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

doi:10.4252/wjsc.v9.i5.77

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World Journal of Stem Cells

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1948-0210

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Baishideng Publishing Group Inc, 7041 Koll Center Parkway, Suite 160, Pleasanton, CA 94566, USA

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World J Stem Cells. May 26, 2017; 9(5): 77-88
Published online May 26, 2017. doi: 10.4252/wjsc.v9.i5.77

Table 4 Sequence depth

	Theoretical depth¹		Observed depth²
Sample	Total bases (Mb)	Depth³	Effective bases on target (Mb)	Average depth on target
NCC1	3689	1173.31	1399	445.06
CC1	3375	1073.43	1084	344.89
CC1-1	2635	838.23	999	317.89
CC1-2	3581	1138.94	1279	406.72
CC1-7	2986	949.69	1195	380.13
CC1-8	3497	1112.35	1352	430.01
CC1-9	3366	1070.72	1355	431.06
CC1-11	3122	993.07	1077	342.50
CC1-12	3109	988.94	1359	432.12
CC1-17	3840	1221.45	1407	447.66
CC1-18	3989	1268.76	1559	495.99
CC1-25	3129	995.45	1083	344.37

¹Theoretical depth calculated from the total number of bases obtained by DNA sequencing;

²Observed depth used for single-nucleotide variant/InDel identification;

³Theoretical depth [Total Bases (Mb)]/[Target region (Mb)]. Target region: SureSelect Human Kinome Kit (approximately 3.1 Mb). 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.

Citation: Ishikawa T. Next-generation sequencing traces human induced pluripotent stem cell lines clonally generated from heterogeneous cancer tissue. World J Stem Cells 2017; 9(5): 77-88
URL: https://www.wjgnet.com/1948-0210/full/v9/i5/77.htm
DOI: https://dx.doi.org/10.4252/wjsc.v9.i5.77