Table 2. Effect of second-tier NGS... | Rockefeller University Press

Table 2.

Effect of second-tier NGS approaches on the PPV for SCID and other T cell deficiencies with a genetic cause

	First-tier TREC results^{^a}, n		Referrals, n			Performance, %
	≤2	>2 and ≤10^{^b}	Total	Genetic findings	False-positive	Reduction in referrals	PPV
Current NBS	22	46	68	15	53	NA	22.1%
Second-tier NGS
Without safety net^{^c}	22	46	16	16	0	76.5%	100%^{^e}
With safety net^{^d}	22	46	29	16	13	57.4%	55.2%^{^e}

	First-tier TREC results^a, n		Referrals, n			Performance, %
	≤2	>2 and ≤10^b	Total	Genetic findings	False-positive	Reduction in referrals	PPV
Current NBS	22	46	68	15	53	NA	22.1%
Second-tier NGS
Without safety net^c	22	46	16	16	0	76.5%	100%^e
With safety net^d	22	46	29	16	13	57.4%	55.2%^e

NA, not applicable.

Copies/3.2 mm DBS punch (ImmunoIVD).

Five newborns with TRECs >2 and ≤10 were indirectly referred after repeat analysis on a second NBS card according to the adjusted referral schema after national implementation (see Materials and methods).

Second-tier NGS algorithm without a safety net, where only newborns with positive second-tier NGS results would be referred (Fig. 3 B).

Second-tier NGS algorithm with a safety net, where newborns with TRECs ≤2 would be referred directly, and those with TRECs >2 and ≤10 only if NGS results are positive (Fig. 3 C).

Considering all identified cases true-positive, although one new case was not (yet) diagnostically confirmed.

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