Systematic evaluation of signal-to-noise ratio in variant detection from single cell genome multiple displacement amplification and exome sequencing

BMC Genomics
Anita T SimonsenAnni Aggerholm

Abstract

The current literature on single cell genomic analyses on the DNA level is conflicting regarding requirements for cell quality, amplification success rates, allelic dropouts and resolution, lacking a systematic comparison of multiple cell input down to the single cell. We hypothesized that such a correlation assay would provide an approach to address the latter issues, utilizing the leukemic cell line OCI-AML3 with a known set of genetic aberrations. By analyzing single and multiple cell replicates (2 to 50 cells) purified by micromanipulation and serial dilution we stringently assessed the signal-to-noise ratio (SNR) from single as well as a discrete number of cells based on a multiple displacement amplification method, with whole exome sequencing as signal readout. In this setting, known OCI-AML3 mutations as well as large copy number alterations could be identified, adding to the current knowledge of cytogenetic status. The presence of DNMT3A R882C, NPM1 W288 fs and NRAS Q61L was consistent, in spite of uneven allelic read depths. In contrast, at the level of single cells, we observed that one-third to half of all variants were not reproduced in the replicate sample, and this allelic mismatch displayed an exponential functio...Continue Reading

References

Sep 30, 2005·Cytogenetic and Genome Research·A BuweM Schmid
Nov 6, 2014·British Journal of Haematology·Gro G PløenAnni Aggerholm
Jun 17, 2015·Annual Review of Genomics and Human Genetics·Lei HuangXiaoliang Sunney Xie
Sep 6, 2015·Proceedings of the National Academy of Sciences of the United States of America·Yusi FuYanyi Huang
Jan 26, 2016·Nature Reviews. Genetics·Charles GawadStephen R Quake
Feb 19, 2016·Genome Biology·Tomislav IlicicSarah A Teichmann
Apr 16, 2016·Genome Biology·Siyuan John LiuDaniel A Lim
Apr 1, 2017·Science·Celia Pilar Martinez-JimenezDuncan T Odom

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Citations

Jun 7, 2019·Integrative and Comparative Biology·Wendy R HoodGeoffrey E Hill
Aug 3, 2019·British Journal of Haematology·Peter HoklandMarie Bill
Oct 12, 2019·British Journal of Haematology·Marcus C HansenCharlotte G Nyvold
Jun 19, 2021·Nature Medicine·Daniela CesanaEugenio Montini
Aug 31, 2021·The EMBO Journal·Roberto VendraminCharles Swanton

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Methods Mentioned

BETA
exome sequencing
PCR
MDA
FCS
dissection
genotyping
single cell assay
single cell sequencing

Software Mentioned

Mathematica
BWA
Genome Analysis ToolKit ( GATK
Fluidigm
Picard
COSMIC
GATK
MDA

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