Table 2.

Effect of Tumor Sample Coverage on Gene-Level Log2(FC) and MAD

Sample	Gene and alteration type	Tumor purity, %	Coverage	Sample MAD	TCH solid SCNA log2(FC)	TCH solid SCNA call
T01	CCND1 amplification	70	834×	0.22	3.78	Yes
			700×	0.22	3.78
			600×	0.22	3.78
			500×	0.23	3.79
			400×	0.23	3.78
			300×	0.24	3.77
			200×	0.26	3.77
			100×	0.3	3.77
			50×	0.37∗	3.77
			25×	0.48∗	3.77
			10×	0.69∗	3.73
			5×	0.99∗	3.72
			1×	6.14∗	4.67
T07	SMARCB1 homozygous deletion	90	337×	0.23	−3.97	Yes
			200×	0.26	−3.99
			100×	0.31	−4.07
			50×	0.4∗	−3.94
			25×	0.52∗	−3.56
			10×	0.78∗	−3.05
			5×	1.1∗	−1.08
			1×	8.43∗	0.03∗	No
T06	PTEN heterozygous deletion	80	104×	0.26	−0.9	Yes
			50×	0.32	−0.9
			25×	0.42∗	−0.88
			10×	0.61∗	−0.93
			5×	0.86∗	−1.07
			1×	4.25∗	1.02∗	No

MAD, median absolute deviation; TCH, Texas Children's Hospital.

^∗The measure fails to be within the expected limits. Tumor purity estimated by pathology review.