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Table 2 Nominal and actual results of the mutation analyses of KIT exons 9 and 11 and PDGFRA exon 18 performed in trial 2.

From: Pitfalls in mutational testing and reporting of common KIT and PDGFRA mutations in gastrointestinal stromal tumors

sample

exon

nominal result

Lab A

Lab B

Lab Ca

Lab D

Lab Ea

Lab F

T2.1

11

c.IVS10(-5)_(-1);

      
  

1648_1672del30

    

p.Q567_577Pdel

 
  

p.K550_558del

      

T2.2

18

c.2528_2539del12

c.2530_2538del9

     
  

p.I843T;

   

p.I843_S847insT

p.I843_S847del

 
  

M844_S847del

      

T2.3

11

c.1669T>A

      
  

p.W557R

      

T2.4

11

c.1712_1738dup27

c.b

c.b

c.wild-type

  

c.b

  

p.H580L;

p.b

p.b

p.wild-type

p.insLDPTQLPYD

p.D572_H580ins

p.b

  

D572_H580dup

      

T2.5

11

c.1727T>C

      
  

p.L576P

      

T2.6

 

c.wild-type

      
  

p.wild-type

      

T2.7

11

c.1669T>A

    

p.W557_R558del

c.wild-type

  

p.W557R

     

p.wild-type

T2.8

11

c.1679T>A

    

c.wild-type

c.1811T>A

  

p.V560D

    

p.wild-type

p.V604D

T2.9

11

c.c

c.1693_1716del24;

c.1693_1720del28;

   

c.1692_1720del

   

1720del

insC

p.G565P;

p.G564_D572del

p.G565_D572del

 
  

p.c

p.G565_D572del;

p.G565_T574delinsP

N566_T574del

  

p.G565_P573del

   

T774del

     

T2.10

11

c.1668_1723del57d

c.1679T>A

c.1672_1716del45

c.wild-type

c.wild-type

 

c.wild-type

  

p.W557_Q575deld

p.V560D

p.K558_D572del

p.wild-type

p.wild-type

 

p.wild-type

T2.11

11

c.1669_1674del6

      
  

p.W557_K558del

    

p.W557_R558del

 

T2.12

11

c.1676T>A

      
  

p.V559D

    

p.W557_R558del

 
  1. Only the nominal results of the relevant exons are given, other exons are wild-type; for the individual panel labs only the results differing from the nominal results are denoted on DNA and protein level, matching results are not shown.
  2. a changes in DNA sequence were not specified in Lab C and E
  3. b in Lab A and Lab F the DNA was not amplifiable; in Lab B mutation was detected from frozen tissue
  4. c complex deletion, different specifications are possible (see Lab A, Lab B and Lab C)
  5. d mutation could not be detected from FFPE material in the second trial; in Lab E mutation was detected from frozen tissue