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

Table 5

Mutational analysis by tTDS on ctDNA.

Oncomine Breast liquid Biopsy v2.0 Analysis Ion Reporter: Workflow Oncomine TagSeq Breast v2 Liquid Biopsy w2.1—Single Sample
A		FFPE biopsy (% MAF)	Prerelapse (% MAF)	Relapse (% MAF)
Relapsed patients	UPN1	TP 53 p.R273H(0,3); ESR1 P.V392I (0,4); TP53 p.V157I (0,3); TP53 p.P82L(0,4)	T4_nondetected SNV	T5_nondetected SNV
	UPN6	PIK3CA p.H1047R (23,2); Tp53 p. R282W (1,1)	T5_ PIK3CA H1047R (0,1); PIK3CA E726K (0,2); Tp53 p. R282W (0,1)	T6_PIK3CA H1047R (0,2)
	UPN 10	TP53 c.919 + 1G>C p.? chr17:7577018 (50)N,P	T5_ CCND1 loss; T7_TP53 c.919 + 1G>C p.? chr17:7577018 (0,2)N,P	T8_not available
	UPN 8	PIK3CA p.E542K (1,5)	T4_KRAS G12D (0,1)	T5_G12V(0,4); T6 _G12V (0,2)
B		FFPE biopsy (% MAF)	Follow-up 24 months (T7) (% MAF)
Nonrelapsed patients	UPN2	PIK3CA p.Glu542Gly (8,4)	Nondetected SNV
	UPN 4	ERBB3 p. V104M(0,5); TP53 R248W (0,3)	TP53 p.R248W (3,9); PIK3CA H1047R (0,6)
	UPN 3	Nondetected SNV	Nondetected SNV
	UPN 7	TP53 chr17:7574034 p? (48,6)N,P; TP53 p.R273H(0,3)_CCND1 gain	TP53 p.R273H (1,1); PIK3CA H1047R (0,3); KRAS p.G12A (0,4)
	UPN 5	Nondetected SNV_ERBB2 gain	Nondetected SNV
	UPN9	FBXW7 p.S582L(0,6)	Nondetected SNV

Mutational analysis on ctDNA and FFPE biopsy by tTDS. A: relapsed patients and B: nonrelapsed patients.