Extended Data Table 1. Validation of mutation calling.

To determine validation rate for mutation calling, a custom capture SureSelect design was used to sequence selected coding/non-coding loci to an average depth of 360-2000X. For loci with sufficient depth (>=20X), the validation rate (the proportion of somatic variants) was calculated as described in Extended Data Table 2 and Supplementary Information, section 3c. On average 95% and 86% of the substitutions and indels, respectively, were somatic. Validation for rearrangement calls was performed by PCR-gel electrophoresis, as described in Supplementary Information, section 3d. PCR-gel experiments yielded a high validation rate for three of the four patients included in the validation. For A22, there was a high rate of PCR failure. For this sample, we therefore assessed the veracity of the breakpoints by visual inspection of the associated copy number segments and confirmed that 82% were high-confidence events resulting in visible copy number changes.

	Patient	# coding subs	# subs from mutation clusters	# total unique subs	# subs with coverage*	% somatic
substitutions	A10	109	163	270	269	90.70%
	A22	97	265	356	356	98.60%
	A29	76	70	144	143	93.00%
	A31	43	109	150	150	89.30%
	A32	74	388	450	450	97.80%
	A12	54	144	192	191	88.50%
	A24	50	147	196	196	97.00%
	A34	258	554	800	795	99.20%
	A21	72	203	275	273	96.30%
	A17	155	377	523	522	100%
	AVERAGE					95.04%
	Patient	# coding indels	# indels from mutation clusters	# total unique indels	# indels with coverage*	% somatic
indels	A10	11	145	156	155	80.70%
	A22	9	74	80	79	78.50%
	A29	6	44	49	49	87.80%
	A31	5	48	52	51	82.40%
	A32	11	93	101	100	86%
	A12	14	76	84	83	86.80%
	A24	9	66	73	72	83.30%
	A34	43	258	284	282	96.10%
	A21	9	85	89	88	81.80%
	A17	15	123	123	122	99.20%
	AVERAGE					86.26%
	Patient	# rearrs validated	PCR failed	% somatic
Rearrangements	A22	49	21	57% (82% with rearrs confirmed by the visual inspection of copy number changes)
	A31	21	1	95%
	A32	32	1	96%
	A24	27	3	89%