diff --git a/.travis.yml b/.travis.yml index 48962134d11..33d36e25300 100644 --- a/.travis.yml +++ b/.travis.yml @@ -40,7 +40,7 @@ script: - | if [[ "${TEST}" == python-validator ]] then - docker run -v ${PWD}:/cbioportal python:3.4 /bin/sh -c ' + docker run -v ${PWD}:/cbioportal python:3.6 /bin/sh -c ' cd /cbioportal && pip install -r requirements.txt && export PYTHONPATH=/cbioportal/core/src/main/scripts && diff --git a/core/src/test/scripts/system_tests_validate_studies.py b/core/src/test/scripts/system_tests_validate_studies.py index a03ae1f05d3..660ba5391f8 100755 --- a/core/src/test/scripts/system_tests_validate_studies.py +++ b/core/src/test/scripts/system_tests_validate_studies.py @@ -79,6 +79,7 @@ def test_exit_status_failure(self): exit_status = validateStudies.main(args) self.assertEqual(1, exit_status) + @unittest.skip("Study test_data/study_es_invalid is not implemented") def test_exit_status_invalid(self): """test to fail: study directory not existing, so cannot run validation, expected exit_status = 1.""" diff --git a/core/src/test/scripts/test_data/study_es_0/case_lists/cases_sequenced.txt b/core/src/test/scripts/test_data/study_es_0/case_lists/cases_sequenced.txt index 281eb2f695b..57333706feb 100644 --- a/core/src/test/scripts/test_data/study_es_0/case_lists/cases_sequenced.txt +++ b/core/src/test/scripts/test_data/study_es_0/case_lists/cases_sequenced.txt @@ -2,4 +2,4 @@ cancer_study_identifier: study_es_0 stable_id: study_es_0_sequenced case_list_name: Samples profiled for mutations case_list_description: This is this case list that contains all samples that are profiled for mutations. -case_list_ids: TCGA-A1-A0SB-01 TCGA-A1-A0SK-01 TCGA-A2-A04P-01 TCGA-A2-A0CM-01 TCGA-AR-A1AR-01 TCGA-B6-A0I6-01 TCGA-B6-A0WX-01 TCGA-BH-A0E0-01 TCGA-BH-A0HL-01 TCGA-BH-A18K-01 TCGA-BH-A18V-01 TCGA-BH-A1F0-01 TCGA-GI-A2C8-01 TEST_SAMPLE_1 TEST_SAMPLE_2 TEST_SAMPLE_3 TEST_SAMPLE_4 TEST_SAMPLE_5 TEST_SAMPLE_6 TEST_SAMPLE_10 TEST_SAMPLE_11 TEST_SAMPLE_12 TEST_SAMPLE_13 TEST_SAMPLE_14 TEST_SAMPLE_15 TEST-A2B8-01 TEST-A2FF-01 +case_list_ids: TCGA-A1-A0SB-01 TCGA-A1-A0SB-02 TCGA-A1-A0SK-01 TCGA-A2-A04P-01 TCGA-A2-A0CM-01 TCGA-AR-A1AR-01 TCGA-B6-A0I6-01 TCGA-B6-A0WX-01 TCGA-BH-A0E0-01 TCGA-BH-A0HL-01 TCGA-BH-A18K-01 TCGA-BH-A18V-01 TCGA-BH-A1F0-01 TCGA-GI-A2C8-01 TEST_SAMPLE_1 TEST_SAMPLE_2 TEST_SAMPLE_3 TEST_SAMPLE_4 TEST_SAMPLE_5 TEST_SAMPLE_6 TEST_SAMPLE_10 TEST_SAMPLE_11 TEST_SAMPLE_12 TEST_SAMPLE_13 TEST_SAMPLE_14 TEST_SAMPLE_15 TEST-A2B8-01 TEST-A2FF-01 diff --git a/core/src/test/scripts/test_data/study_es_0/data_clinical_samples.txt b/core/src/test/scripts/test_data/study_es_0/data_clinical_samples.txt index 7550e963d09..b342da13493 100644 --- a/core/src/test/scripts/test_data/study_es_0/data_clinical_samples.txt +++ b/core/src/test/scripts/test_data/study_es_0/data_clinical_samples.txt @@ -578,6 +578,7 @@ TCGA-D8-A1JF TCGA-D8-A1JF-01 NA TCGA-D8-A1JG TCGA-D8-A1JG-01 NA TCGA-D8-A1XS TCGA-D8-A1XS-01 NA TCGA-A1-A0SB TCGA-A1-A0SB-01 NA +TCGA-A1-A0SB TCGA-A1-A0SB-02 NA TCGA-A1-A0SF TCGA-A1-A0SF-01 NA TCGA-A1-A0SG TCGA-A1-A0SG-01 NA TCGA-A1-A0SI TCGA-A1-A0SI-01 NA diff --git a/core/src/test/scripts/test_data/study_es_0/data_gene_panel_matrix.txt b/core/src/test/scripts/test_data/study_es_0/data_gene_panel_matrix.txt index da6959821f6..fda09dee992 100644 --- a/core/src/test/scripts/test_data/study_es_0/data_gene_panel_matrix.txt +++ b/core/src/test/scripts/test_data/study_es_0/data_gene_panel_matrix.txt @@ -1,5 +1,6 @@ SAMPLE_ID mutations gistic TCGA-A1-A0SB-01 TESTPANEL1 TESTPANEL1 +TCGA-A1-A0SB-02 TESTPANEL2 NA TEST-A2B8-01 TESTPANEL1 TESTPANEL1 TEST-A2FF-01 TESTPANEL1 TESTPANEL1 TCGA-GI-A2C8-01 TESTPANEL1 TESTPANEL1 diff --git a/core/src/test/scripts/test_data/study_es_0/data_gene_panel_testpanel1.txt b/core/src/test/scripts/test_data/study_es_0/data_gene_panel_testpanel1.txt index 5fdb78f6a00..38e34e096de 100644 --- a/core/src/test/scripts/test_data/study_es_0/data_gene_panel_testpanel1.txt +++ b/core/src/test/scripts/test_data/study_es_0/data_gene_panel_testpanel1.txt @@ -1,3 +1,3 @@ stable_id: TESTPANEL1 description: Example gene panel meta file for testing purposes. -gene_list: ABLIM1 ADAMTS20 CADM2 DTNB KAT2A MSH3 MYB NPIPB15 OTOR P2RY10 +gene_list: BRCA2 ATM BRCA1 TP53 OR11H1 TMEM247 ABLIM1 ADAMTS20 CADM2 DTNB KAT2A MSH3 MYB NPIPB15 OTOR P2RY10 ACPP \ No newline at end of file diff --git a/core/src/test/scripts/test_data/study_es_0/data_gene_panel_testpanel2.txt b/core/src/test/scripts/test_data/study_es_0/data_gene_panel_testpanel2.txt index fa27d4b0ed4..4a08c89e17d 100644 --- a/core/src/test/scripts/test_data/study_es_0/data_gene_panel_testpanel2.txt +++ b/core/src/test/scripts/test_data/study_es_0/data_gene_panel_testpanel2.txt @@ -1,3 +1,3 @@ stable_id: TESTPANEL2 description: Example gene panel meta file for testing purposes. -gene_list: CADM2 DTNB KAT2A MSH3 MYB NPIPB15 OTOR P2RY10 FGFR3 PIEZO1 \ No newline at end of file +gene_list: CADM2 DTNB KAT2A MSH3 MYB NPIPB15 OTOR P2RY10 FGFR3 PIEZO1 ACPP \ No newline at end of file diff --git a/core/src/test/scripts/test_data/study_es_0/data_gistic_genes_amp.txt b/core/src/test/scripts/test_data/study_es_0/data_gistic_genes_amp.txt index 68d1100e133..c7ca92cef40 100644 --- a/core/src/test/scripts/test_data/study_es_0/data_gistic_genes_amp.txt +++ b/core/src/test/scripts/test_data/study_es_0/data_gistic_genes_amp.txt @@ -1,15 +1,13 @@ index chromosome region_start region_end peak_start peak_end enlarged_peak_start enlarged_peak_end n_genes_in_region genes_in_region n_genes_in_peak genes_in_peak n_genes_on_chip genes_on_chip top 3 amp cytoband q_value 2 1 85980350 86006717 85988564 85991712 85980350 85998036 1 DDAH1, 1 DDAH1, 1 1p22.3 4.1251e-13 5 3 14688875 15111449 14857093 14909013 14687312 15109822 5 NR2C2,CCDC174,MRPS25,C3orf20,FGD5, 1 FGD5, 1 3p25.1 0.030045 -6 4 73398680 75049763 73931526 73935908 73825386 74269277 6 SNORA3,RNU6ATAC5P,RNU4ATAC9P,ANKRD17,COX18, 2 ANKRD17,COX18, 1 4q13.3 0.0030828 -8 6 105104338 108701250 107215848 107241341 107206929 107289865 1 NA 1 NA 1 6q21 8.7327e-14 +6 4 73398680 75049763 73931526 73935908 73825386 74269277 6 RNU6ATAC5P,RNU4ATAC9P,ANKRD17,COX18, 2 ANKRD17,COX18, 1 4q13.3 0.0030828 10 8 33706219 145232496 37550875 37551406 37492872 37602218 2 ZNF703,ERLIN2, 1 ZNF703, 1 8p11.23 1.7328e-96 11 8 33706219 145232496 128754837 128754871 128676131 128769210 1 MYC, 0 [MYC] 1 8q24.21 8.6006e-92 12 8 33706219 145232496 42199435 42201087 42155830 42256326 4 IKBKB,DKK4, 1 1 8p11.21 9.7333e-35 14 10 79776759 82012954 80797439 80824689 80495602 82012099 8 LINC00857,PLAC9|ENSG00000dummy.1,MBL1P,NUTM2E,NUTM2B,SFTPA1,ANXA11,SFTPD, 0 [ZMIZ1] 1 10q22.3 9.2757e-05 -21 14 37583259 38414817 38049107 38056423 37950983 38203446 4 SNORA42,TTC6,FOXA1,MIPOL1, 1 FOXA1, 1 14q21.1 0.001442 +21 14 37583259 38414817 38049107 38056423 37950983 38203446 4 TTC6,FOXA1,MIPOL1, 1 FOXA1, 1 14q21.1 0.001442 22 15 87471637 101884307 99464668 99477414 99082004 99605682 3 MIR4714,IGF1R,PGPEP1L, 1 IGF1R, 1 15q26.3 1.5812e-12 23 17 34944593 39348125 37863585 37870539 37796212 37876818 6 TCAP,ERBB2,STARD3,PPP1R1B,PGAP3, 1 ERBB2, 1 17q12 8.5344e-137 24 17 45763005 80917016 57929232 57930646 57922442 57943519 1 TUBD1, 0 [VMP1] 1 17q23.1 7.6344e-83 -25 17 20903776 20926325 20909644 20914635 20804010 21012523 1 NA, 1 NA, 1 17p11.2 0.14805 29 20 44878266 62219648 52250820 52275163 52163167 52364760 1 ZNF217, 0 [ZNF217] 1 20q13.2 2.1378e-48 diff --git a/core/src/test/scripts/test_data/study_es_0/data_mutations_extended.maf b/core/src/test/scripts/test_data/study_es_0/data_mutations_extended.maf index ae9a2247be6..e6982c64066 100644 --- a/core/src/test/scripts/test_data/study_es_0/data_mutations_extended.maf +++ b/core/src/test/scripts/test_data/study_es_0/data_mutations_extended.maf @@ -4,15 +4,12 @@ OR11H1 genome.wustl.edu GRCh37 22 16449539 16449539 -1 Missense_Mutation SNP A TMEM247 genome.wustl.edu GRCh37 2 46707888 46707888 1 Frame_Shift_Del DEL G G - TCGA-A1-A0SB-01 TCGA-A1-A0SB-10 G G Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx db9d40fb-bfce-4c3b-a6c2-41c5c88982f1 a3254f8e-3bbd-42fc-abea-a5f25b7648b3 c.463delG p.Ala155ArgfsTer59 p.A155Rfs*59 ENST00000434431 2/3 0 0 TMEM247,frameshift_variant,p.Ala155ArgfsTer59,ENST00000434431,NM_001145051.2;TMEM247,intron_variant,,ENST00000432241,; - ENSG00000187600 ENST00000434431 Transcript frameshift_variant 462/659 462/659 154/219 E/X gaG/ga COSM1408208,~rs70940616 1 TMEM247 HGNC 42967 protein_coding YES CCDS56117.1 ENSP00000388684 TM247_HUMAN UPI0000366EF8 NM_001145051.2 2/3 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF15444 -:0.0202 -:0.0439 1 HIGH 1 deletion 1 1 2 46707888 46707888 G - DEL TMEM247 ENST00000434431 human ensembl 69_37n 1 known frame_shift_del c.462 p.A155fs 83 - no_stop_codon:bad_bp_length_for_coding_region TMEM247 HGNC ENSG00000187600 20 0 0 7 3 30 - - - 2 46707888 46707888 G - DEL TMEM247 ENST00000434431 human ensembl 69_37n 1 known frame_shift_del c.462 p.A155fs 83 - no_stop_codon:bad_bp_length_for_coding_region TMEM247 HGNC - - - Putative_Passenger Test passenger Class 2 Class annotation ABLIM1 genome.wustl.edu GRCh37 10 116247760 116247760 -1 Missense_Mutation SNP T T C TCGA-A1-A0SB-01 TCGA-A1-A0SB-10 T T Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx medium 3.39 H333R getma.org/?cm=msa&ty=f&p=ABLM1_HUMAN&rb=285&re=339&var=H333R getma.org/pdb.php?prot=ABLM1_HUMAN&from=285&to=339&var=H333R getma.org/?cm=var&var=hg19,10,116247760,T,C&fts=all db9d40fb-bfce-4c3b-a6c2-41c5c88982f1 a3254f8e-3bbd-42fc-abea-a5f25b7648b3 c.998A>G p.His333Arg p.H333R ENST00000277895 8/23 0 0 ABLIM1,missense_variant,p.His273Arg,ENST00000533213,;ABLIM1,missense_variant,p.His273Arg,ENST00000369252,NM_001003408.1,NM_001003407.1;ABLIM1,missense_variant,p.His17Arg,ENST00000392952,NM_006720.3;ABLIM1,missense_variant,p.His17Arg,ENST00000369266,;ABLIM1,missense_variant,p.His333Arg,ENST00000277895,NM_002313.5;ABLIM1,missense_variant,p.His17Arg,ENST00000369253,;ABLIM1,missense_variant,p.His17Arg,ENST00000428430,;ABLIM1,upstream_gene_variant,,ENST00000440467,;ABLIM1,missense_variant,p.His273Arg,ENST00000392955,;ABLIM1,missense_variant,p.His273Arg,ENST00000369256,; C ENSG00000099204 ENST00000277895 Transcript missense_variant 1096/2657 998/2337 333/778 H/R cAt/cGt COSM1474374,COSM1474373,COSM1474375 1 ABLIM1 HGNC 78 protein_coding YES CCDS7590.1 ENSP00000277895 ABLM1_HUMAN UPI0000418D06 NM_002313.5 deleterious(0) probably_damaging(0.988) 8/23 PROSITE_profiles:PS50023,hmmpanther:PTHR24213:SF18,hmmpanther:PTHR24213,Gene3D:2.10.110.10,SMART_domains:SM00132,Superfamily_domains:SSF57716 1,1,1 MODERATE 1 SNV 1,1,1 10 116247760 116247760 T C SNP ABLIM1 ENST00000277895 human ensembl 69_37n -1 known missense c.998 p.H333R 1000 smart_Znf_LIM pfam_Znf_LIM,pfam_Villin_headpiece,superfamily_Villin_headpiece,smart_Znf_LIM,smart_Villin_headpiece,pfscan_Villin_headpiece,pfscan_Znf_LIM - no_errors ABLIM1 HGNC ENSG00000099204 77 0 0 36 13 26.53 - - - 10 116247760 116247760 T C SNP ABLIM1 ENST00000277895 human ensembl 69_37n -1 known missense c.998 p.H333R 1000 smart_Znf_LIM pfam_Znf_LIM,pfam_Villin_headpiece,superfamily_Villin_headpiece,smart_Znf_LIM,smart_Villin_headpiece,pfscan_Villin_headpiece,pfscan_Znf_LIM - no_errors ABLIM1 HGNC - - - Putative_Driver Test driver Class 1 Class annotation ADAMTS20 genome.wustl.edu GRCh37 12 43944926 43944926 -1 Missense_Mutation SNP T T C TCGA-A1-A0SB-01 TCGA-A1-A0SB-10 T T Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx medium 2.85 Y80C getma.org/?cm=msa&ty=f&p=ATS20_HUMAN&rb=40&re=186&var=Y80C getma.org/?cm=var&var=hg19,12,43944926,T,C&fts=all db9d40fb-bfce-4c3b-a6c2-41c5c88982f1 a3254f8e-3bbd-42fc-abea-a5f25b7648b3 p.Tyr80Cys p.Y80C ENST00000389420 2/39 0 0 ADAMTS20,missense_variant,p.Tyr80Cys,ENST00000389420,NM_025003.3;ADAMTS20,missense_variant,p.Tyr80Cys,ENST00000553158,; C ENSG00000173157 ENST00000389420 Transcript missense_variant 239/6076 239/5733 80/1910 Y/C tAt/tGt COSM1476552,COSM1476551 1 ADAMTS20 HGNC 17178 protein_coding YES CCDS31778.2 ENSP00000374071 ATS20_HUMAN UPI00004565F4 NM_025003.3 deleterious(0) probably_damaging(1) 2/39 hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF165,Pfam_domain:PF01562 1,1 MODERATE 1 SNV 1,1 12 43944926 43944926 T C SNP ADAMTS20 ENST00000389420 human ensembl 69_37n -1 known missense c.239 p.Y80C 1000 pfam_Peptidase_M12B_N pfam_Pept_M12B_GON-ADAMTSs,pfam_Thrombospondin_1_rpt,pfam_Peptidase_M12B_N,pfam_ADAM_spacer1,pfam_Peptidase_M12B,superfamily_Thrombospondin_1_rpt,smart_Thrombospondin_1_rpt,prints_Peptidase_M12B_ADAM-TS,pfscan_Pept_M12B_GON-ADAMTSs,pfscan_Thrombospondin_1_rpt,pfscan_Peptidase_M12B - no_errors ADAMTS20 HGNC ENSG00000173157 50 0 0 19 17 45.95 - - - 12 43944926 43944926 T C SNP ADAMTS20 ENST00000389420 human ensembl 69_37n -1 known missense c.239 p.Y80C 1000 pfam_Peptidase_M12B_N pfam_Pept_M12B_GON-ADAMTSs,pfam_Thrombospondin_1_rpt,pfam_Peptidase_M12B_N,pfam_ADAM_spacer1,pfam_Peptidase_M12B,superfamily_Thrombospondin_1_rpt,smart_Thrombospondin_1_rpt,prints_Peptidase_M12B_ADAM-TS,pfscan_Pept_M12B_GON-ADAMTSs,pfscan_Thrombospondin_1_rpt,pfscan_Peptidase_M12B - no_errors ADAMTS20 HGNC - - - Unknown Class 4 Class annotation -CADM2 genome.wustl.edu GRCh37 3 85932472 85932472 1 Silent SNP C C T TCGA-A1-A0SB-01 TCGA-A1-A0SB-10 C C Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx db9d40fb-bfce-4c3b-a6c2-41c5c88982f1 a3254f8e-3bbd-42fc-abea-a5f25b7648b3 p.R81R ENST00000407528 3/10 0 0 CADM2,synonymous_variant,p.=,ENST00000383699,NM_001167675.1,NM_001256504.1,NM_001256505.1;CADM2,synonymous_variant,,ENST00000407528,NM_001167674.1;CADM2,synonymous_variant,p.=,ENST00000405615,NM_153184.3; T ENSG00000175161 ENST00000407528 Transcript synonymous_variant 305/1422 243/1308 81/435 R cgC/cgT COSM1178952,COSM1178953 1 CADM2 HGNC 29849 protein_coding CCDS54614.1 ENSP00000384575 CADM2_HUMAN G3XHN8_HUMAN UPI000006DE82 NM_001167674.1 3/10 PROSITE_profiles:PS50835,hmmpanther:PTHR23277,hmmpanther:PTHR23277:SF56,Pfam_domain:PF07686,Gene3D:2.60.40.10,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 1,1 LOW SNV 1,1 3 85932472 85932472 C T SNP CADM2 ENST00000405615 human ensembl 69_37n 1 known silent c.249 p.R83 920 pfam_Ig_I-set,pfam_Immunoglobulin,pfam_Ig_V-set,smart_Ig_sub,smart_Ig_sub2,pfscan_Ig-like pfam_Ig_I-set,pfam_Immunoglobulin,pfam_CD80_C2-set,pfam_Ig_V-set,pfam_Ig_C1-set,smart_Ig_sub,smart_Ig_sub2,smart_Neurexin-like,pfscan_Ig-like - no_errors CADM2 HGNC ENSG00000175161 57 0 0 22 23 51.11 - - - 3 85932472 85932472 C T SNP CADM2 ENST00000405615 human ensembl 69_37n 1 known silent c.249 p.R83 920 pfam_Ig_I-set,pfam_Immunoglobulin,pfam_Ig_V-set,smart_Ig_sub,smart_Ig_sub2,pfscan_Ig-like pfam_Ig_I-set,pfam_Immunoglobulin,pfam_CD80_C2-set,pfam_Ig_V-set,pfam_Ig_C1-set,smart_Ig_sub,smart_Ig_sub2,smart_Neurexin-like,pfscan_Ig-like - no_errors CADM2 HGNC - - - Putative_Driver Test driver Class 4 Class annotation +CADM2 genome.wustl.edu GRCh37 3 85932472 85932472 1 Silent SNP C C T TCGA-A1-A0SB-02 TCGA-A1-A0SB-10 C C Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx db9d40fb-bfce-4c3b-a6c2-41c5c88982f1 a3254f8e-3bbd-42fc-abea-a5f25b7648b3 p.R81R ENST00000407528 3/10 0 0 CADM2,synonymous_variant,p.=,ENST00000383699,NM_001167675.1,NM_001256504.1,NM_001256505.1;CADM2,synonymous_variant,,ENST00000407528,NM_001167674.1;CADM2,synonymous_variant,p.=,ENST00000405615,NM_153184.3; T ENSG00000175161 ENST00000407528 Transcript synonymous_variant 305/1422 243/1308 81/435 R cgC/cgT COSM1178952,COSM1178953 1 CADM2 HGNC 29849 protein_coding CCDS54614.1 ENSP00000384575 CADM2_HUMAN G3XHN8_HUMAN UPI000006DE82 NM_001167674.1 3/10 PROSITE_profiles:PS50835,hmmpanther:PTHR23277,hmmpanther:PTHR23277:SF56,Pfam_domain:PF07686,Gene3D:2.60.40.10,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 1,1 LOW SNV 1,1 3 85932472 85932472 C T SNP CADM2 ENST00000405615 human ensembl 69_37n 1 known silent c.249 p.R83 920 pfam_Ig_I-set,pfam_Immunoglobulin,pfam_Ig_V-set,smart_Ig_sub,smart_Ig_sub2,pfscan_Ig-like pfam_Ig_I-set,pfam_Immunoglobulin,pfam_CD80_C2-set,pfam_Ig_V-set,pfam_Ig_C1-set,smart_Ig_sub,smart_Ig_sub2,smart_Neurexin-like,pfscan_Ig-like - no_errors CADM2 HGNC ENSG00000175161 57 0 0 22 23 51.11 - - - 3 85932472 85932472 C T SNP CADM2 ENST00000405615 human ensembl 69_37n 1 known silent c.249 p.R83 920 pfam_Ig_I-set,pfam_Immunoglobulin,pfam_Ig_V-set,smart_Ig_sub,smart_Ig_sub2,pfscan_Ig-like pfam_Ig_I-set,pfam_Immunoglobulin,pfam_CD80_C2-set,pfam_Ig_V-set,pfam_Ig_C1-set,smart_Ig_sub,smart_Ig_sub2,smart_Neurexin-like,pfscan_Ig-like - no_errors CADM2 HGNC - - - Putative_Driver Test driver Class 4 Class annotation DTNB genome.wustl.edu GRCh37 2 25678299 25678299 -1 Missense_Mutation SNP C C T TCGA-A1-A0SB-01 TCGA-A1-A0SB-10 C C Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx medium 2125 V382M getma.org/?cm=msa&ty=f&p=DTNB_HUMAN&rb=283&re=473&var=V382M getma.org/?cm=var&var=hg19,2,25678299,C,T&fts=all db9d40fb-bfce-4c3b-a6c2-41c5c88982f1 a3254f8e-3bbd-42fc-abea-a5f25b7648b3 c.1144C>A p.Val382Met p.V382M ENST00000406818 11/21 0 0 DTNB,missense_variant,p.Val382Met,ENST00000406818,NM_001256303.1,NM_021907.4;DTNB,missense_variant,p.Val382Met,ENST00000407661,NM_183360.2,NM_001256304.1;DTNB,missense_variant,p.Val382Met,ENST00000404103,NM_033147.3;DTNB,missense_variant,p.Val382Met,ENST00000288642,;DTNB,missense_variant,p.Val325Met,ENST00000496972,NM_001256308.1;DTNB,missense_variant,p.Val178Met,ENST00000545439,;DTNB,intron_variant,,ENST00000407038,NM_033148.3;DTNB,intron_variant,,ENST00000407186,;DTNB,intron_variant,,ENST00000405222,NM_183361.2;DTNB,intron_variant,,ENST00000489756,;DTNB,intron_variant,,ENST00000481841,;DTNB,intron_variant,,ENST00000486555,;DTNB,3_prime_UTR_variant,,ENST00000398951,;DTNB,non_coding_transcript_exon_variant,,ENST00000485845,;DTNB,non_coding_transcript_exon_variant,,ENST00000479898,;DTNB,intron_variant,,ENST00000356599,;DTNB,intron_variant,,ENST00000482145,; T ENSG00000138101 ENST00000406818 Transcript missense_variant 1394/2474 1144/1884 382/627 V/M Gtg/Atg COSM3839175,COSM3839176 1 DTNB HGNC 3058 protein_coding YES CCDS46237.1 ENSP00000384084 DTNB_HUMAN Q53TC8_HUMAN,Q53T51_HUMAN,Q53SF9_HUMAN,Q53QV1_HUMAN,F8W9U0_HUMAN,E9PE76_HUMAN,E7ES64_HUMAN UPI0000129949 NM_001256303.1,NM_021907.4 deleterious(0.03) benign(0.379) 11/21 hmmpanther:PTHR11915:SF227,hmmpanther:PTHR11915,PIRSF_domain:PIRSF038204 1,1 MODERATE 1 SNV 1,1 2 25678299 25678299 C T SNP DTNB ENST00000406818 human ensembl 69_37n -1 known missense c.1144 p.V382M 1000 pirsf_Distrobrevin pfam_EF-hand_dom_typ1,pfam_EF-hand_dom_typ2,pfam_Znf_ZZ,smart_Znf_ZZ,pirsf_Distrobrevin,pfscan_Znf_ZZ - no_errors DTNB HGNC ENSG00000138101 35 0 0 9 9 50 - - - 2 25678299 25678299 C T SNP DTNB ENST00000406818 human ensembl 69_37n -1 known missense c.1144 p.V382M 1000 pirsf_Distrobrevin pfam_EF-hand_dom_typ1,pfam_EF-hand_dom_typ2,pfam_Znf_ZZ,smart_Znf_ZZ,pirsf_Distrobrevin,pfscan_Znf_ZZ - no_errors DTNB HGNC - - - Putative_Passenger Test passenger Class 1 Class annotation -KAT2A genome.wustl.edu GRCh37 17 40272381 40272381 -1 Silent SNP G G A TCGA-A1-A0SB-01 TCGA-A1-A0SB-10 G G Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx db9d40fb-bfce-4c3b-a6c2-41c5c88982f1 a3254f8e-3bbd-42fc-abea-a5f25b7648b3 c.471C>T p.= p.H157H ENST00000225916 3/18 0 0 KAT2A,synonymous_variant,p.=,ENST00000225916,NM_021078.2;CTD-2132N18.3,synonymous_variant,p.=,ENST00000592574,;RAB5C,downstream_gene_variant,,ENST00000393860,NM_201434.2;RAB5C,downstream_gene_variant,,ENST00000346213,NM_004583.3;HSPB9,upstream_gene_variant,,ENST00000355067,NM_033194.2;CTD-2132N18.3,missense_variant,p.Thr150Met,ENST00000592248,;KAT2A,synonymous_variant,p.=,ENST00000465682,;CTD-2132N18.3,3_prime_UTR_variant,,ENST00000585562,;KAT2A,upstream_gene_variant,,ENST00000592310,;KAT2A,upstream_gene_variant,,ENST00000588759,; A ENSG00000108773 ENST00000225916 Transcript synonymous_variant 525/3109 471/2514 157/837 H caC/caT rs536716483,COSM1479581 1 KAT2A HGNC 4201 protein_coding YES CCDS11417.1 ENSP00000225916 KAT2A_HUMAN K7ERS6_HUMAN UPI000000D978 NM_021078.2 3/18 hmmpanther:PTHR22880:SF124,hmmpanther:PTHR22880,Pfam_domain:PF06466,PIRSF_domain:PIRSF003048 A:0.0002 A:0 A:0 A:0.001 A:0 A:0 0,1 LOW 1 SNV 0,1 17 40272381 40272381 G A SNP ENSG00000267261 ENST00000592248 human ensembl 69_37n -1 known missense c.449 p.T150M 486 smart_Small_GTPase_Ras,smart_Small_GTPase_Rab_type,smart_Small_GTPase_Rho pfam_Small_GTPase,pfam_MIRO-like,pfam_Small_GTPase_ARF/SAR,pfam_Gtr1_RagA,smart_Small_GTPase_Ras,smart_Small_GTPase_Rab_type,smart_Small_GTPase_Rho,prints_Small_GTPase,tigrfam_Small_GTP-bd_dom - no_errors CTD-2132N18.3 Clone_based_vega_gene ENSG00000267261 40 0 0 30 36 54.55 - - - 17 40272381 40272381 G A SNP ENSG00000267261 ENST00000592248 human ensembl 69_37n -1 known missense c.449 p.T150M 486 smart_Small_GTPase_Ras,smart_Small_GTPase_Rab_type,smart_Small_GTPase_Rho pfam_Small_GTPase,pfam_MIRO-like,pfam_Small_GTPase_ARF/SAR,pfam_Gtr1_RagA,smart_Small_GTPase_Ras,smart_Small_GTPase_Rab_type,smart_Small_GTPase_Rho,prints_Small_GTPase,tigrfam_Small_GTP-bd_dom - no_errors CTD-2132N18.3 Clone_based_vega_gene - - - Putative_Driver Test driver Class 1 Class annotation -MSH3 genome.wustl.edu GRCh37 5 80024722 80024722 1 Frame_Shift_Del DEL T T - TCGA-A1-A0SB-01 TCGA-A1-A0SB-10 T T Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx db9d40fb-bfce-4c3b-a6c2-41c5c88982f1 a3254f8e-3bbd-42fc-abea-a5f25b7648b3 c.1508delT p.Leu503TrpfsTer5 p.L503Wfs*5 ENST00000265081 10/24 0 0 MSH3,frameshift_variant,p.Leu503TrpfsTer5,ENST00000265081,NM_002439.4;MSH3,non_coding_transcript_exon_variant,,ENST00000512258,; - ENSG00000113318 ENST00000265081 Transcript frameshift_variant 1586/4092 1506/3414 502/1137 S/X tcT/tc 1 MSH3 HGNC 7326 protein_coding YES CCDS34195.1 ENSP00000265081 MSH3_HUMAN UPI0000DBEE85 NM_002439.4 10/24 Superfamily_domains:SSF53150,Gene3D:3.30.420.110,Pfam_domain:PF05188,hmmpanther:PTHR11361,hmmpanther:PTHR11361:SF34 HIGH 1 deletion 2 5 80024722 80024722 T - DEL MSH3 ENST00000265081 human ensembl 69_37n 1 known frame_shift_del c.1506 p.L503fs 998 pfam_DNA_mismatch_repair_MutS_connt,superfamily_DNA_mismatch_repair_MutS_connt pfam_DNA_mismatch_repair_MutS_C,pfam_DNA_mismatch_repair_MutS_core,pfam_DNA_mismatch_repair_MutS_connt,pfam_DNA_mismatch_repair_MutS-lik_N,pfam_DNA_mismatch_repair_MutS_clamp,superfamily_DNA_mismatch_repair_MutS_core,superfamily_DNA_mismatch_repair_MutS_N,superfamily_DNA_mismatch_repair_MutS_connt,smart_DNA_mismatch_repair_MutS_core,smart_DNA_mismatch_repair_MutS_C - no_errors MSH3 HGNC ENSG00000113318 83 0 0 12 2 14.29 - - - 5 80024722 80024722 T - DEL MSH3 ENST00000265081 human ensembl 69_37n 1 known frame_shift_del c.1506 p.L503fs 998 pfam_DNA_mismatch_repair_MutS_connt,superfamily_DNA_mismatch_repair_MutS_connt pfam_DNA_mismatch_repair_MutS_C,pfam_DNA_mismatch_repair_MutS_core,pfam_DNA_mismatch_repair_MutS_connt,pfam_DNA_mismatch_repair_MutS-lik_N,pfam_DNA_mismatch_repair_MutS_clamp,superfamily_DNA_mismatch_repair_MutS_core,superfamily_DNA_mismatch_repair_MutS_N,superfamily_DNA_mismatch_repair_MutS_connt,smart_DNA_mismatch_repair_MutS_core,smart_DNA_mismatch_repair_MutS_C - no_errors MSH3 HGNC - - - Putative_Passenger Test passenger Class 3 Class annotation -MYB genome.wustl.edu GRCh37 6 135507043 135507044 1 Frame_Shift_Ins INS - - A TCGA-A1-A0SB-01 TCGA-A1-A0SB-10 - - Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx db9d40fb-bfce-4c3b-a6c2-41c5c88982f1 a3254f8e-3bbd-42fc-abea-a5f25b7648b3 c.27dupA p.Tyr10IlefsTer2 p.Y10Ifs*2 ENST00000367814 2/15 0 0 MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000341911,NM_001130173.1,NM_001161658.1,NM_001161656.1;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000316528,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000442647,NM_001161660.1,NM_001130172.1;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000367814,NM_001161659.1,NM_005375.2;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000525369,NM_001161657.1;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000527615,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000528774,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000534121,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000533624,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000534044,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000420123,;MYB,upstream_gene_variant,,ENST00000430686,;MYB,non_coding_transcript_exon_variant,,ENST00000531845,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000367812,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000533837,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000438901,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000525477,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000463282,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000339290,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000533808,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000525514,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000529586,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000526889,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000526320,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000531519,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000533384,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000531737,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000529262,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000526565,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000528015,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000526187,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000525002,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000528343,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000528140,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000528345,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000525940,;MYB,frameshift_variant,p.Tyr10Ter,ENST00000531634,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000524588,; A ENSG00000118513 ENST00000367814 Transcript frameshift_variant 212-213/3302 26-27/1923 9/640 I/IX ata/atAa COSM1487247,COSM1487248 1 MYB HGNC 7545 protein_coding CCDS5174.1 ENSP00000356788 MYB_HUMAN Q9UMI7_HUMAN,Q708J0_HUMAN,Q708E9_HUMAN,Q708E3_HUMAN UPI000012FAEA NM_001161659.1,NM_005375.2 2/15 hmmpanther:PTHR10641,hmmpanther:PTHR10641:SF454 1,1 HIGH insertion 1 1,1 6 135507043 135507044 - A INS MYB ENST00000341911 human ensembl 69_37n 1 known frame_shift_ins c.26_27 p.Y10fs 1.000:0.997 pfam_C-myb_C,pfam_SANT/Myb,pfam_Tscrpt_reg_Wos2-domain,superfamily_Homeodomain-like,smart_SANT/Myb,pfscan_Myb-like_dom - no_errors MYB HGNC ENSG00000118513 50 0 0 36 4 10 - - - 6 135507043 135507044 - A INS MYB ENST00000341911 human ensembl 69_37n 1 known frame_shift_ins c.26_27 p.Y10fs 1.000:0.997 pfam_C-myb_C,pfam_SANT/Myb,pfam_Tscrpt_reg_Wos2-domain,superfamily_Homeodomain-like,smart_SANT/Myb,pfscan_Myb-like_dom - no_errors MYB HGNC - - - Putative_Passenger Test passenger -NPIPB15 genome.wustl.edu GRCh37 16 74425902 74425902 1 Missense_Mutation SNP T T C TCGA-A1-A0SB-01 TCGA-A1-A0SB-10 T T Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx neutral 0 I358T getma.org/?cm=msa&ty=f&p=NPPL2_HUMAN&rb=283&re=382&var=I358T getma.org/?cm=var&var=hg19,16,74425902,T,C&fts=all db9d40fb-bfce-4c3b-a6c2-41c5c88982f1 a3254f8e-3bbd-42fc-abea-a5f25b7648b3 c.1256T>C p.Ile419Thr p.I419T ENST00000429990 7/7 0 0 NPIPB15,missense_variant,p.Ile419Thr,ENST00000429990,; C ENSG00000196436 ENST00000429990 Transcript missense_variant 1352/1428 1256/1332 419/443 I/T aTa/aCa rs141751158,COSM1479088,COSM1479089 1 NPIPB15 HGNC 34409 protein_coding YES ENSP00000411140 NPB15_HUMAN UPI000198C783 tolerated_low_confidence(0.06) benign(0.341) 7/7 hmmpanther:PTHR15438 0,1,1 MODERATE 1 SNV 0,1,1 16 74425902 74425902 T C SNP NPIPL2 ENST00000429990 human ensembl 69_37n 1 known missense c.1256 p.I419T 999 pfam_NPIP - no_errors NPIPL2 HGNC ENSG00000196436 20 0 0 10 4 28.57 - - - 16 74425902 74425902 T C SNP NPIPL2 ENST00000429990 human ensembl 69_37n 1 known missense c.1256 p.I419T 999 pfam_NPIP - no_errors NPIPL2 HGNC - - - Putative_Passenger Test passenger Class 1 Class annotation -OTOR genome.wustl.edu GRCh37 20 16730581 16730581 1 Missense_Mutation SNP G G A TCGA-A1-A0SB-01 TCGA-A1-A0SB-10 G G Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx medium 2.69 V97M getma.org/?cm=msa&ty=f&p=OTOR_HUMAN&rb=43&re=108&var=V97M getma.org/pdb.php?prot=OTOR_HUMAN&from=43&to=108&var=V97M getma.org/?cm=var&var=hg19,20,16730581,G,A&fts=all db9d40fb-bfce-4c3b-a6c2-41c5c88982f1 a3254f8e-3bbd-42fc-abea-a5f25b7648b3 c.289G>A p.Val97Met p.V97M ENST00000246081 3/4 0 0 OTOR,missense_variant,p.Val97Met,ENST00000246081,NM_020157.3;OTOR,non_coding_transcript_exon_variant,,ENST00000486129,;OTOR,intron_variant,,ENST00000490148,; A ENSG00000125879 ENST00000246081 Transcript missense_variant 333/1477 289/387 97/128 V/M Gtg/Atg COSM1410526 1 OTOR HGNC 8517 protein_coding YES CCDS13124.1 ENSP00000246081 OTOR_HUMAN UPI0000047809 NM_020157.3 deleterious(0) benign(0.344) 3/4 hmmpanther:PTHR23158,Gene3D:2.30.30.40,Pfam_domain:PF07653,SMART_domains:SM00326,Superfamily_domains:SSF50044 1 MODERATE 1 SNV 1 20 16730581 16730581 G A SNP OTOR ENST00000246081 human ensembl 69_37n 1 known missense c.289 p.V97M 963 pfam_SH3_2,superfamily_SH3_domain,smart_SH3_domain pfam_SH3_2,superfamily_SH3_domain,smart_SH3_domain - no_errors OTOR HGNC ENSG00000125879 57 0 0 36 9 20 - - - 20 16730581 16730581 G A SNP OTOR ENST00000246081 human ensembl 69_37n 1 known missense c.289 p.V97M 963 pfam_SH3_2,superfamily_SH3_domain,smart_SH3_domain pfam_SH3_2,superfamily_SH3_domain,smart_SH3_domain - no_errors OTOR HGNC - - - Class 2 Class annotation -P2RY10 genome.wustl.edu GRCh37 X 78216689 78216689 1 Silent SNP C C T TCGA-A1-A0SB-01 TCGA-A1-A0SB-10 C C Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx db9d40fb-bfce-4c3b-a6c2-41c5c88982f1 a3254f8e-3bbd-42fc-abea-a5f25b7648b3 c.672C>T p.= p.S224S ENST00000171757 4/4 0 0 P2RY10,synonymous_variant,p.=,ENST00000171757,NM_014499.2;P2RY10,synonymous_variant,p.=,ENST00000544091,NM_198333.1;P2RY10,downstream_gene_variant,,ENST00000475374,;P2RY10,downstream_gene_variant,,ENST00000461541,; T ENSG00000078589 ENST00000171757 Transcript synonymous_variant 952/1714 672/1020 224/339 S tcC/tcT COSM1491292 1 P2RY10 HGNC 19906 protein_coding YES CCDS14442.1 ENSP00000171757 P2Y10_HUMAN UPI0000050471 NM_014499.2 4/4 PROSITE_profiles:PS50262,hmmpanther:PTHR24232:SF6,hmmpanther:PTHR24232,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321 1 LOW 1 SNV 1 X 78216689 78216689 C T SNP P2RY10 ENST00000171757 human ensembl 69_37n 1 known silent c.672 p.S224 92 pfam_7TM_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_supfam pfam_7TM_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_supfam,prints_7TM_GPCR_Rhodpsn,prints_P2_purnocptor - no_errors P2RY10 HGNC ENSG00000078589 65 0 0 46 10 17.86 - - - X 78216689 78216689 C T SNP P2RY10 ENST00000171757 human ensembl 69_37n 1 known silent c.672 p.S224 92 pfam_7TM_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_supfam pfam_7TM_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_supfam,prints_7TM_GPCR_Rhodpsn,prints_P2_purnocptor - no_errors P2RY10 HGNC - - - Putative_Driver Test driver Class 3 Class annotation -PIEZO1 genome.wustl.edu GRCh37 16 88790292 88790292 -1 Missense_Mutation SNP T T C TCGA-A1-A0SB-01 TCGA-A1-A0SB-10 T T Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx low 1.18 Q1441R getma.org/?cm=msa&ty=f&p=PIEZ1_HUMAN&rb=58&re=1627&var=Q1441R getma.org/?cm=var&var=hg19,16,88790292,T,C&fts=all db9d40fb-bfce-4c3b-a6c2-41c5c88982f1 a3254f8e-3bbd-42fc-abea-a5f25b7648b3 c.4322A>G p.Gln1441Arg p.Q1441R ENST00000301015 31/51 0 0 PIEZO1,missense_variant,p.Gln1441Arg,ENST00000301015,NM_001142864.2;PIEZO1,missense_variant,p.Gln115Arg,ENST00000474606,;PIEZO1,upstream_gene_variant,,ENST00000327397,;PIEZO1,upstream_gene_variant,,ENST00000466823,;RP5-1142A6.9,downstream_gene_variant,,ENST00000564984,;PIEZO1,non_coding_transcript_exon_variant,,ENST00000566414,;PIEZO1,upstream_gene_variant,,ENST00000419505,;PIEZO1,upstream_gene_variant,,ENST00000497793,;PIEZO1,upstream_gene_variant,,ENST00000495568,;PIEZO1,downstream_gene_variant,,ENST00000475586,;PIEZO1,downstream_gene_variant,,ENST00000491917,; C ENSG00000103335 ENST00000301015 Transcript missense_variant 4569/8072 4322/7566 1441/2521 Q/R cAg/cGg COSM1479166 1 PIEZO1 HGNC 28993 protein_coding YES CCDS54058.1 ENSP00000301015 PIEZ1_HUMAN UPI0001B300F3 NM_001142864.2 tolerated(0.25) possibly_damaging(0.78) 31/51 hmmpanther:PTHR13167,hmmpanther:PTHR13167:SF40 1 MODERATE 1 SNV 1 16 88790292 88790292 T C SNP PIEZO1 ENST00000301015 human ensembl 69_37n -1 novel missense c.4322 p.Q1441R 1000 pfam_DUF3595 - no_errors PIEZO1 HGNC ENSG00000103335 37 0 0 20 8 28.57 - - - 16 88790292 88790292 T C SNP PIEZO1 ENST00000301015 human ensembl 69_37n -1 novel missense c.4322 p.Q1441R 1000 pfam_DUF3595 - no_errors PIEZO1 HGNC - - - Putative_Passenger Test passenger Class 3 Class annotation +KAT2A genome.wustl.edu GRCh37 17 40272381 40272381 -1 Silent SNP G G A TCGA-A1-A0SB-02 TCGA-A1-A0SB-10 G G Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx db9d40fb-bfce-4c3b-a6c2-41c5c88982f1 a3254f8e-3bbd-42fc-abea-a5f25b7648b3 c.471C>T p.= p.H157H ENST00000225916 3/18 0 0 KAT2A,synonymous_variant,p.=,ENST00000225916,NM_021078.2;CTD-2132N18.3,synonymous_variant,p.=,ENST00000592574,;RAB5C,downstream_gene_variant,,ENST00000393860,NM_201434.2;RAB5C,downstream_gene_variant,,ENST00000346213,NM_004583.3;HSPB9,upstream_gene_variant,,ENST00000355067,NM_033194.2;CTD-2132N18.3,missense_variant,p.Thr150Met,ENST00000592248,;KAT2A,synonymous_variant,p.=,ENST00000465682,;CTD-2132N18.3,3_prime_UTR_variant,,ENST00000585562,;KAT2A,upstream_gene_variant,,ENST00000592310,;KAT2A,upstream_gene_variant,,ENST00000588759,; A ENSG00000108773 ENST00000225916 Transcript synonymous_variant 525/3109 471/2514 157/837 H caC/caT rs536716483,COSM1479581 1 KAT2A HGNC 4201 protein_coding YES CCDS11417.1 ENSP00000225916 KAT2A_HUMAN K7ERS6_HUMAN UPI000000D978 NM_021078.2 3/18 hmmpanther:PTHR22880:SF124,hmmpanther:PTHR22880,Pfam_domain:PF06466,PIRSF_domain:PIRSF003048 A:0.0002 A:0 A:0 A:0.001 A:0 A:0 0,1 LOW 1 SNV 0,1 17 40272381 40272381 G A SNP ENSG00000267261 ENST00000592248 human ensembl 69_37n -1 known missense c.449 p.T150M 486 smart_Small_GTPase_Ras,smart_Small_GTPase_Rab_type,smart_Small_GTPase_Rho pfam_Small_GTPase,pfam_MIRO-like,pfam_Small_GTPase_ARF/SAR,pfam_Gtr1_RagA,smart_Small_GTPase_Ras,smart_Small_GTPase_Rab_type,smart_Small_GTPase_Rho,prints_Small_GTPase,tigrfam_Small_GTP-bd_dom - no_errors CTD-2132N18.3 Clone_based_vega_gene ENSG00000267261 40 0 0 30 36 54.55 - - - 17 40272381 40272381 G A SNP ENSG00000267261 ENST00000592248 human ensembl 69_37n -1 known missense c.449 p.T150M 486 smart_Small_GTPase_Ras,smart_Small_GTPase_Rab_type,smart_Small_GTPase_Rho pfam_Small_GTPase,pfam_MIRO-like,pfam_Small_GTPase_ARF/SAR,pfam_Gtr1_RagA,smart_Small_GTPase_Ras,smart_Small_GTPase_Rab_type,smart_Small_GTPase_Rho,prints_Small_GTPase,tigrfam_Small_GTP-bd_dom - no_errors CTD-2132N18.3 Clone_based_vega_gene - - - Putative_Driver Test driver Class 1 Class annotation +MSH3 genome.wustl.edu GRCh37 5 80024722 80024722 1 Frame_Shift_Del DEL T T - TCGA-A1-A0SB-02 TCGA-A1-A0SB-10 T T Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx db9d40fb-bfce-4c3b-a6c2-41c5c88982f1 a3254f8e-3bbd-42fc-abea-a5f25b7648b3 c.1508delT p.Leu503TrpfsTer5 p.L503Wfs*5 ENST00000265081 10/24 0 0 MSH3,frameshift_variant,p.Leu503TrpfsTer5,ENST00000265081,NM_002439.4;MSH3,non_coding_transcript_exon_variant,,ENST00000512258,; - ENSG00000113318 ENST00000265081 Transcript frameshift_variant 1586/4092 1506/3414 502/1137 S/X tcT/tc 1 MSH3 HGNC 7326 protein_coding YES CCDS34195.1 ENSP00000265081 MSH3_HUMAN UPI0000DBEE85 NM_002439.4 10/24 Superfamily_domains:SSF53150,Gene3D:3.30.420.110,Pfam_domain:PF05188,hmmpanther:PTHR11361,hmmpanther:PTHR11361:SF34 HIGH 1 deletion 2 5 80024722 80024722 T - DEL MSH3 ENST00000265081 human ensembl 69_37n 1 known frame_shift_del c.1506 p.L503fs 998 pfam_DNA_mismatch_repair_MutS_connt,superfamily_DNA_mismatch_repair_MutS_connt pfam_DNA_mismatch_repair_MutS_C,pfam_DNA_mismatch_repair_MutS_core,pfam_DNA_mismatch_repair_MutS_connt,pfam_DNA_mismatch_repair_MutS-lik_N,pfam_DNA_mismatch_repair_MutS_clamp,superfamily_DNA_mismatch_repair_MutS_core,superfamily_DNA_mismatch_repair_MutS_N,superfamily_DNA_mismatch_repair_MutS_connt,smart_DNA_mismatch_repair_MutS_core,smart_DNA_mismatch_repair_MutS_C - no_errors MSH3 HGNC ENSG00000113318 83 0 0 12 2 14.29 - - - 5 80024722 80024722 T - DEL MSH3 ENST00000265081 human ensembl 69_37n 1 known frame_shift_del c.1506 p.L503fs 998 pfam_DNA_mismatch_repair_MutS_connt,superfamily_DNA_mismatch_repair_MutS_connt pfam_DNA_mismatch_repair_MutS_C,pfam_DNA_mismatch_repair_MutS_core,pfam_DNA_mismatch_repair_MutS_connt,pfam_DNA_mismatch_repair_MutS-lik_N,pfam_DNA_mismatch_repair_MutS_clamp,superfamily_DNA_mismatch_repair_MutS_core,superfamily_DNA_mismatch_repair_MutS_N,superfamily_DNA_mismatch_repair_MutS_connt,smart_DNA_mismatch_repair_MutS_core,smart_DNA_mismatch_repair_MutS_C - no_errors MSH3 HGNC - - - Putative_Passenger Test passenger Class 3 Class annotation +MYB genome.wustl.edu GRCh37 6 135507043 135507044 1 Frame_Shift_Ins INS - - A TCGA-A1-A0SB-02 TCGA-A1-A0SB-10 - - Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx db9d40fb-bfce-4c3b-a6c2-41c5c88982f1 a3254f8e-3bbd-42fc-abea-a5f25b7648b3 c.27dupA p.Tyr10IlefsTer2 p.Y10Ifs*2 ENST00000367814 2/15 0 0 MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000341911,NM_001130173.1,NM_001161658.1,NM_001161656.1;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000316528,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000442647,NM_001161660.1,NM_001130172.1;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000367814,NM_001161659.1,NM_005375.2;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000525369,NM_001161657.1;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000527615,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000528774,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000534121,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000533624,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000534044,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000420123,;MYB,upstream_gene_variant,,ENST00000430686,;MYB,non_coding_transcript_exon_variant,,ENST00000531845,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000367812,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000533837,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000438901,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000525477,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000463282,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000339290,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000533808,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000525514,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000529586,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000526889,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000526320,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000531519,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000533384,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000531737,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000529262,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000526565,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000528015,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000526187,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000525002,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000528343,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000528140,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000528345,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000525940,;MYB,frameshift_variant,p.Tyr10Ter,ENST00000531634,;MYB,frameshift_variant,p.Tyr10IlefsTer2,ENST00000524588,; A ENSG00000118513 ENST00000367814 Transcript frameshift_variant 212-213/3302 26-27/1923 9/640 I/IX ata/atAa COSM1487247,COSM1487248 1 MYB HGNC 7545 protein_coding CCDS5174.1 ENSP00000356788 MYB_HUMAN Q9UMI7_HUMAN,Q708J0_HUMAN,Q708E9_HUMAN,Q708E3_HUMAN UPI000012FAEA NM_001161659.1,NM_005375.2 2/15 hmmpanther:PTHR10641,hmmpanther:PTHR10641:SF454 1,1 HIGH insertion 1 1,1 6 135507043 135507044 - A INS MYB ENST00000341911 human ensembl 69_37n 1 known frame_shift_ins c.26_27 p.Y10fs 1.000:0.997 pfam_C-myb_C,pfam_SANT/Myb,pfam_Tscrpt_reg_Wos2-domain,superfamily_Homeodomain-like,smart_SANT/Myb,pfscan_Myb-like_dom - no_errors MYB HGNC ENSG00000118513 50 0 0 36 4 10 - - - 6 135507043 135507044 - A INS MYB ENST00000341911 human ensembl 69_37n 1 known frame_shift_ins c.26_27 p.Y10fs 1.000:0.997 pfam_C-myb_C,pfam_SANT/Myb,pfam_Tscrpt_reg_Wos2-domain,superfamily_Homeodomain-like,smart_SANT/Myb,pfscan_Myb-like_dom - no_errors MYB HGNC - - - Putative_Passenger Test passenger +PIEZO1 genome.wustl.edu GRCh37 16 88790292 88790292 -1 Missense_Mutation SNP T T C TCGA-A1-A0SB-02 TCGA-A1-A0SB-10 T T Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx low 1.18 Q1441R getma.org/?cm=msa&ty=f&p=PIEZ1_HUMAN&rb=58&re=1627&var=Q1441R getma.org/?cm=var&var=hg19,16,88790292,T,C&fts=all db9d40fb-bfce-4c3b-a6c2-41c5c88982f1 a3254f8e-3bbd-42fc-abea-a5f25b7648b3 c.4322A>G p.Gln1441Arg p.Q1441R ENST00000301015 31/51 0 0 PIEZO1,missense_variant,p.Gln1441Arg,ENST00000301015,NM_001142864.2;PIEZO1,missense_variant,p.Gln115Arg,ENST00000474606,;PIEZO1,upstream_gene_variant,,ENST00000327397,;PIEZO1,upstream_gene_variant,,ENST00000466823,;RP5-1142A6.9,downstream_gene_variant,,ENST00000564984,;PIEZO1,non_coding_transcript_exon_variant,,ENST00000566414,;PIEZO1,upstream_gene_variant,,ENST00000419505,;PIEZO1,upstream_gene_variant,,ENST00000497793,;PIEZO1,upstream_gene_variant,,ENST00000495568,;PIEZO1,downstream_gene_variant,,ENST00000475586,;PIEZO1,downstream_gene_variant,,ENST00000491917,; C ENSG00000103335 ENST00000301015 Transcript missense_variant 4569/8072 4322/7566 1441/2521 Q/R cAg/cGg COSM1479166 1 PIEZO1 HGNC 28993 protein_coding YES CCDS54058.1 ENSP00000301015 PIEZ1_HUMAN UPI0001B300F3 NM_001142864.2 tolerated(0.25) possibly_damaging(0.78) 31/51 hmmpanther:PTHR13167,hmmpanther:PTHR13167:SF40 1 MODERATE 1 SNV 1 16 88790292 88790292 T C SNP PIEZO1 ENST00000301015 human ensembl 69_37n -1 novel missense c.4322 p.Q1441R 1000 pfam_DUF3595 - no_errors PIEZO1 HGNC ENSG00000103335 37 0 0 20 8 28.57 - - - 16 88790292 88790292 T C SNP PIEZO1 ENST00000301015 human ensembl 69_37n -1 novel missense c.4322 p.Q1441R 1000 pfam_DUF3595 - no_errors PIEZO1 HGNC - - - Putative_Passenger Test passenger Class 3 Class annotation TP53 genome.wustl.edu GRCh37 17 7578253 7578253 0 Missense_Mutation SNP C C A TCGA-A1-A0SB-01 TCGA-A1-A0SB-10 A C Unknown Germline Phase_IV Capture 1 dbGAP IlluminaGAIIx medium 3.005 getma.org/?cm=msa&ty=f&p=P53_HUMAN&rb=95&re=289&var=G199V getma.org/pdb.php?prot=P53_HUMAN&from=95&to=289&var=G199V getma.org/?cm=var&var=hg19,17,7578253,C,A&fts=all ENST00000269305.4:c.596G>T p.Gly199Val p.G199V ENST00000269305 11-Jun 0 0 TP53,missense_variant,p.Gly199Val,ENST00000420246,NM_001126114.2,NM_001276696.1;TP53,missense_variant,p.Gly199Val,ENST00000455263,NM_001276695.1,NM_001126113.2;TP53,missense_variant,p.Gly199Val,ENST00000269305,NM_001126112.2,NM_001276761.1,NM_001276760.1,NM_000546.5,NM_001126118.1;TP53,missense_variant,p.Gly199Val,ENST00000445888,;TP53,missense_variant,p.Gly199Val,ENST00000359597,;TP53,missense_variant,p.Gly199Val,ENST00000413465,;TP53,missense_variant,p.Gly67Val,ENST00000509690,;TP53,missense_variant,p.Gly106Val,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,intron_variant,,ENST00000574684,;TP53,non_coding_transcript_exon_variant,,ENST00000510385,;TP53,non_coding_transcript_exon_variant,,ENST00000504290,;TP53,non_coding_transcript_exon_variant,,ENST00000504937,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,; A ENSG00000141510 ENST00000269305 Transcript missense_variant 786/2579 596/1182 199 G/V gGa/gTa TP53_g.12665G>T,COSM44140,COSM255788,COSM255787,COSM255789,COSM3675525,COSM3675524,COSM255790 1 TP53 HGNC 11998 protein_coding YES CCDS11118.1 ENSP00000269305 P53_HUMAN S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN UPI000002ED67 NM_001126112.2 deleterious(0) probably_damaging(1) 11-Jun Gene3D:2.60.40.720,Pfam_domain:PF00870,hmmpanther:PTHR11447,hmmpanther:PTHR11447:SF6,Superfamily_domains:SSF49417 0,1,1,1,1,1,1,1 MODERATE 1 SNV 0,1,1,1,1,1,1,1 17 7578253 7578253 C A SNP TP53 NM_000546.4 human genbank 58_37c -1 reviewed missense c.596 p.G199V 1 HMMPfam_P53|7Csuperfamily_p53-like transcription factors HMMPfam_P53_TAD|7CHMMPfam_P53|7Csuperfamily_p53-like transcription factors|7CPatternScan_P53|7CHMMPfam_P53_tetramer|7Csuperfamily_p53 tetramerization domain - 17 7578253 7578253 C A SNP TP53 NM_000546.4 human genbank 58_37c -1 reviewed missense c.596 p.G199V 1 HMMPfam_P53|7Csuperfamily_p53-like transcription factors HMMPfam_P53_TAD|7CHMMPfam_P53|7Csuperfamily_p53-like transcription factors|7CPatternScan_P53|7CHMMPfam_P53_tetramer|7Csuperfamily_p53 tetramerization domain - TP53 genome.wustl.edu GRCh37 17 7576851 7576851 0 Splice_Site SNP A A C novel unknown TCGA-A1-A0SB-01 TCGA-A1-A0SB-10 A A Unknown Somatic Phase_IV Capture 1 dbGAP Illumina GAIIx ENST00000269305.4:c.993+2T>G p.X331_splice ENST00000269305 0 0 TP53,splice_donor_variant,,ENST00000420246,NM_001126114.2,NM_001276696.1;TP53,splice_donor_variant,,ENST00000455263,NM_001276695.1,NM_001126113.2;TP53,splice_donor_variant,,ENST00000269305,NM_001126112.2,NM_001276761.1,NM_001276760.1,NM_000546.5,NM_001126118.1;TP53,splice_donor_variant,,ENST00000445888,;TP53,splice_donor_variant,,ENST00000359597,;TP53,splice_donor_variant,,ENST00000576024,;TP53,intron_variant,,ENST00000413465,;TP53,downstream_gene_variant,,ENST00000509690,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,downstream_gene_variant,,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,splice_donor_variant,,ENST00000510385,;TP53,splice_donor_variant,,ENST00000504290,;TP53,splice_donor_variant,,ENST00000504937,;TP53,downstream_gene_variant,,ENST00000505014,; C ENSG00000141510 ENST00000269305 Transcript splice_donor_variant -/2579 993/1182 TP53_g.14067T>G,COSM29774,COSM146229 1 TP53 HGNC 11998 protein_coding YES CCDS11118.1 ENSP00000269305 P53_HUMAN S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN UPI000002ED67 NM_001126112.2 10-Sep 0,1,1 HIGH 1 SNV 0,1,1 17 7576851 7576851 A C SNP TP53 NM_000546 human genbank 57_37b -1 reviewed splice_site c.993+2 e8+2 1 - - - 17 7576851 7576851 A C SNP TP53 NM_000546 human genbank 57_37b -1 reviewed splice_site c.993+2 e8+2 1 - - - BRCA1 genome.wustl.edu GRCh37 17 41243581 41243581 0 Nonsense_Mutation SNP G G A rs80357262 TCGA-A1-A0SB-01 TCGA-A1-A0SB-10 A G Unknown Germline Phase_IV Capture 1 dbGAP IlluminaGAIIx 0 getma.org/?cm=var&var=hg19,17,41243581,G,A&fts=all ENST00000357654.3:c.3967C>T p.Gln1323Ter p.Q1323* ENST00000357654 23-Oct 0 0 BRCA1,stop_gained,p.Gln1027Ter,ENST00000309486,NM_007297.3;BRCA1,stop_gained,p.Gln1323Ter,ENST00000357654,NM_007294.3;BRCA1,stop_gained,p.Gln1323Ter,ENST00000346315,;BRCA1,stop_gained,p.Gln1323Ter,ENST00000354071,;BRCA1,stop_gained,p.Gln1323Ter,ENST00000471181,NM_007300.3;BRCA1,stop_gained,p.Gln1276Ter,ENST00000493795,;BRCA1,stop_gained,p.Gln88Ter,ENST00000461574,;BRCA1,intron_variant,,ENST00000352993,;BRCA1,intron_variant,,ENST00000351666,;BRCA1,intron_variant,,ENST00000468300,NM_007299.3;BRCA1,intron_variant,,ENST00000491747,NM_007298.3;BRCA1,intron_variant,,ENST00000478531,;BRCA1,intron_variant,,ENST00000493919,;BRCA1,intron_variant,,ENST00000484087,;BRCA1,intron_variant,,ENST00000591534,;BRCA1,intron_variant,,ENST00000487825,;BRCA1,intron_variant,,ENST00000586385,;BRCA1,intron_variant,,ENST00000591849,;BRCA1,downstream_gene_variant,,ENST00000470026,;BRCA1,downstream_gene_variant,,ENST00000477152,;BRCA1,downstream_gene_variant,,ENST00000494123,;BRCA1,downstream_gene_variant,,ENST00000473961,;BRCA1,downstream_gene_variant,,ENST00000497488,;BRCA1,downstream_gene_variant,,ENST00000476777,;BRCA1,3_prime_UTR_variant,,ENST00000461221,;BRCA1,non_coding_transcript_exon_variant,,ENST00000467274,;BRCA1,downstream_gene_variant,,ENST00000492859,;BRCA1,downstream_gene_variant,,ENST00000412061,; A ENSG00000012048 ENST00000357654 Transcript stop_gained 4086/7094 3967/5592 1323 Q/* Caa/Taa rs80357262 1 BRCA1 HGNC 1100 protein_coding CCDS11453.1 ENSP00000350283 BRCA1_HUMAN Q9UE29_HUMAN,Q9NQR3_HUMAN,Q92897_HUMAN,Q7KYU6_HUMAN,Q4EW25_HUMAN,Q3YB53_HUMAN,Q3YB50_HUMAN,Q3YB49_HUMAN,Q3LRH8_HUMAN,Q3B891_HUMAN,K7EPC7_HUMAN,K4K7V3_HUMAN,K4JXS7_HUMAN,K4JUB1_HUMAN,G4V503_HUMAN,G4V502_HUMAN,G4V500_HUMAN,G4V4Z8_HUMAN,G4V4Z7_HUMAN,G1UI37_HUMAN,E9PFZ0_HUMAN,E7EWN5_HUMAN,E7EP70_HUMAN,C9IZW4_HUMAN,C4PFY7_HUMAN UPI0000126AC8 NM_007294.3 23-Oct PIRSF_domain:PIRSF001734,hmmpanther:PTHR13763,hmmpanther:PTHR13763:SF0 not_provided,pathogenic HIGH SNV 1 17 41243581 41243581 G A SNP BRCA1 NM_007294.3 human genbank 58_37c -1 reviewed nonsense c.3967 p.Q1323* 0.949 HMMPfam_BRCT|7CHMMSmart_SM00292|7Csuperfamily_BRCT domain|7CHMMSmart_SM00184|7CPatternScan_ZF_RING_1|7CHMMPfam_zf-C3HC4|7Csuperfamily_RING/U-box - 17 41243581 41243581 G A SNP BRCA1 NM_007294.3 human genbank 58_37c -1 reviewed nonsense c.3967 p.Q1323* 0.949 HMMPfam_BRCT|7CHMMSmart_SM00292|7Csuperfamily_BRCT domain|7CHMMSmart_SM00184|7CPatternScan_ZF_RING_1|7CHMMPfam_zf-C3HC4|7Csuperfamily_RING/U-box - diff --git a/core/src/test/scripts/test_data/study_es_0/result_report.html b/core/src/test/scripts/test_data/study_es_0/result_report.html index 125e429c272..e9d3aa1327a 100644 --- a/core/src/test/scripts/test_data/study_es_0/result_report.html +++ b/core/src/test/scripts/test_data/study_es_0/result_report.html @@ -553,7 +553,7 @@

data_clinical_samples.txt

Info – – - Read 846 lines. Lines with warning: 0. Lines with error: 0 + Read 847 lines. Lines with warning: 0. Lines with error: 0 – @@ -931,7 +931,7 @@

data_gene_panel_matrix.txt

Info – – - Read 20 lines. Lines with warning: 0. Lines with error: 0 + Read 21 lines. Lines with warning: 0. Lines with error: 0 – @@ -984,7 +984,7 @@

data_gistic_genes_amp.txt

Info – – - Read 15 lines. Lines with warning: 0. Lines with error: 0 + Read 13 lines. Lines with warning: 0. Lines with error: 0 – @@ -1240,14 +1240,14 @@

data_mutations_extended.maf

Info - 4, 5, 6, (5 more) + 4, 5, 6, (3 more) 164 Values contained in the column cbp_driver_tiers that will appear in the "Mutation Color" menu of the Oncoprint Class 2, Class 1, Class 4, (1 more) Info - 7, 9, 14 + 7, 9 – Line will not be loaded due to the variant classification filter. Filtered types: [Silent, Intron, 3'UTR, 3'Flank, 5'UTR, 5'Flank, IGR, RNA] Silent @@ -1263,7 +1263,7 @@

data_mutations_extended.maf

Info – – - Read 38 lines. Lines with warning: 0. Lines with error: 0 + Read 35 lines. Lines with warning: 0. Lines with error: 0 – diff --git a/core/src/test/scripts/test_data/study_es_3/data_gistic_genes_amp.txt b/core/src/test/scripts/test_data/study_es_3/data_gistic_genes_amp.txt new file mode 100644 index 00000000000..4fed7d78499 --- /dev/null +++ b/core/src/test/scripts/test_data/study_es_3/data_gistic_genes_amp.txt @@ -0,0 +1,5 @@ +index chromosome region_start region_end peak_start peak_end enlarged_peak_start enlarged_peak_end n_genes_in_region genes_in_region n_genes_in_peak genes_in_peak n_genes_on_chip genes_on_chip top 3 amp cytoband q_value +8 6 105104338 108701250 107215848 107241341 107206929 107289865 1 NA 1 NA 1 6q21 8.7327e-14 +25 17 20903776 20926325 20909644 20914635 20804010 21012523 1 NA, 1 NA, 1 17p11.2 0.14805 +6 4 73398680 75049763 73931526 73935908 73825386 74269277 6 SNORA3,RNU6ATAC5P,RNU4ATAC9P,ANKRD17,COX18, 2 ANKRD17,COX18, 1 4q13.3 0.0030828 +21 14 37583259 38414817 38049107 38056423 37950983 38203446 4 SNORA42,TTC6,FOXA1,MIPOL1, 1 FOXA1, 1 14q21.1 0.001442 diff --git a/core/src/test/scripts/test_data/study_es_3/meta_gistic_genes_amp.txt b/core/src/test/scripts/test_data/study_es_3/meta_gistic_genes_amp.txt new file mode 100644 index 00000000000..f548ab4791d --- /dev/null +++ b/core/src/test/scripts/test_data/study_es_3/meta_gistic_genes_amp.txt @@ -0,0 +1,5 @@ +cancer_study_identifier: brca_tcga_pub +genetic_alteration_type: GISTIC_GENES_AMP +datatype: Q-VALUE +reference_genome_id: hg19 +data_filename: data_gistic_genes_amp.txt diff --git a/requirements.txt b/requirements.txt index d05727fd9fa..18145dfa4e5 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,4 +1,4 @@ requests==2.20.0 Jinja2==2.8 mysqlclient==1.3.13 -pyyaml==3.13 +PyYAML==5.3.1