Original Article

PCR-RFLP method enhance DNA sequencing of IDH1 somatic mutations detection in gliomas


  • Wei Chiang Goh
  • Badrisyah Idris
  • Regunath Kandasamy
  • Shaharum Shamsuddin
  • Hasnan Jaafar
  • Farizan Ahmad

Received Date: 24.06.2019 Accepted Date: 11.09.2019 Gulhane Med J 2019;61(4):167-171


Isocitrate dehydrogenase 1 (IDH1) mutations are commonly found in lower grade gliomas and secondary GBMs. Glioblastomas (GBMs) are the most common and most malignant gliomas in adult with a median survival of 15 months only. Discovery of IDH1 mutations have made a significant positive impact on glioma patient’s diagnosis, prognosis, and treatments. Thus, IDH1 mutation screening method in gliomas is necessary to improve survival rate. The gold standard for somatic mutation screening, DNA sequencing was performed to detect IDH1 gene mutation status in glioma samples.


Forty-seven formalin fixed paraffin-embedded glioma samples were subjected for DNA sequencing. The ambiguous glioma samples from DNA sequencing were subjected to PCR-RFLP for IDH1 mutation confirmation.


Three out of 47 glioma samples (6.4%) were found to harbor IDH1 mutations. Two IDH1 R132H and one IDH1 R132L were found in the glioma samples. From the DNA sequencing results, we found that the mutant nucleotide spectrum was lower than the wild-type nucleotide results in failure of IDH1 mutations detection. PCR-RFLP method was implemented to confirm the ambiguous IDH1 mutations. We found that the ambiguous IDH1 mutations from DNA sequencing were indeed IDH1 mutants using PCR-RFLP method.


In conclusion, DNA sequencing method has a considerable low sensitivity level which leads to false negative results. Thus, combination of DNA sequencing and PCR-RFLP method in heterogeneous glioma samples can be applied to avoid false negative result and cost-effective.

Keywords: Glioma, IDH1 R132L, IDH1 R132H, DNA sequencing, PCR-RFLP.