Detection of Genetic Alterations in Oral Squamous Cell Carcinoma Using Multiplex Ligation-Dependent Probe Amplification (MLPA)


  • Zachary Wei Ern Yong
  • Lee Peng Karen-Ng Universiti Malaya
  • Thomas George Kallarakkal Universiti Malaya
  • Zainal Ariff Abdul Rahman Universiti Malaya
  • Siti Mazlipah Ismail Universiti Malaya
  • Mannil Thomas Abraham Hospital Tengku Ampuan Rahimah, Klang
  • Keng Kiong Tay Hospital Umum Sarawak, Kuching
  • Rosnah Binti Zain MAHSA University
  • Zuraiza Mohamad Zaini Universiti Malaya



Biomarkers, DNA copy number, Dysplasia, Chromosome alteration


Deletions and amplifications of genes often occur during multistep progression from oral precancer, seen as oral epithelial dysplasia (OED) to cancerous stage. These genetic alterations could be used as markers to aid in detection of oral squamous cell carcinomas (OSCC). This study explored the use of multiplex ligation-dependent probe amplification (MLPA) technique in detecting OSCC and OED specific genetic alterations. MLPA was used to detect gains and losses of 106 genes in DNA extracted from frozen tissue samples of 10 OSCC and 10 non-cancer patients. Two biopsies of OED were analyzed to explore the alterations in oral potentially malignant disorders. There were significant differences (p<0.001) in the number of alterations in OSCC and dysplasia compared to non-cancer samples respectively.  The most frequently altered genes in OSCC were PTP4A3, RECQL4, ATM, and KLK3 (60%). Five genes (MYC, SLA, TNFRSF1A, MESDC1, MIF) were altered in 50% of OSCC samples. These nine genes were specific to OSCC samples (p<0.05). Some genes, including MYB, MET, CASP2, SLA and PTEN occurred in 50% of OED samples. MLPA was able to detect genetic alterations, that are present only in OSCC samples and showed potential to be used as an adjunctive tool in early diagnosis of OSCC.


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