Merge pull request #44 from genomic-medicine-sweden/rm_CDH1

fix: rm CDH1 from cnv deletioner
genomic-medicine-sweden · Jun 19, 2024 · 4d5e5f3 · 4d5e5f3
2 parents 0697ec3 + b3c6268
commit 4d5e5f3
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diff --git a/cnv/cnv_deletion_genes_240618.tsv 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
@@ -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
@@ -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
@@ -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