Whole genome deep sequencing analysis of cell-free DNA in samples with low tumour content

BMC Cancer

Table 1 HiSeqXTen Sequencing output per sample

Specimen Type	Sample^a	Number of reads	Sequencing Yield (Mb)	% Bases > = Q30	% Duplicated reads	Sequencing Coverage^b
Germline DNA	1084_N0^c	885,589,680	132,838	83.88	15.82	35
	1249_N0	927,175,866	138,149	87.61	37.67	28
	1494_N0	830,442,242	123,736	85.08	27.42	29
	1524_N0	937,319,184	139,661	86.33	25.54	34
	065_N0^c	897,176,584	134,576	85.10	8.30	40
	098_N0^c	1,014,190,632	152,129	86.09	11.31	44
Tumour DNA	1084_T0	1,785,014,202	265,967	82.32	31.09	58
	1249_ T0	1,919,380,364	285,987	83.99	26.70	67
	1494_T0	1,833,108,412	273,133	80.67	22.14	66
	1524_T0	1,819,092,474	271,044	83.42	24.43	65
Plasma DNA	1084_P0	3,978,736,468	592,832	88.76	25.10	97
	1249_P0	3,742,076,682	557,569	87.92	28.30	82
	1494_P0	3,703,572,042	551,832	89.22	29.78	83
	1524_P0	3,993,601,472	595,047	89.77	26.60	93
	065_P0^c	4,247,100,536	637,065	85.56	12.77	112
	098_P0^c	4,145,998,174	621,900	84.70	10.96	116

^aN0 germline, T0 tumour, P0 plasma
^bSequencing coverage was estimated using Isaac [36] provided by the sequencing provider; duplicated reads and overlapping bases are excluded for the coverage calculation
^cSequenced in a separate batch

ISSN: 1471-2407