Table 3 Summary of genomic PCR, RT-PCR and MSP analysis

From: Identification of homozygous deletions of tumor suppressor gene FAT in oral cancer using CGH-array

OSCC cell lines Other SCC cell lines
Genomic PCR  
  HSC2 HSC3 HSC4 OSC4 OSC5 OSC6 SCC9 SCC25 Ca9–22 SAS HO1-U1 KB KN TE4 TE8 EBC1 ME180
Exon 1          HD HD    2/13 (15%)     
Exon 2          HD HD    2/13 (15%)     
Exon 3          HD     1/13 (7%)     
Exon 4          HD HD HD   3/13 (23%)     
RT-PCR
  HSC2 HSC3 HSC4 OSC4 OSC5 OSC6 SCC9 SCC25 Ca9–22 SAS HO1-U1 KB KN TE4 TE8 EBC1 ME180
Exon 2 NE         NE NE    3/13 (23%) NE    
Exon 3          NE NE    2/13 (15%) NE    
Exon 3–4          NE NE    2/13 (15%) NE    
Methylation-specific PCR (+: methylated , −: unmethylated)
HSC2 HSC3 HSC4 OSC4 OSC5 OSC6 SCC9 SCC25 Ca9–22 SAS HO1-U1 KB KN TE4 TE8 EBC1 ME180  
+ + + +  
OSCC primary tumors
  T1 T2 T3 T4 T5 T6 T7 T8 T9 T10        
Exon 1   HD   HD HD    HD   HD        
Exon 2 HD       HD           
Exon 3      HD HD            
Exon 4     HD              
  T11 T12 T13 T14 T15 T16 T17 T18 T19 T20        
Exon 1   HD      HD HD HD   9/20 (45%)       
Exon 2 HD HD          4/20 (20%)       
Exon 3            2/20 (10%)       
Exon 4 HD HD HD HD HD HD      7/20 (35%)       
  1. HD, homozygous deletion; NE, no expression.