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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