Quality assessment of a clinical next-generation sequencing melanoma panel within the Italian Melanoma Intergroup (IMI)

Table 3 NGS data quality

		ID #1	ID #2	ID #3	ID #4	ID #5	ID #6	ID #7	ID #8	ID #9	ID #10	ID #11
A	N°Amplicons ≥500x	322	318	320	317	324	313	331	318	225	302	295
	% Amplicons ≥500x	93.9	92.7	93.3	92.4	94.5	91.3	96.5	92.7	65.6	88.0	86.0
	N°Amplicons ≥200x	337	334	332	336	334	331	338	335	240	327	328
	% Amplicons ≥200x	98.3	97.4	96.8	98.0	97.4	96.5	98.5	97.7	70.0	95.3	95.6
	N°Amplicons <100x	4	6	6	5	4	10	5	5	91	6	8
	% Amplicons <100X	1.2	1,7	1,7	1,5	1,2	2,9	1,5	1,5	26,5	1,7	2,3
	Average amplicon coverage	3,93	4002	3375	3,26	3522	3126	4083	3302	3714	2146	1737
	Uniformity (%)	90.1	89.8	88.2	91.15	91.44	82.3	92.5	90.7	65.1	91.1	91.8
B	N°Amplicons ≥500x	337	340	340	338	341	290	289	294	338	302	254
	% Amplicons ≥500x	98.3	99.1	99.1	98.5	99.4	84.5	84.3	85.7	98.5	88.0	74.1
	N°Amplicons ≥200x	342	342	342	342	343	330	332	338	339	331	324
	% Amplicons ≥200x	99.7	99.7	99.7	99.7	100.0	96.2	96.8	98.5	98.8	97.1	94.5
	N°Amplicons <100x	0	0	0	0	0	6	3	4	3	5	7
	% Amplicons <100x	0.0	0.0	0.0	0.0	0.0	1.7	0.9	1.2	0.9	1.5	2.0
	Average amplicon coverage	9,75	15,009	12,239	11,254	14,842	967	1137	1102	1647	1308	1083
	Uniformity (%)	94.7	92.7	93.9	96.2	93.9	95.6	96.0	97.1	92.0	95.7	93.8
C	N°Amplicons ≥500x	307	277	307	306	321	240	310	310	209	310	339
	% Amplicons ≥500x	89.5	80.8	89.5	89.2	93.6	70.0	90.4	90.4	60.9	90.4	98.8
	N°Amplicons ≥200x	336	326	336	335	337	300	336	334	286	334	340
	% Amplicons ≥200x	98.0	95.0	98.0	97.7	98.3	87.5	98.0	97.4	83.4	97.4	99.1
	N°Amplicons <100x	3	11	4	4	4	23	4	6	26	2	2
	% Amplicons <100x	0.9	3.2	1.2	1.2	1.2	6,7	1,2	1,7	7,6	0,6	0,6
	Average amplicon coverage	1,91	1267	1825	1617	2016	1531	2085	2292	1217	1387	3,73
	Uniformity (%)	93.9	93.3	93.0	94.2	95.6	81.2	92.7	91.3	80.5	94.2	96.2

The table shows for each NGS platforms ((A) PGM™ platform, (B) Proton™ platform, and (C) MiSeq™ Illumina platform) data quality for the eleven tumor samples in terms of uniformity (the percentage of bases in all target regions covered by at least 20% of the average base coverage depth reads), average amplicon coverage depth and number (%) of amplicons at different coverage

ISSN: 1746-1596