Table 2.

NGS QC Metrics and Results in the Analytical Validation Study for NCI-MATCH NGS Assay

NGS QC metrics	Threshold, call	Failed samples, n	Flagged samples, n	Mean (range)
				FNLCR	MDACC	MGH	YSM	Four laboratories
DNA library yield (pmol/L)	≥20, Fail	0	NA	1966 (112–7720)	1638 (36–13,786)	1556 (90–4994)	1734 (117–9306)	1724 (36–13,786)
RNA library yield (pmol/L)	≥20, Fail	0	NA	2443 (192–7892)	1827 (137–12,621)	2099 (198–5195)	2408 (188–8680)	2197 (137–12,621)
DNA total reads (million counts)	≥3, Flag	NA	8	4.20 (0.90–5.51)	4.30 (0.91–6.10)	4.37 (0.67–5.17)	5.04 (1.82–6.22)	4.46 (0.67–6.22)
DNA uniformity (%)∗	≥80, Fail; ≥90, flag	2	52	93.70 (85.65–96.61)	93.99 (80.98–98.70)	95.31 (84.81–98.00)	91.75 (67.66–97.44)	93.67 (67.66–98.70)
DNA percentage of amplicons 100× (%)	≥90, Fail	6†	NA	97.80 (81.00–99.05)	98.39 (85.93–99.49)	98.63 (85.22–99.45)	97.78 (85.89–99.21)	98.15 (81.00–99.49)
DNA MAPD‡	≤0.9, Fail	0	NA	0.277 (0.14–0.574)	0.403 (0.196–0.762)	0.27 (0.134–0.534)	0.385 (0.225–0.691)	0.333 (0.134–0.762)
RNA total reads (thousand counts)	≥100, Flag	NA	0	918 (405–1313)	925 (186–2266)	1037 (510–2725)	1112 (182–2884)	998 (182–2884)
RNA read length (bp)	≥40, Flag	NA	0	93 (77–99)	98 (74–112)	98 (84–116)	96 (79–104)	96 (74–116)

FNLCR, Frederick National Laboratory for Cancer Research; MAPD, median of the absolute values of all pairwise differences; MDACC, MD Anderson Cancer Center; MGH, Massachusetts General Hospital; NA, not applicable; QC, quality control; YSM, Yale University School of Medicine.

^∗Uniformity is the percentage of bases in all amplicon-targeted regions covered by at least 0.2× the mean base read depth.

^†Two of 6 samples failed by percentage of amplicon >100× also failed by uniformity.

^‡The MAPD between log2 ratios of two adjacent amplicons (except at the beginning and end of a chromosome).