Table 1.

Mutation-reactive T cells in metastatic GI cancers. NE, not evaluated.

Patient ID	Age/sex	Tumor type	Number of mutations†	Number of mutations assessed‡	Number of TIL cultures assessed	Number of TIL cultures with mutation reactivity§	Mutated protein recognized	Amino acid change	T cell type	Frequency of mutation-reactive TCR in tumor (%)	Rank of mutation-reactive TCR in tumor
3737*	45/F	Bile duct	26	25	5	5	ERBB2IP	E805G	CD4	0.009	2718
								E805G	CD4	0.375	10
3812	44/M	Bile duct	48	179	5	0	–	–	–	–	–
3942	46/F	Rectal	155	144	6	2	NUP98	A359D	CD8	0.67	5
						4	KARS	D356	CD8	0.020	1143
						3	GPD2	E426K	CD4	0.037	862
3948	48/M	Esophageal	84	211	5	2	PLEC	E1179K	CD4	NE	NE
						2	XPO7	P274S	CD4	NE	NE
						2	AKAP2	Q418K	CD4	NE	NE
3971	49/M	Colon	118	118	23	11	CASP8	F67V	CD8	1.25	3
3978	46/F	Bile duct	39	38	9∥	1¶	ITGB4	S1002I	CD4	NE	NE
3995	50/M	Colon	58	154	19∥	2	TUBGCP2	P293L	CD8	0.023	1056
						15	RNF213	N1702S	CD8	0.60	15
						2	KRAS	G12D	CD8	0.055	527
4007	52/M	Colon	134	264	23	4	SKIV2L	R653H	CD8	0.090	121
								R653H	CD8	0.014	887
						5	H3F3B	A48T	CD8	1.19	4
4032	46/M	Colon	101	222	24	12	API5	R243Q	CD8	0.083	126
								R243Q	CD8	0.059	187
						1	RNF10	E572K	CD8	0.030	423
						7	PHLPP1	G566E	CD8	0.081	129
4069	57/M	Pancreatic	10	97	15	1	ZFYVE27	R6H	CD8	0.088	278

^*Patient 3737 was previously reported in (14).

^†As determined by Personal Genome Diagnostics (PGDx) from whole-exome sequencing (17).

^‡determined when mutation call criteria was relaxed (17). The mutation call criteria was not relaxed for patients 3737, 3942, and 3978.

^§Reactivity was determined with IFN-γ ELISPOT or flow cytometry for 4-1BB or OX40 up-regulation upon coculture with mutated TMGs or peptides.

^∥The indicated number of TIL cultures includes T cell populations that were sorted and expanded from a tumor digest based on PD-1 expression as described in the supplementary materials.

^¶Identified from a FACS-purified TIL population as described in the supplementary text.