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Public Release (June) #2186

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edf36cb
public studies
Rima-Waleed Jun 4, 2025
de0b501
public studies
Rima-Waleed Jun 16, 2025
7565198
Merge branch 'master' into june_release
rmadupuri Jul 1, 2025
1fd39c6
review updates
Rima-Waleed Jul 17, 2025
b611f49
Merge branch 'master' into june_release
sbabyanusha Sep 2, 2025
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6 changes: 6 additions & 0 deletions public/blca_msk_2024/case_lists/cases_all.txt
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cancer_study_identifier: blca_msk_2024
stable_id: blca_msk_2024_all
case_list_name: All samples
case_list_description: All samples (184 samples)
case_list_category: all_cases_in_study
case_list_ids: s_C_CTF5YF_P001_d s_C_2VU6CW_P001_d s_C_D719AD_P001_d s_C_M9LRUU_P001_d s_C_AC46KC_P001_d s_C_H6KW86_P001_d s_C_RA99UW_P001_d s_C_ND3PF6_P001_d s_C_VV3UK5_P001_d s_C_679EAR_P001_d s_C_MP6REX_P001_d s_C_ADTAL5_P001_d s_C_003HA8_P001_d s_C_XHTVXK_P001_d s_C_CPMWYP_P001_d s_C_FNM4WR_P001_d s_C_16WVCF_P001_d s_C_VJXJFU_P001_d s_C_1R1WNJ_P001_d s_C_UDRKF3_P001_d s_C_XKCKC4_P001_d s_C_74P9P5_P001_d s_C_N9HPT3_P001_d s_C_3F494V_P001_d s_C_FXE2UD_P001_d s_C_38PJEF_P001_d s_C_F2M8WF_P001_d s_C_PM5TJ7_P001_d s_C_6D84WP_P001_d s_C_JLJYPK_P001_d s_C_207N1F_P001_d s_C_K317TX_P001_d s_C_L6W2CJ_P001_d s_C_H4W1K4_P001_d s_C_463ART_P001_d s_C_87E3EJ_P001_d s_C_43DJ06_P001_d s_C_PDDMRT_P001_d s_C_AHNE99_P001_d s_C_NVUUKL_P001_d s_C_MA94C5_P001_d s_C_VYYFDM_P001_d s_C_D86FFD_P001_d s_C_2M7T23_P001_d s_C_1X92N8_P001_d s_C_KERR2T_P001_d s_C_U55NDX_P001_d s_C_89C4M2_P001_d s_C_PD7WJ5_P001_d s_C_J8LXYH_P001_d s_C_7EJL8A_P001_d s_C_AML0FT_P001_d s_C_VN5R9F_P001_d s_C_560HVF_P001_d s_C_0TCWAD_P001_d s_C_7DC7TE_P001_d s_C_WWVAUA_P001_d s_C_37NVKX_P001_d s_C_J6VM3L_P001_d s_C_CUNWLL_P001_d s_C_2NNWRW_P001_d s_C_4E8PUE_P001_d s_C_R46WLK_P001_d s_C_3J08Y0_P001_d s_C_K2N1TF_P001_d s_C_LE0374_P001_d s_C_X6CKRC_P001_d s_C_TUPDLD_P001_d s_C_9KL29X_P001_d s_C_WWX7F3_P001_d s_C_232307_P001_d s_C_CLWNJ3_P001_d s_C_EVTW87_P001_d s_C_K8EJXJ_P001_d s_C_W7RKP6_P001_d s_C_3DDFJ1_P001_d s_C_H2TY6P_P001_d s_C_FFDRA3_P001_d s_C_63A3CN_P001_d s_C_EC82A3_P001_d s_C_WETKKF_P001_d s_C_PN4P3L_P001_d s_C_FFAVJN_P001_d s_C_F666AJ_P001_d s_C_2LFVFJ_P001_d s_C_YW97WL_P001_d s_C_JNR9X3_P001_d s_C_UT983P_P001_d s_C_54LU1W_P001_d s_C_0XTAKJ_P001_d s_C_78NDH0_P001_d s_C_EX51R7_P001_d s_C_5CD5F4_P001_d s_C_VK8J4L_P001_d s_C_ECY328_P001_d s_C_R02LP8_P001_d s_C_73ALEN_P001_d s_C_EKXV7Y_P001_d s_C_E2UHXJ_P001_d s_C_YDVXUW_P001_d s_C_6J9XA7_P001_d s_C_A53JAX_P001_d s_C_V7KV1F_P001_d s_C_0KDD84_P001_d s_C_UX8338_P001_d s_C_JC2AAV_P001_d s_C_43CW84_P001_d s_C_NKC9KT_P001_d s_C_YVFD2D_P001_d s_C_YD1V7A_P001_d s_C_6HDFCW_P001_d s_C_7985Y0_P001_d s_C_8P85VJ_P001_d s_C_A83PUJ_P001_d s_C_WKATAH_P001_d s_C_FCV3TX_P001_d s_C_0TH9KN_P001_d s_C_W5LDW5_P001_d s_C_WD75HA_P001_d s_C_UWM6VE_P001_d s_C_AKF3DV_P001_d s_C_HD11U7_P001_d s_C_EFW6MX_P001_d s_C_K77HCW_P001_d s_C_JJ288E_P001_d s_C_6XRKTE_P001_d s_C_XEE6T3_P001_d s_C_DY80YJ_P001_d s_C_EWURPF_P001_d s_C_HVF41F_P001_d s_C_C0R4XV_P001_d s_C_7C3FH7_P001_d s_C_086CTC_P001_d s_C_85EFWK_P001_d s_C_UJD97R_P001_d s_C_E5959J_P001_d s_C_NR69F3_P001_d s_C_T0F2EP_P001_d s_C_EDRAFY_P001_d s_C_7M996U_P001_d s_C_UR3KPW_P001_d s_C_JLMFY4_P001_d s_C_452P26_P001_d s_C_9F3MTV_P001_d s_C_R0UH0K_P001_d s_C_DV4NE2_P001_d s_C_433LEN_P001_d s_C_XCJM63_P001_d s_C_UC4HNA_P001_d s_C_4CXPCD_P001_d s_C_30E67P_P001_d s_C_CKPXK0_P001_d s_C_VW7737_P001_d s_C_U1R4KF_P001_d s_C_RHFHTD_P001_d s_C_V2M1XF_P001_d s_C_T495A5_P001_d s_C_40DXFP_P001_d s_C_5RMT0X_P001_d s_C_XNLAPP_P001_d s_C_WNJMJL_P001_d s_C_WK4PUE_P001_d s_C_DJY8FJ_P001_d s_C_K6PU9E_P001_d s_C_T0H067_P001_d s_C_EMA9TY_P001_d s_C_RRRVF4_P001_d s_C_N677E4_P001_d s_C_C15KVL_P001_d s_C_T246L8_P001_d s_C_CW7N4C_P001_d s_C_35A8RK_P001_d s_C_YEPU8K_P001_d s_C_XEAY67_P001_d s_C_AN6LCV_P001_d s_C_CWJ45P_P001_d s_C_X2RNX1_P001_d s_C_323C2E_P001_d s_C_KHKDUM_P001_d s_C_M2L33T_P001_d s_C_6MA9R0_P001_d s_C_15J678_P001_d s_C_RP1DED_P001_d s_C_LY7NRX_P001_d
6 changes: 6 additions & 0 deletions public/blca_msk_2024/case_lists/cases_cna.txt
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cancer_study_identifier: blca_msk_2024
stable_id: blca_msk_2024_cna
case_list_name: Samples with CNA data
case_list_description: Samples with CNA data (184 samples)
case_list_category: all_cases_with_cna_data
case_list_ids: s_C_CTF5YF_P001_d s_C_2VU6CW_P001_d s_C_D719AD_P001_d s_C_M9LRUU_P001_d s_C_AC46KC_P001_d s_C_H6KW86_P001_d s_C_RA99UW_P001_d s_C_ND3PF6_P001_d s_C_VV3UK5_P001_d s_C_679EAR_P001_d s_C_MP6REX_P001_d s_C_ADTAL5_P001_d s_C_003HA8_P001_d s_C_XHTVXK_P001_d s_C_CPMWYP_P001_d s_C_FNM4WR_P001_d s_C_16WVCF_P001_d s_C_VJXJFU_P001_d s_C_1R1WNJ_P001_d s_C_UDRKF3_P001_d s_C_XKCKC4_P001_d s_C_74P9P5_P001_d s_C_N9HPT3_P001_d s_C_3F494V_P001_d s_C_FXE2UD_P001_d s_C_38PJEF_P001_d s_C_F2M8WF_P001_d s_C_PM5TJ7_P001_d s_C_6D84WP_P001_d s_C_JLJYPK_P001_d s_C_207N1F_P001_d s_C_K317TX_P001_d s_C_L6W2CJ_P001_d s_C_H4W1K4_P001_d s_C_463ART_P001_d s_C_87E3EJ_P001_d s_C_43DJ06_P001_d s_C_PDDMRT_P001_d s_C_AHNE99_P001_d s_C_NVUUKL_P001_d s_C_MA94C5_P001_d s_C_VYYFDM_P001_d s_C_D86FFD_P001_d s_C_2M7T23_P001_d s_C_1X92N8_P001_d s_C_KERR2T_P001_d s_C_U55NDX_P001_d s_C_89C4M2_P001_d s_C_PD7WJ5_P001_d s_C_J8LXYH_P001_d s_C_7EJL8A_P001_d s_C_AML0FT_P001_d s_C_VN5R9F_P001_d s_C_560HVF_P001_d s_C_0TCWAD_P001_d s_C_7DC7TE_P001_d s_C_WWVAUA_P001_d s_C_37NVKX_P001_d s_C_J6VM3L_P001_d s_C_CUNWLL_P001_d s_C_2NNWRW_P001_d s_C_4E8PUE_P001_d s_C_R46WLK_P001_d s_C_3J08Y0_P001_d s_C_K2N1TF_P001_d s_C_LE0374_P001_d s_C_X6CKRC_P001_d s_C_TUPDLD_P001_d s_C_9KL29X_P001_d s_C_WWX7F3_P001_d s_C_232307_P001_d s_C_CLWNJ3_P001_d s_C_EVTW87_P001_d s_C_K8EJXJ_P001_d s_C_W7RKP6_P001_d s_C_3DDFJ1_P001_d s_C_H2TY6P_P001_d s_C_FFDRA3_P001_d s_C_63A3CN_P001_d s_C_EC82A3_P001_d s_C_WETKKF_P001_d s_C_PN4P3L_P001_d s_C_FFAVJN_P001_d s_C_F666AJ_P001_d s_C_2LFVFJ_P001_d s_C_YW97WL_P001_d s_C_JNR9X3_P001_d s_C_UT983P_P001_d s_C_54LU1W_P001_d s_C_0XTAKJ_P001_d s_C_78NDH0_P001_d s_C_EX51R7_P001_d s_C_5CD5F4_P001_d s_C_VK8J4L_P001_d s_C_ECY328_P001_d s_C_R02LP8_P001_d s_C_73ALEN_P001_d s_C_EKXV7Y_P001_d s_C_E2UHXJ_P001_d s_C_YDVXUW_P001_d s_C_6J9XA7_P001_d s_C_A53JAX_P001_d s_C_V7KV1F_P001_d s_C_0KDD84_P001_d s_C_UX8338_P001_d s_C_JC2AAV_P001_d s_C_43CW84_P001_d s_C_NKC9KT_P001_d s_C_YVFD2D_P001_d s_C_YD1V7A_P001_d s_C_6HDFCW_P001_d s_C_7985Y0_P001_d s_C_8P85VJ_P001_d s_C_A83PUJ_P001_d s_C_WKATAH_P001_d s_C_FCV3TX_P001_d s_C_0TH9KN_P001_d s_C_W5LDW5_P001_d s_C_WD75HA_P001_d s_C_UWM6VE_P001_d s_C_AKF3DV_P001_d s_C_HD11U7_P001_d s_C_EFW6MX_P001_d s_C_K77HCW_P001_d s_C_JJ288E_P001_d s_C_6XRKTE_P001_d s_C_XEE6T3_P001_d s_C_DY80YJ_P001_d s_C_EWURPF_P001_d s_C_HVF41F_P001_d s_C_C0R4XV_P001_d s_C_7C3FH7_P001_d s_C_086CTC_P001_d s_C_85EFWK_P001_d s_C_UJD97R_P001_d s_C_E5959J_P001_d s_C_NR69F3_P001_d s_C_T0F2EP_P001_d s_C_EDRAFY_P001_d s_C_7M996U_P001_d s_C_UR3KPW_P001_d s_C_JLMFY4_P001_d s_C_452P26_P001_d s_C_9F3MTV_P001_d s_C_R0UH0K_P001_d s_C_DV4NE2_P001_d s_C_433LEN_P001_d s_C_XCJM63_P001_d s_C_UC4HNA_P001_d s_C_4CXPCD_P001_d s_C_30E67P_P001_d s_C_CKPXK0_P001_d s_C_VW7737_P001_d s_C_U1R4KF_P001_d s_C_RHFHTD_P001_d s_C_V2M1XF_P001_d s_C_T495A5_P001_d s_C_40DXFP_P001_d s_C_5RMT0X_P001_d s_C_XNLAPP_P001_d s_C_WNJMJL_P001_d s_C_WK4PUE_P001_d s_C_DJY8FJ_P001_d s_C_K6PU9E_P001_d s_C_T0H067_P001_d s_C_EMA9TY_P001_d s_C_RRRVF4_P001_d s_C_N677E4_P001_d s_C_C15KVL_P001_d s_C_T246L8_P001_d s_C_CW7N4C_P001_d s_C_35A8RK_P001_d s_C_YEPU8K_P001_d s_C_XEAY67_P001_d s_C_AN6LCV_P001_d s_C_CWJ45P_P001_d s_C_X2RNX1_P001_d s_C_323C2E_P001_d s_C_KHKDUM_P001_d s_C_M2L33T_P001_d s_C_6MA9R0_P001_d s_C_15J678_P001_d s_C_RP1DED_P001_d s_C_LY7NRX_P001_d
6 changes: 6 additions & 0 deletions public/blca_msk_2024/case_lists/cases_cnaseq.txt
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cancer_study_identifier: blca_msk_2024
stable_id: blca_msk_2024_cnaseq
case_list_name: Samples with mutation and CNA data
case_list_description: Samples with mutation and CNA data (184 samples)
case_list_category: all_cases_with_mutation_and_cna_data
case_list_ids: s_C_CTF5YF_P001_d s_C_D719AD_P001_d s_C_2VU6CW_P001_d s_C_H6KW86_P001_d s_C_AC46KC_P001_d s_C_M9LRUU_P001_d s_C_RA99UW_P001_d s_C_ND3PF6_P001_d s_C_VV3UK5_P001_d s_C_679EAR_P001_d s_C_MP6REX_P001_d s_C_ADTAL5_P001_d s_C_FNM4WR_P001_d s_C_003HA8_P001_d s_C_CPMWYP_P001_d s_C_XHTVXK_P001_d s_C_16WVCF_P001_d s_C_VJXJFU_P001_d s_C_1R1WNJ_P001_d s_C_UDRKF3_P001_d s_C_XKCKC4_P001_d s_C_74P9P5_P001_d s_C_N9HPT3_P001_d s_C_3F494V_P001_d s_C_F2M8WF_P001_d s_C_38PJEF_P001_d s_C_FXE2UD_P001_d s_C_PM5TJ7_P001_d s_C_6D84WP_P001_d s_C_JLJYPK_P001_d s_C_207N1F_P001_d s_C_K317TX_P001_d s_C_L6W2CJ_P001_d s_C_H4W1K4_P001_d s_C_463ART_P001_d s_C_87E3EJ_P001_d s_C_43DJ06_P001_d s_C_PDDMRT_P001_d s_C_AHNE99_P001_d s_C_MA94C5_P001_d s_C_NVUUKL_P001_d s_C_VYYFDM_P001_d s_C_2M7T23_P001_d s_C_D86FFD_P001_d s_C_1X92N8_P001_d s_C_U55NDX_P001_d s_C_KERR2T_P001_d s_C_89C4M2_P001_d s_C_PD7WJ5_P001_d s_C_J8LXYH_P001_d s_C_7EJL8A_P001_d s_C_AML0FT_P001_d s_C_VN5R9F_P001_d s_C_560HVF_P001_d s_C_0TCWAD_P001_d s_C_7DC7TE_P001_d s_C_WWVAUA_P001_d s_C_37NVKX_P001_d s_C_J6VM3L_P001_d s_C_CUNWLL_P001_d s_C_2NNWRW_P001_d s_C_4E8PUE_P001_d s_C_R46WLK_P001_d s_C_3J08Y0_P001_d s_C_K2N1TF_P001_d s_C_LE0374_P001_d s_C_X6CKRC_P001_d s_C_TUPDLD_P001_d s_C_9KL29X_P001_d s_C_WWX7F3_P001_d s_C_232307_P001_d s_C_CLWNJ3_P001_d s_C_K8EJXJ_P001_d s_C_EVTW87_P001_d s_C_W7RKP6_P001_d s_C_3DDFJ1_P001_d s_C_H2TY6P_P001_d s_C_FFDRA3_P001_d s_C_63A3CN_P001_d s_C_EC82A3_P001_d s_C_WETKKF_P001_d s_C_PN4P3L_P001_d s_C_FFAVJN_P001_d s_C_F666AJ_P001_d s_C_2LFVFJ_P001_d s_C_YW97WL_P001_d s_C_JNR9X3_P001_d s_C_UT983P_P001_d s_C_0XTAKJ_P001_d s_C_54LU1W_P001_d s_C_78NDH0_P001_d s_C_EX51R7_P001_d s_C_5CD5F4_P001_d s_C_VK8J4L_P001_d s_C_ECY328_P001_d s_C_R02LP8_P001_d s_C_73ALEN_P001_d s_C_EKXV7Y_P001_d s_C_E2UHXJ_P001_d s_C_YDVXUW_P001_d s_C_6J9XA7_P001_d s_C_A53JAX_P001_d s_C_V7KV1F_P001_d s_C_0KDD84_P001_d s_C_UX8338_P001_d s_C_JC2AAV_P001_d s_C_43CW84_P001_d s_C_6HDFCW_P001_d s_C_YVFD2D_P001_d s_C_8P85VJ_P001_d s_C_A83PUJ_P001_d s_C_7985Y0_P001_d s_C_NKC9KT_P001_d s_C_YD1V7A_P001_d s_C_WKATAH_P001_d s_C_HD11U7_P001_d s_C_WD75HA_P001_d s_C_W5LDW5_P001_d s_C_0TH9KN_P001_d s_C_UWM6VE_P001_d s_C_AKF3DV_P001_d s_C_FCV3TX_P001_d s_C_6XRKTE_P001_d s_C_EFW6MX_P001_d s_C_JJ288E_P001_d s_C_K77HCW_P001_d s_C_XEE6T3_P001_d s_C_DY80YJ_P001_d s_C_EWURPF_P001_d s_C_HVF41F_P001_d s_C_C0R4XV_P001_d s_C_7C3FH7_P001_d s_C_086CTC_P001_d s_C_UJD97R_P001_d s_C_85EFWK_P001_d s_C_E5959J_P001_d s_C_NR69F3_P001_d s_C_T0F2EP_P001_d s_C_EDRAFY_P001_d s_C_7M996U_P001_d s_C_JLMFY4_P001_d s_C_UR3KPW_P001_d s_C_452P26_P001_d s_C_9F3MTV_P001_d s_C_R0UH0K_P001_d s_C_DV4NE2_P001_d s_C_UC4HNA_P001_d s_C_XCJM63_P001_d s_C_433LEN_P001_d s_C_4CXPCD_P001_d s_C_30E67P_P001_d s_C_CKPXK0_P001_d s_C_VW7737_P001_d s_C_U1R4KF_P001_d s_C_RHFHTD_P001_d s_C_V2M1XF_P001_d s_C_T495A5_P001_d s_C_40DXFP_P001_d s_C_5RMT0X_P001_d s_C_XNLAPP_P001_d s_C_WNJMJL_P001_d s_C_WK4PUE_P001_d s_C_DJY8FJ_P001_d s_C_K6PU9E_P001_d s_C_T0H067_P001_d s_C_EMA9TY_P001_d s_C_RRRVF4_P001_d s_C_N677E4_P001_d s_C_C15KVL_P001_d s_C_T246L8_P001_d s_C_CW7N4C_P001_d s_C_35A8RK_P001_d s_C_YEPU8K_P001_d s_C_XEAY67_P001_d s_C_AN6LCV_P001_d s_C_CWJ45P_P001_d s_C_X2RNX1_P001_d s_C_323C2E_P001_d s_C_KHKDUM_P001_d s_C_M2L33T_P001_d s_C_6MA9R0_P001_d s_C_15J678_P001_d s_C_RP1DED_P001_d s_C_LY7NRX_P001_d
6 changes: 6 additions & 0 deletions public/blca_msk_2024/case_lists/cases_sequenced.txt
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cancer_study_identifier: blca_msk_2024
stable_id: blca_msk_2024_sequenced
case_list_name: Samples with mutation data
case_list_description: Samples with mutation data (184 samples)
case_list_category: all_cases_with_mutation_data
case_list_ids: s_C_CTF5YF_P001_d s_C_D719AD_P001_d s_C_2VU6CW_P001_d s_C_H6KW86_P001_d s_C_AC46KC_P001_d s_C_M9LRUU_P001_d s_C_RA99UW_P001_d s_C_ND3PF6_P001_d s_C_VV3UK5_P001_d s_C_679EAR_P001_d s_C_MP6REX_P001_d s_C_ADTAL5_P001_d s_C_FNM4WR_P001_d s_C_003HA8_P001_d s_C_CPMWYP_P001_d s_C_XHTVXK_P001_d s_C_16WVCF_P001_d s_C_VJXJFU_P001_d s_C_1R1WNJ_P001_d s_C_UDRKF3_P001_d s_C_XKCKC4_P001_d s_C_74P9P5_P001_d s_C_N9HPT3_P001_d s_C_3F494V_P001_d s_C_F2M8WF_P001_d s_C_38PJEF_P001_d s_C_FXE2UD_P001_d s_C_PM5TJ7_P001_d s_C_6D84WP_P001_d s_C_JLJYPK_P001_d s_C_207N1F_P001_d s_C_K317TX_P001_d s_C_L6W2CJ_P001_d s_C_H4W1K4_P001_d s_C_463ART_P001_d s_C_87E3EJ_P001_d s_C_43DJ06_P001_d s_C_PDDMRT_P001_d s_C_AHNE99_P001_d s_C_MA94C5_P001_d s_C_NVUUKL_P001_d s_C_VYYFDM_P001_d s_C_2M7T23_P001_d s_C_D86FFD_P001_d s_C_1X92N8_P001_d s_C_U55NDX_P001_d s_C_KERR2T_P001_d s_C_89C4M2_P001_d s_C_PD7WJ5_P001_d s_C_J8LXYH_P001_d s_C_7EJL8A_P001_d s_C_AML0FT_P001_d s_C_VN5R9F_P001_d s_C_560HVF_P001_d s_C_0TCWAD_P001_d s_C_7DC7TE_P001_d s_C_WWVAUA_P001_d s_C_37NVKX_P001_d s_C_J6VM3L_P001_d s_C_CUNWLL_P001_d s_C_2NNWRW_P001_d s_C_4E8PUE_P001_d s_C_R46WLK_P001_d s_C_3J08Y0_P001_d s_C_K2N1TF_P001_d s_C_LE0374_P001_d s_C_X6CKRC_P001_d s_C_TUPDLD_P001_d s_C_9KL29X_P001_d s_C_WWX7F3_P001_d s_C_232307_P001_d s_C_CLWNJ3_P001_d s_C_K8EJXJ_P001_d s_C_EVTW87_P001_d s_C_W7RKP6_P001_d s_C_3DDFJ1_P001_d s_C_H2TY6P_P001_d s_C_FFDRA3_P001_d s_C_63A3CN_P001_d s_C_EC82A3_P001_d s_C_WETKKF_P001_d s_C_PN4P3L_P001_d s_C_FFAVJN_P001_d s_C_F666AJ_P001_d s_C_2LFVFJ_P001_d s_C_YW97WL_P001_d s_C_JNR9X3_P001_d s_C_UT983P_P001_d s_C_0XTAKJ_P001_d s_C_54LU1W_P001_d s_C_78NDH0_P001_d s_C_EX51R7_P001_d s_C_5CD5F4_P001_d s_C_VK8J4L_P001_d s_C_ECY328_P001_d s_C_R02LP8_P001_d s_C_73ALEN_P001_d s_C_EKXV7Y_P001_d s_C_E2UHXJ_P001_d s_C_YDVXUW_P001_d s_C_6J9XA7_P001_d s_C_A53JAX_P001_d s_C_V7KV1F_P001_d s_C_0KDD84_P001_d s_C_UX8338_P001_d s_C_JC2AAV_P001_d s_C_43CW84_P001_d s_C_6HDFCW_P001_d s_C_YVFD2D_P001_d s_C_8P85VJ_P001_d s_C_A83PUJ_P001_d s_C_7985Y0_P001_d s_C_NKC9KT_P001_d s_C_YD1V7A_P001_d s_C_WKATAH_P001_d s_C_HD11U7_P001_d s_C_WD75HA_P001_d s_C_W5LDW5_P001_d s_C_0TH9KN_P001_d s_C_UWM6VE_P001_d s_C_AKF3DV_P001_d s_C_FCV3TX_P001_d s_C_6XRKTE_P001_d s_C_EFW6MX_P001_d s_C_JJ288E_P001_d s_C_K77HCW_P001_d s_C_XEE6T3_P001_d s_C_DY80YJ_P001_d s_C_EWURPF_P001_d s_C_HVF41F_P001_d s_C_C0R4XV_P001_d s_C_7C3FH7_P001_d s_C_086CTC_P001_d s_C_UJD97R_P001_d s_C_85EFWK_P001_d s_C_E5959J_P001_d s_C_NR69F3_P001_d s_C_T0F2EP_P001_d s_C_EDRAFY_P001_d s_C_7M996U_P001_d s_C_JLMFY4_P001_d s_C_UR3KPW_P001_d s_C_452P26_P001_d s_C_9F3MTV_P001_d s_C_R0UH0K_P001_d s_C_DV4NE2_P001_d s_C_UC4HNA_P001_d s_C_XCJM63_P001_d s_C_433LEN_P001_d s_C_4CXPCD_P001_d s_C_30E67P_P001_d s_C_CKPXK0_P001_d s_C_VW7737_P001_d s_C_U1R4KF_P001_d s_C_RHFHTD_P001_d s_C_V2M1XF_P001_d s_C_T495A5_P001_d s_C_40DXFP_P001_d s_C_5RMT0X_P001_d s_C_XNLAPP_P001_d s_C_WNJMJL_P001_d s_C_WK4PUE_P001_d s_C_DJY8FJ_P001_d s_C_K6PU9E_P001_d s_C_T0H067_P001_d s_C_EMA9TY_P001_d s_C_RRRVF4_P001_d s_C_N677E4_P001_d s_C_C15KVL_P001_d s_C_T246L8_P001_d s_C_CW7N4C_P001_d s_C_35A8RK_P001_d s_C_YEPU8K_P001_d s_C_XEAY67_P001_d s_C_AN6LCV_P001_d s_C_CWJ45P_P001_d s_C_X2RNX1_P001_d s_C_323C2E_P001_d s_C_KHKDUM_P001_d s_C_M2L33T_P001_d s_C_6MA9R0_P001_d s_C_15J678_P001_d s_C_RP1DED_P001_d s_C_LY7NRX_P001_d
6 changes: 6 additions & 0 deletions public/blca_msk_2024/case_lists/cases_sv.txt
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cancer_study_identifier: blca_msk_2024
stable_id: blca_msk_2024_sv
case_list_name: Samples with mutation data
case_list_description: Samples with SV data (184 samples)
case_list_category: all_cases_with_sv_data
case_list_ids: s_C_CTF5YF_P001_d s_C_D719AD_P001_d s_C_2VU6CW_P001_d s_C_H6KW86_P001_d s_C_AC46KC_P001_d s_C_M9LRUU_P001_d s_C_RA99UW_P001_d s_C_ND3PF6_P001_d s_C_VV3UK5_P001_d s_C_679EAR_P001_d s_C_MP6REX_P001_d s_C_ADTAL5_P001_d s_C_FNM4WR_P001_d s_C_003HA8_P001_d s_C_CPMWYP_P001_d s_C_XHTVXK_P001_d s_C_16WVCF_P001_d s_C_VJXJFU_P001_d s_C_1R1WNJ_P001_d s_C_UDRKF3_P001_d s_C_XKCKC4_P001_d s_C_74P9P5_P001_d s_C_N9HPT3_P001_d s_C_3F494V_P001_d s_C_F2M8WF_P001_d s_C_38PJEF_P001_d s_C_FXE2UD_P001_d s_C_PM5TJ7_P001_d s_C_6D84WP_P001_d s_C_JLJYPK_P001_d s_C_207N1F_P001_d s_C_K317TX_P001_d s_C_L6W2CJ_P001_d s_C_H4W1K4_P001_d s_C_463ART_P001_d s_C_87E3EJ_P001_d s_C_43DJ06_P001_d s_C_PDDMRT_P001_d s_C_AHNE99_P001_d s_C_MA94C5_P001_d s_C_NVUUKL_P001_d s_C_VYYFDM_P001_d s_C_2M7T23_P001_d s_C_D86FFD_P001_d s_C_1X92N8_P001_d s_C_U55NDX_P001_d s_C_KERR2T_P001_d s_C_89C4M2_P001_d s_C_PD7WJ5_P001_d s_C_J8LXYH_P001_d s_C_7EJL8A_P001_d s_C_AML0FT_P001_d s_C_VN5R9F_P001_d s_C_560HVF_P001_d s_C_0TCWAD_P001_d s_C_7DC7TE_P001_d s_C_WWVAUA_P001_d s_C_37NVKX_P001_d s_C_J6VM3L_P001_d s_C_CUNWLL_P001_d s_C_2NNWRW_P001_d s_C_4E8PUE_P001_d s_C_R46WLK_P001_d s_C_3J08Y0_P001_d s_C_K2N1TF_P001_d s_C_LE0374_P001_d s_C_X6CKRC_P001_d s_C_TUPDLD_P001_d s_C_9KL29X_P001_d s_C_WWX7F3_P001_d s_C_232307_P001_d s_C_CLWNJ3_P001_d s_C_K8EJXJ_P001_d s_C_EVTW87_P001_d s_C_W7RKP6_P001_d s_C_3DDFJ1_P001_d s_C_H2TY6P_P001_d s_C_FFDRA3_P001_d s_C_63A3CN_P001_d s_C_EC82A3_P001_d s_C_WETKKF_P001_d s_C_PN4P3L_P001_d s_C_FFAVJN_P001_d s_C_F666AJ_P001_d s_C_2LFVFJ_P001_d s_C_YW97WL_P001_d s_C_JNR9X3_P001_d s_C_UT983P_P001_d s_C_0XTAKJ_P001_d s_C_54LU1W_P001_d s_C_78NDH0_P001_d s_C_EX51R7_P001_d s_C_5CD5F4_P001_d s_C_VK8J4L_P001_d s_C_ECY328_P001_d s_C_R02LP8_P001_d s_C_73ALEN_P001_d s_C_EKXV7Y_P001_d s_C_E2UHXJ_P001_d s_C_YDVXUW_P001_d s_C_6J9XA7_P001_d s_C_A53JAX_P001_d s_C_V7KV1F_P001_d s_C_0KDD84_P001_d s_C_UX8338_P001_d s_C_JC2AAV_P001_d s_C_43CW84_P001_d s_C_6HDFCW_P001_d s_C_YVFD2D_P001_d s_C_8P85VJ_P001_d s_C_A83PUJ_P001_d s_C_7985Y0_P001_d s_C_NKC9KT_P001_d s_C_YD1V7A_P001_d s_C_WKATAH_P001_d s_C_HD11U7_P001_d s_C_WD75HA_P001_d s_C_W5LDW5_P001_d s_C_0TH9KN_P001_d s_C_UWM6VE_P001_d s_C_AKF3DV_P001_d s_C_FCV3TX_P001_d s_C_6XRKTE_P001_d s_C_EFW6MX_P001_d s_C_JJ288E_P001_d s_C_K77HCW_P001_d s_C_XEE6T3_P001_d s_C_DY80YJ_P001_d s_C_EWURPF_P001_d s_C_HVF41F_P001_d s_C_C0R4XV_P001_d s_C_7C3FH7_P001_d s_C_086CTC_P001_d s_C_UJD97R_P001_d s_C_85EFWK_P001_d s_C_E5959J_P001_d s_C_NR69F3_P001_d s_C_T0F2EP_P001_d s_C_EDRAFY_P001_d s_C_7M996U_P001_d s_C_JLMFY4_P001_d s_C_UR3KPW_P001_d s_C_452P26_P001_d s_C_9F3MTV_P001_d s_C_R0UH0K_P001_d s_C_DV4NE2_P001_d s_C_UC4HNA_P001_d s_C_XCJM63_P001_d s_C_433LEN_P001_d s_C_4CXPCD_P001_d s_C_30E67P_P001_d s_C_CKPXK0_P001_d s_C_VW7737_P001_d s_C_U1R4KF_P001_d s_C_RHFHTD_P001_d s_C_V2M1XF_P001_d s_C_T495A5_P001_d s_C_40DXFP_P001_d s_C_5RMT0X_P001_d s_C_XNLAPP_P001_d s_C_WNJMJL_P001_d s_C_WK4PUE_P001_d s_C_DJY8FJ_P001_d s_C_K6PU9E_P001_d s_C_T0H067_P001_d s_C_EMA9TY_P001_d s_C_RRRVF4_P001_d s_C_N677E4_P001_d s_C_C15KVL_P001_d s_C_T246L8_P001_d s_C_CW7N4C_P001_d s_C_35A8RK_P001_d s_C_YEPU8K_P001_d s_C_XEAY67_P001_d s_C_AN6LCV_P001_d s_C_CWJ45P_P001_d s_C_X2RNX1_P001_d s_C_323C2E_P001_d s_C_KHKDUM_P001_d s_C_M2L33T_P001_d s_C_6MA9R0_P001_d s_C_15J678_P001_d s_C_RP1DED_P001_d s_C_LY7NRX_P001_d
3 changes: 3 additions & 0 deletions public/blca_msk_2024/data_clinical_sample.txt
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3 changes: 3 additions & 0 deletions public/blca_msk_2024/data_cna.txt
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3 changes: 3 additions & 0 deletions public/blca_msk_2024/data_cna_hg19.seg
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3 changes: 3 additions & 0 deletions public/blca_msk_2024/data_mutations.txt
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3 changes: 3 additions & 0 deletions public/blca_msk_2024/data_sv.txt
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4 changes: 4 additions & 0 deletions public/blca_msk_2024/meta_clinical_sample.txt
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cancer_study_identifier: blca_msk_2024
genetic_alteration_type: CLINICAL
datatype: SAMPLE_ATTRIBUTES
data_filename: data_clinical_sample.txt
8 changes: 8 additions & 0 deletions public/blca_msk_2024/meta_cna.txt
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cancer_study_identifier: blca_msk_2024
data_filename: data_cna.txt
datatype: DISCRETE
genetic_alteration_type: COPY_NUMBER_ALTERATION
profile_description: Discrete Copy Number Data
profile_name: Discrete Copy Number Data
show_profile_in_analysis_tab: true
stable_id: cna
8 changes: 8 additions & 0 deletions public/blca_msk_2024/meta_cna_hg19_seg.txt
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cancer_study_identifier: blca_msk_2024
data_filename: data_cna_hg19.seg
genetic_alteration_type: COPY_NUMBER_ALTERATION
datatype: SEG
show_profile_in_analysis_tab: FALSE
profile_name: Segment data values
description: Somatic CNA data (copy number ratio from tumor samples minus ratio from matched normals) from TCGA.
reference_genome_id: hg19
8 changes: 8 additions & 0 deletions public/blca_msk_2024/meta_mutations.txt
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cancer_study_identifier: blca_msk_2024
data_filename: data_mutations.txt
datatype: MAF
genetic_alteration_type: MUTATION_EXTENDED
profile_description: Mutation data
profile_name: Mutations
show_profile_in_analysis_tab: true
stable_id: mutations
7 changes: 7 additions & 0 deletions public/blca_msk_2024/meta_study.txt
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cancer_study_identifier: blca_msk_2024
description: Targeted sequencing of 184 muscle-invasive bladder cancer (MIBC) samples and their matched normals using MSK-IMPACT.
name: Bladder Urothelial Carcinoma (MSK, JCO Precis Oncol 2024)
short_name: Bladder Carcinoma
type_of_cancer: blca
citation: Iyer, Gopa et al. JCO precision oncology 2024
pmid: 39499893
8 changes: 8 additions & 0 deletions public/blca_msk_2024/meta_sv.txt
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cancer_study_identifier: blca_msk_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
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