1,3 @@`
	`1`	`+version https://git-lfs.github.com/spec/v1`
	`2`	`+oid sha256:68e0d9aebad94efa0af95b987457e88b1b30ba25a2b9704fd24ab5f72c787913`
	`3`	`+size 4664567`