Table 2.

Analysis of predicted HLA-A2 binding mutated or tumor associated peptides that trigger activation of tumor-infiltrating lymphocytes and/or are detected in pMHC complexes by MS.

Patient	Mutated epitope	Mutated position	Mutated sequence	Wild type sequence	Predicted HLA-A2 binding by mutated epitope (nM)	Predicted HLA-A2 binding by wild type epitope (nM)	Expression of mutant allele	Expression of gene compared to β-actin (fold)	Detection of mutant epitope on tumor cells by MS	Detection of wild type epitope on tumor cells by MS	Expression of gene compared to β-actin after IFNγ treatment (fold)	Detection of mutant epitope on tumor cells after IFNγ treatment	Detection of wild type epitope on tumor cells after IFNγ treatment
KADA	AGPS 9mer#	2	ALWDRVVDL	APWDRVVDL	18.12	18335.02	65%	3.28	Yes	No	4.14	Yes	No
	ENC1 9mer#	3	YLSELLQTV	YLPELLQTV	2.25	3.1	58%	0.72	Yes	Yes	1.47	Yes	Yes
	KDELR2 9mer	4	ILWIFSIYL	ILWTFSIYL	16.96	4.95	67%	8.07	ND	ND	11.39	ND	ND
	CCT4 9mer	1	FLLDSCTKL	SLLDSCTKL	4.31	23.02v	48%	12.45	Yes	Yes	22.79	Yes	Yes
	MYLIP 9mer	2	RLDAVLMEV	RPDAVLMEV	5.75	6090.18	52%	0.16	No	No	0.36	No	No
	SVIL 9mer	5	YLTDKDFEF	YLTDEDFEF	75.01	156.56	35%	0.62	No	No	0.43	No	No
	SVIL 10mer	5	YLTDKDFEFA	YLTDEDFEFA	13.53	14.11	35%	0.62	No	No	0.43	No	No
	WDR75 9mer	1	FMFVNSLLL	SMFVNSLLL	7.36	62.76	37%	5.18	No	No	9.67	No	No
	Flu M1 9mer	NA£	NA	GILGFVFTL	NA	15.03	NA	NA	NA	NA	NA	NA	NA
ANRU	ETV6 9mer	1	VLWDYVYQL	LLWDYVYQL	2.24	2.16	55%	0.92	No	No	3.68	Yes	Yes
	ETV6 10mer	1	VLWDYVYQLL	LLWDYVYQLL	4.8	4.34	55%	0.92	ND	ND	3.68	ND	ND
	NUP210 9mer	8	AIDAALTFV	AIDAALTSV	17.01	34.36	42%	1.78	No	No	2.17	No	No
	MART 10mer	2*	ELAGIGILTV	EAAGIGILTV	375.16	7627.98	NA	71.4	NA	No	28.91	NA	No
	MART 9mer	NA¤	NA	AAGIGILTV	NA	3448.53	NA	71.4	NA	No	28.91	NA	No
	gp100 9mer	2*	IMDQVPFSV	ITDQVPFSV	5.47	188.19	NA	591	NA	ND	175	NA	ND

^#Undetected by TIL activation.

^£Viral peptide without mutations.

^¤Unmutated peptide.

^*Heteroclitic peptide with optimized aminoacid at mentioned position.

NA, Not applicable; ND, Not determined.