A Pilot Study Comparing HPV-Positive and HPV-Negative Head and Neck Squamous Cell Carcinomas by Whole Exome Sequencing

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.