Table 2

Number of reads containing mutant versus wildtype base at position of interest

Tissue type	Fluidigm Access Array run 1							Fluidigm Access Array run 2							HaloPlex (standard)							HaloPlex^HS							% Average reads
Patient 1: c.5125G>A	Total reads	T	G	C	A	WT%	Mut%	Total reads	T	G	C	A	WT%	Mut%	Total reads	T	G	C	A	WT%	Mut%	Total reads*	T	G	C	A	WT%	Mut%	WT average	Mutant average
PPB type II†	1102	0	432	0	670	39.20	60.80	6563	4	4404	2	2153	67.10	32.81	10	0	6	0	4	60.0	40.0	73*	0	40	1	32	54.79	43.84	55.27	44.36
Skin fibroblasts (cultured)	5313	3	5027	2	281	94.62	5.29	22 907	10	21 154	4	1739	92.35	7.59	317	0	292	0	24	92.11	7.57	568*	1	541	2	24	95.25	4.23	93.58	6.17
Saliva DNA	5463	5	5178	1	279	94.78	5.11	26 511	6	26 487	4	14	99.91	0.05	1208	0	1184	0	24	98.01	1.99	792*	0	770	0	22	97.22	2.78	97.48	2.48

Patient 2: c.5437G>C	Total reads	T	G	C	A	WT%	Mut%	Total reads	T	G	C	A	WT%	Mut%	Total reads	T	G	C	A	WT%	Mut%	Total reads*	T	G	C	A	WT%	Mut%	WT average	Mutant average
Blood DNA	7987	4	7978	0	5	99.89	0	68 572	24	68 503	14	31	99.90	0.02	3223	6	3213	4	0	99.69	0.12	9650*	4	9642	4	0	99.92	0.04	99.85	0.05
Saliva DNA	ND	–	–	–	–	–	–	31 414	6	31 254	139	15	99.49	0.44	795	0	793	1	1	99.75	0.13	1972*	1	1966	5	0	99.70	0.25	99.64	0.27
Urine DNA	ND	–	–	–	–	–	–	14 662	5	14 458	195	4	98.61	1.33	821	0	818	2	1	99.63	0.24	3014*	2	3000	12	0	99.54	0.40	99.26	0.66

Patient 3: c.5439G>C	Total reads	T	G	C	A	WT%	Mut%	Total reads	T	G	C	A	WT%	Mut%	Total reads	T	G	C	A	WT%	Mut%	Total reads*	T	G	C	A	WT%	Mut%	WT average	Mutant average
Normal right kidney (#1)†	ND	–	–	–	–	–	–	656	0	656	0	0	100	0	100	0	89	11	0	89.00	11.00	2303*	0	2228	75	0	96.74	3.26	95.25	4.75
Normal right kidney (#2)†	1494	0	1020	474	0	68.27	31.73	3863	1	3791	71	0	98.14	1.84	102	0	90	12	0	88.24	11.76	739*	0	643	95	0	87.01	12.86	85.41	14.55
Blood DNA	ND	–	–	–	–	–	–	ND	–	–	–	–	–	–	ND	–	–	–	–	–	–	2455*	1	2454	0	0	100	0	–	–

Patient 4: c.5425G>A	Total reads	T	G	C	A	WT%	Mut%	Total reads	T	G	C	A	WT%	Mut%	Total reads	T	G	C	A	WT%	Mut%	Total reads*	T	G	C	A	WT%	Mut%	WT average	Mutant average
Reactive right lung†	3580	0	3336	0	244	93.18	6.82	7543	0	6541	0	1002	86.72	13.28	1964	2	1937	0	25	98.63	1.27	4401*	1	4091	4	305	92.96	6.93	92.87	7.08
Blood DNA	8266	6	8253	1	6	99.84	0.07	15 501	9	15 481	0	11	99.87	0.00	840	1	838	1	0	99.76	0	16 081*	3	16 073	3	1	99.95	0.01	99.86	0.02
Saliva DNA	ND	–	–	–	–	–	–	ND	–	–	–	–	–	–	647	3	644	0	0	99.54	0	2533*	0	2532	1	0	99.96	0	99.75	0

*Duplicate reads removed (HaloPlex^HS data); -, no data. Wildtype allele at position of interest is italicised and the mutant allele is underlined.
†Formalin-fixed paraffin-embedded samples.
Mut, mutant; ND, not done; PPB, pleuropulmonary blastoma, WT, wildtype.