Exploring DNA quality of single cells for genome analysis with simultaneous whole-genome amplification

Scientific Reports
Christiane BäumerChristian Korfhage

Abstract

Single cell genome analysis methods are powerful tools to define features of single cells and to identify differences between them. Since the DNA amount of a single cell is very limited, cellular DNA usually needs to be amplified by whole-genome amplification before being subjected to further analysis. A single nucleus only contains two haploid genomes. Thus, any DNA damage that prevents amplification results in loss of damaged DNA sites and induces an amplification bias. Therefore, the assessment of single cell DNA quality is urgently required. As of today, there is no simple method to determine the quality of a single cell DNA in a manner that will still retain the entire cellular DNA for amplification and downstream analysis. Here, we describe a method for whole-genome amplification with simultaneous quality control of single cell DNA by using a competitive spike-in DNA template.

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Citations

Apr 15, 2020·Biomedical Papers of the Medical Faculty of the University Palacký, Olomouc, Czechoslovakia·Aneta Brisudova, Jozef Skarda
Feb 9, 2020·Genome Biology·David LähnemannAlexander Schönhuth
Aug 19, 2020·Genome Biology·Xian F MalloryLuay Nakhleh
Nov 26, 2020·Clinical Reviews in Allergy & Immunology·Mingming ZhaoQianjin Lu
Jan 11, 2021·Forensic Science International. Genetics·Piyamas KanokwongnuwutAdrian Linacre

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Methods Mentioned

BETA
chromosomal aberrations
PCR
MDA

Software Mentioned

coWGA
R
package ineq
BEDTools

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