Table 4.

Coding mutations in the HPV-negative tumor.

Chr	Position	Reference allele	Tumor allele	Zygosity	dbSNP ID	Region	Type	Gene	Transcript name	Exon	CDS position	Protein change	Stansky*	Agrawal**
2	73679256	C	G	Homo		Exonic	Nonsynonymous	ALMS1	NM_015120	8	c.C5599G	p.L1867V	Yes
10	37451586	G	A	Hetero	rs12766884	Exonic	Nonsynonymous	ANKRD30A	NM_052997	16	c.G1742A	p.G581E	Yes
9	33385733	C	T	Hetero		Exonic	Nonsynonymous	AQP7	NM_001170	7	c.G657A	p.M219I
17	42271663	G	C	Homo		Exonic	Nonsynonymous	ATXN7L3	NM_001098833	12	c.C1012G	p.P338A
6	136599913	A	T	Hetero		Exonic	Nonsynonymous	BCLAF1	NM_001077441	4	c.T106A	p.S36T
1	26646726	A	G	Hetero	rs1071849	Exonic	Nonsynonymous	CD52	NM_001803	2	c.A119G	p.N40S
1	26646730	A	G	Homo	rs17645	Exonic	Nonsynonymous	CD52	NM_001803	2	c.A123G	p.I41M
19	42213948	C	G	Hetero		Exonic	Nonsynonymous	CEACAM5	NM_004363	2	c.C414G	p.F138L
12	31242362	A	G	Hetero	rs3950588	Exonic	Nonsynonymous	DDX11	NM_030653	8	c.A818G	p.K273R	Yes
15	83657820	G	C	Hetero		Exonic	Stoploss	FAM103A1	NM_031452	3	c.G50C	p.X17S
6	76023130	T	G	Homo		Exonic	Nonsynonymous	FILIP1	NM_015687	5	c.A2418C	p.Q806H,	Yes
1	152191709	C	G	Hetero	rs6662450	Exonic	Nonsynonymous	HRNR	NM_001009931	3	c.G2396C	p.S799T	Yes
9	21202136	A	G	Hetero	rs145794215	Exonic	Nonsynonymous	IFNA7	NM_021057	1	c.T29C	p.V10A
7	100635103	A	C	Hetero		Exonic	Nonsynonymous	MUC12	NM_001164462	2	c.A1259C	p.E420A
17	10404435	T	G	Hetero		Exonic	Nonsynonymous	MYH1	NM_005963	27	c.A3730C	p.K1244Q	Yes	Yes
18	47364086	C	T	Hetero		Exonic	Nonsynonymous	MYO5B	NM_001080467	37	c.G4939A	p.D1647N	Yes
12	57106659	C	G	Hetero		Exonic	Nonsynonymous	NACA	NM_001113203	10	c.G2674C	p.E892Q	Yes
1	21795333	C	G	Hetero		Exonic	Nonsynonymous	NBPF3	NM_032264	3	c.C286G	p.Q96E	Yes	Yes
10	115370274	T	C	Homo	rs10749138	Exonic	Nonsynonymous	NRAP	NM_006175	30	c.A3442G	p.I1148V	Yes	Yes
11	48346916	G	C	Homo	rs77069283	Exonic	Nonsynonymous	OR4C3	NM_001004702	1	c.G424C	p.V142L	Yes
11	4608046	T	A	Hetero		Exonic	Nonsynonymous	OR52I2	NM_001005170	1	c.T4A	p.C2S
11	56128081	A	G	Hetero	rs10896290	Exonic	Nonsynonymous	OR8J1	NM_001005205	1	c.A359G	p.Y120C	Yes
11	56143823	G	A	Homo	rs77614949	Exonic	Nonsynonymous	OR8U1, OR8U8	NM_001005204	1	c.G724A	p.G242S
X	82764042	G	C	Hetero	rs5921979	Exonic	Nonsynonymous	POU3F4	NM_000307	1	c.G710C	p.G237A	Yes
19	43709656	C	G	Homo	rs11883278	Exonic	Nonsynonymous	PSG4	NM_213633	1	c.G33C	p.Q11H	Yes
14	21511497	C	T	Homo	rs1243469	Exonic	Nonsynonymous	RNASE7	NM_032572	2	c.C346T	p.H116Y
1	153004853	C	T	Homo	rs3795382	Exonic	Nonsynonymous	SPRR1B	NM_003125	2	c.C32T	p.T11I
6	33410273	T	A	Homo		Splicing	NA	SYNGAP1	NM_006772	14	c.2336+2T>A
12	11174327	C	T	Hetero	rs72475481	Exonic	Nonsynonymous	TAS2R19	NM_176888	1	c.G844A	p.G282R
12	11183676	C	T	Hetero	rs73049072	Exonic	Nonsynonymous	TAS2R31	NM_176885	1	c.G259A	p.V87I
7	35244086	A	T	Hetero		Exonic	Nonsynonymous	TBX20	NM_001077653	7	c.T999A	p.N333K
21	10910347	A	G	Hetero	rs150482	Exonic	Nonsynonymous	TPTE	NM_199261	22	c.T1409C	p.L470P
7	99669149	C	T	Hetero		Exonic	Nonsynonymous	ZNF3	NM_032924	6	c.G958A	p.A320T
19	57839150	A	G	Homo	rs8100491	Exonic	Nonsynonymous	ZNF543	NM_213598	4	c.A320G	p.Q107R	Yes
12	124497119	T	A	Hetero		Exonic	Nonsynonymous	ZNF664	NM_001204298	5	c.T428A	p.F143Y
19	12501852	C	T	Hetero		Exonic	Nonsynonymous	ZNF799	NM_001080821	4	c.G1360A	p.G454R	Yes

Chr: chromosome, *mutations present in Stransky et al., Science 2011 [7], **mutations present in Agrawal et al., Science 2011 [6], Homo: homozygous, Hetero: heterozygous.