ArticleScientific reports2015
Quantitative assessment of single-cell whole genome amplification methods for detecting copy number variation using hippocampal neurons.
Article in Scientific reports, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed, 109 citations in OpenAlex.
- Differential performance of strategies for single-cell whole-genome amplification.Cell reports methods · 2025Article
- Metagenomic detection of protozoan parasites on leafy greens aided by a rapid and efficient DNA extraction protocol.Frontiers in microbiology · 2025Article
- Single-cell somatic copy number variants in brain using different amplification methods and reference genomes.Communications biology · 2024Article
- Single-cell somatic copy number variants in brain using different amplification methods and reference genomes.bioRxiv : the preprint server for biology · 2023Article
- Chromosome instability and aneuploidy in the mammalian brain.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2023Review
- Appropriate whole genome amplification and pathogenic loci detection can improve the accuracy of preimplantation genetic diagnosis for deletional α-thalassemia.Frontiers in endocrinology · 2023Article
- Leveraging single-cell sequencing to unravel intratumour heterogeneity and tumour evolution in human cancers.The Journal of pathology · 2022Review
- HBV genome-enriched single cell sequencing revealed heterogeneity in HBV-driven hepatocellular carcinoma (HCC).BMC medical genomics · 2022Article
- Whole-Genome Amplification-Surveying Yield, Reproducibility, and Heterozygous Balance, Reported by STR-Targeting MIPs.International journal of molecular sciences · 2022Article
- Improvement in the risk assessment of oral leukoplakia through morphology-related copy number analysis.Science China. Life sciences · 2021Article
- Comparison of seven single cell whole genome amplification commercial kits using targeted sequencing.Scientific reports · 2021Article
- scDPN for High-throughput Single-cell CNV Detection to Uncover Clonal Evolution During HCC Recurrence.Genomics, proteomics & bioinformatics · 2021Article
- Single-cell sequencing of the small and AT-skewed genome of malaria parasites.Genome medicine · 2021Article
- Article
- Experimental and bioinformatics considerations in cancer application of single cell genomics.Computational and structural biotechnology journal · 2021Article
- Investigation of somatic CNVs in brains of synucleinopathy cases using targeted SNCA analysis and single cell sequencing.Acta neuropathologica communications · 2019Article
- DNA Analysis by Restriction Enzyme (DARE) enables concurrent genomic and epigenomic characterization of single cells.Nucleic acids research · 2019Article
- A low cost and input tailing method of quality control on multiple annealing, and looping-based amplification cycles-based whole-genome amplification products.Journal of clinical laboratory analysis · 2019Article
- Defining Cell Identity with Single-Cell Omics.Proteomics · 2018Review
- Application of single-cell sequencing in human cancer.Briefings in functional genomics · 2018Review
Corrections and comments
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Authors and funding
13 authors at 4 institutions in 2 countries.
Funding
Abstract
Single-cell genomic analysis has grown rapidly in recent years and finds widespread applications in various fields of biology, including cancer biology, development, immunology, pre-implantation genetic diagnosis, and neurobiology. To date, the amplification bias, amplification uniformity and reproducibility of the three major single cell whole genome amplification methods (GenomePlex WGA4, MDA and MALBAC) have not been systematically investigated using mammalian cells. In this study, we amplified genomic DNA from individual hippocampal neurons using three single-cell DNA amplification methods, and sequenced them at shallow depth. We then systematically evaluated the GC-bias, reproducibility, and copy number variations among individual neurons. Our results showed that single-cell genome sequencing results obtained from the MALBAC and WGA4 methods are highly reproducible and have a high success rate. The MALBAC displays significant biases towards high GC content. We then attempted to correct the GC bias issue by developing a bioinformatics pipeline, which allows us to call CNVs in single cell sequencing data, and chromosome level and sub-chromosomal level CNVs among individual neurons can be detected. We also proposed a metric to determine the CNV detection limits. Overall, MALBAC and WGA4 have better performance than MDA in detecting CNVs.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.