diff --git a/public/es_dsrct_msk_2023/case_lists/cases_all.txt b/public/es_dsrct_msk_2023/case_lists/cases_all.txt new file mode 100644 index 0000000000..04c8c9e157 --- /dev/null +++ b/public/es_dsrct_msk_2023/case_lists/cases_all.txt @@ -0,0 +1,6 @@ +cancer_study_identifier: es_dsrct_msk_2023 +stable_id: es_dsrct_msk_2023_all +case_list_name: All samples +case_list_description: All samples (290 samples) +case_list_category: all_cases_in_study +case_list_ids: P-0000232-T01-IM3 P-0000253-T02-IM5 P-0000257-T01-IM3 P-0000258-T02-IM5 P-0000564-T01-IM3 P-0000609-T01-IM3 P-0000719-T01-IM3 P-0001233-T01-IM3 P-0001377-T01-IM3 P-0001725-T01-IM3 P-0001896-T01-IM3 P-0002170-T01-IM3 P-0002240-T01-IM3 P-0003290-T01-IM5 P-0003405-T01-IM5 P-0003435-T01-IM5 P-0003554-T01-IM5 P-0004071-T01-IM5 P-0004079-T01-IM5 P-0004163-T01-IM5 P-0004498-T01-IM5 P-0004671-T01-IM5 P-0004931-T02-IM5 P-0005297-T01-IM5 P-0005614-T01-IM5 P-0005710-T01-IM5 P-0005716-T01-IM5 P-0005841-T01-IM5 P-0005977-T01-IM5 P-0006040-T01-IM5 P-0006092-T01-IM5 P-0006208-T01-IM5 P-0006274-T01-IM5 P-0006506-T01-IM5 P-0006792-T01-IM5 P-0007117-T01-IM5 P-0007908-T01-IM5 P-0008030-T01-IM5 P-0008102-T01-IM5 P-0008265-T01-IM5 P-0008320-T01-IM5 P-0008352-T01-IM5 P-0008355-T01-IM5 P-0008523-T01-IM5 P-0008731-T01-IM5 P-0008749-T01-IM5 P-0009359-T01-IM5 P-0009733-T01-IM5 P-0012131-T01-IM5 P-0012316-T01-IM5 P-0012454-T01-IM5 P-0012482-T02-IM5 P-0012923-T01-IM5 P-0013601-T01-IM5 P-0013746-T02-IM5 P-0013841-T01-IM5 P-0013874-T01-IM5 P-0013922-T01-IM5 P-0014314-T01-IM6 P-0014984-T02-IM6 P-0015517-T01-IM6 P-0015619-T03-IM6 P-0016346-T01-IM6 P-0016417-T01-IM6 P-0016515-T02-IM6 P-0016658-T01-IM6 P-0016723-T01-IM6 P-0017027-T01-IM6 P-0017225-T01-IM6 P-0017427-T01-IM6 P-0018508-T01-IM6 P-0018530-T01-IM6 P-0018663-T01-IM6 P-0019080-T02-IM6 P-0019756-T01-IM6 P-0020416-T01-IM6 P-0020463-T01-IM6 P-0020783-T01-IM6 P-0021068-T01-IM6 P-0021189-T01-IM6 P-0021655-T02-IM6 P-0021868-T01-IM6 P-0021939-T01-IM6 P-0021981-T01-IM6 P-0022234-T01-IM6 P-0022452-T01-IM6 P-0022500-T01-IM6 P-0024067-T01-IM6 P-0024101-T02-IM6 P-0024608-T01-IM6 P-0024807-T01-IM6 P-0024845-T02-IM6 P-0024945-T01-IM6 P-0025251-T01-IM6 P-0026404-T01-IM6 P-0027315-T01-IM6 P-0028358-T01-IM6 P-0029161-T01-IM6 P-0029258-T01-IM6 P-0029448-T01-IM6 P-0029619-T02-IM6 P-0030044-T02-IM6 P-0030220-T01-IM6 P-0030279-T02-IM6 P-0030349-T03-IM6 P-0030397-T02-IM6 P-0030650-T02-IM6 P-0030917-T02-IM6 P-0032119-T01-IM6 P-0032382-T01-IM6 P-0032610-T01-IM6 P-0032909-T02-IM6 P-0033623-T01-IM6 P-0033922-T02-IM6 P-0034612-T01-IM6 P-0036245-T01-IM6 P-0036376-T01-IM6 P-0036601-T02-IM6 P-0036604-T02-IM6 P-0037173-T01-IM6 P-0037182-T02-IM6 P-0038127-T01-IM6 P-0038131-T01-IM6 P-0038570-T02-IM6 P-0038749-T01-IM6 P-0039202-T02-IM7 P-0039406-T01-IM6 P-0039579-T01-IM6 P-0039688-T01-IM6 P-0040254-T02-IM6 P-0040442-T01-IM6 P-0041551-T01-IM6 P-0041943-T01-IM6 P-0042292-T02-IM6 P-0042302-T02-IM6 P-0042438-T01-IM6 P-0042571-T02-IM6 P-0042798-T02-IM6 P-0042913-T01-IM6 P-0043526-T01-IM6 P-0043649-T02-IM6 P-0043958-T01-IM6 P-0044088-T02-IM6 P-0044126-T01-IM6 P-0044233-T02-IM6 P-0044523-T02-IM6 P-0044551-T01-IM6 P-0044826-T01-IM6 P-0044896-T02-IM6 P-0045323-T02-IM6 P-0045722-T01-IM6 P-0046904-T01-IM6 P-0047109-T02-IM6 P-0047480-T03-IM6 P-0047625-T02-IM6 P-0047990-T02-IM6 P-0048335-T02-IM6 P-0048359-T01-IM6 P-0048417-T02-IM6 P-0048577-T03-IM6 P-0048734-T02-IM6 P-0050027-T02-IM6 P-0051333-T01-IM6 P-0051569-T01-IM6 P-0052277-T01-IM6 P-0052635-T01-IM6 P-0052745-T02-IM6 P-0052809-T02-IM6 P-0053879-T02-IM6 P-0053991-T01-IM6 P-0054475-T01-IM6 P-0055038-T02-IM6 P-0055090-T01-IM6 P-0055519-T01-IM6 P-0055733-T02-IM7 P-0055969-T02-IM6 P-0056323-T02-IM6 P-0056509-T02-IM6 P-0056693-T02-IM6 P-0056712-T01-IM6 P-0057151-T02-IM7 P-0057192-T01-IM6 P-0057669-T01-IM6 P-0057766-T01-IM6 P-0057913-T02-IM6 P-0058582-T01-IM7 P-0059067-T02-IM7 P-0059068-T02-IM7 P-0059143-T01-IM7 P-0059432-T01-IM7 P-0059518-T02-IM7 P-0060347-T02-IM7 P-0060461-T02-IM7 P-0061850-T02-IM7 P-0062142-T03-IM7 P-0062355-T03-IM7 P-0062632-T03-IM7 P-0062785-T01-IM7 P-0063940-T02-IM7 P-0064511-T02-IM7 P-0065014-T01-IM7 P-0065643-T01-IM7 P-0065672-T01-IM7 P-0065945-T03-IM7 P-0066169-T01-IM7 P-0066379-T02-IM7 P-0066564-T02-IM7 P-0066725-T02-IM7 P-0067360-T02-IM7 P-0067493-T01-IM7 P-0067897-T01-IM7 P-0067959-T01-IM7 P-0068227-T02-IM7 P-0068585-T02-IM7 P-0068866-T02-IM7 P-0070056-T01-IM7 P-0070230-T01-IM7 P-0070856-T02-IM7 P-0070866-T02-IM7 P-0071598-T02-IM7 P-0072413-T02-IM7 P-0072507-T02-IM7 P-0072628-T01-IM7 P-0073074-T02-IM7 P-0074020-T01-IM7 P-0074320-T02-IM7 P-0074365-T02-IM7 P-0074505-T03-IM7 P-0074560-T02-IM7 P-0075471-T02-IM7 P-0076337-T01-IM7 P-0076441-T01-IM7 P-0076499-T01-IM7 P-0077035-T01-IM7 P-0077435-T01-IM7 P-0077472-T01-IM7 P-0078214-T01-IM7 P-0078251-T02-IM7 P-0078549-T01-IM7 P-0079165-T01-IM7 P-0079703-T01-IM7 P-0079803-T01-IM7 P-0080440-T01-IM7 P-0080464-T01-IM7 P-0080998-T01-IM7 P-0082096-T01-IM7 P-0082175-T01-IM7 P-0082664-T02-IM7 P-0082988-T01-IM7 P-0083231-T01-IM7 P-0083855-T03-IM7 P-0085187-T01-IM7 P-0086263-T01-IM7 P-0086684-T01-IM7 P-0086760-T01-IM7 P-0087046-T02-IM7 P-0088279-T02-IM7 P-0089249-T01-IM7 P-0089525-T01-IM7 P-0089564-T01-IM7 P-0089643-T02-IM7 P-0090846-T01-IM7 P-0091528-T01-IM7 P-0091606-T01-IM7 P-0091886-T01-IM7 P-0092621-T01-IM7 P-0015217-T01-IM6 P-0060558-T01-IM7 P-0077156-T01-IM7 P-0079707-T01-IM7 P-0090152-T02-IM7 P-0086880-T01-IM7 P-0087224-T02-IM7 P-0091798-T01-IM7 P-0091032-T01-IM7 P-0091928-T01-IM7 P-0009452-T01-IM5 P-0006506-T02-IM6 P-0013746-T04-IM7 P-0029161-T02-IM6 P-0032909-T05-IM6 P-0032909-T06-IM7 P-0032909-T08-IM7 P-0037182-T03-IM6 P-0039579-T03-IM7 P-0043526-T03-IM6 P-0047109-T03-IM7 P-0056509-T03-IM7 P-0082096-T02-IM7 P-0082175-T02-IM7 \ No newline at end of file diff --git a/public/es_dsrct_msk_2023/case_lists/cases_cna.txt b/public/es_dsrct_msk_2023/case_lists/cases_cna.txt new file mode 100644 index 0000000000..0833d42b8f --- /dev/null +++ b/public/es_dsrct_msk_2023/case_lists/cases_cna.txt @@ -0,0 +1,6 @@ +cancer_study_identifier: es_dsrct_msk_2023 +stable_id: es_dsrct_msk_2023_cna +case_list_name: Samples with CNA data +case_list_description: Samples with CNA data (290 samples) +case_list_category: all_cases_with_cna_data +case_list_ids: P-0000232-T01-IM3 P-0000253-T02-IM5 P-0000257-T01-IM3 P-0000258-T02-IM5 P-0000564-T01-IM3 P-0000609-T01-IM3 P-0000719-T01-IM3 P-0001233-T01-IM3 P-0001377-T01-IM3 P-0001725-T01-IM3 P-0001896-T01-IM3 P-0002170-T01-IM3 P-0002240-T01-IM3 P-0003290-T01-IM5 P-0003405-T01-IM5 P-0003435-T01-IM5 P-0003554-T01-IM5 P-0004071-T01-IM5 P-0004079-T01-IM5 P-0004163-T01-IM5 P-0004498-T01-IM5 P-0004671-T01-IM5 P-0004931-T02-IM5 P-0005297-T01-IM5 P-0005614-T01-IM5 P-0005710-T01-IM5 P-0005716-T01-IM5 P-0005841-T01-IM5 P-0005977-T01-IM5 P-0006040-T01-IM5 P-0006092-T01-IM5 P-0006208-T01-IM5 P-0006274-T01-IM5 P-0006506-T01-IM5 P-0006792-T01-IM5 P-0007117-T01-IM5 P-0007908-T01-IM5 P-0008030-T01-IM5 P-0008102-T01-IM5 P-0008265-T01-IM5 P-0008320-T01-IM5 P-0008352-T01-IM5 P-0008355-T01-IM5 P-0008523-T01-IM5 P-0008731-T01-IM5 P-0008749-T01-IM5 P-0009359-T01-IM5 P-0009733-T01-IM5 P-0012131-T01-IM5 P-0012316-T01-IM5 P-0012454-T01-IM5 P-0012482-T02-IM5 P-0012923-T01-IM5 P-0013601-T01-IM5 P-0013746-T02-IM5 P-0013841-T01-IM5 P-0013874-T01-IM5 P-0013922-T01-IM5 P-0014314-T01-IM6 P-0014984-T02-IM6 P-0015517-T01-IM6 P-0015619-T03-IM6 P-0016346-T01-IM6 P-0016417-T01-IM6 P-0016515-T02-IM6 P-0016658-T01-IM6 P-0016723-T01-IM6 P-0017027-T01-IM6 P-0017225-T01-IM6 P-0017427-T01-IM6 P-0018508-T01-IM6 P-0018530-T01-IM6 P-0018663-T01-IM6 P-0019080-T02-IM6 P-0019756-T01-IM6 P-0020416-T01-IM6 P-0020463-T01-IM6 P-0020783-T01-IM6 P-0021068-T01-IM6 P-0021189-T01-IM6 P-0021655-T02-IM6 P-0021868-T01-IM6 P-0021939-T01-IM6 P-0021981-T01-IM6 P-0022234-T01-IM6 P-0022452-T01-IM6 P-0022500-T01-IM6 P-0024067-T01-IM6 P-0024101-T02-IM6 P-0024608-T01-IM6 P-0024807-T01-IM6 P-0024845-T02-IM6 P-0024945-T01-IM6 P-0025251-T01-IM6 P-0026404-T01-IM6 P-0027315-T01-IM6 P-0028358-T01-IM6 P-0029161-T01-IM6 P-0029258-T01-IM6 P-0029448-T01-IM6 P-0029619-T02-IM6 P-0030044-T02-IM6 P-0030220-T01-IM6 P-0030279-T02-IM6 P-0030349-T03-IM6 P-0030397-T02-IM6 P-0030650-T02-IM6 P-0030917-T02-IM6 P-0032119-T01-IM6 P-0032382-T01-IM6 P-0032610-T01-IM6 P-0032909-T02-IM6 P-0033623-T01-IM6 P-0033922-T02-IM6 P-0034612-T01-IM6 P-0036245-T01-IM6 P-0036376-T01-IM6 P-0036601-T02-IM6 P-0036604-T02-IM6 P-0037173-T01-IM6 P-0037182-T02-IM6 P-0038127-T01-IM6 P-0038131-T01-IM6 P-0038570-T02-IM6 P-0038749-T01-IM6 P-0039202-T02-IM7 P-0039406-T01-IM6 P-0039579-T01-IM6 P-0039688-T01-IM6 P-0040254-T02-IM6 P-0040442-T01-IM6 P-0041551-T01-IM6 P-0041943-T01-IM6 P-0042292-T02-IM6 P-0042302-T02-IM6 P-0042438-T01-IM6 P-0042571-T02-IM6 P-0042798-T02-IM6 P-0042913-T01-IM6 P-0043526-T01-IM6 P-0043649-T02-IM6 P-0043958-T01-IM6 P-0044088-T02-IM6 P-0044126-T01-IM6 P-0044233-T02-IM6 P-0044523-T02-IM6 P-0044551-T01-IM6 P-0044826-T01-IM6 P-0044896-T02-IM6 P-0045323-T02-IM6 P-0045722-T01-IM6 P-0046904-T01-IM6 P-0047109-T02-IM6 P-0047480-T03-IM6 P-0047625-T02-IM6 P-0047990-T02-IM6 P-0048335-T02-IM6 P-0048359-T01-IM6 P-0048417-T02-IM6 P-0048577-T03-IM6 P-0048734-T02-IM6 P-0050027-T02-IM6 P-0051333-T01-IM6 P-0051569-T01-IM6 P-0052277-T01-IM6 P-0052635-T01-IM6 P-0052745-T02-IM6 P-0052809-T02-IM6 P-0053879-T02-IM6 P-0053991-T01-IM6 P-0054475-T01-IM6 P-0055038-T02-IM6 P-0055090-T01-IM6 P-0055519-T01-IM6 P-0055733-T02-IM7 P-0055969-T02-IM6 P-0056323-T02-IM6 P-0056509-T02-IM6 P-0056693-T02-IM6 P-0056712-T01-IM6 P-0057151-T02-IM7 P-0057192-T01-IM6 P-0057669-T01-IM6 P-0057766-T01-IM6 P-0057913-T02-IM6 P-0058582-T01-IM7 P-0059067-T02-IM7 P-0059068-T02-IM7 P-0059143-T01-IM7 P-0059432-T01-IM7 P-0059518-T02-IM7 P-0060347-T02-IM7 P-0060461-T02-IM7 P-0061850-T02-IM7 P-0062142-T03-IM7 P-0062355-T03-IM7 P-0062632-T03-IM7 P-0062785-T01-IM7 P-0063940-T02-IM7 P-0064511-T02-IM7 P-0065014-T01-IM7 P-0065643-T01-IM7 P-0065672-T01-IM7 P-0065945-T03-IM7 P-0066169-T01-IM7 P-0066379-T02-IM7 P-0066564-T02-IM7 P-0066725-T02-IM7 P-0067360-T02-IM7 P-0067493-T01-IM7 P-0067897-T01-IM7 P-0067959-T01-IM7 P-0068227-T02-IM7 P-0068585-T02-IM7 P-0068866-T02-IM7 P-0070056-T01-IM7 P-0070230-T01-IM7 P-0070856-T02-IM7 P-0070866-T02-IM7 P-0071598-T02-IM7 P-0072413-T02-IM7 P-0072507-T02-IM7 P-0072628-T01-IM7 P-0073074-T02-IM7 P-0074020-T01-IM7 P-0074320-T02-IM7 P-0074365-T02-IM7 P-0074505-T03-IM7 P-0074560-T02-IM7 P-0075471-T02-IM7 P-0076337-T01-IM7 P-0076441-T01-IM7 P-0076499-T01-IM7 P-0077035-T01-IM7 P-0077435-T01-IM7 P-0077472-T01-IM7 P-0078214-T01-IM7 P-0078251-T02-IM7 P-0078549-T01-IM7 P-0079165-T01-IM7 P-0079703-T01-IM7 P-0079803-T01-IM7 P-0080440-T01-IM7 P-0080464-T01-IM7 P-0080998-T01-IM7 P-0082096-T01-IM7 P-0082175-T01-IM7 P-0082664-T02-IM7 P-0082988-T01-IM7 P-0083231-T01-IM7 P-0083855-T03-IM7 P-0085187-T01-IM7 P-0086263-T01-IM7 P-0086684-T01-IM7 P-0086760-T01-IM7 P-0087046-T02-IM7 P-0088279-T02-IM7 P-0089249-T01-IM7 P-0089525-T01-IM7 P-0089564-T01-IM7 P-0089643-T02-IM7 P-0090846-T01-IM7 P-0091528-T01-IM7 P-0091606-T01-IM7 P-0091886-T01-IM7 P-0092621-T01-IM7 P-0015217-T01-IM6 P-0060558-T01-IM7 P-0077156-T01-IM7 P-0079707-T01-IM7 P-0090152-T02-IM7 P-0086880-T01-IM7 P-0087224-T02-IM7 P-0091798-T01-IM7 P-0091032-T01-IM7 P-0091928-T01-IM7 P-0009452-T01-IM5 P-0006506-T02-IM6 P-0013746-T04-IM7 P-0029161-T02-IM6 P-0032909-T05-IM6 P-0032909-T06-IM7 P-0032909-T08-IM7 P-0037182-T03-IM6 P-0039579-T03-IM7 P-0043526-T03-IM6 P-0047109-T03-IM7 P-0056509-T03-IM7 P-0082096-T02-IM7 P-0082175-T02-IM7 \ No newline at end of file diff --git a/public/es_dsrct_msk_2023/case_lists/cases_cnaseq.txt b/public/es_dsrct_msk_2023/case_lists/cases_cnaseq.txt new file mode 100644 index 0000000000..3f8ef4f4dc --- /dev/null +++ b/public/es_dsrct_msk_2023/case_lists/cases_cnaseq.txt @@ -0,0 +1,6 @@ +cancer_study_identifier: es_dsrct_msk_2023 +stable_id: es_dsrct_msk_2023_cnaseq +case_list_name: Samples with mutation and CNA data +case_list_description: Samples with mutation and CNA data (290 samples) +case_list_category: all_cases_with_mutation_and_cna_data +case_list_ids: P-0000232-T01-IM3 P-0000253-T02-IM5 P-0000257-T01-IM3 P-0000258-T02-IM5 P-0000564-T01-IM3 P-0000609-T01-IM3 P-0000719-T01-IM3 P-0001233-T01-IM3 P-0001377-T01-IM3 P-0001725-T01-IM3 P-0001896-T01-IM3 P-0002170-T01-IM3 P-0002240-T01-IM3 P-0003290-T01-IM5 P-0003405-T01-IM5 P-0003435-T01-IM5 P-0003554-T01-IM5 P-0004071-T01-IM5 P-0004079-T01-IM5 P-0004163-T01-IM5 P-0004498-T01-IM5 P-0004671-T01-IM5 P-0004931-T02-IM5 P-0005297-T01-IM5 P-0005614-T01-IM5 P-0005710-T01-IM5 P-0005716-T01-IM5 P-0005841-T01-IM5 P-0005977-T01-IM5 P-0006040-T01-IM5 P-0006092-T01-IM5 P-0006208-T01-IM5 P-0006274-T01-IM5 P-0006506-T01-IM5 P-0006792-T01-IM5 P-0007117-T01-IM5 P-0007908-T01-IM5 P-0008030-T01-IM5 P-0008102-T01-IM5 P-0008265-T01-IM5 P-0008320-T01-IM5 P-0008352-T01-IM5 P-0008355-T01-IM5 P-0008523-T01-IM5 P-0008731-T01-IM5 P-0008749-T01-IM5 P-0009359-T01-IM5 P-0009733-T01-IM5 P-0012131-T01-IM5 P-0012316-T01-IM5 P-0012454-T01-IM5 P-0012482-T02-IM5 P-0012923-T01-IM5 P-0013601-T01-IM5 P-0013746-T02-IM5 P-0013841-T01-IM5 P-0013874-T01-IM5 P-0013922-T01-IM5 P-0014314-T01-IM6 P-0014984-T02-IM6 P-0015517-T01-IM6 P-0015619-T03-IM6 P-0016346-T01-IM6 P-0016417-T01-IM6 P-0016515-T02-IM6 P-0016658-T01-IM6 P-0016723-T01-IM6 P-0017027-T01-IM6 P-0017225-T01-IM6 P-0017427-T01-IM6 P-0018508-T01-IM6 P-0018530-T01-IM6 P-0018663-T01-IM6 P-0019080-T02-IM6 P-0019756-T01-IM6 P-0020416-T01-IM6 P-0020463-T01-IM6 P-0020783-T01-IM6 P-0021068-T01-IM6 P-0021189-T01-IM6 P-0021655-T02-IM6 P-0021868-T01-IM6 P-0021939-T01-IM6 P-0021981-T01-IM6 P-0022234-T01-IM6 P-0022452-T01-IM6 P-0022500-T01-IM6 P-0024067-T01-IM6 P-0024101-T02-IM6 P-0024608-T01-IM6 P-0024807-T01-IM6 P-0024845-T02-IM6 P-0024945-T01-IM6 P-0025251-T01-IM6 P-0026404-T01-IM6 P-0027315-T01-IM6 P-0028358-T01-IM6 P-0029161-T01-IM6 P-0029258-T01-IM6 P-0029448-T01-IM6 P-0029619-T02-IM6 P-0030044-T02-IM6 P-0030220-T01-IM6 P-0030279-T02-IM6 P-0030349-T03-IM6 P-0030397-T02-IM6 P-0030650-T02-IM6 P-0030917-T02-IM6 P-0032119-T01-IM6 P-0032382-T01-IM6 P-0032610-T01-IM6 P-0032909-T02-IM6 P-0033623-T01-IM6 P-0033922-T02-IM6 P-0034612-T01-IM6 P-0036245-T01-IM6 P-0036376-T01-IM6 P-0036601-T02-IM6 P-0036604-T02-IM6 P-0037173-T01-IM6 P-0037182-T02-IM6 P-0038127-T01-IM6 P-0038131-T01-IM6 P-0038570-T02-IM6 P-0038749-T01-IM6 P-0039202-T02-IM7 P-0039406-T01-IM6 P-0039579-T01-IM6 P-0039688-T01-IM6 P-0040254-T02-IM6 P-0040442-T01-IM6 P-0041551-T01-IM6 P-0041943-T01-IM6 P-0042292-T02-IM6 P-0042302-T02-IM6 P-0042438-T01-IM6 P-0042571-T02-IM6 P-0042798-T02-IM6 P-0042913-T01-IM6 P-0043526-T01-IM6 P-0043649-T02-IM6 P-0043958-T01-IM6 P-0044088-T02-IM6 P-0044126-T01-IM6 P-0044233-T02-IM6 P-0044523-T02-IM6 P-0044551-T01-IM6 P-0044826-T01-IM6 P-0044896-T02-IM6 P-0045323-T02-IM6 P-0045722-T01-IM6 P-0046904-T01-IM6 P-0047109-T02-IM6 P-0047480-T03-IM6 P-0047625-T02-IM6 P-0047990-T02-IM6 P-0048335-T02-IM6 P-0048359-T01-IM6 P-0048417-T02-IM6 P-0048577-T03-IM6 P-0048734-T02-IM6 P-0050027-T02-IM6 P-0051333-T01-IM6 P-0051569-T01-IM6 P-0052277-T01-IM6 P-0052635-T01-IM6 P-0052745-T02-IM6 P-0052809-T02-IM6 P-0053879-T02-IM6 P-0053991-T01-IM6 P-0054475-T01-IM6 P-0055038-T02-IM6 P-0055090-T01-IM6 P-0055519-T01-IM6 P-0055733-T02-IM7 P-0055969-T02-IM6 P-0056323-T02-IM6 P-0056509-T02-IM6 P-0056693-T02-IM6 P-0056712-T01-IM6 P-0057151-T02-IM7 P-0057192-T01-IM6 P-0057669-T01-IM6 P-0057766-T01-IM6 P-0057913-T02-IM6 P-0058582-T01-IM7 P-0059067-T02-IM7 P-0059068-T02-IM7 P-0059143-T01-IM7 P-0059432-T01-IM7 P-0059518-T02-IM7 P-0060347-T02-IM7 P-0060461-T02-IM7 P-0061850-T02-IM7 P-0062142-T03-IM7 P-0062355-T03-IM7 P-0062632-T03-IM7 P-0062785-T01-IM7 P-0063940-T02-IM7 P-0064511-T02-IM7 P-0065014-T01-IM7 P-0065643-T01-IM7 P-0065672-T01-IM7 P-0065945-T03-IM7 P-0066169-T01-IM7 P-0066379-T02-IM7 P-0066564-T02-IM7 P-0066725-T02-IM7 P-0067360-T02-IM7 P-0067493-T01-IM7 P-0067897-T01-IM7 P-0067959-T01-IM7 P-0068227-T02-IM7 P-0068585-T02-IM7 P-0068866-T02-IM7 P-0070056-T01-IM7 P-0070230-T01-IM7 P-0070856-T02-IM7 P-0070866-T02-IM7 P-0071598-T02-IM7 P-0072413-T02-IM7 P-0072507-T02-IM7 P-0072628-T01-IM7 P-0073074-T02-IM7 P-0074020-T01-IM7 P-0074320-T02-IM7 P-0074365-T02-IM7 P-0074505-T03-IM7 P-0074560-T02-IM7 P-0075471-T02-IM7 P-0076337-T01-IM7 P-0076441-T01-IM7 P-0076499-T01-IM7 P-0077035-T01-IM7 P-0077435-T01-IM7 P-0077472-T01-IM7 P-0078214-T01-IM7 P-0078251-T02-IM7 P-0078549-T01-IM7 P-0079165-T01-IM7 P-0079703-T01-IM7 P-0079803-T01-IM7 P-0080440-T01-IM7 P-0080464-T01-IM7 P-0080998-T01-IM7 P-0082096-T01-IM7 P-0082175-T01-IM7 P-0082664-T02-IM7 P-0082988-T01-IM7 P-0083231-T01-IM7 P-0083855-T03-IM7 P-0085187-T01-IM7 P-0086263-T01-IM7 P-0086684-T01-IM7 P-0086760-T01-IM7 P-0087046-T02-IM7 P-0088279-T02-IM7 P-0089249-T01-IM7 P-0089525-T01-IM7 P-0089564-T01-IM7 P-0089643-T02-IM7 P-0090846-T01-IM7 P-0091528-T01-IM7 P-0091606-T01-IM7 P-0091886-T01-IM7 P-0092621-T01-IM7 P-0015217-T01-IM6 P-0060558-T01-IM7 P-0077156-T01-IM7 P-0079707-T01-IM7 P-0090152-T02-IM7 P-0086880-T01-IM7 P-0087224-T02-IM7 P-0091798-T01-IM7 P-0091032-T01-IM7 P-0091928-T01-IM7 P-0009452-T01-IM5 P-0006506-T02-IM6 P-0013746-T04-IM7 P-0029161-T02-IM6 P-0032909-T05-IM6 P-0032909-T06-IM7 P-0032909-T08-IM7 P-0037182-T03-IM6 P-0039579-T03-IM7 P-0043526-T03-IM6 P-0047109-T03-IM7 P-0056509-T03-IM7 P-0082096-T02-IM7 P-0082175-T02-IM7 \ No newline at end of file diff --git a/public/es_dsrct_msk_2023/case_lists/cases_sequenced.txt b/public/es_dsrct_msk_2023/case_lists/cases_sequenced.txt new file mode 100644 index 0000000000..ccffb7772d --- /dev/null +++ b/public/es_dsrct_msk_2023/case_lists/cases_sequenced.txt @@ -0,0 +1,6 @@ +cancer_study_identifier: es_dsrct_msk_2023 +stable_id: es_dsrct_msk_2023_sequenced +case_list_name: Samples with mutation data +case_list_description: Samples with mutation data (290 samples) +case_list_category: all_cases_with_mutation_data +case_list_ids: P-0000232-T01-IM3 P-0000253-T02-IM5 P-0000257-T01-IM3 P-0000258-T02-IM5 P-0000564-T01-IM3 P-0000609-T01-IM3 P-0000719-T01-IM3 P-0001233-T01-IM3 P-0001377-T01-IM3 P-0001725-T01-IM3 P-0001896-T01-IM3 P-0002170-T01-IM3 P-0002240-T01-IM3 P-0003290-T01-IM5 P-0003405-T01-IM5 P-0003435-T01-IM5 P-0003554-T01-IM5 P-0004071-T01-IM5 P-0004079-T01-IM5 P-0004163-T01-IM5 P-0004498-T01-IM5 P-0004671-T01-IM5 P-0004931-T02-IM5 P-0005297-T01-IM5 P-0005614-T01-IM5 P-0005710-T01-IM5 P-0005716-T01-IM5 P-0005841-T01-IM5 P-0005977-T01-IM5 P-0006040-T01-IM5 P-0006092-T01-IM5 P-0006208-T01-IM5 P-0006274-T01-IM5 P-0006506-T01-IM5 P-0006792-T01-IM5 P-0007117-T01-IM5 P-0007908-T01-IM5 P-0008030-T01-IM5 P-0008102-T01-IM5 P-0008265-T01-IM5 P-0008320-T01-IM5 P-0008352-T01-IM5 P-0008355-T01-IM5 P-0008523-T01-IM5 P-0008731-T01-IM5 P-0008749-T01-IM5 P-0009359-T01-IM5 P-0009733-T01-IM5 P-0012131-T01-IM5 P-0012316-T01-IM5 P-0012454-T01-IM5 P-0012482-T02-IM5 P-0012923-T01-IM5 P-0013601-T01-IM5 P-0013746-T02-IM5 P-0013841-T01-IM5 P-0013874-T01-IM5 P-0013922-T01-IM5 P-0014314-T01-IM6 P-0014984-T02-IM6 P-0015517-T01-IM6 P-0015619-T03-IM6 P-0016346-T01-IM6 P-0016417-T01-IM6 P-0016515-T02-IM6 P-0016658-T01-IM6 P-0016723-T01-IM6 P-0017027-T01-IM6 P-0017225-T01-IM6 P-0017427-T01-IM6 P-0018508-T01-IM6 P-0018530-T01-IM6 P-0018663-T01-IM6 P-0019080-T02-IM6 P-0019756-T01-IM6 P-0020416-T01-IM6 P-0020463-T01-IM6 P-0020783-T01-IM6 P-0021068-T01-IM6 P-0021189-T01-IM6 P-0021655-T02-IM6 P-0021868-T01-IM6 P-0021939-T01-IM6 P-0021981-T01-IM6 P-0022234-T01-IM6 P-0022452-T01-IM6 P-0022500-T01-IM6 P-0024067-T01-IM6 P-0024101-T02-IM6 P-0024608-T01-IM6 P-0024807-T01-IM6 P-0024845-T02-IM6 P-0024945-T01-IM6 P-0025251-T01-IM6 P-0026404-T01-IM6 P-0027315-T01-IM6 P-0028358-T01-IM6 P-0029161-T01-IM6 P-0029258-T01-IM6 P-0029448-T01-IM6 P-0029619-T02-IM6 P-0030044-T02-IM6 P-0030220-T01-IM6 P-0030279-T02-IM6 P-0030349-T03-IM6 P-0030397-T02-IM6 P-0030650-T02-IM6 P-0030917-T02-IM6 P-0032119-T01-IM6 P-0032382-T01-IM6 P-0032610-T01-IM6 P-0032909-T02-IM6 P-0033623-T01-IM6 P-0033922-T02-IM6 P-0034612-T01-IM6 P-0036245-T01-IM6 P-0036376-T01-IM6 P-0036601-T02-IM6 P-0036604-T02-IM6 P-0037173-T01-IM6 P-0037182-T02-IM6 P-0038127-T01-IM6 P-0038131-T01-IM6 P-0038570-T02-IM6 P-0038749-T01-IM6 P-0039202-T02-IM7 P-0039406-T01-IM6 P-0039579-T01-IM6 P-0039688-T01-IM6 P-0040254-T02-IM6 P-0040442-T01-IM6 P-0041551-T01-IM6 P-0041943-T01-IM6 P-0042292-T02-IM6 P-0042302-T02-IM6 P-0042438-T01-IM6 P-0042571-T02-IM6 P-0042798-T02-IM6 P-0042913-T01-IM6 P-0043526-T01-IM6 P-0043649-T02-IM6 P-0043958-T01-IM6 P-0044088-T02-IM6 P-0044126-T01-IM6 P-0044233-T02-IM6 P-0044523-T02-IM6 P-0044551-T01-IM6 P-0044826-T01-IM6 P-0044896-T02-IM6 P-0045323-T02-IM6 P-0045722-T01-IM6 P-0046904-T01-IM6 P-0047109-T02-IM6 P-0047480-T03-IM6 P-0047625-T02-IM6 P-0047990-T02-IM6 P-0048335-T02-IM6 P-0048359-T01-IM6 P-0048417-T02-IM6 P-0048577-T03-IM6 P-0048734-T02-IM6 P-0050027-T02-IM6 P-0051333-T01-IM6 P-0051569-T01-IM6 P-0052277-T01-IM6 P-0052635-T01-IM6 P-0052745-T02-IM6 P-0052809-T02-IM6 P-0053879-T02-IM6 P-0053991-T01-IM6 P-0054475-T01-IM6 P-0055038-T02-IM6 P-0055090-T01-IM6 P-0055519-T01-IM6 P-0055733-T02-IM7 P-0055969-T02-IM6 P-0056323-T02-IM6 P-0056509-T02-IM6 P-0056693-T02-IM6 P-0056712-T01-IM6 P-0057151-T02-IM7 P-0057192-T01-IM6 P-0057669-T01-IM6 P-0057766-T01-IM6 P-0057913-T02-IM6 P-0058582-T01-IM7 P-0059067-T02-IM7 P-0059068-T02-IM7 P-0059143-T01-IM7 P-0059432-T01-IM7 P-0059518-T02-IM7 P-0060347-T02-IM7 P-0060461-T02-IM7 P-0061850-T02-IM7 P-0062142-T03-IM7 P-0062355-T03-IM7 P-0062632-T03-IM7 P-0062785-T01-IM7 P-0063940-T02-IM7 P-0064511-T02-IM7 P-0065014-T01-IM7 P-0065643-T01-IM7 P-0065672-T01-IM7 P-0065945-T03-IM7 P-0066169-T01-IM7 P-0066379-T02-IM7 P-0066564-T02-IM7 P-0066725-T02-IM7 P-0067360-T02-IM7 P-0067493-T01-IM7 P-0067897-T01-IM7 P-0067959-T01-IM7 P-0068227-T02-IM7 P-0068585-T02-IM7 P-0068866-T02-IM7 P-0070056-T01-IM7 P-0070230-T01-IM7 P-0070856-T02-IM7 P-0070866-T02-IM7 P-0071598-T02-IM7 P-0072413-T02-IM7 P-0072507-T02-IM7 P-0072628-T01-IM7 P-0073074-T02-IM7 P-0074020-T01-IM7 P-0074320-T02-IM7 P-0074365-T02-IM7 P-0074505-T03-IM7 P-0074560-T02-IM7 P-0075471-T02-IM7 P-0076337-T01-IM7 P-0076441-T01-IM7 P-0076499-T01-IM7 P-0077035-T01-IM7 P-0077435-T01-IM7 P-0077472-T01-IM7 P-0078214-T01-IM7 P-0078251-T02-IM7 P-0078549-T01-IM7 P-0079165-T01-IM7 P-0079703-T01-IM7 P-0079803-T01-IM7 P-0080440-T01-IM7 P-0080464-T01-IM7 P-0080998-T01-IM7 P-0082096-T01-IM7 P-0082175-T01-IM7 P-0082664-T02-IM7 P-0082988-T01-IM7 P-0083231-T01-IM7 P-0083855-T03-IM7 P-0085187-T01-IM7 P-0086263-T01-IM7 P-0086684-T01-IM7 P-0086760-T01-IM7 P-0087046-T02-IM7 P-0088279-T02-IM7 P-0089249-T01-IM7 P-0089525-T01-IM7 P-0089564-T01-IM7 P-0089643-T02-IM7 P-0090846-T01-IM7 P-0091528-T01-IM7 P-0091606-T01-IM7 P-0091886-T01-IM7 P-0092621-T01-IM7 P-0015217-T01-IM6 P-0060558-T01-IM7 P-0077156-T01-IM7 P-0079707-T01-IM7 P-0090152-T02-IM7 P-0086880-T01-IM7 P-0087224-T02-IM7 P-0091798-T01-IM7 P-0091032-T01-IM7 P-0091928-T01-IM7 P-0009452-T01-IM5 P-0006506-T02-IM6 P-0013746-T04-IM7 P-0029161-T02-IM6 P-0032909-T05-IM6 P-0032909-T06-IM7 P-0032909-T08-IM7 P-0037182-T03-IM6 P-0039579-T03-IM7 P-0043526-T03-IM6 P-0047109-T03-IM7 P-0056509-T03-IM7 P-0082096-T02-IM7 P-0082175-T02-IM7 \ No newline at end of file diff --git a/public/es_dsrct_msk_2023/case_lists/cases_sv.txt b/public/es_dsrct_msk_2023/case_lists/cases_sv.txt new file mode 100644 index 0000000000..fa9567410f --- /dev/null +++ b/public/es_dsrct_msk_2023/case_lists/cases_sv.txt @@ -0,0 +1,6 @@ +cancer_study_identifier: es_dsrct_msk_2023 +stable_id: es_dsrct_msk_2023_sv +case_list_name: Samples with SV data +case_list_description: All samples with SV data (290 samples) +case_list_category: all_cases_with_sv_data +case_list_ids: P-0000232-T01-IM3 P-0000253-T02-IM5 P-0000257-T01-IM3 P-0000258-T02-IM5 P-0000564-T01-IM3 P-0000609-T01-IM3 P-0000719-T01-IM3 P-0001233-T01-IM3 P-0001377-T01-IM3 P-0001725-T01-IM3 P-0001896-T01-IM3 P-0002170-T01-IM3 P-0002240-T01-IM3 P-0003290-T01-IM5 P-0003405-T01-IM5 P-0003435-T01-IM5 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diff --git a/public/es_dsrct_msk_2023/data_clinical_patient.txt b/public/es_dsrct_msk_2023/data_clinical_patient.txt new file mode 100644 index 0000000000..e0d927a43f --- /dev/null +++ b/public/es_dsrct_msk_2023/data_clinical_patient.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:2a1d58cbaa4c0f80150ba940d63096ead4309dedf4c0aecd8872abc3e4cfd198 +size 38944 diff --git a/public/es_dsrct_msk_2023/data_clinical_sample.txt b/public/es_dsrct_msk_2023/data_clinical_sample.txt new file mode 100644 index 0000000000..938b89122c --- /dev/null +++ b/public/es_dsrct_msk_2023/data_clinical_sample.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:16bb0e8533aec809d63126f33743870f1180c26df433be2f4e9bc53a5171b4ba +size 60916 diff --git a/public/es_dsrct_msk_2023/data_cna.txt b/public/es_dsrct_msk_2023/data_cna.txt new file mode 100644 index 0000000000..d5ffd6e1a2 --- /dev/null +++ b/public/es_dsrct_msk_2023/data_cna.txt @@ -0,0 +1,3 @@ +version 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100644 index 0000000000..256c95114a --- /dev/null +++ b/public/es_dsrct_msk_2023/data_mutations.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:a9a5d66ec646475ecdd3e3e46c08eb9c331c1a6ffb91096f53301944017056e9 +size 113998 diff --git a/public/es_dsrct_msk_2023/data_sv.txt b/public/es_dsrct_msk_2023/data_sv.txt new file mode 100644 index 0000000000..7faa2396ac --- /dev/null +++ b/public/es_dsrct_msk_2023/data_sv.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:909e70a5a3676443d0f50ae07f6fe240b4de759bc320789e9a1eff1c826e6db3 +size 48738 diff --git a/public/es_dsrct_msk_2023/data_timeline.txt b/public/es_dsrct_msk_2023/data_timeline.txt new file mode 100644 index 0000000000..91219b062c --- /dev/null +++ b/public/es_dsrct_msk_2023/data_timeline.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:f6e33d08eda03ddefec2dab6e6289dac9dea58cc2526416e6f7348006b76a549 +size 1148 diff --git a/public/es_dsrct_msk_2023/meta_clinical_patient.txt b/public/es_dsrct_msk_2023/meta_clinical_patient.txt new file mode 100644 index 0000000000..ccf089e49d --- /dev/null +++ b/public/es_dsrct_msk_2023/meta_clinical_patient.txt @@ -0,0 +1,4 @@ +cancer_study_identifier: es_dsrct_msk_2023 +genetic_alteration_type: CLINICAL +datatype: PATIENT_ATTRIBUTES +data_filename: data_clinical_patient.txt diff --git a/public/es_dsrct_msk_2023/meta_clinical_sample.txt b/public/es_dsrct_msk_2023/meta_clinical_sample.txt new file mode 100644 index 0000000000..174c3ec607 --- /dev/null +++ b/public/es_dsrct_msk_2023/meta_clinical_sample.txt @@ -0,0 +1,4 @@ +cancer_study_identifier: es_dsrct_msk_2023 +genetic_alteration_type: CLINICAL +datatype: SAMPLE_ATTRIBUTES +data_filename: data_clinical_sample.txt diff --git a/public/es_dsrct_msk_2023/meta_cna.txt b/public/es_dsrct_msk_2023/meta_cna.txt new file mode 100644 index 0000000000..a3eaa5dc12 --- /dev/null +++ b/public/es_dsrct_msk_2023/meta_cna.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: es_dsrct_msk_2023 +genetic_alteration_type: COPY_NUMBER_ALTERATION +datatype: DISCRETE +stable_id: cna +show_profile_in_analysis_tab: true +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. +profile_name: Putative copy-number alterations from GISTIC +data_filename: data_cna.txt diff --git a/public/es_dsrct_msk_2023/meta_cna_hg19_seg.txt b/public/es_dsrct_msk_2023/meta_cna_hg19_seg.txt new file mode 100644 index 0000000000..e086549a35 --- /dev/null +++ b/public/es_dsrct_msk_2023/meta_cna_hg19_seg.txt @@ -0,0 +1,7 @@ +cancer_study_identifier: es_dsrct_msk_2023 +reference_genome_id: hg19 +description: Somatic segment CNA data (copy number ratio from tumor samples minus ratio from matched normals). +show_profile_in_analysis_tab: true +datatype: SEG +genetic_alteration_type: COPY_NUMBER_ALTERATION +data_filename: data_cna_hg19.seg diff --git a/public/es_dsrct_msk_2023/meta_gene_panel_matrix.txt b/public/es_dsrct_msk_2023/meta_gene_panel_matrix.txt new file mode 100644 index 0000000000..fc3364aae5 --- /dev/null +++ b/public/es_dsrct_msk_2023/meta_gene_panel_matrix.txt @@ -0,0 +1,4 @@ +cancer_study_identifier: es_dsrct_msk_2023 +genetic_alteration_type: GENE_PANEL_MATRIX +datatype: GENE_PANEL_MATRIX +data_filename: data_gene_panel_matrix.txt diff --git a/public/es_dsrct_msk_2023/meta_mutations.txt b/public/es_dsrct_msk_2023/meta_mutations.txt new file mode 100644 index 0000000000..0924b300bd --- /dev/null +++ b/public/es_dsrct_msk_2023/meta_mutations.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: es_dsrct_msk_2023 +genetic_alteration_type: MUTATION_EXTENDED +stable_id: mutations +datatype: MAF +show_profile_in_analysis_tab: true +profile_description: Mutation data. +profile_name: Mutations +data_filename: data_mutations.txt diff --git a/public/es_dsrct_msk_2023/meta_study.txt b/public/es_dsrct_msk_2023/meta_study.txt new file mode 100755 index 0000000000..29011c4145 --- /dev/null +++ b/public/es_dsrct_msk_2023/meta_study.txt @@ -0,0 +1,6 @@ +type_of_cancer: es +cancer_study_identifier: es_dsrct_msk_2023 +name: Ewing Sarcoma (MSK, 2023) +description: Targeted Sequencing of 290 Ewing sarcoma tumor/normal pairs via MSK-IMPACT platform. +groups: PUBLIC +reference_genome: hg19 diff --git a/public/es_dsrct_msk_2023/meta_sv.txt b/public/es_dsrct_msk_2023/meta_sv.txt new file mode 100644 index 0000000000..dc92152358 --- /dev/null +++ b/public/es_dsrct_msk_2023/meta_sv.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: es_dsrct_msk_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 variants data. +data_filename: data_sv.txt diff --git a/public/es_dsrct_msk_2023/meta_timeline.txt b/public/es_dsrct_msk_2023/meta_timeline.txt new file mode 100644 index 0000000000..4701ae2691 --- /dev/null +++ b/public/es_dsrct_msk_2023/meta_timeline.txt @@ -0,0 +1,4 @@ +cancer_study_identifier: es_dsrct_msk_2023 +genetic_alteration_type: CLINICAL +datatype: TIMELINE +data_filename: data_timeline.txt diff --git a/public/ilc_msk_2023/case_lists/cases_all.txt b/public/ilc_msk_2023/case_lists/cases_all.txt new file mode 100644 index 0000000000..dec2afa3bd --- /dev/null +++ b/public/ilc_msk_2023/case_lists/cases_all.txt @@ -0,0 +1,6 @@ +cancer_study_identifier: ilc_msk_2023 +stable_id: ilc_msk_2023_all +case_list_name: All samples +case_list_description: All samples (25 samples) +case_list_category: all_cases_in_study +case_list_ids: CDW1 CDW2 CDW3 CDW4 CDW5 CDW6 CDW7 CDW8 CDW10 CDW11 CDW12 CDW13 CDW16 CDW17 CDW18 CDW19 CDW20 CDW29 CDW21 CDW22 CDW30 CDW23 CDW24 CDW25 CDW28 diff --git a/public/ilc_msk_2023/case_lists/cases_cna.txt b/public/ilc_msk_2023/case_lists/cases_cna.txt new file mode 100644 index 0000000000..c24f5da178 --- /dev/null +++ b/public/ilc_msk_2023/case_lists/cases_cna.txt @@ -0,0 +1,6 @@ +cancer_study_identifier: ilc_msk_2023 +stable_id: ilc_msk_2023_cna +case_list_name: Samples with CNA data +case_list_description: Samples with CNA data (25 samples) +case_list_category: all_cases_with_cna_data +case_list_ids: CDW1 CDW2 CDW3 CDW4 CDW5 CDW6 CDW7 CDW8 CDW10 CDW11 CDW12 CDW13 CDW16 CDW17 CDW18 CDW19 CDW20 CDW29 CDW21 CDW22 CDW30 CDW23 CDW24 CDW25 CDW28 diff --git a/public/ilc_msk_2023/case_lists/cases_cnaseq.txt b/public/ilc_msk_2023/case_lists/cases_cnaseq.txt new file mode 100644 index 0000000000..5b5c9f4e24 --- /dev/null +++ b/public/ilc_msk_2023/case_lists/cases_cnaseq.txt @@ -0,0 +1,6 @@ +cancer_study_identifier: ilc_msk_2023 +stable_id: ilc_msk_2023_cnaseq +case_list_name: Samples with mutation and CNA data +case_list_description: Samples with mutation and CNA data (25 samples) +case_list_category: all_cases_with_mutation_and_cna_data +case_list_ids: CDW1 CDW2 CDW3 CDW4 CDW5 CDW6 CDW7 CDW8 CDW10 CDW11 CDW12 CDW13 CDW16 CDW17 CDW18 CDW19 CDW20 CDW29 CDW21 CDW22 CDW30 CDW23 CDW24 CDW25 CDW28 diff --git a/public/ilc_msk_2023/case_lists/cases_sequenced.txt b/public/ilc_msk_2023/case_lists/cases_sequenced.txt new file mode 100644 index 0000000000..e8c19cdc31 --- /dev/null +++ b/public/ilc_msk_2023/case_lists/cases_sequenced.txt @@ -0,0 +1,6 @@ +cancer_study_identifier: ilc_msk_2023 +stable_id: ilc_msk_2023_sequenced +case_list_name: Samples with mutation data +case_list_description: Samples with mutation data (25 samples) +case_list_category: all_cases_with_mutation_data +case_list_ids: CDW1 CDW2 CDW3 CDW4 CDW5 CDW6 CDW7 CDW8 CDW10 CDW11 CDW12 CDW13 CDW16 CDW17 CDW18 CDW19 CDW20 CDW29 CDW21 CDW22 CDW30 CDW23 CDW24 CDW25 CDW28 diff --git a/public/ilc_msk_2023/case_lists/cases_sv.txt b/public/ilc_msk_2023/case_lists/cases_sv.txt new file mode 100644 index 0000000000..70cac0d79b --- /dev/null +++ b/public/ilc_msk_2023/case_lists/cases_sv.txt @@ -0,0 +1,6 @@ +cancer_study_identifier: ilc_msk_2023 +stable_id: ilc_msk_2023_sv +case_list_name: Samples with SV data +case_list_description: All samples with SV data (25 samples) +case_list_category: all_cases_with_sv_data +case_list_ids: CDW1 CDW2 CDW3 CDW4 CDW5 CDW6 CDW7 CDW8 CDW10 CDW11 CDW12 CDW13 CDW16 CDW17 CDW18 CDW19 CDW20 CDW29 CDW21 CDW22 CDW30 CDW23 CDW24 CDW25 CDW28 diff --git a/public/ilc_msk_2023/data_clinical_patient.txt b/public/ilc_msk_2023/data_clinical_patient.txt new file mode 100644 index 0000000000..39ee521f9e --- /dev/null +++ b/public/ilc_msk_2023/data_clinical_patient.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:12062d620417357bbeb165f2cf5ac27921394e3c9b596e2ae9a0d8f10508be1c +size 2840 diff --git a/public/ilc_msk_2023/data_clinical_sample.txt b/public/ilc_msk_2023/data_clinical_sample.txt new file mode 100644 index 0000000000..6da9da0bd5 --- /dev/null +++ b/public/ilc_msk_2023/data_clinical_sample.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:987fb3f83beaabba62b05d95aaf36a91d6b1c16aa63227970d316e417b6bbe19 +size 7501 diff --git a/public/ilc_msk_2023/data_cna.txt b/public/ilc_msk_2023/data_cna.txt new file mode 100644 index 0000000000..30b9ca7da6 --- /dev/null +++ b/public/ilc_msk_2023/data_cna.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:bc7c4f7de6b7db25f814caed6afe51cbcf6dc5917130e341ff543b90b74438f2 +size 43428 diff --git a/public/ilc_msk_2023/data_cna_hg19.seg b/public/ilc_msk_2023/data_cna_hg19.seg new file mode 100644 index 0000000000..1b0c0b2e5d --- /dev/null +++ b/public/ilc_msk_2023/data_cna_hg19.seg @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:4393b4271d48e85e5e76717a9220fa7e8ca08b8a06b0fcd6f0ed041b14b52679 +size 50208 diff --git a/public/ilc_msk_2023/data_gene_panel_matrix.txt b/public/ilc_msk_2023/data_gene_panel_matrix.txt new file mode 100755 index 0000000000..b60fceec0c --- /dev/null +++ b/public/ilc_msk_2023/data_gene_panel_matrix.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:7d5d09e6a5cb0e2077e3517d8b3d15dd40aa63f8d2d7c1ff387a8b71261a8105 +size 935 diff --git a/public/ilc_msk_2023/data_mutations.txt b/public/ilc_msk_2023/data_mutations.txt new file mode 100644 index 0000000000..9002ae42e9 --- /dev/null +++ b/public/ilc_msk_2023/data_mutations.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:85e7283557fab8f6ed04251632fa64b312ba011e090ebb1cb6faff26fa471b31 +size 31670 diff --git a/public/ilc_msk_2023/data_sv.txt b/public/ilc_msk_2023/data_sv.txt new file mode 100644 index 0000000000..6df1dc358d --- /dev/null +++ b/public/ilc_msk_2023/data_sv.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:9e2eb817237cad2bd7166df5db92d74f683a1b2c6e87b075df3e8daf5b4d3844 +size 3975 diff --git a/public/ilc_msk_2023/meta_clinical_patient.txt b/public/ilc_msk_2023/meta_clinical_patient.txt new file mode 100644 index 0000000000..060ad29ba8 --- /dev/null +++ b/public/ilc_msk_2023/meta_clinical_patient.txt @@ -0,0 +1,4 @@ +cancer_study_identifier: ilc_msk_2023 +data_filename: data_clinical_patient.txt +genetic_alteration_type: CLINICAL +datatype: PATIENT_ATTRIBUTES diff --git a/public/ilc_msk_2023/meta_clinical_sample.txt b/public/ilc_msk_2023/meta_clinical_sample.txt new file mode 100644 index 0000000000..fe1526ad44 --- /dev/null +++ b/public/ilc_msk_2023/meta_clinical_sample.txt @@ -0,0 +1,4 @@ +cancer_study_identifier: ilc_msk_2023 +genetic_alteration_type: CLINICAL +datatype: SAMPLE_ATTRIBUTES +data_filename: data_clinical_sample.txt diff --git a/public/ilc_msk_2023/meta_cna.txt b/public/ilc_msk_2023/meta_cna.txt new file mode 100644 index 0000000000..b341f8b03f --- /dev/null +++ b/public/ilc_msk_2023/meta_cna.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: ilc_msk_2023 +genetic_alteration_type: COPY_NUMBER_ALTERATION +datatype: DISCRETE +stable_id: cna +show_profile_in_analysis_tab: true +profile_description: Discrete copy-number data from IMPACT +profile_name: Copy Number Alterations +data_filename: data_cna.txt diff --git a/public/ilc_msk_2023/meta_cna_hg19_seg.txt b/public/ilc_msk_2023/meta_cna_hg19_seg.txt new file mode 100644 index 0000000000..b2d70056d0 --- /dev/null +++ b/public/ilc_msk_2023/meta_cna_hg19_seg.txt @@ -0,0 +1,10 @@ +cancer_study_identifier: ilc_msk_2023 +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 + + diff --git a/public/ilc_msk_2023/meta_gene_panel_matrix.txt b/public/ilc_msk_2023/meta_gene_panel_matrix.txt new file mode 100755 index 0000000000..4994b1cbcc --- /dev/null +++ b/public/ilc_msk_2023/meta_gene_panel_matrix.txt @@ -0,0 +1,4 @@ +cancer_study_identifier: ilc_msk_2023 +genetic_alteration_type: GENE_PANEL_MATRIX +datatype: GENE_PANEL_MATRIX +data_filename: data_gene_panel_matrix.txt diff --git a/public/ilc_msk_2023/meta_mutations.txt b/public/ilc_msk_2023/meta_mutations.txt new file mode 100644 index 0000000000..921fbfb270 --- /dev/null +++ b/public/ilc_msk_2023/meta_mutations.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: ilc_msk_2023 +genetic_alteration_type: MUTATION_EXTENDED +datatype: MAF +stable_id: mutations +show_profile_in_analysis_tab: true +profile_description: Mutation data. +profile_name: Mutations +data_filename: data_mutations.txt diff --git a/public/ilc_msk_2023/meta_study.txt b/public/ilc_msk_2023/meta_study.txt new file mode 100644 index 0000000000..0d0da5a5a7 --- /dev/null +++ b/public/ilc_msk_2023/meta_study.txt @@ -0,0 +1,4 @@ +cancer_study_identifier: ilc_msk_2023 +type_of_cancer: breast +name: Non-CDH1 Invasive Lobular Carcinoma (MSK, 2023) +description: Targeted Sequencing of breast Invasive Lobular Carcinoma tumors and their matched normals via MSK-IMPACT. \ No newline at end of file diff --git a/public/ilc_msk_2023/meta_sv.txt b/public/ilc_msk_2023/meta_sv.txt new file mode 100644 index 0000000000..68f6fd99c2 --- /dev/null +++ b/public/ilc_msk_2023/meta_sv.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: ilc_msk_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