Integrated multi-omics analyses on patient-derived CRC organoids highlight altered molecular pathways in colorectal cancer progression involving PTEN

Table 3 Summary of WES deleterious and potentially deleterious somatic variants. We performed twenty-five comparisons, identifying hundreds of SNVs and indels in each iteration (n = 472 on average)

Comparison	# Variants	Type			Localization
Comparison		SIFT	ClinVar	Non-Synonymous	Exonic	ncRNA_exonic	Splicing	5’UTR	3’UTR
P12T primary tissue_P12N primary tissue	532	108	7	417	141	51	5	50	285
P12N early_P12N primary tissue	248	56	1	191	80	30	4	26	108
P12N late_P12N early	139	24	1	114	37	20	1	18	63
P12T primary tissue_P12N early	506	103	7	396	135	47	5	45	274
P12T + W early_P12N early	328	93	7	228	114	30	2	38	144
P12T -W early_P12N early	435	113	9	313	150	41	6	58	180
P12T -W late_P12N late	313	82	7	224	107	20	2	33	151
P12T -W late_P12T -W early	155	22	0	133	30	19	0	23	83
P12T + W early_P12T primary tissue	153	30	1	122	39	24	0	25	65
P12T -W early_P12T primary tissue	223	38	2	183	54	31	5	43	90
P12T + W early_P12T -W early	152	26	0	127	33	26	0	23	71
P14T primary tissue_P14N primary tissue	592	90	3	499	134	49	6	72	331
P14N early_P14N primary tissue	257	60	2	195	85	26	1	38	107
P14T primary tissue_P14N early	661	95	3	563	142	61	6	77	375
P14T + W early_P14N early	815	219	8	588	265	71	11	122	346
P14T + W late_P14N early	728	192	10	526	238	69	8	107	306
P14T + W very late_P14N early	747	203	9	535	255	69	7	110	306
P14T -W early_P14N early	789	213	10	566	261	66	9	98	355
P14T -W late_P14N early	858	234	11	613	296	86	9	106	361
P14T + W early_P14T primary tissue	604	150	7	447	188	55	9	84	268
P14T -W early_P14T primary tissue	585	142	8	435	183	61	8	66	267
P14T + W early_P14T -W early	301	58	0	243	74	34	5	56	132
P14T + W late_P14T primary tissue	518	123	8	387	160	47	6	74	231
P14T -W late_P14T primary tissue	712	179	10	523	240	71	8	77	316
P14T + W late_P14T -W late	450	101	6	343	134	47	7	74	188

ISSN: 1756-9966