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Table 3 List of variants grouped according to gene function

From: Circulating DNA as prognostic biomarker in patients with advanced hepatocellular carcinoma: a translational exploratory study from the SORAMIC trial

Gene group

Location

AA

Codon

Patients (%)

DNA repair

 ATM

chr11:108121426

–

c.1236-2A>T

2 (15.4)

 BLM

chr15:91304138

p.N515fs

na

c.1544delA

c.*468delA

1 (7.7)

 BRCA2

chr13:32954022

p.T18fs

p.T3033fs

c.52insA

c.9097insA

1 (7.7)

 ERCC5

chr13:103524611

p.K150fs

p.K917fs

c.450delA

c.2751delA

5 (38.4)

 MSH6

chr2:48030639

p.F56fs

p.F1088fs

–

p.F958fs

p.F786fs

c.165delC

c.3261delC

c.*2608delC

c.2871delC

c.2355delC

6 (46.1)

 RAD50

chr5:131931451

p.K722fs

–

–

p.?661fs

c.2165delA

c.*1791delA

c.*351delA

c.1982delA

4 (30.8)

 WRN

chr8:30915970

p.K5fs

c.15delA

2 (15.4)

Multidrug resistance/xenobiotic metabolism

 ABCB1

chr7:87160618

p.S893A

p.S829A

c.2677T>G

c.2485T>G

3 (23.0)

 CYP2B6

chr19:41515263

p.K262R

c.785A>G

6 (46.1)

 CYP2C9

chr10:96702047

p.R144C

c.430C>T

1 (7.7)

 CYP2D6

chr22:42524994

p.P34S

p.P12S

c.100C>T

c.34C>T

2 (15.4)

 GSTP1

chr11:67352689

–

p.I105V

c.*137A>G

c.313A>G

2 (15.4)

 SLCO1B1

chr12:21331549

p.V174A

c.521T>C

2 (15.4)

Cell cycle control/proliferation

 CTNNB1

chr3:41266098

p.D32V

p.D25V

c.95A>T

c.74A>T

1 (7.75)

 FGFR2

chr10:123274794

p.Y261C

p.Y147C

p.Y287C

p.Y263C

p.Y286C

p.Y375C

p.Y376C

p.Y377C

p.Y260C

–

c.782A>G

c.440A>G

c.860A>G

c.788A>G

c.857A>G

c.1124A>G

c.1127A>G

c.1130A>G

c.779A>G

c.*171A>G

1 (7.75)

 FGFR4

chr5:176520243

p.G23R

p.G388R

c.67G>A

c.1162G>A

1 (7.75)

 TP53

chr17:7579447

p.G254D

p.G113D

p.G206D

p.G152D

p.G86D

p.G234D

c.374G>A

c.338G>A

c.617G>A

c.455G>A

c.257G>A

c.701G>A

1 (7.75)

 TP53*

chr17:7579407

p.A86fs

p.A47fs

c.257del279

c.140del162

1 (7.75)

Signal transduction signalling

 PIK3CA

chr3:178952085

p.H1047R

c.3140A>G

1 (7.75)

 PIK3CA*

chr3:178952085

p.H1047L

c.3140A>T

1 (7.75)

 SOS1

chr2:39249927

p.S548R

c.1642A>C

1 (7.75)

Chromatin structure

 ASXL1

chr20:31022441

p.G641fs

p.G646fs

c.1919insG

c.1934insG

3 (23.0)

Liver transcription factor

 HNF1A

chr12:121432114

p.P291fs

p.G226fs

–

c.864delG

c.677delG

c.*304delG

12 (92.3)

Apoptosis

 BAX

chr19:49458970

p.E41fs

p.R24fs

p.E24fs

c.121insG

c.69insG

c.70insG

9 (69.2)

DNA methylation

 DNMT3A

chr2:25457242

–

p.R693H

p.R659H

p.R882H

c.*498G>A

c.2078G>A

c.1976G>A

c.2645G>A

2 (15.4)

  1. Chromosome location, amino acid (AA) change and codon change are indicated
  2. (na, not available)
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Journal of Translational Medicine

ISSN: 1479-5876

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