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Digital PCR pp 173-190 | Cite as

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. UrbanEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1768)

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%.

Key words

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

Notes

Acknowledgments

Research reported in this chapter was supported by the National Institute of Mental Health of the National Institutes of Health under award numbers R01MH094740 and R01MH100914. We also acknowledge additional funds from Stanford University (Department of Psychiatry and Behavioral Sciences, and Department of Genetics).

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • Bo Zhou
    • 1
    • 2
  • Michael S. Haney
    • 1
    • 2
  • Xiaowei Zhu
    • 1
    • 2
  • Reenal Pattni
    • 1
    • 2
  • Alexej Abyzov
    • 3
  • Alexander E. Urban
    • 1
    • 2
    Email author
  1. 1.Department of Psychiatry and Behavioral Sciences, Stanford Center for Genomics and Personalized MedicineStanford University School of MedicinePalo AltoUSA
  2. 2.Program on Genetics of Brain Function, Department of GeneticsStanford Center for Genomics and Personalized MedicinePalo AltoUSA
  3. 3.Department of Health Sciences Research, Center for Individualized MedicineMayo ClinicRochesterUSA

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