Droplet Digital PCR (ddPCR)

Overview

Droplet digital PCR (ddPCR) is an absolute quantification method that partitions a PCR reaction into thousands of nanoliter droplets, each serving as an independent reaction. Positive and negative droplets are counted after endpoint PCR amplification, enabling highly sensitive detection and quantification of rare variants without the need for a standard curve. In cancer genomics it is used primarily for validation of low-frequency somatic mutations identified by next-generation sequencing and for quantification of subclonal variant allele frequencies.

Used by

  • Applied to validate subclonal/heterogeneity findings from whole-exome sequencing in grade II glioma paired initial/recurrent tumor cohort (n=23), confirming variant allele frequencies at low clonal abundance PMID:24336570
  • Used in 5/5 tested COADREAD cases to confirm frameshifted splice product from the recurrent APC intronic splice-acceptor mutation chr5:112151184 A>G in MSS CRC PMID:29316426

Notes

  • Sensitivity typically reaches 0.01–0.1% variant allele frequency, well below standard WES detection thresholds (~5–10%).
  • Used as an orthogonal validation method for mutations present at low allele frequencies in intratumoral heterogeneity studies.
  • Unverified corpus-grown slug; not a cBioPortal gene panel identifier.

Sources

This page was processed by crosslinker on 2026-05-09. - PMID:29316426

This page was processed by wiki-cli on 2026-05-15.