Table 2. Comparison between the number of variants detected with the MPS and Sanger sequencing technologies.

		PGMa									MiSeqb
Sample	Sangersequencing	Ion shearenzymes			Covaris			NEBNext dsDNAFragmentase			Covaris			NEBNext dsDNAFragmentase				Nextera XT
		vs Sanger	FN	extra	vs Sanger	FN	extra	vs Sanger	FN	extra	vs Sanger	FN	extra	vs Sanger	FN		extra	vs Sanger	FN	extra
1	33	32	1	1	32	1	1	32	1	1	33	–	1	33		–	1	33	–	1
2	13	11	2	1	12	1	1	12	1	1	13	–	1	13		–	1	13	–	1
4	33	32	1	–	31	2	–	31	2	–	33	–	–	33		–	–	33	–	0
9	36	35	1	2	35	1	2	35	1	2	36	–	3	36		–	2	36	–	2
14	57	56	1	–	56	1	–	56	1	–	57	–	1	57		–	1	57	–	–
21	42	40	2	–	41	1	–	41	1	–	41	1	–	41		1	–	41	1	–
Total	214	206	8	4	207	7	4	207	7	4	213	1	6	213		1	6	213

FN: false negative result, extra: additional low allele frequency variants identified compared to Sanger sequencing.

^aIon Torrent PGM results obtained with the TS4.2 software.

^bMiSeq data obtained with the in-house GATK pipeline.