Measurement of copy number variation in single cancer cells using rapid-emulsification digital droplet MDA

Microsystems & Nanoengineering
Samuel C KimAdam R Abate

Abstract

Uniform amplification of low input DNA is important for applications across biology, including single-cell genomics, forensic science, and microbial and viral sequencing. However, the requisite biochemical amplification methods are prone to bias, skewing sequence proportions and obscuring signals relating to copy number. Digital droplet multiple displacement amplification enables uniform amplification, but requires expert knowledge of microfluidics to generate monodisperse emulsions. In addition, existing microfluidic methods are tedious and labor intensive for preparing many samples. Here, we introduce rapid emulsification multiple displacement amplification, a method to generate monodisperse droplets with a hand-held syringe and hierarchical droplet splitter. While conventional microfluidic devices require >10 minutes to emulsify a sample, our system takes tens of seconds and yields data of equivalent quality. We demonstrate the approach by using it to accurately measure copy number variation in single cancer cells.

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Citations

Oct 8, 2019·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Javier FlorenzaStefan Bertilsson
May 28, 2020·Lab on a Chip·Fangli ZhangYanyi Huang
May 26, 2018·Wiley Interdisciplinary Reviews. Nanomedicine and Nanobiotechnology·Aniruddha M KaushikTza-Huei Wang
Jul 11, 2020·Advanced Biosystems·Jacky Fong-Chuen LooYi-Ping Ho

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Methods Mentioned

BETA
MDA
biopsy
PCR
Feature Extraction
Assay
fluorescence-activated cell sorting
biopsies

Software Mentioned

re
stats
ddMDA
MDA
ggplot2
GenomicAlignments
Feature Extraction CytoGenomics
R
BWA Aligner
ShortRead

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