Methods: DNA from frozen tissue samples of 10 OSCC and 10 gingiva flaps (obtained from healthy normal individuals during the minor impacted 8 surgery) as controls was used in this study. Three MLPA kits were used to detect 107 genes. The upper and lower limits of the 99.99% confidence interval were used to determine the cut-off point for copy number gains and losses. Using MLPA copy number ratios, chromosomal aberrations obtained were validated using the array comparative genomic hybridization (aCGH).
Results: Four genes (PTP4A3, RECQL4, ATM and KLK3) showed alterations in 60% (n=10) OSCC samples while five other genes (MYC, SLA, TNFRSF1A, MESDC1 and MIF) showed alterations in 50% (n=10) and both sets of genes were significantly different compared to the normal samples (p=0.011 and p=0.033 respectively). The genes which showed the highest frequency of gains (60%, n=10) were PTP4A3 and RECQL4 in the region 8q24.3 while the highest frequency of loses (50%, n=10) were ATM and KLK3 found in the region 11q23 and 19q13.33 respectively. Both MLPA and aCGH copy number ratios for each gene yielded very similar patterns.
Conclusions: MLPA was able to identify genetic alterations which are present only in the OSCCs samples suggestive of a potential use as an adjunctive tool for assisting in screening and diagnosis of OSCC.