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

Bo Zhou, Michael S. Haney, Xiaowei Zhu, Reenal Pattni, Alexej Abyzov, Alexander E. Urban

Research output: Chapter in Book/Report/Conference proceedingChapter

2 Citations (Scopus)

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%.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Pages173-190
Number of pages18
DOIs
StatePublished - Jan 1 2018

Publication series

NameMethods in Molecular Biology
Volume1768
ISSN (Print)1064-3745

Fingerprint

DNA Transposable Elements
Nucleotides
Polymerase Chain Reaction
DNA

Keywords

  • Copy number variations (CNVs)
  • Droplet digital PCR (ddPCR)
  • Mobile elements
  • Single nucleotide variations (SNVs)
  • Somatic mosaicism

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

Cite this

Zhou, B., Haney, M. S., Zhu, X., Pattni, R., Abyzov, A., & Urban, A. E. (2018). 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. In Methods in Molecular Biology (pp. 173-190). (Methods in Molecular Biology; Vol. 1768). Humana Press Inc.. https://doi.org/10.1007/978-1-4939-7778-9_11

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. / Zhou, Bo; Haney, Michael S.; Zhu, Xiaowei; Pattni, Reenal; Abyzov, Alexej; Urban, Alexander E.

Methods in Molecular Biology. Humana Press Inc., 2018. p. 173-190 (Methods in Molecular Biology; Vol. 1768).

Research output: Chapter in Book/Report/Conference proceedingChapter

Zhou, Bo ; Haney, Michael S. ; Zhu, Xiaowei ; Pattni, Reenal ; Abyzov, Alexej ; Urban, Alexander E. / 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 in Molecular Biology. Humana Press Inc., 2018. pp. 173-190 (Methods in Molecular Biology).
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