Circulating Tumor DNA Using Tagged Targeted Deep Sequencing to Assess Minimal Residual Disease in Breast Cancer Patients Undergoing Neoadjuvant Chemotherapy

Table 4

Mutational analysis by MPS and tTDS on FFPE biopsy, comparison between MPS and tTDS on FFPE biopsies samples at diagnosis.

		Target mutation selected by MPS (% frequency)	Target mutations selected by tTDS (% VAF)
		AmpliSeq CCP w1.1—Tumor-Normal pair	Oncomine TagSeq Breast v2 Liquid Biopsy w2.1—Single Sample
Relapsed patients	UPN 1	TP 53 p.Tyr205Cys (18)^#	TP 53 p.R273H(0.3); ESR1 P.V392I (0.4); TP53 p.V157I
			(0.4); TP53 p.P82L(0.4)
	UPN 6	PIK3CA p.His1047Arg (29.7)	PIK3CA p.H1047R (23.2); Tp53 p. R282W (1.1)
	UPN 10	GATA3 p.Pro409fs (28.0)^#
		TP53c.919 + 1G>C p.?chr 17:7577018(43.0)	TP53c.919 + 1G>C p.?chr 17:7577018 (50.0)
	UPN 8	PIK3CA p.E542K (5.9)	PIK3CA p.E542K (1.5)
Nonrelapsed patients	UPN 2	PIK3CA p.Glu542Gly (9.0)	PIK3CA p.Glu542Gly (8.4)
	UPN 4	TP 53 p.Trp53Thr (21.0)^#	ERBB3 p. V104M(0.5); TP53 R248W (0.3)
	UPN 5	Nondetected SNV	Nondetected SNV/ERBB2 gain
	UPN 7	TP53c.994 − 1G>C; chr17:7574034 p? (48.2)	TP53 chr17:7574034 p? (48.6); TP53 p. R273H (0.3)
			CCND1 gain
	UPN 9	Nondetected SNV	FBXW7 p.S582L (0.6)

^#Mutation not present in Oncomine Breast cfDNA panel.