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Table 1 List of targeted genes, site of mutations, and design of gRNA

From: Preparation of the standard cell lines for reference mutations in cancer gene-panels by genome editing in HEK 293 T/17 cells

Gene

NCC Oncopanel (ver 2)

Thermo Fisher Oncomine Dx Test

Personails ACE CancerPlus™ Test

Illumina Trusight Tumor 26

Ion AmpliSeq Cancer Hotspot Panel v2

No of mutations in COSMIC

COSMIC_ID

CDS Mutation

FATHMM

gRNA sequense

(No of mismatch)

Distanse from PAM

0

1

2

3

AKT1

*

*

*

*

*

975

COSM33765

49G > A

Pathogenic

(score 1.00)

CACCACCCGCACGTCTGTAGGGG

1

1

1

1

12

AKT3

*

 

*

  

269

COSM242892

232C > A

Pathogenic (score 0.99)

 

TCTCTATAACAGTAGTCCACTGG

1

1

0

0

27

ALK

*

*

*

*

*

1522

COSM28056

3824G > A

Pathogenic

(score 0.98)

TACTCACCTGTAGATGTCTCGGG

4

1

1

1

16

BAP1

*

 

*

  

1221

COSM110721

178C > T

Pathogenic

(score 0.98)

CCAAGGTAGAGACCTTTCGCCGG

5

1

1

1

9

BCL2L11(BIM)

*

 

*

  

116

COSM389356

585G > C

Pathogenic (score 0.98)

 

GTTACATTGTCCGCCTGGTGTGG

1

1

0

0

7

BRAF

*

*

*>

*

*

27,630

COSM476

1799 T > A

Pathogenic (score 0.99)

 

TAGCTACAGTGAAATCTCGATGG

12

1

0

1

20

BRAF’

*

*

*

*

*

4

COSM1137

1817G > A

Pathogenic (score 0.98)

 

ACAGTGAAATCTCGATGGAGTGG

1

1

1

0

25

CDK4

*

*

*

  

101

COSM1677139

70C > T

Pathogenic

(score 0.98)

AGTGGCCACTGTGGGGATCACGG

2

1

1

2

45

CDKN2A(p16)

*

*

*

 

*

5911

COSM12475

238C > T

Pathogenic

(score 0.88)

GGGCAGCGTCGTGCACGGGTCGG

2

1

1

1

4

CTNNB1(β-catenin)

*

*

*

*

*

7307

COSM5664

121A > G

Pathogenic

(score 0.98)

CAGAGAAGGAGCTGTGGTAGTGG

6

1

1

11

195

DNMT3A

 

*

*

  

3679

COSM52944

2645G > A

Pathogenic

(score 0.98)

CGTCTCCAACATGAGCCGCTTGG

6

1

1

2

18

ERBB2(HER2)

*

*

*

*

*

1596

COSM48358

929C > T

Pathogenic

(score 0.97)

CAGGGGGCAGACGAGGGTGCAGG

1

1

1

21

201

ERBB3

*

*

*

  

900

COSM20710

310G > A

Pathogenic

(score 0.88)

ACCATTGCCCAACCTCCGCGTGG

4

1

1

1

7

EZH2

*

*

*

 

*

1273

COSM37028

1937A > T

Pathogenic

(score 0.99)

GAATTCATCTCAGAATACTGTGG

7

1

1

5

77

FBXW7

*

*

 

*

*

1972

COSM22975

1513C > T

Pathogenic

(score 0.94)

TGCCATCATATTGAACACAGCGG

2

1

1

1

18

FGFR3

*

*

*

 

*

4354

COSM715

746C > G

Pathogenic

(score 0.96)

CTGCAGGATGGGCCGGTGCGGGG

1

2

4

7

58

FOXL2

 

*

 

*

 

933

COSM33661

402C > G

Pathogenic

(score 0.95)

CTTCTCGAACATGTCTTCGCAGG

5

1

1

1

12

HRAS

*

*

*

 

*

2023

COSM502

183G > T

none

(score 0.53)

CATCCTGGATACCGCCGGCCAGG

2

2

2

2

16

IDH2

*

*

*

 

*

2430

COSM33733

515G > A

Pathogenic

(score 0.99)

CCAAGCCCATCACCATTGGCAGG

2

1

1

4

86

IGF2

*

    

132

COSM1561457

293C > T

Pathogenic (score 0.97)

 

ACCCTCACCGGAAGCACGGTCGG

2

1

0

0

1

JAK2

*

*

*

 

*

50,556

COSM12600

1849G > T

Pathogenic

(score 0.94)

AATTATGGAGTATGTGTCTGTGG

8

1

1

1

75

KIT

*

*

*

*

*

8856

COSM1314

2447A > T

Pathogenic

(score 0.99)

AGAATCATTCTTGATGTCTCTGG

7

1

1

1

133

KNSTRN

 

*

   

118

COSM140056

71C > T

Neutral

(score 0.00)

GTAGCTAGGCGGAAGTGGGTGGG

1

1

1

2

28

KRAS

*

*

*

*

*

43,548

No ID

124G > A

 

CTTGTGGTAGTTGGAGCTGGTGG

4

1

1

1

46

MAGOH

 

*

   

43

COSM535605

410 T > C

Pathogenic

(score 0.99)

TGTTTGGTCTTCAGTCTTATTGG

4

1

2

3

76

MAP 2 K1

*

*

*

*

 

496

COSM235614

370C > T

Pathogenic

(score 0.99)

CCATAGAAGCCCACGATGTACGG

1

1

4

4

10

MAPK1

 

*

*

  

173

COSM461148

964G > A

Pathogenic

(score 0.98)

GTATTACGACCCGAGTGACGAGG

4

1

1

1

2

MDM2

*

 

*

  

110

COSM431747

994C > T

Pathogenic

(score 0.91)

AGGAAGCCAATTCTCACGAAGGG

6

1

1

2

25

MET

*

*

*

*

*

1142

COSM707

3029C > T

Pathogenic

(score 0.98)

TTTGAAACCATTTCTGTAGTTGG

5

1

1

2

78

MTOR

*

*

*

  

1195

COSM20417

6644C > A

Pathogenic

(score 1.00)

CCAATGACCCAACATCTCTTCGG

8

1

1

1

12

MYCN

*

    

305

COSM35624

131C > T

Pathogenic (score 0.96)

 

CTTCCAGATGTCCTCCCCCGGGG

1

1

0

0

24

NOTCH1

*

*

*

 

*

3921

COSM12771

4799 T > C

Pathogenic

(score 0.99)

CCACGTTGGTGTGCAGCACGCGG

9

1

1

1

53

NRAS

*

*

*

*

*

6676

COSM5930625

112G > A

Pathogenic

(score 0.99)

AAACTGGTGGTGGTTGGAGCAGG

1

1

1

1

67

PDGFRA

*

*

*

*

*

2354

COSM736

2525A > T

Pathogenic

(score 0.99)

CGAATCATGCATGATGTCTCTGG

7

1

1

1

24

PIK3CA

*

*

*

*

*

13,613

COSM775

3140A > G

Pathogenic

(score 0.96)

ATGAATGATGCACATCATGGTGG

1

1

0

1

56

PTCH1

*

*

*

  

1331

COSM1638394

3944C > T

Pathogenic

(score 1.00)

AGCGTCTCTGCGCGGTCTGTAGG

1

1

1

1

7

PTEN

*

*

*

*

*

4778

No ID

697C > T

 

AACTTGTCTTCCCGTCGTGTGGG

7

1

0

1

7

SMO

*

*

*

 

*

593

COSM216037

1234C > T

Pathogenic

(score 0.96)

AGCCTCCCACGATGAGCACCAGG

8

1

1

1

102

STAT3

*

*

   

805

COSM1155743

1919A > T

Pathogenic

(score 0.97)

TTCAGCTGCTGCTTTGTGTATGG

5

1

1

6

92

TP53(p53)

*

*

*

*

*

39,196

COSM10662

743G > A

Pathogenic

(score 0.98)

GCATGGGCGGCATGAACCGGAGG

5

1

0

0

3