Detection and Quantification of Mosaic Genomic DNA Variation in Primary Somatic Tissues Using ddPCR: Analysis of Mosaic Transposable-Element Insertions, Copy-Number Variants, and Single-Nucleotide Variants

Methods Mol Biol. 2018;1768:173-190. doi: 10.1007/978-1-4939-7778-9_11.

Abstract

Here, we describe approaches using droplet digital polymerase chain reaction (ddPCR) to validate and quantify somatic mosaic events contributed by transposable-element insertions, copy-number variants, and single-nucleotide variants. In the ddPCR assay, sample or template DNA is partitioned into tens of thousands of individual droplets such that when DNA input is low, the vast majority of droplets contains no more than one copy of template DNA. PCR takes place in each individual droplet and produces a fluorescent readout to indicate the presence or absence of the target of interest allowing for the accurate "counting" of the number of copies present in the sample. The number of partitions is large enough to assay somatic mosaic events with frequencies down to less than 1%.

Keywords: Copy number variations (CNVs); Droplet digital PCR (ddPCR); Mobile elements; Single nucleotide variations (SNVs); Somatic mosaicism.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA / genetics
  • DNA / isolation & purification*
  • DNA Copy Number Variations / genetics*
  • DNA Transposable Elements / genetics*
  • Humans
  • Mosaicism*
  • Polymerase Chain Reaction / methods*
  • Polymorphism, Single Nucleotide

Substances

  • DNA Transposable Elements
  • DNA