Most Common Sample Types in ddPCR

Digital droplet PCR can be run with a variety of sample types, making it versatile for numerous applications in research and diagnostics. Some of the most common sample types compatible with ddPCR are listed below:

DNA Samples

  • Genomic DNA: Extracted from a variety of organisms, such as humans, animals, plants, and microbes.
  • Cell-free DNA (cfDNA): Found in plasma, used in liquid biopsies for cancer detection and prenatal screening.
  • Circulating tumor DNA (ctDNA): Derived from tumors and released into the bloodstream, used for cancer diagnostics and monitoring.
  • Formalin-fixed paraffin-embedded (FFPE) tissue DNA: Used in cancer research and diagnostics, as well as for archival tissue studies.

RNA Samples

  • Total RNA: Extracted from cells or tissues and reverse transcribed into cDNA for quantification of gene expression.
  • Cell-free RNA: Found in plasma or other bodily fluids, used in non-invasive diagnostics.
  • Viral RNA: Used in the detection and quantification of viral infections (e.g., HIV, SARS-CoV-2) after reverse transcription to cDNA.

Tissue Samples

  • Fresh or frozen tissues: Used in research for gene expression or mutation analysis.
  • Biopsies: Small tissue samples, including fine needle aspirations, for disease research or diagnostics.

Bodily Fluids

  • Blood/Plasma/Serum: Commonly used for liquid biopsy applications, monitoring disease biomarkers, and quantifying circulating nucleic acids.
  • Urine: Contains cfDNA and other biomarkers, useful in non-invasive diagnostics.
  • Saliva: Can be used for detecting viral or bacterial DNA, as well as human DNA for genetic testing.
  • Cerebrospinal fluid (CSF): Useful in detecting the presence of some pathogens such as Mycobacterium tuberculosis.

Microbial and Viral Samples

  • Bacterial and viral DNA/RNA: ddPCR is used for quantifying microbial loads in environmental samples, infections, or microbiome studies.

Environmental Samples

  • Soil and water samples: Can be used to detect and quantify microbial or viral DNA present in the environment.