Single-Cell-Based Platform for Copy Number Variation Profiling through Digital Counting of Amplified Genomic DNA Fragments.
We develop a novel single-cell-based platform through digital counting of amplified genomic DNA fragments, named multifraction amplification (mfA), to detect the copy number variations (CNVs) in a single cell. Amplification is required to acquire genomic information from a single cell, while introducing unavoidable bias. Unlike prevalent methods that directly infer CNV profiles from the pattern of sequencing depth, our mfA platform denatures and separates the DNA molecules from a single cell into multiple fractions of a reaction mix before amplification. By examining the sequencing result of each fraction for a specific fragment and applying a segment-merge maximum likelihood algorithm to the calculation of copy number, we digitize the sequencing-depth-based CNV identification and thus provide a method that is less sensitive to the amplification bias. In this paper, we demonstrate a mfA platform through multiple displacement amplification (MDA) chemistry. When performing the mfA platform, the noise of MDA is reduced; therefore, the resolution of single-cell CNV identification can be improved to 100 kb. We can also determine the genomic region free of allelic drop-out with mfA platform, which is impossible for conventional single-cell amplification methods.
Beijing Advanced Innovation Center for Genomics (ICG), Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University , Beijing 100871, China.
Chunmei
C
Li
Beijing Advanced Innovation Center for Genomics (ICG), Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University , Beijing 100871, China.
Zhilong
Z
Yu
Beijing Advanced Innovation Center for Genomics (ICG), Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University , Beijing 100871, China.
Yusi
Y
Fu
Beijing Advanced Innovation Center for Genomics (ICG), Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University , Beijing 100871, China.
Yuhong
Y
Pang
Beijing Advanced Innovation Center for Genomics (ICG), Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University , Beijing 100871, China.
Yanyi
http://orcid.org/0000-0002-7297-1266
Y
Huang
D004247:DNA; D056915:DNA Copy Number Variations; D023281:Genomics; D017422:Sequence Analysis, DNA
D004247:DNA
DNA amplification; copy number variation; digital counting; genomic sequencing; maximum likelihood; single-cell