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Table 1 Shown are the results of exome sequencing in the 12 tumor nodules. Relevant information are given such as the position in thechromosome, the reference and alternative alleles, the type of mutation, the amino acid substitution and variant allele frequency

From: Multi-omics data integration reveals novel drug targets in hepatocellular carcinoma

TUMOR_SAMPLE

NORMAL_SAMPLE

CHROM

POS

REF

ALT

GENE

EFFECT

Alteration (cDNA)

Alteration (AA)

Depth in tumor

Variant allele fraction

368N4

368muscle

1

65050991

C

T

Cryge

missense_variant

c.31G>A

p.Gly11Ser

58

8.80%

357N1

357muscle

1

85577158

G

C

G530012D18Rik

missense_variant

c.283G>C

p.Glu95Gln

15

26.70%

368N2

368muscle

1

86426453

C

A

1700019O17Rik

missense_variant

c.83C>A

p.Ala28Asp

42

7.10%

373N4

373muscle

1

92942579

C

A

Capn10

missense_variant

c.786C>A

p.His262Gln

48

6.30%

373N4

373muscle

1

1.06E+08

C

T

Phlpp1

stop_gained

c.4243C>T

p.Arg1415*

110

21.80%

358N3

358muscle

1

1.28E+08

C

A

Lct

missense_variant

c.3054G>T

p.Met1018Ile

43

7.00%

373N4

373muscle

1

1.31E+08

C

A

Pfkfb2

missense_variant

c.619G>T

p.Asp207Tyr

89

4.50%

358N3

358muscle

1

1.66E+08

C

A

Gm4846

missense_variant

c.1305G>T

p.Met435Ile

72

5.60%

358N3

358muscle

1

1.67E+08

G

T

Aldh9a1

missense_variant

c.712G>T

p.Ala238Ser

44

6.80%

368N2

368muscle

1

1.81E+08

C

A

Acbd3

missense_variant

c.337C>A

p.His113Asn

25

12.00%

358N3

358muscle

2

13486755

C

A

Cubn

missense_variant&splice_region_variant

c.480G>T

p.Lys160Asn

47

6.40%

357N1

357muscle

2

25911320

C

A

Kcnt1

synonymous_variant

c.3409C>A

p.Arg1137Arg

35

8.60%

368N2

368muscle

2

58982966

G

T

Ccdc148

missense_variant

c.614C>A

p.Ala205Asp

28

10.70%

358N3

358muscle

2

66565161

C

A

Scn9a

stop_gained

c.538G>T

p.Glu180*

24

12.50%

368N4

368muscle

2

1.04E+08

A

C

D430041D05Rik

missense_variant

c.1942T>G

p.Leu648Val

267

13.10%

373N4

373muscle

2

1.12E+08

A

G

Olfr1308

missense_variant

c.344T>C

p.Leu115Pro

51

11.80%

368N2

368muscle

2

1.2E+08

C

A

Rpap1

missense_variant

c.1903G>T

p.Ala635Ser

34

8.80%

373N4

373muscle

2

1.2E+08

C

A

Pla2g4e

missense_variant

c.665G>T

p.Cys222Phe

38

7.90%

373N3

373muscle

2

1.46E+08

C

A

Cfap61

missense_variant

c.1976C>A

p.Ala659Asp

46

6.50%

368N2

368muscle

2

1.53E+08

C

A

Asxl1

missense_variant

c.3191C>A

p.Pro1064Gln

84

4.80%

368N4

368muscle

2

1.62E+08

A

G

Ptprt

synonymous_variant

c.295T>C

p.Leu99Leu

75

16.00%

368N2

368muscle

2

1.67E+08

C

A

B4galt5

missense_variant

c.766G>T

p.Ala256Ser

16

18.80%

368N2

368muscle

3

86780226

G

T

Lrba

missense_variant

c.8437G>T

p.Ala2813Ser

48

6.30%

358N3

358muscle

3

88360373

G

A

Smg5

synonymous_variant

c.2799G>A

p.Arg933Arg

86

4.70%

357N1

357muscle

3

88367297

G

A

Paqr6

missense_variant

c.685G>A

p.Ala229Thr

22

18.20%

373N3

373muscle

3

1.03E+08

C

A

Csde1

missense_variant

c.845C>A

p.Pro282Gln

47

6.40%

357N5

357muscle

3

1.04E+08

C

A

Rsbn1

missense_variant

c.1871C>A

p.Ala624Asp

27

11.10%

358N3

358muscle

4

24536440

G

T

Mms22l

synonymous_variant

c.2028G>T

p.Ala676Ala

77

5.20%

357N1

357muscle

4

40738329

G

T

Smu1

stop_gained

c.1404C>A

p.Cys468*

35

8.60%

358N3

358muscle

4

41034270

G

T

Aqp7

synonymous_variant

c.888C>A

p.Gly296Gly

17

17.60%

358N1

358muscle

4

56937908

C

A

Tmem245

missense_variant

c.639G>T

p.Leu213Phe

19

15.80%

358N2

358muscle

4

1.01E+08

G

T

Jak1

synonymous_variant

c.1245C>A

p.Leu415Leu

41

7.30%

368N4

368muscle

4

1.26E+08

C

T

Csf3r

synonymous_variant

c.2145C>T

p.Ser715Ser

53

13.20%

358N3

358muscle

4

1.53E+08

G

T

Nphp4

synonymous_variant

c.1500G>T

p.Ser500Ser

46

6.50%

373N4

373muscle

4

1.54E+08

A

G

Cep104

missense_variant

c.1544A>G

p.Lys515Arg

121

4.10%

373N4

373muscle

4

1.55E+08

G

A

Plch2

synonymous_variant

c.3087C>T

p.Ala1029Ala

38

8.10%

373N3

373muscle

4

1.56E+08

A

G

Mib2

synonymous_variant

c.966T>C

p.Ala322Ala

102

5.90%

358N3

358muscle

4

1.56E+08

C

A

Agrn

missense_variant

c.4334G>T

p.Arg1445Leu

46

6.50%

368N2

368muscle

5

34813050

C

A

Htt

missense_variant

c.1541C>A

p.Ser514Tyr

50

6.00%

358N3

358muscle

5

63937830

C

A

Rell1

stop_gained

c.292G>T

p.Glu98*

83

4.80%

357N1

357muscle

5

1.12E+08

C

A

Hps4

synonymous_variant

c.1359C>A

p.Pro453Pro

39

7.70%

373N3

373muscle

5

1.22E+08

C

A

Rad9b

missense_variant

c.727G>T

p.Ala243Ser

40

7.50%

368N2

368muscle

6

29283208

G

T

Fam71f2

missense_variant

c.204G>T

p.Met68Ile

35

8.60%

357N1

357muscle

6

89342587

G

A

Plxna1

missense_variant&splice_region_variant

c.1735C>T

p.Pro579Ser

31

9.70%

358N2

358muscle

6

91486900

C

G

Tmem43

missense_variant

c.1156C>G

p.Pro386Ala

89

5.60%

358N3

358muscle

6

92189633

C

T

Zfyve20

missense_variant

c.2029G>A

p.Ala677Thr

75

20.00%

373N4

373muscle

6

1.29E+08

G

T

BC048546

missense_variant

c.2389C>A

p.Pro797Thr

41

7.30%

358N3

358muscle

7

24710200

C

A

BC049730

missense_variant

c.43C>A

p.Leu15Met

28

10.70%

368N2

368muscle

7

29292075

C

A

Ppp1r14a

missense_variant

c.307C>A

p.Pro103Thr

44

6.80%

368N2

368muscle

7

34204130

T

C

Gpi1

missense_variant

c.1297A>G

p.Thr433Ala

46

6.50%

373N3

373muscle

7

80738221

G

A

Iqgap1

missense_variant

c.2677C>T

p.Arg893Cys

46

6.50%

358N2

358muscle

7

1.18E+08

C

G

Xylt1

missense_variant

c.2763C>G

p.Cys921Trp

38

10.50%

368N4

368muscle

7

1.26E+08

G

A

Gsg1l

synonymous_variant

c.918C>T

p.His306His

121

5.00%

368N2

368muscle

7

1.27E+08

C

A

Zfp768

missense_variant

c.937G>T

p.Gly313Cys

41

7.30%

373N1

373muscle

7

1.4E+08

G

T

Olfr525

missense_variant

c.686G>T

p.Arg229Leu

95

4.20%

368N2

368muscle

7

1.44E+08

C

A

Ppfia1

missense_variant

c.2471G>T

p.Ser824Ile

48

6.30%

373N1

373muscle

8

11517878

C

G

Cars2

missense_variant

c.1216G>C

p.Val406Leu

169

8.30%

368N2

368muscle

8

13955760

C

A

Tdrp

stop_gained

c.160G>T

p.Glu54*

50

6.00%

368N2

368muscle

8

15041975

C

T

BB014433

missense_variant

c.877G>A

p.Val293Met

42

14.30%

358N3

358muscle

8

68358564

G

T

Csgalnact1

missense_variant

c.1453C>A

p.Pro485Thr

50

6.00%

373N4

373muscle

8

72346037

C

A

Eps15l1

missense_variant

c.2509G>T

p.Asp837Tyr

18

16.70%

373N4

373muscle

8

80730168

C

T

Smarca5

synonymous_variant

c.444G>A

p.Glu148Glu

91

5.50%

368N2

368muscle

8

95327967

G

A

Zfp319

missense_variant

c.1607C>T

p.Ala536Val

50

6.00%

358N3

358muscle

8

1.05E+08

G

A

Rrad

missense_variant

c.118C>T

p.Pro40Ser

41

7.30%

358N3

358muscle

8

1.08E+08

G

T

Wwp2

missense_variant

c.1034G>T

p.Arg345Met

43

7.00%

358N3

358muscle

8

1.11E+08

C

A

Fuk

missense_variant

c.970G>T

p.Gly324Cys

40

7.50%

358N3

358muscle

8

1.26E+08

C

A

Ntpcr

synonymous_variant

c.21C>A

p.Leu7Leu

42

7.10%

357N1

357muscle

9

24582820

C

A

Dpy19l2

synonymous_variant

c.2013G>T

p.Val671Val

44

6.80%

358N2

358muscle

9

43311472

G

A

Trim29

synonymous_variant

c.597G>A

p.Leu199Leu

173

4.00%

357N5

357muscle

9

45450529

C

T

Dscaml1

missense_variant

c.586C>T

p.Arg196Cys

50

8.00%

368N8

368muscle

9

55168284

G

A

Ube2q2

missense_variant

c.376G>A

p.Asp126Asn

71

7.00%

368N8

368muscle

9

55168290

C

T

Ube2q2

missense_variant

c.382C>T

p.Pro128Ser

69

7.20%

373N1

373muscle

9

56260482

C

T

Peak1

missense_variant

c.161G>A

p.Arg54Gln

340

2.90%

358N3

358muscle

9

92287625

C

A

Plscr2

missense_variant

c.127C>A

p.Gln43Lys

97

4.10%

357N4

357muscle

9

1.08E+08

G

C

Bsn

missense_variant

c.4976C>G

p.Pro1659Arg

47

21.30%

368N2

368muscle

10

20246611

C

A

Map7

missense_variant

c.422C>A

p.Ala141Asp

37

8.10%

358N3

358muscle

10

20322064

C

G

Bclaf1

missense_variant

c.52C>G

p.Gln18Glu

21

14.30%

368N2

368muscle

10

38966046

C

A

Lama4

missense_variant

c.92C>A

p.Ala31Glu

47

6.40%

358N2

358muscle

10

70534879

G

A

Fam13c

missense_variant

c.848G>A

p.Ser283Asn

40

20.00%

357N5

357muscle

10

80773112

C

A

Dot1l

missense_variant

c.502C>A

p.Gln168Lys

39

7.70%

373N4

373muscle

10

81420600

G

A

Nfic

synonymous_variant

c.229C>T

p.Leu77Leu

150

8.70%

357N1

357muscle

10

1.27E+08

G

T

Mettl1

missense_variant

c.577G>T

p.Asp193Tyr

45

6.70%

373N4

373muscle

11

5707370

G

A

Mrps24

missense_variant

c.148C>T

p.Pro50Ser

97

4.10%

358N3

358muscle

11

60202880

C

A

Srebf1

synonymous_variant

c.2232G>T

p.Ser744Ser

74

5.60%

357N4

357muscle

11

69853226

A

G

Tnk1

missense_variant

c.1306T>C

p.Phe436Leu

114

30.70%

373N3

373muscle

11

78499753

C

A

Vtn

missense_variant

c.237C>A

p.Asp79Glu

48

6.30%

368N4

368muscle

11

87889211

G

A

Olfr462

synonymous_variant

c.684C>T

p.His228His

50

6.00%

357N4

357muscle

11

98250228

A

G

Cdk12

missense_variant

c.4294A>G

p.Lys1432Glu

35

8.60%

368N2

368muscle

11

1.01E+08

A

G

Aoc2

synonymous_variant

c.195A>G

p.Thr65Thr

38

7.90%

368N2

368muscle

11

1.01E+08

A

G

Aoc2

missense_variant

c.269A>G

p.Asn90Ser

35

20.00%

357N4

357muscle

11

1.03E+08

C

G

Fzd2

synonymous_variant

c.1419C>G

p.Leu473Leu

109

28.40%

368N2

368muscle

11

1.08E+08

C

A

Helz

synonymous_variant

c.1356C>A

p.Thr452Thr

32

9.40%

368N2

368muscle

12

4209383

C

A

Adcy3

synonymous_variant

c.2659C>A

p.Arg887Arg

44

9.10%

368N4

368muscle

12

33342134

C

A

Atxn7l1

synonymous_variant

c.771C>A

p.Thr257Thr

85

4.70%

368N4

368muscle

12

70246446

C

A

Trim9

synonymous_variant

c.2310G>T

p.Thr770Thr

67

6.00%

373N1

373muscle

12

72567232

G

A

Pcnxl4

synonymous_variant

c.1950G>A

p.Leu650Leu

47

6.40%

368N2

368muscle

12

82387603

C

A

Sipa1l1

missense_variant

c.2146C>A

p.Gln716Lys

29

10.30%

358N3

358muscle

12

1.02E+08

G

T

Slc24a4

synonymous_variant

c.117G>T

p.Leu39Leu

46

6.50%

368N2

368muscle

12

1.02E+08

C

A

Golga5

missense_variant

c.197C>A

p.Ala66Asp

49

6.10%

358N3

358muscle

13

73672769

G

T

Slc6a18

missense_variant

c.695C>A

p.Ala232Glu

26

11.50%

357N5

357muscle

13

73821238

G

T

Nkd2

missense_variant

c.1108C>A

p.Pro370Thr

46

6.50%

357N1

357muscle

13

93387596

C

A

Homer1

synonymous_variant

c.648C>A

p.Ala216Ala

25

12.00%

373N4

373muscle

14

7945932

G

T

Flnb

missense_variant

c.7336G>T

p.Ala2446Ser

36

8.30%

368N4

368muscle

14

54907149

C

T

Slc22a17

synonymous_variant

c.1128G>A

p.Arg376Arg

99

4.00%

357N1

357muscle

14

55745048

C

A

Dhrs1

missense_variant

c.20G>T

p.Gly7Val

20

15.00%

358N3

358muscle

15

81692128

G

T

Chadl

synonymous_variant

c.2239C>A

p.Arg747Arg

66

6.10%

358N3

358muscle

15

99104471

G

T

Dnajc22

missense_variant

c.996G>T

p.Gln332His

36

8.60%

373N4

373muscle

16

5240002

G

T

Alg1

synonymous_variant

c.837G>T

p.Leu279Leu

63

6.30%

368N4

368muscle

16

14233649

C

A

Myh11

missense_variant

c.1292G>T

p.Arg431Leu

74

5.40%

373N3

373muscle

16

23357761

C

T

St6gal1

missense_variant

c.1103C>T

p.Pro368Leu

155

5.80%

357N1

357muscle

16

45731773

G

T

Abhd10

missense_variant

c.736C>A

p.Gln246Lys

73

5.50%

373N4

373muscle

16

56000642

C

A

Zbtb11

missense_variant

c.2101C>A

p.Gln701Lys

38

7.90%

373N4

373muscle

16

96673771

G

T

Dscam

missense_variant

c.3590C>A

p.Ala1197Glu

47

6.40%

368N2

368muscle

16

97576326

C

A

Tmprss2

missense_variant&splice_region_variant

c.570G>T

p.Lys190Asn

47

6.40%

373N4

373muscle

17

24265204

C

A

Abca17

missense_variant&splice_region_variant

c.4938G>T

p.Lys1646Asn

48

6.30%

358N3

358muscle

17

27101185

C

A

Itpr3

synonymous_variant

c.3009C>A

p.Pro1003Pro

97

5.20%

358N3

358muscle

17

28877021

C

A

Pnpla1

synonymous_variant

c.415C>A

p.Arg139Arg

50

6.00%

373N4

373muscle

17

28982146

T

C

Stk38

synonymous_variant

c.555A>G

p.Thr185Thr

39

25.60%

368N2

368muscle

17

34685203

G

T

Tnxb

missense_variant

c.3686G>T

p.Gly1229Val

48

6.40%

357N4

357muscle

17

80145171

C

A

Galm

missense_variant

c.537C>A

p.Phe179Leu

46

6.50%

368N2

368muscle

18

38259948

G

T

0610009O20Rik

missense_variant

c.1204G>T

p.Ala402Ser

20

15.00%

358N1

358muscle

18

42337039

C

A

Rbm27

missense_variant

c.2900C>A

p.Ser967Tyr

44

6.80%

358N3

358muscle

18

44886378

C

A

Ythdc2

missense_variant

c.4213C>A

p.Pro1405Thr

37

8.10%

368N4

368muscle

19

4733741

G

A

Sptbn2

missense_variant

c.1741G>A

p.Ala581Thr

213

5.20%

373N4

373muscle

19

8896787

A

G

Ints5

synonymous_variant

c.2109A>G

p.Leu703Leu

49

6.10%

373N4

373muscle

19

8896820

C

T

Ints5

synonymous_variant

c.2142C>T

p.Thr714Thr

42

9.50%

368N4

368muscle

19

8978064

G

T

Eef1g

missense_variant

c.1276G>T

p.Val426Leu

24

12.50%

357N1

357muscle

19

34950052

G

T

Kif20b

missense_variant

c.2713G>T

p.Ala905Ser

45

6.70%

373N3

373muscle

19

40072400

G

A

Cyp2c54

missense_variant

c.298C>T

p.Leu100Phe

101

5.00%

373N3

373muscle

19

50225150

G

A

Sorcs1

missense_variant

c.2138C>T

p.Ala713Val

47

6.40%

357N4

357muscle

19

55207920

C

T

Gucy2g

missense_variant

c.2582G>A

p.Arg861His

244

6.10%

358N2

358muscle

19

56851528

C

T

Tdrd1

synonymous_variant

c.2019C>T

p.Asp673Asp

71

9.90%

358N2

358muscle

X

6583974

A

C

Shroom4

missense_variant

c.1187A>C

p.Asn396Thr

26

15.40%

373N3

373muscle

X

20936595

G

A

Elk1

synonymous_variant

c.726C>T

p.Gly242Gly

53

7.50%

358N3

358muscle

X

56501662

G

T

Ddx26b

missense_variant&splice_region_variant

c.1775G>T

p.Gly592Val

43

7.00%

357N1

357muscle

X

1.67E+08

G

T

Tlr7

missense_variant

c.2212C>A

p.Gln738Lys

31

16.10%

357N5

357muscle

17

24267574

GCA

G

Abca17

frameshift_variant

c.4476_4477delTG

p.Ala1493fs

120

3.33%

358N1

358muscle

6

47554188

GTCA

G

Ezh2

disruptive_inframe_deletion

c.558_560delTGA

p.Asp187del

57

5.26%

358N1

358muscle

10

58223101

CA

C

AW822073

frameshift_variant

c.1007delT

p.Leu336fs

74

5.41%

358N1

358muscle

15

78935001

C

CAAG

Nol12

disruptive_inframe_insertion

c.24_26dupGAA

p.Lys9dup

13

30.77%

358N2

358muscle

11

3524692

CGTG

C

Smtn

disruptive_inframe_deletion

c.2115_2117delCAC

p.Thr706del

208

2.88%

358N3

358muscle

2

1.55E+08

GT

G

Itch

splice_donor_variant&intron_variant

c.1430+2delT

.

55

5.45%

358N3

358muscle

4

1.37E+08

GCTT

G

Zbtb40

inframe_deletion

c.2461_2463delAAG

p.Lys821del

134

3.73%

358N3

358muscle

5

1.11E+08

TTGC

T

Ep400

disruptive_inframe_deletion

c.7974_7976delGCA

p.Gln2659del

90

3.33%

358N3

358muscle

5

1.35E+08

ATC

A

Fkbp6

frameshift_variant

c.927_928delGA

p.Glu309fs

84

3.57%

358N3

358muscle

7

1.01E+08

GAC

G

Atg16l2

frameshift_variant

c.972_973delGT

p.Ser325fs

191

3.66%

358N3

358muscle

9

5302474

TC

T

Casp1

frameshift_variant

c.396delC

p.Lys133fs

64

6.25%

358N3

358muscle

10

1.1E+08

TGAA

T

Nav3

disruptive_inframe_deletion

c.5574_5576delTTC

p.Ser1859del

78

3.85%

358N3

358muscle

11

84860577

TG

T

Ggnbp2

frameshift_variant

c.395delC

p.Ala132fs

86

3.49%

358N3

358muscle

16

32793328

AATAG

A

Muc20

frameshift_variant

c.1674_1677delCTAT

p.Tyr559fs

76

3.95%

368N2

368muscle

12

1.04E+08

TAC

T

Serpina3k

frameshift_variant

c.1161_1162delAC

p.Leu387fs

108

3.70%

368N4

368muscle

11

71182505

TGAA

T

Nlrp1b

inframe_deletion

c.508_510delTTC

p.Phe170del

225

1.78%

373N3

373muscle

9

38449182

C

CT

Olfr902

frameshift_variant

c.313dupT

p.Cys105fs

131

3.82%

373N4

373muscle

2

85770217

CTG

C

Olfr1013

frameshift_variant

c.425_426delGT

p.Cys142fs

85

3.53%

373N4

373muscle

11

23745586

TG

T

Rel

frameshift_variant

c.695delC

p.Ser232fs

67

4.48%

373N4

373muscle

12

76609154

GGC

G

Sptb

frameshift_variant

c.4151_4152delGC

p.Arg1384fs

95

4.21%

373N4

373muscle

14

48659272

TCTG

T

Otx2

inframe_deletion

c.325_327delCAG

p.Gln109del

68

4.41%

  1. Shown are the results of exome sequencing in the 12 tumor nodules. Relevant information are given such as the position in the chromosome, the reference and alternative alleles, the type of mutation, the amino acid substitution and variant allele frequency.