Table 1. Genomic alterations in the Hedgehog pathways genes detected in 19 of 186 GIST patients by the FoundationOne^® assays.

Patient	Hh Pathway Gene	Alteration	Foundation Medicine Category	Allelic Frequency	Genomic Alteration	Depth of NGS Coverage	GIST Driver Gene (s)	KIT/PDGFRΑ Exon(s)	GIST Driver Gene Alteration(s)
1	PTCH1	E44G	VUS	0.88	missense	478	KIT	11	W557_V559>C
1	PTCH1	S827G	VUS	0.89	missense	714	KIT	11	W557_V559>C
2	PTCH1	E44G	VUS	0.85	missense	506	KIT	11, 17	K550_K558del, D820Y
3	PTCH1	R1239Q	VUS	0.51	missense	480	SDHA	-	R171H, R451C
3	PTCH1	E44del	VUS	0.33	inframe indel	621	SDHA	-	R171H, R451C
4	PTCH1	V1418I	VUS	0.51	missense	349	KIT	11, 13	W557_K558del, V654A
5	PTCH1	W1339_R1345del	likely deleterious	0.16	inframe indel	535	KIT	11	W557_K558del
5	PTCH1	E44G	VUS	0.51	missense	359	KIT	11	W557_K558del
6	PTCH1	PTCH1_C9orf153_truncation	likely deleterious		truncation		NF1	-	V1146I
7	PTCH1	S181*	likely deleterious	0.42	nonsense	553	KIT	11	V560D
8	PTCH2	S1189T	VUS	0.61	missense	345	KIT	11, 14	W557_K558del, T670I
9	PTCH2	A531V	VUS	0.46	missense	362	KIT	11, 13	W557_K558>Q, V654A
7	PTCH2	P881Q	VUS	0.11	missense	338	KIT	11	V560D
10	SMO	G16_L17insL	VUS	0.21	inframe indel	439	KIT	9	S501_A502insAY
11	SMO	R671W	VUS	0.51	missense	414	KIT	11	V560E
12	SMO	R726Q	VUS	0.89	missense	310	KIT	11, 17	V560_E561>E, D820V, Y823D
13	SMO	V54M	VUS	0.53	missense	131	PDGFRΑ	18	D842V
14	SUFU	A425V	VUS	0.05	missense	618	WT	-
15	SUFU	R362C	VUS	0.5	missense	479	WT	-
16	GLI1	R293C	VUS	0.46	missense	428	WT	-
15	GLI1	A745V	VUS	0.49	missense	475	WT	-
17	GLI1	splice site 913-1G>A	VUS	0.38	splicing	519	KIT	11	W557_K558del
18	GLI1	G274C	VUS	0.52	missense	923	KIT	11	D579_H580insDPTQLPYD
19	GLI1	P666S	VUS	0.48	missense	705	KIT	9	Y503_F504insAY
19	GLI1	G421S	VUS	0.48	missense	688	KIT	9	Y503_F504insAY

Abbreviations: NGS, next-generation sequencing; VUS, variant of unknown significance; WT, wild type tumor (lacking mutations in KIT, PDGFRA, BRAF, KRAS, HRAS, NF1, and SDH subunits).