Next-generation sequencing traces human induced pluripotent stem cell lines clonally generated from heterogeneous cancer tissue

Table 5 Target capture

	NCC1	CC1	CC1-1	CC1-2	CC1-7	CC1-8	CC1-9	CC1-11	CC1-12	CC1-17	CC1-18	CC1-25
Initial bases on target ①	3143812	3143812	3143812	3143812	3143812	3143812	3143812	3143812	3143812	3143812	3143812	3143812
Initial bases near target ②	3790645	3790645	3790645	3790645	3790645	3790645	3790645	3790645	3790645	3790645	3790645	3790645
Initial bases on or near target ③	6934457	6934457	6934457	6934457	6934457	6934457	6934457	6934457	6934457	6934457	6934457	6934457
Total effective reads ④	26950921	26357798	21898501	25997648	21511158	26825314	26718931	25414259	25117934	29541030	30894642	21641723
Total effective bases (Mb) ⑤	2663	2602	2157	2573	2125	2643	2637	2503	2480	2914	3047	2133
Read length mean (b)	98.91	98.83	98.58	99.02	98.84	98.61	98.77	98.58	98.79	98.74	98.69	98.65
Read length median (b)	101	101	101	101	101	101	101	101	101	101	101	101
Effective bases on target (Mb) ⑥	1399	1084	999	1279	1195	1352	1355	1077	1359	1407	1559	1083
Effective bases near target (Mb) ⑦	440	342	355	405	380	438	448	327	445	430	450	342
Effective bases on or near target (Mb) ⑧	1839	1426	1354	1683	1575	1790	1804	1403	1804	1837	2009	1425
Fraction of effective bases on target (%) (⑥/⑤)	52.54	41.67	46.32	49.70	56.25	51.14	51.38	43.01	54.78	48.30	51.18	50.75
Fraction of effective bases near target (%) (⑦/⑤)	16.52	13.14	16.45	15.73	17.88	16.56	17.00	13.05	17.96	14.75	14.77	16.05
Fraction of effective bases on or near target (%) (⑧/⑤)	69.06	54.82	62.78	65.43	74.12	67.70	68.38	56.06	72.74	63.05	65.95	66.80
Average sequencing depth on target (⑥/①)	445.06	344.89	317.89	406.72	380.13	430.01	431.06	342.50	432.12	447.66	495.99	344.37
Average sequencing depth near target (⑦/②)	116.05	90.22	93.63	106.76	100.21	115.48	118.31	86.16	117.51	113.43	118.68	90.33
Average sequencing depth on or near target (⑧/③)	265.21	205.68	195.30	242.75	227.11	258.07	260.10	202.38	260.14	264.96	289.74	205.50
Base covered on target ⑨	3143221	3143152	3142784	3143540	3143280	3143263	3143277	3142887	3143338	3143035	3143296	3142818
Coverage of target region (%) (⑨/①)	99.98	99.98	99.97	99.99	99.98	99.98	99.98	99.97	99.98	99.98	99.98	99.97
Base covered near target ⑩	3775671	3773869	3774076	3771915	3768892	3773823	3776942	3760218	3776060	3766215	3762031	3762823
Coverage of near target region (%) (⑩/②)	99.60	99.56	99.56	99.51	99.43	99.56	99.64	99.20	99.62	99.36	99.25	99.27
Fraction of target covered with at least 15 × (%)	99.72	99.62	99.59	99.69	99.65	99.68	99.70	99.55	99.69	99.60	99.68	99.58
Fraction of target covered with at least 8 × (%)	99.86	99.78	99.78	99.83	99.81	99.82	99.83	99.76	99.83	99.78	99.83	99.77
Fraction of target covered with at least 4 × (%)	99.93	99.89	99.89	99.90	99.90	99.90	99.91	99.87	99.92	99.89	99.91	99.89
Fraction of flanking region covered with at least 15 × (%)	86.88	84.24	87.52	85.84	84.62	87.92	89.85	79.85	90.17	84.50	80.72	82.36
Fraction of flanking region covered with at least 8 × (%)	94.32	93.13	94.66	93.66	92.95	94.70	95.77	89.93	95.87	92.55	89.96	91.39
Fraction of flanking region covered with at least 4 × (%)	97.85	97.33	97.91	97.50	97.15	97.87	98.27	95.76	98.32	96.86	95.71	96.37

The target region, as covered by the SureSelect Human Kinome Kit, was approx. 3.1 Mb. Near target region was 200 bases forward and backward of the target region. "⑥/⑤" means "each number of ⑥ devided by each number of ⑤"; "⑦/⑤" means "each number of ⑦ devided by each number of ⑤"; "⑧/⑤" means "each number of ⑧ devided by each number of ⑤"; "⑥/①" means "each number of ⑥ devided by each number of ①"; "⑦/②" means "each number of ⑦ devided by each number of ②"; "⑧/③" means "each number of ⑧ devided by each number of ③"; "⑨/①" means "each number of ⑨ devided by each number of ①"; "⑩/②" means "each number of ⑩ devided by each number of ②". NCC1: The matched adjacent non-cancerous tissue; CC1: The starting cancer tissue of the induced pluripotent stem cell lines; CC1-1 to CC1-25: Each induced pluripotent stem cell line.