Abstract
In this study, we aimed to assess the performance of two whole-genome amplification methods, multiple displacement amplification (MDA), and multiple annealing and looping-based amplification cycle (MALBAC), for β-thalassemia genotyping and single-nucleotide polymorphism (SNP)/copy-number variant (CNV) detection using two DNA sequencing assays. We collected peripheral blood, cell lines, and discarded embryos, and carried out MALBAC and MDA on single-cell and five-cell samples. We detected and statistically analyzed differences in the amplification efficiency, positive predictive value, sensitivity, allele dropout (ADO) rate, SNPs, and CV values between the two methods. Through Sanger sequencing at the single-cell and five-cell levels, we showed that both the amplification rate and ADO rate of MDA were better than those using MALBAC, and the sensitivity and positive predictive value obtained from MDA were higher than those from MALBAC for β-thalassemia genotyping. Using next-generation sequencing (NGS) at the single-cell level, we confirmed that MDA has better properties than MALBAC for SNP detection. However, MALBAC was more stable and homogeneous than MDA using low-depth NGS at the single-cell level for CNV detection. We conclude that MALBAC is the better option for CNV detection, while MDA is better suited for SNV detection.
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Acknowledgements
We are grateful to the Liuzhou Municipal Maternity and Child Healthcare Hospital for helping collect discarded embryos, including cleavage-stage and blastocyst-stage embryos. The study was supported by the Natural Science Foundation of China (code: 31671314, 81370670), Science and Technology Planning Project of Guangzhou (201604020045), and Science and Technology Planning Project of Guangdong Province (2016A020214011).
Author contributions
F.H. and W.Z. conceived the study, participated in the design, carried out the experimental work, and drafted the manuscript. R.C. and T.Y. participated in the sample collection. X.X. conceived the study, participated in the design, and drafted the manuscript. All authors read and approved the final manuscript.
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He, F., Zhou, W., Cai, R. et al. Systematic assessment of the performance of whole-genome amplification for SNP/CNV detection and β-thalassemia genotyping. J Hum Genet 63, 407–416 (2018). https://doi.org/10.1038/s10038-018-0411-5
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DOI: https://doi.org/10.1038/s10038-018-0411-5
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