Comparison of whole genome amplification techniques for human single cell exome sequencing
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BACKGROUND: Whole genome amplification (WGA) is currently a prerequisite for single cell whole genome or exome sequencing. Depending on the method used the rate of artifact formation, allelic dropout and sequence coverage over the genome may differ significantly. RESULTS: The largest difference between the evaluated protocols was observed when analyzing the target coverage and read depth distribution. These differences also had impact on the downstream variant calling. Conclusively, the products from the AMPLI1 and MALBAC kits were shown to be most similar to the bulk samples and are therefore recommended for WGA of single cells. DISCUSSION: In this study four commercial kits for WGA (AMPLI1, MALBAC, Repli-G and PicoPlex) were used to amplify human single cells. The WGA products were exome sequenced together with non-amplified bulk samples from the same source. The resulting data was evaluated in terms of genomic coverage, allelic dropout and SNP calling.
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MDA is known to have high allelic dropout and preferential amplification rates.
“which is common in single cell applications but is known to have high allelic dropout and preferential amplification rates (22).”
From Frequent loss of heterozygosity in CRISPR-Cas9–edited early human embryos (2021) · cites this paper as [22]
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- Authors
- Borgström, E., Paterlini, M., Mold, J. E., Frisen, J., & Lundeberg, J.
- Affiliations
- Science for Life Laboratory (SE)
- Karolinska Institutet (SE)
- Corresponding author
- Lundeberg, Joakim
- Venue
- PLOS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2017-02-16
- Volume
- 12
- Issue
- 2
- Pages
- e0171566
- ISSN
- 1932-6203 (ISSN-L)
- PMC
- PMC5313163
- OpenAlex
- W2587987600
- Cited by
- 77
- References
- 25
- Citations by year
- 2026: 5 · 2025: 3 · 2024: 8 · 2023: 6 · 2022: 7 · 2021: 13 · 2020: 7 · 2019: 5 · 2018: 18 · 2017: 4
- FWCI
- 3.80
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- PLoS ONE (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- Figshare (submittedVersion, cc-by)
- Funders
- The Swedish Cancer Society
- European Research Council (BE)
- Knut och Alice Wallenbergs Stiftelse (SE)
- Vetenskapsrådet (SE)
- Karolinska Institutet (SE)
- Tobias Foundation
- Torsten Söderbergs Stiftelse (SE)
- StratRegen
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Keywords
- whole genome amplification, single-cell sequencing, allele dropout, variant calling, MALBAC, human cells, SNP calling
- MeSH terms
- Humans, Genome, Human, Sequence Analysis, DNA, Polymorphism, Single Nucleotide, Nucleic Acid Amplification Techniques, Single-Cell Analysis, High-Throughput Nucleotide Sequencing, Exome
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