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Single-cell whole-genome analyses by Linear Amplification via Transposon Insertion (LIANTI)

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Science  14 Apr 2017:
Vol. 356, Issue 6334, pp. 189-194
DOI: 10.1126/science.aak9787

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Making an unbiased library

Sequencing the genome of single cells gives insight into issues such as cell-to-cell heterogeneity and genome instability. Key to single-cell sequencing techniques are whole-genome amplification (WGA) methods that provide sufficient DNA for next-generation sequencing. Current WGA methods have been hampered by low accuracy and spatial resolution of gene copy numbers and by low amplification fidelity. Chen et al. report an improved single-cell WGA method, Linear Amplification via Transposon Insertion (LIANTI). The DNA is randomly fragmented by Tn5 transposition of a transposon that includes a T7 promoter, which allows linear amplification. The authors used the method to determine the spectrum of single-nucleotide variations in a single human cell after ultraviolet radiation.

Science, this issue p. 189

Abstract

Single-cell genomics is important for biology and medicine. However, current whole-genome amplification (WGA) methods are limited by low accuracy of copy-number variation (CNV) detection and low amplification fidelity. Here we report an improved single-cell WGA method, Linear Amplification via Transposon Insertion (LIANTI), which outperforms existing methods, enabling micro-CNV detection with kilobase resolution. This allowed direct observation of stochastic firing of DNA replication origins, which differs from cell to cell. We also show that the predominant cytosine-to-thymine mutations observed in single-cell genomics often arise from the artifact of cytosine deamination upon cell lysis. However, identifying single-nucleotide variations (SNVs) can be accomplished by sequencing kindred cells. We determined the spectrum of SNVs in a single human cell after ultraviolet radiation, revealing their nonrandom genome-wide distribution.

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