Rare mutation detection
Detecting rare mutations is a cornerstone of cancer and disease research, essential for applications ranging from biomarker to minimal residual disease research studies. Rare mutation detection involves identifying sequence variants present at very low frequencies (down to 0.1%) in a pool of wild-type background.
The challenge in rare mutation detection is discriminating between two highly similar sequences, where one is significantly more abundant than the other. This challenge is compounded when working with sample types like FFPE tissue and liquid biopsies where nucleic acids are often fragmented and present at very low levels.
For detecting and quantifying rare events, such as point mutations or single nucleotide polymorphisms (SNPs), you need a sensitive, accurate and precise method. Digital PCR (dPCR) provides the absolute quantification and reproducibility required for confident rare mutation analysis.
Why use nanoplate dPCR for rare mutation detection?
- Ability to load a larger input reaction volume into 26,000 partitions, which substantially increases the chances of finding a rare target
- Multiplexing for mutant and wild-type sequencing to detect low fractions of rare mutant molecules against an abundant wild-type background
- No need for a standard curve
Rare mutation analysis with nanoplate dPCR
Related products
Scientific publications
Tanaka J, et al. Highly multiplexed digital PCR assay for simultaneous quantification of variant allele frequencies and copy number alterations of KRAS and GNAS in pancreatic cancer precursors. Mol Oncol. 2025. doi:10.1002/1878-0261.70011.
Shek RCM, et al. A novel digital PCR assay for accurate detection and differentiation of focal and non-focal subtypes of mesenchymal-epithelial transition (MET) gene amplification in lung cancer. Cancers. 2025;17(5):811.
Carvalho-Moore P, et al. A rearranged Amaranthus palmeri extrachromosomal circular DNA confers resistance to glyphosate and glufosinate. Plant Cell. 2025;37(4):koaf069.
FAQs on dPCR for rare mutation analysis
Q1:What types of rare mutations can dPCR detect?
A1: dPCR can detect a wide variety of variant types, including: Single nucleotide variants (SNVs), small insertions or deletions (indels), copy number variations (CNVs), gene fusions (via expression or DNA breakpoints) and methylation differences (after bisulfite conversion or restriction digest). Any disease-associated mutation can be detected by dPCR with high sensitivity and specificity, such as mutations in EGFR, BRAF, KRAS, TP53, BRCA1&2 and other mutations relevant in cancer, hereditary disorders and mitochondrial diseases.
Q1: What mutations can I detect with dPCR?
A1: Digital PCR enables highly sensitive detection of mutations such as the EGFR T790M mutation, the BRAF V600E mutation, KRAS gene mutation, TP53 mutations, BRCA2 mutations, BRCA1 mutations and other relevant mutations in cancer, hereditary disorders and mitochondrial diseases.
Q2: How sensitive is digital PCR for mutation detection?
A2: Literature shows that digital PCR systems can identify low-abundant molecular alterations (0.01–1.0 %) to help detect minor allele frequency (MAF) variants in driver biomarkers or monitor minimal residual disease (MRD) (Scimone C et al, 2024; Crucitta S et al, 2023).
Q3: Why use digital PCR instead of qPCR for mutation analysis?
A3: The many advantages of dPCR, such as high sensitivity and reproducibility, absolute quantification, reduced competition between DNA targets (minimizing bias from PCR efficiency differences), lower susceptibility to PCR inhibitors, simplified analysis, and the need for smaller sample volumes with faster turnaround times establish dPCR as a powerful tool for rare mutation detection (Trouchet et al, 2025).
Q4: Can dPCR be used for liquid biopsy?
A4: Yes, dPCR is widely used in analysis of cell-free DNA (cfDNA) and circulating tumor DNA (ctDNA) and monitoring of treatment response (Scimone C et at., 2024; Rosing F et al, 2024; Crucitta S et al, 2023). dPCR can also be used with more challenging sample types, like FFPE tissue.