From b3c626855e5a3cb8b104539ad2186ad98394ad92 Mon Sep 17 00:00:00 2001 From: jonca79 Date: Tue, 18 Jun 2024 16:42:04 +0200 Subject: [PATCH] fix: rm CDH1 from cnv deletioner --- cnv/cnv_deletion_genes_240618.tsv | 19 +++++++++++++++++++ cnv/cnv_deletion_genes_240618_hg38.tsv | 19 +++++++++++++++++++ cnv/cnv_loh_genes_240618.bed | 19 +++++++++++++++++++ cnv/cnv_loh_genes_240618_hg38.bed | 19 +++++++++++++++++++ 4 files changed, 76 insertions(+) create mode 100644 cnv/cnv_deletion_genes_240618.tsv create mode 100644 cnv/cnv_deletion_genes_240618_hg38.tsv create mode 100644 cnv/cnv_loh_genes_240618.bed create mode 100644 cnv/cnv_loh_genes_240618_hg38.bed diff --git a/cnv/cnv_deletion_genes_240618.tsv b/cnv/cnv_deletion_genes_240618.tsv new file mode 100644 index 0000000..ebffbcb --- /dev/null +++ b/cnv/cnv_deletion_genes_240618.tsv @@ -0,0 +1,19 @@ +#gene(s) chrmosome start_cnv_region stop_cnv_region gene_start gene_end +CDKN2A,CDKN2B chr9 19645614 24999615 21968207 22008972 +BRCA2 chr13 29566848 36647253 32889005 32973172 +BRCA1 chr17 38487450 43985736 41197105 41276778 +PTEN chr10 86278390 92430351 89623686 89725324 +BAP1 chr3 49459013 55281722 52436283 52443914 +FAT1 chr4 184290736 190436199 187509725 187631001 +CHD1 chr5 95192063 101262110 98192063 98262110 +MCPH1 chr8 3409643 9212540 6264168 6357470 +TSC1 chr9 132895849 138662761 135771601 135804279 +ATM chr11 105481578 111078515 108098331 108236255 +RB1 chr13 45997245 51796943 48878028 49054227 +SPRED1 chr15 35422573 41541070 38496523 38643885 +TSC2 chr16 132409 6140579 2098250 2138631 +PALB2 chr16 20647820 26576399 23614759 23652498 +FANCA chr16 86992145 90095377 89809187 89883043 +TP53 chr17 4638383 10578134 7572906 7579932 +NF1 chr17 26653787 32780860 29422307 29701193 +RAD51C chr17 53818678 59675481 56769984 56811603 diff --git a/cnv/cnv_deletion_genes_240618_hg38.tsv b/cnv/cnv_deletion_genes_240618_hg38.tsv new file mode 100644 index 0000000..d103ede --- /dev/null +++ b/cnv/cnv_deletion_genes_240618_hg38.tsv @@ -0,0 +1,19 @@ +#gene(s) chrmosome start_cnv_region stop_cnv_region gene_start gene_end +CDKN2A,CDKN2B chr9 19645616 24999617 21968208 22008973 +BRCA2 chr13 28992711 36073116 32314868 32399035 +BRCA1 chr17 40331198 45908370 43045088 43124761 +PTEN chr10 84518634 90670594 87863929 87965567 +BAP1 chr3 49421580 55247694 52402267 52409898 +FAT1 chr4 183369583 189515045 186588571 186709847 +CHD1 chr5 95856359 101926406 98856359 98926406 +MCPH1 chr8 3552121 9355030 6406647 6499949 +TSC1 chr9 130133570 135770915 132896214 132928892 +ATM chr11 105610851 111207791 108227604 108365528 +RB1 chr13 45423110 51222807 48303892 48480091 +SPRED1 chr15 35130372 41248872 38204322 38351684 +TSC2 chr16 82410 6090578 2048249 2088630 +PALB2 chr16 20636498 26565078 23603438 23641177 +FANCA chr16 86958539 90028969 89742779 89816635 +TP53 chr17 4735088 10674817 7669588 7676614 +NF1 chr17 28326761 34453841 31095289 31374175 +RAD51C chr17 55741317 61598120 58692623 58734242 diff --git a/cnv/cnv_loh_genes_240618.bed b/cnv/cnv_loh_genes_240618.bed new file mode 100644 index 0000000..b8e72cf --- /dev/null +++ b/cnv/cnv_loh_genes_240618.bed @@ -0,0 +1,19 @@ +chr3 52436283 52443914 BAP1 +chr4 187509725 187631001 FAT1 +chr5 98192063 98262110 CHD1 +chr8 6264168 6357470 MCPH1 +chr9 21968207 21994350 CDKN2A +chr9 22005965 22008972 CDKN2B +chr9 135771601 135804279 TSC1 +chr10 89623686 89725324 PTEN +chr11 108098331 108236255 ATM +chr13 32889005 32973172 BRCA2 +chr13 48878028 49054227 RB1 +chr15 38545366 38643885 SPRED1 +chr16 2098250 2138631 TSC2 +chr16 23614759 23652498 PALB2 +chr16 89809187 89883043 FANCA +chr17 7572906 7579932 TP53 +chr17 29422307 29701193 NF1 +chr17 41197105 41276778 BRCA1 +chr17 56769984 56811603 RAD51C diff --git a/cnv/cnv_loh_genes_240618_hg38.bed b/cnv/cnv_loh_genes_240618_hg38.bed new file mode 100644 index 0000000..90e27f4 --- /dev/null +++ b/cnv/cnv_loh_genes_240618_hg38.bed @@ -0,0 +1,19 @@ +chr3 52402267 52409898 BAP1 +chr4 186588571 186709847 FAT1 +chr5 98856359 98926406 CHD1 +chr8 6406647 6499949 MCPH1 +chr9 21968208 21994351 CDKN2A +chr9 22005966 22008973 CDKN2B +chr9 132896214 132928892 TSC1 +chr10 87863929 87965567 PTEN +chr11 108227604 108365528 ATM +chr13 32314868 32399035 BRCA2 +chr13 48303892 48480091 RB1 +chr15 38253165 38351684 SPRED1 +chr16 2048249 2088630 TSC2 +chr16 23603438 23641177 PALB2 +chr16 89742779 89816635 FANCA +chr17 7669588 7676614 TP53 +chr17 31095289 31374175 NF1 +chr17 43045088 43124761 BRCA1 +chr17 58692623 58734242 RAD51C