Merge pull request #2020 from cBioPortal/pdx_mdanderson

New Stuyd: prad_msk_mdanderson_2023

public/prad_msk_mdanderson_2023/case_lists/cases_RNA_Seq_v2_mRNA.txt

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+cancer_study_identifier: prad_msk_mdanderson_2023
+stable_id: prad_msk_mdanderson_2023_rna_seq_v2_mrna
+case_list_name: Samples with mRNA data (RNA Seq V2)
+case_list_description: Samples with mRNA expression data
+case_list_category: all_cases_with_mrna_rnaseq_data
+case_list_ids: MDA-PCa-117-9	MDA-PCa-117-9-T200	MDA-PCa-118b	MDA-PCa-118b-T200	MDA-PCa-133-4	MDA-PCa-133-4-T200	MDA-PCa-144-4	MDA-PCa-144-4-T200	MDA-PCa-144-13	MDA-PCa-144-13-T200	MDA-PCa-146-10	MDA-PCa-146-10-T200	MDA-PCa-146-12	MDA-PCa-146-12-T200	MDA-PCa-150-7	MDA-PCa-150-7-T200	MDA-PCa-152-1	MDA-PCa-152-1-T200	MDA-PCa-153-7	MDA-PCa-153-7-T200	MDA-PCa-155-2	MDA-PCa-155-2-T200	MDA-PCa-163-A	MDA-PCa-163-A-T200	MDA-PCa-173-2	MDA-PCa-173-2-T200	MDA-PCa-174-6	MDA-PCa-174-6-T200	MDA-PCa-175-6	MDA-PCa-175-6-T200	MDA-PCa-177-B	MDA-PCa-177-B-T200	MDA-PCa-178-11	MDA-PCa-178-11-T200	MDA-PCa-180-30	MDA-PCa-180-30-T200	MDA-PCa-183-A	MDA-PCa-183-A-T200	MDA-PCa-200-0	MDA-PCa-200-0-T200	MDA-PCa-203-A	MDA-PCa-203-A-T200	MDA-PCa-250-15	MDA-PCa-250-15-T200	MDA-PCa-265-8	MDA-PCa-265-8-T200	MDA-PCa-266-A	MDA-PCa-266-A-T200	MDA-PCa-270-A	MDA-PCa-270-A-T200	MDA-PCa-273-A	MDA-PCa-273-A-T200	MDA-PCa-274-2	MDA-PCa-274-2-T200	MDA-PCa-277-6	MDA-PCa-277-6-T200	MDA-PCa-280-9	MDA-PCa-280-9-T200	MDA-PCa-285-3	MDA-PCa-285-3-T200	MDA-PCa-306-14	MDA-PCa-306-14-T200	MDA-PCa-312-7	MDA-PCa-312-7-T200	MDA-PCa-315-8	MDA-PCa-315-8-T200	MDA-PCa-316-1	MDA-PCa-316-1-T200	MDA-PCa-316-2	MDA-PCa-316-2-T200	MDA-PCa-320-1	MDA-PCa-320-1-T200	MDA-PCa-322-2	MDA-PCa-322-2-T200	MDA-PCa-327-2	MDA-PCa-327-2-T200	MDA-PCa-328-5	MDA-PCa-328-5-T200	MDA-PCa-337-A	MDA-PCa-337-A-T200	MDA-PCa-342-B	MDA-PCa-342-B-T200	MDA-PCa-352-8	MDA-PCa-352-8-T200	MDA-PCa-355-9	MDA-PCa-355-9-T200	MDA-PCa-377-1	MDA-PCa-377-1-T200

public/prad_msk_mdanderson_2023/case_lists/cases_all.txt

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+cancer_study_identifier: prad_msk_mdanderson_2023
+stable_id: prad_msk_mdanderson_2023_all
+case_list_name: All samples
+case_list_description: All samples
+case_list_category: all_cases_in_study
+case_list_ids: MDA-PCa-117-9	MDA-PCa-117-9-T200	MDA-PCa-118b	MDA-PCa-118b-T200	MDA-PCa-133-4	MDA-PCa-133-4-T200	MDA-PCa-144-4	MDA-PCa-144-4-T200	MDA-PCa-144-13	MDA-PCa-144-13-T200	MDA-PCa-146-10	MDA-PCa-146-10-T200	MDA-PCa-146-12	MDA-PCa-146-12-T200	MDA-PCa-150-7	MDA-PCa-150-7-T200	MDA-PCa-152-1	MDA-PCa-152-1-T200	MDA-PCa-153-7	MDA-PCa-153-7-T200	MDA-PCa-155-2	MDA-PCa-155-2-T200	MDA-PCa-163-A	MDA-PCa-163-A-T200	MDA-PCa-173-2	MDA-PCa-173-2-T200	MDA-PCa-174-6	MDA-PCa-174-6-T200	MDA-PCa-175-6	MDA-PCa-175-6-T200	MDA-PCa-177-B	MDA-PCa-177-B-T200	MDA-PCa-178-11	MDA-PCa-178-11-T200	MDA-PCa-180-30	MDA-PCa-180-30-T200	MDA-PCa-183-A	MDA-PCa-183-A-T200	MDA-PCa-200-0	MDA-PCa-200-0-T200	MDA-PCa-203-A	MDA-PCa-203-A-T200	MDA-PCa-250-15	MDA-PCa-250-15-T200	MDA-PCa-265-8	MDA-PCa-265-8-T200	MDA-PCa-266-A	MDA-PCa-266-A-T200	MDA-PCa-270-A	MDA-PCa-270-A-T200	MDA-PCa-273-A	MDA-PCa-273-A-T200	MDA-PCa-274-2	MDA-PCa-274-2-T200	MDA-PCa-277-6	MDA-PCa-277-6-T200	MDA-PCa-280-9	MDA-PCa-280-9-T200	MDA-PCa-285-3	MDA-PCa-285-3-T200	MDA-PCa-306-14	MDA-PCa-306-14-T200	MDA-PCa-312-7	MDA-PCa-312-7-T200	MDA-PCa-315-8	MDA-PCa-315-8-T200	MDA-PCa-316-1	MDA-PCa-316-1-T200	MDA-PCa-316-2	MDA-PCa-316-2-T200	MDA-PCa-320-1	MDA-PCa-320-1-T200	MDA-PCa-322-2	MDA-PCa-322-2-T200	MDA-PCa-327-2	MDA-PCa-327-2-T200	MDA-PCa-328-5	MDA-PCa-328-5-T200	MDA-PCa-337-A	MDA-PCa-337-A-T200	MDA-PCa-342-B	MDA-PCa-342-B-T200	MDA-PCa-352-8	MDA-PCa-352-8-T200	MDA-PCa-355-9	MDA-PCa-355-9-T200	MDA-PCa-377-1	MDA-PCa-377-1-T200

public/prad_msk_mdanderson_2023/case_lists/cases_cna.txt

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+cancer_study_identifier: prad_msk_mdanderson_2023
+stable_id: prad_msk_mdanderson_2023_cna
+case_list_name: Samples with CNA data
+case_list_description: Samples with CNA data
+case_list_category: all_cases_with_cna_data
+case_list_ids: MDA-PCa-117-9	MDA-PCa-118b	MDA-PCa-133-4	MDA-PCa-144-4	MDA-PCa-144-13	MDA-PCa-146-10	MDA-PCa-146-12	MDA-PCa-150-7	MDA-PCa-152-1	MDA-PCa-153-7	MDA-PCa-155-2	MDA-PCa-163-A	MDA-PCa-173-2	MDA-PCa-174-6	MDA-PCa-175-6	MDA-PCa-177-B	MDA-PCa-178-11	MDA-PCa-180-30	MDA-PCa-183-A	MDA-PCa-200-0	MDA-PCa-203-A	MDA-PCa-250-15	MDA-PCa-265-8	MDA-PCa-266-A	MDA-PCa-270-A	MDA-PCa-273-A	MDA-PCa-274-2	MDA-PCa-277-6	MDA-PCa-280-9	MDA-PCa-285-3	MDA-PCa-306-14	MDA-PCa-312-7	MDA-PCa-315-8	MDA-PCa-316-1	MDA-PCa-316-2	MDA-PCa-320-1	MDA-PCa-322-2	MDA-PCa-327-2	MDA-PCa-328-5	MDA-PCa-337-A	MDA-PCa-342-B	MDA-PCa-352-8	MDA-PCa-355-9	MDA-PCa-377-1

public/prad_msk_mdanderson_2023/case_lists/cases_cnaseq.txt

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+cancer_study_identifier: prad_msk_mdanderson_2023
+stable_id: prad_msk_mdanderson_2023_cnaseq
+case_list_name: Samples with mutation and CNA data
+case_list_description: Samples with mutation and CNA data
+case_list_category: all_cases_with_mutation_and_cna_data
+case_list_ids: MDA-PCa-117-9	MDA-PCa-118b	MDA-PCa-133-4	MDA-PCa-144-4	MDA-PCa-144-13	MDA-PCa-146-10	MDA-PCa-146-12	MDA-PCa-150-7	MDA-PCa-152-1	MDA-PCa-153-7	MDA-PCa-155-2	MDA-PCa-163-A	MDA-PCa-173-2	MDA-PCa-174-6	MDA-PCa-175-6	MDA-PCa-177-B	MDA-PCa-178-11	MDA-PCa-180-30	MDA-PCa-183-A	MDA-PCa-200-0	MDA-PCa-203-A	MDA-PCa-250-15	MDA-PCa-265-8	MDA-PCa-266-A	MDA-PCa-270-A	MDA-PCa-273-A	MDA-PCa-274-2	MDA-PCa-277-6	MDA-PCa-280-9	MDA-PCa-285-3	MDA-PCa-306-14	MDA-PCa-312-7	MDA-PCa-315-8	MDA-PCa-316-1	MDA-PCa-316-2	MDA-PCa-320-1	MDA-PCa-322-2	MDA-PCa-327-2	MDA-PCa-328-5	MDA-PCa-337-A	MDA-PCa-342-B	MDA-PCa-352-8	MDA-PCa-355-9	MDA-PCa-377-1

public/prad_msk_mdanderson_2023/case_lists/cases_log2CNA.txt

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+cancer_study_identifier: prad_msk_mdanderson_2023
+stable_id: prad_msk_mdanderson_2023_log2CNA
+case_list_name: Samples with log2 copy-number data
+case_list_description: Samples with log2 copy-number data
+case_list_category: all_cases_with_log2_cna_data
+case_list_ids: MDA-PCa-265-8	MDA-PCa-266-A	MDA-PCa-270-A	MDA-PCa-273-A	MDA-PCa-274-2	MDA-PCa-277-6	MDA-PCa-280-9	MDA-PCa-285-3	MDA-PCa-306-14	MDA-PCa-312-7	MDA-PCa-315-8	MDA-PCa-316-1	MDA-PCa-316-2	MDA-PCa-320-1	MDA-PCa-322-2	MDA-PCa-327-2	MDA-PCa-328-5	MDA-PCa-337-A	MDA-PCa-342-B	MDA-PCa-352-8	MDA-PCa-355-9	MDA-PCa-377-1	MDA-PCa-117-9	MDA-PCa-153-7	MDA-PCa-155-2	MDA-PCa-163-A	MDA-PCa-173-2	MDA-PCa-174-6	MDA-PCa-175-6	MDA-PCa-177-B	MDA-PCa-178-11	MDA-PCa-180-30	MDA-PCa-118b	MDA-PCa-183-A	MDA-PCa-200-0	MDA-PCa-203-A	MDA-PCa-250-15	MDA-PCa-133-4	MDA-PCa-144-13	MDA-PCa-144-4	MDA-PCa-146-10	MDA-PCa-146-12	MDA-PCa-150-7	MDA-PCa-152-1	MDA-PCa-117-9-T200	MDA-PCa-153-7-T200	MDA-PCa-155-2-T200	MDA-PCa-163-A-T200	MDA-PCa-173-2-T200	MDA-PCa-174-6-T200	MDA-PCa-175-6-T200	MDA-PCa-177-B-T200	MDA-PCa-178-11-T200	MDA-PCa-180-30-T200	MDA-PCa-118b-T200	MDA-PCa-183-A-T200	MDA-PCa-200-0-T200	MDA-PCa-203-A-T200	MDA-PCa-250-15-T200	MDA-PCa-265-8-T200	MDA-PCa-266-A-T200	MDA-PCa-270-A-T200	MDA-PCa-273-A-T200	MDA-PCa-133-4-T200	MDA-PCa-274-2-T200	MDA-PCa-277-6-T200	MDA-PCa-280-9-T200	MDA-PCa-285-3-T200	MDA-PCa-306-14-T200	MDA-PCa-312-7-T200	MDA-PCa-315-8-T200	MDA-PCa-316-1-T200	MDA-PCa-316-2-T200	MDA-PCa-144-13-T200	MDA-PCa-320-1-T200	MDA-PCa-322-2-T200	MDA-PCa-327-2-T200	MDA-PCa-328-5-T200	MDA-PCa-337-A-T200	MDA-PCa-342-B-T200	MDA-PCa-352-8-T200	MDA-PCa-355-9-T200	MDA-PCa-377-1-T200	MDA-PCa-144-4-T200	MDA-PCa-146-10-T200	MDA-PCa-146-12-T200	MDA-PCa-150-7-T200	MDA-PCa-152-1-T200

public/prad_msk_mdanderson_2023/case_lists/cases_sequenced.txt

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+cancer_study_identifier: prad_msk_mdanderson_2023
+stable_id: prad_msk_mdanderson_2023_sequenced
+case_list_name: Samples with mutation data
+case_list_description: Samples with mutation data
+case_list_category: all_cases_with_mutation_data
+case_list_ids: MDA-PCa-117-9	MDA-PCa-117-9-T200	MDA-PCa-118b	MDA-PCa-118b-T200	MDA-PCa-133-4	MDA-PCa-133-4-T200	MDA-PCa-144-4	MDA-PCa-144-4-T200	MDA-PCa-144-13	MDA-PCa-144-13-T200	MDA-PCa-146-10	MDA-PCa-146-10-T200	MDA-PCa-146-12	MDA-PCa-146-12-T200	MDA-PCa-150-7	MDA-PCa-150-7-T200	MDA-PCa-152-1	MDA-PCa-152-1-T200	MDA-PCa-153-7	MDA-PCa-153-7-T200	MDA-PCa-155-2	MDA-PCa-155-2-T200	MDA-PCa-163-A	MDA-PCa-163-A-T200	MDA-PCa-173-2	MDA-PCa-173-2-T200	MDA-PCa-174-6	MDA-PCa-174-6-T200	MDA-PCa-175-6	MDA-PCa-175-6-T200	MDA-PCa-177-B	MDA-PCa-177-B-T200	MDA-PCa-178-11	MDA-PCa-178-11-T200	MDA-PCa-180-30	MDA-PCa-180-30-T200	MDA-PCa-183-A	MDA-PCa-183-A-T200	MDA-PCa-200-0	MDA-PCa-200-0-T200	MDA-PCa-203-A	MDA-PCa-203-A-T200	MDA-PCa-250-15	MDA-PCa-250-15-T200	MDA-PCa-265-8	MDA-PCa-265-8-T200	MDA-PCa-266-A	MDA-PCa-266-A-T200	MDA-PCa-270-A	MDA-PCa-270-A-T200	MDA-PCa-273-A	MDA-PCa-273-A-T200	MDA-PCa-274-2	MDA-PCa-274-2-T200	MDA-PCa-277-6	MDA-PCa-277-6-T200	MDA-PCa-280-9	MDA-PCa-280-9-T200	MDA-PCa-285-3	MDA-PCa-285-3-T200	MDA-PCa-306-14	MDA-PCa-306-14-T200	MDA-PCa-312-7	MDA-PCa-312-7-T200	MDA-PCa-315-8	MDA-PCa-315-8-T200	MDA-PCa-316-1	MDA-PCa-316-1-T200	MDA-PCa-316-2	MDA-PCa-316-2-T200	MDA-PCa-320-1	MDA-PCa-320-1-T200	MDA-PCa-322-2	MDA-PCa-322-2-T200	MDA-PCa-327-2	MDA-PCa-327-2-T200	MDA-PCa-328-5	MDA-PCa-328-5-T200	MDA-PCa-337-A	MDA-PCa-337-A-T200	MDA-PCa-342-B	MDA-PCa-342-B-T200	MDA-PCa-352-8	MDA-PCa-352-8-T200	MDA-PCa-355-9	MDA-PCa-355-9-T200	MDA-PCa-377-1	MDA-PCa-377-1-T200

public/prad_msk_mdanderson_2023/case_lists/cases_sv.txt

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+cancer_study_identifier: prad_msk_mdanderson_2023
+stable_id: prad_msk_mdanderson_2023_sv
+case_list_name: Samples with SV data
+case_list_description: All samples
+case_list_category: all_cases_with_sv_data
+case_list_ids: MDA-PCa-117-9	MDA-PCa-118b	MDA-PCa-133-4	MDA-PCa-144-4	MDA-PCa-144-13	MDA-PCa-146-10	MDA-PCa-146-12	MDA-PCa-150-7	MDA-PCa-152-1	MDA-PCa-153-7	MDA-PCa-155-2	MDA-PCa-163-A	MDA-PCa-173-2	MDA-PCa-174-6	MDA-PCa-175-6	MDA-PCa-177-B	MDA-PCa-178-11	MDA-PCa-180-30	MDA-PCa-183-A	MDA-PCa-200-0	MDA-PCa-203-A	MDA-PCa-250-15	MDA-PCa-265-8	MDA-PCa-266-A	MDA-PCa-270-A	MDA-PCa-273-A	MDA-PCa-274-2	MDA-PCa-277-6	MDA-PCa-280-9	MDA-PCa-285-3	MDA-PCa-306-14	MDA-PCa-312-7	MDA-PCa-315-8	MDA-PCa-316-1	MDA-PCa-316-2	MDA-PCa-320-1	MDA-PCa-322-2	MDA-PCa-327-2	MDA-PCa-328-5	MDA-PCa-337-A	MDA-PCa-342-B	MDA-PCa-352-8	MDA-PCa-355-9	MDA-PCa-377-1

public/prad_msk_mdanderson_2023/meta_clinical_patient.txt

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+cancer_study_identifier: prad_msk_mdanderson_2023
+genetic_alteration_type: CLINICAL
+datatype: PATIENT_ATTRIBUTES
+data_filename: data_clinical_patient.txt

public/prad_msk_mdanderson_2023/meta_clinical_sample.txt

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+cancer_study_identifier: prad_msk_mdanderson_2023
+genetic_alteration_type: CLINICAL
+datatype: SAMPLE_ATTRIBUTES
+data_filename: data_clinical_sample.txt

public/prad_msk_mdanderson_2023/meta_cna.txt

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+cancer_study_identifier: prad_msk_mdanderson_2023
+genetic_alteration_type: COPY_NUMBER_ALTERATION
+stable_id: cna
+show_profile_in_analysis_tab: TRUE
+profile_name: Putative copy-number alterations.
+profile_description: Putative copy-number calls. Values: -2 = homozygous deletion; -1 = hemizygous deletion; 0 = neutral / no change; 1 = gain; 2 = high level amplification.
+datatype: DISCRETE
+data_filename: data_cna.txt

public/prad_msk_mdanderson_2023/meta_cna_hg19_seg.txt

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+cancer_study_identifier: prad_msk_mdanderson_2023
+genetic_alteration_type: COPY_NUMBER_ALTERATION
+datatype: SEG
+reference_genome_id: hg19
+description: Somatic CNA data
+data_filename: data_cna_hg19.seg

public/prad_msk_mdanderson_2023/meta_gene_panel_matrix.txt

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+cancer_study_identifier: prad_msk_mdanderson_2023
+genetic_alteration_type: GENE_PANEL_MATRIX
+datatype: GENE_PANEL_MATRIX
+data_filename: data_gene_panel_matrix.txt

public/prad_msk_mdanderson_2023/meta_log2_cna.txt

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+cancer_study_identifier: prad_msk_mdanderson_2023
+genetic_alteration_type: COPY_NUMBER_ALTERATION
+datatype: LOG2-VALUE
+stable_id: log2CNA
+show_profile_in_analysis_tab: false
+profile_description: Log2 copy-number values for each gene.
+profile_name: Log2 copy-number values
+data_filename: data_log2_cna.txt

public/prad_msk_mdanderson_2023/meta_mrna_seq_v2_rsem.txt

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+cancer_study_identifier: prad_msk_mdanderson_2023
+stable_id: rna_seq_v2_mrna
+genetic_alteration_type: MRNA_EXPRESSION
+datatype: CONTINUOUS
+show_profile_in_analysis_tab: FALSE
+profile_name: mRNA Expression, RSEM (Batch normalized from Illumina HiSeq_RNASeqV2)
+profile_description: mRNA Expression, RSEM (Batch normalized from Illumina HiSeq_RNASeqV2)
+data_filename: data_mrna_seq_v2_rsem.txt

public/prad_msk_mdanderson_2023/meta_mrna_seq_v2_rsem_zscores_ref_all_samples.txt

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+cancer_study_identifier: prad_msk_mdanderson_2023
+genetic_alteration_type: MRNA_EXPRESSION
+datatype: Z-SCORE
+stable_id: rna_seq_v2_mrna_median_all_sample_Zscores
+show_profile_in_analysis_tab: TRUE
+profile_name: mRNA expression z-scores relative to all samples (log RNA Seq V2 RSEM)
+profile_description: Log-transformed mRNA expression z-scores compared to the expression distribution of all samples (RNA Seq V2 RSEM).
+data_filename: data_mrna_seq_v2_rsem_zscores_ref_all_samples.txt

public/prad_msk_mdanderson_2023/meta_mutations.txt

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+cancer_study_identifier: prad_msk_mdanderson_2023
+genetic_alteration_type: MUTATION_EXTENDED
+datatype: MAF
+stable_id: mutations
+profile_name: Mutations
+profile_description: Mutation data.
+show_profile_in_analysis_tab: true
+data_filename: data_mutations.txt

public/prad_msk_mdanderson_2023/meta_study.txt

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+type_of_cancer: prostate
+cancer_study_identifier: prad_msk_mdanderson_2023
+name: Prostate Cancer MDA PCa PDX (MD Anderson, 2023)
+description: Targeted sequencingand whole-genome sequencing of 44 MD Anderson Prostate Cancer PDX models derived from 38 patients with tumor.
+pmid: 38488813
+citation: Anselmino et al. Clin Cancer Res 2024

public/prad_msk_mdanderson_2023/meta_sv.txt

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+cancer_study_identifier: prad_msk_mdanderson_2023
+genetic_alteration_type: STRUCTURAL_VARIANT
+datatype: SV
+stable_id: structural_variants
+show_profile_in_analysis_tab: true
+profile_name: Structural Variants
+profile_description: Structural Variant Data.
+data_filename: data_sv.txt