Detecting DNA methylation of the BCL2, CDKN2A and NID2 genes in urine using a nested methylation specific polymerase chain reaction assay to predict bladder cancer

J Urol. 2012 Dec;188(6):2101-7. doi: 10.1016/j.juro.2012.08.015. Epub 2012 Oct 18.


Purpose: Detection of methylated DNA has been shown to be a good biomarker for bladder cancer. Bladder cancer has the highest recurrence rate of any cancer and, as such, patients are regularly monitored using invasive diagnostic techniques. As urine is easily attainable, bladder cancer is an optimal cancer to detect using DNA methylation. DNA methylation is highly specific in cancer detection. However, it is difficult to detect because of the limited amount of DNA present in the urine of patients with bladder cancer. Therefore, an improved, sensitive and noninvasive diagnostic test is needed.

Materials and methods: We developed a highly specific and sensitive nested methylation specific polymerase chain reaction assay to detect the presence of bladder cancer in small volumes of patient urine. The genes assayed for DNA methylation are BCL2, CDKN2A and NID2. The regions surrounding the DNA methylation sites were amplified in a methylation independent first round polymerase chain reaction and the amplification product from the first polymerase chain reaction was used in a real-time methylation specific polymerase chain reaction. Urine samples were collected from patients receiving treatment at Wolfson Medical Center in Holon, Israel.

Results: In a pilot clinical study using patient urine samples we were able to differentiate bladder cancer from other urogenital malignancies and nonmalignant conditions with a sensitivity of 80.9% and a specificity of 86.4%.

Conclusions: We developed a novel methylation specific polymerase chain reaction assay for the detection and monitoring of bladder cancer using DNA extracted from patient urine. The assay may also be combined with other diagnostic tests to improve accuracy.

MeSH terms

  • Adult
  • Aged
  • Aged, 80 and over
  • Biomarkers, Tumor / urine*
  • Calcium-Binding Proteins
  • Cell Adhesion Molecules / genetics*
  • Cell Adhesion Molecules / urine
  • DNA Methylation*
  • Female
  • Genes, bcl-2*
  • Genes, p16*
  • Humans
  • Male
  • Middle Aged
  • Pilot Projects
  • Polymerase Chain Reaction* / methods
  • Urinary Bladder Neoplasms / diagnosis
  • Urinary Bladder Neoplasms / genetics*
  • Urinary Bladder Neoplasms / urine


  • Biomarkers, Tumor
  • Calcium-Binding Proteins
  • Cell Adhesion Molecules
  • NID2 protein, human