TABLE 3.

Germline and somatic mutations determined in the tumor tissue samples

ID	Chr	Region	Type	Reference	Allele	Frequency	Read count	Read coverage	Gene name	Amino acid change
HPV‐positive responder
517
	3	178927410	SNV	A	G	55.3	3854	6983	PIK3CA	Ile391Met
	17	7579472	SNV	G	C	99.7	3901	3910	TP53	Pro72Arg
558
	4	55972974	SNV	T	A	99.8	1113	1115	KDR	Gln472His
	4	55979558	SNV	C	T	99.8	938	940	KDR	Val297Ile
	17	7579472	SNV	G	C	99.9	3901	1351	TP53	Pro72Arg
738
	4	55972974	SNV	T	A	50.1	584	1162	KDR	Gln472His
	4	55979558	SNV	C	T	46.6	410	884	KDR	Val297Ile
	12	121432117	SNV	G	C	58.6	34	56	HNF1A	Gly226Ala
	17	7579472	SNV	G	C	100	1364	1364	TP53	Pro72Arg
744
	4	153247289	SNV	G	C	30.5	621	2026	FBXW7	Arg505Gly
	9	21971160	SNV	G	C	54.4	506	779	CDKN2A	Arg81Gly
	12	121432117	SNV	G	C	43.8	27	80	HNF1A	Gly226Ala
	17	7574012	SNV	C	T	19.4	239	1226	TP53	Glu339Lys
	17	7579472	SNV	G	C	99.9	2209	2211	TP53	Pro72Arg
749
	3	178936082	SNV	G	A	16.3	1415	8656	PIK3CA	Glu542Lys
	4	55972974	SNV	T	A	49.1	1113	2268	KDR	Gln472His
	17	7579472	SNV	G	C	52.5	951	1814	TP53	Pro72Arg
756
	4	55979558	SNV	C	T	100	983	983	KDR	Val297Ile
780
	3	178927410	SNV	A	G	48.8	1564	3207	PIK3CA	Ile391Met
	4	55593464	SNV	A	C	50.1	1489	2980	KIT	Met541Leu
	12	121432117	SNV	G	C	92.9	128	137	HNF1A	Gly226Ala
	17	7579472	SNV	G	C	99.9	2131	2133	TP53	Pro72Arg
C3‐32
	3	178927410	SNV	A	G	23.7	3367	14253	PIK3CA	Ile391Met
	4	55979558	SNV	C	T	46.3	1315	2845	KDR	Val297Ile
	10	89692905	SNV	G	A	20	546	2800	PTEN	Arg130Gln
	17	7579548	SNV	G	A	48.4	2261	4666	TP53	Pro47Ser
HPV‐positive nonresponder
668
	10	89720779̂89720780	Insertion	‐	A	41.5	1847	4456	PTEN	Asn311fs
	12	121432117	SNV	G	C	51.7	58	113	HNF1A	Gly226Ala
	17	7579472	SNV	G	C	51.9	1684	3260	TP53	Pro72Arg
789
	3	178927410	SNV	A	G	56	4137	7385	PIK3CA	Ile391Met
	4	55979558	SNV	C	T	48	1237	2580	KDR	Val297Ile
	12	121432117	SNV	G	C	93.8	145	153	HNF1A	Gly226Ala
	17	7579472	SNV	G	C	45.2	1231	2746	TP53	Pro72Arg
807
	4	55593464	SNV	A	C	49.7	2092	4225	KIT	Met541Leu
	4	55972974	SNV	T	A	52.1	1326	2550	KDR	Gln472His
	12	121432117	SNV	G	C	96.3	162	159	HNF1A	Gly226Ala
	17	7579472	SNV	G	C	99.9	3057	3059	TP53	Pro72Arg
HPV‐negative responder
723
	4	55979558	SNV	C	T	46.9	714	1521	KDR	Val297Ile
	5	112173899	SNV	C	T	100	1382	1382	APC	Pro870Ser
766
	4	55972974	SNV	T	A	38.7	859	2213	KDR	Gln472His
	17	7578382	SNV	G	T	69.5	2047	2910	TP53	Ser183*
	17	7579472	SNV	G	C	17.3	259	1520	TP53	Pro72Arg
C3‐15
	12	121432117	SNV	G	C	44.3	85	192	HNF1A	Gly226Ala
	17	7578263	SNV	G	A	90.3	6664	7347	TP53	Arg196*
	17	7579472	SNV	G	C	5.5	158	2702	TP53	Pro72Arg
HPV‐negative nonresponder
460
	11	534289	SNV	C	A	36.9	1956	5296	HRAS	Gly12Cys
	12	121432117	SNV	G	C	42.7	58	132	HNF1A	Gly226Ala
	17	7576872	Deletion	C	‐	27	889	3260	TP53	Gly325fs
	17	7577574	SNV	T	C	22.3	294	1317	TP53	Tyr236Cys
	17	7579472	SNV	G	C	99.8	2134	2136	TP53	Pro72Arg
499
	4	55979558	SNV	C	T	48.3	417	859	KDR	Val297Ile
	9	21971017	SNV	G	C	49.8	879	1771	CDKN2A	Pro114Arg
	12	121432117	SNV	G	C	96.9	120	123	HNF1A	Gly226Ala
	17	7577094	SNV	G	A	48.1	1119	2331	TP53	Arg282Trp
	17	7579472	SNV	G	C	25	257	1064	TP53	Pro72Arg
606
	4	55972974	SNV	T	A	43.9	664	1509	KDR	Gln472His
	17	7577046	SNV	C	A	5.9	158	2744	TP53	Glu298*
662
	4	55972974	SNV	T	A	44.6	765	1714	KDR	Gln472His
	17	7579442	Deletion	G	‐	21.4	358	1672	TP53	Pro82fs
767
	9	21970979	SNV	C	A	52	3112	5963	CDKN2A	Ala127Ser
817
	4	55972946	SNV	A	G	33.4	370	1111	KDR	Cys482Arg
	4	55972974	SNV	T	A	33.9	375	1109	KDR	Gln472His
	17	7576853	SNV	C	A	56.5	1646	2906	TP53	Gln331His
	17	7579472	SNV	G	C	80.5	914	1153	TP53	Pro72Arg
836
	4	55972974	SNV	T	A	51.3	924	1798	KDR	Gln472His
	4	153247288	SNV	C	A	30.9	762	2467	FBXW7	Arg505Leu
	12	121432117	SNV	G	C	68.9	58	84	HNF1A	Gly226Ala
	17	7577121	SNV	G	A	38.7	1460	3773	TP53	Arg273Cys
	17	7579472	SNV	G	C	99.9	1839	1841	TP53	Pro72Arg
C3‐12
	4	55972974	SNV	T	A	52.7	1130	2148	KDR	Gln472His
	5	112175711	SNV	G	A	45	1220	2706	APC	Ala1474Thr
	12	121432117	SNV	G	C	54.8	78	143	HNF1A	Gly226Ala
	17	7579472	SNV	G	C	99.8	2060	2064	TP53	Pro72Arg

Note: Samples were segregated based on human papillomavirus (HPV) status and response to treatment.