1Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; 2Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; 3Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China; 4Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing 100871, China
Single-cell genomics is important for biology and medicine. However, current whole genome amplification (WGA) methods do not accurately reflect unamplified samples. Here we report a much improved single-cell WGA method, Linear Amplification via Transposon Insertion (LIANTI). By truly linear amplification of DNA fragments created by transposition, LIANTI supersedes existing methods in all aspects, enabling micro-CNV detection in single cells with kilobase resolution. This allowed us to observe the stochastic firing of DNA replication origins, different from cell to cell. We also proved that the predominant cytosine-to-thymine SNVs observed in single-cell genomics often arise from spontaneous cytosine deamination upon cell lysis. Such artifact can be avoided by sequencing kindred cells. Accordingly, we determined the true spectrum of SNVs in a single human cell after ultraviolet radiation, revealing their nonrandom genome-wide distribution.
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