Development and validation of a droplet digital PCR (ddPCR) assay to detect MGMT promoter methylation in FFPE tumors of glioblastoma (GBM) patients.

Abstract

2072 Background: Methylation of the MGMT gene promoter (MGMTp) is a critical biomarker to inform GBM prognosis and guide treatment decisions, including clinical trial eligibility. Rapid reporting of MGMTp methylation can help stratify patients early and facilitate clinical trial referral during the crucial post-operative period where treatment options are being considered by patients and physicians alike. Methods: We developed a probe-based ddPCR method to detect and quantify MGMTp methylation. Assay specificity was assessed using bisulfite-converted, unmethylated DNA. Assay linearity and Limit of Detection (LoD) were determined using MGMTp methylated cell line DNA samples of decreasing fractional abundances (35%, 5%, and 0.5%) and decreasing DNA inputs (30ng, 10ng, 3ng,1ng and 0.5ng). The limit of Blank (LoB) was calculated using 16 replicates of unmethylated bisulfite-converted PBMC DNA, and DNA from tonsil FFPE samples (n = 9). Reproducibility studies were conducted on two different days with two different operators. Accuracy and concordance were assessed using an in-house MGMTp methylation pyrosequencing assay as an orthogonal method to analyze11 melanoma and one glioblastoma cell line. Preliminary clinical validation was conducted via analysis of FFPE tumor DNA from 34 GBM patients with clinical MGMTp methylation pyrosequencing results. Results: The MGMTp methylation ddPCR assay demonstrated 100% specificity to detect promoter methylation. The method linearly quantified both total DNA and methylated DNA along a range of input DNAs with conserved fractional abundances. The LoB was 0.036% and 0.034% using PBMC and tonsil FFPE DNA, respectively. The LoD was 0.075%. The bisulfite conversion and assay were highly reproducible, with a coefficient of variation < 20%. Among the 12 cell lines analyzed by both pyrosequencing and ddPCR the concordance was 100%. Ten of 11 GBM tumor samples identified as MGMTp methylated by the clinical pyrosequencing assay were also identified as methylated by the ddPCR assay. Five of 23 clinically unmethylated tumors were positive in the ddPCR assay with generally very low fractional abundances (0.08%, 0.12% 0.3%, 0.97% and 10.11%). Conclusions: We report preliminary validation of a highly sensitive and specific ddPCR assay to detect MGMTp methylation. Given the minimal sample requirements and rapid turnaround time for ddPCR assays, this test could eventually be utilized in clinical laboratories to quickly report MGMTp methylation status for GBM patient management.