Scientific Updates

Huang and Xie groups develop a new single cell whole genome amplification method


  Scientists at Biodynamic Optical Imaging Center (BIOPIC) makes great progress in single cell whole genome amplification. Recently Huang and Xie groups published a new single cell amplification method — emulsion whole genome amplification (eWGA) (PNAS, ). Compared to other existing methods for single cell whole genome amplification, eWGA can greatly improve the evenness and accuracy of amplification, enable simultaneous detection of small-size copy number variations (CNVs) and high confidence single nucleotide variations (SNVs). eWGA also increase the genome coverage and depressed the contamination, outperforming the prevailing single-cell amplifi- cation methods in many aspects.

  Single cell research is becoming one of the most active fields of life sciences. Many key functions in life have cell-to-cell heterogeneity, and in many studies the starting material is just around a few single cells. Single cell whole genome sequencing is a promising approach to precisely assess the complexity and heterogeneity of life processes. However, the scarce amount of DNA in a single cell has to undergo whole genome amplification to produce enough material for sequencing. This procedure is challenging. The unevenness of such amplification and copying error of the enzyme may result in the amplified molecules different from the original DNA. Thus, the CNV and SNV patterns identified from the amplified DNA sample may be incorrect.

          eWGA elegantly solves this problem by combining microfluidic technology with isothermal amplification chemistry. The genomic DNA of a single cell was evenly divided into nearly a million separated fractions, each of which was confined as a  pico-liter aqueous droplets in oil. Each droplet contains around one DNA fragment along with the reagent for multiple displacement amplification (MDA) reaction. Although the reaction rate is not the same between droplets, the final amplification yield will be the same after each droplet-reaction reaches saturation. eWGA inherits the low error rate of MDA technology using high-fidelity polymerase, while extraordinarily suppresses amplification bias, the notorious characteristic associated with MDA.  The result shows that eWGA is able to accurately detect small CNVs without inter-sample correction, and to probe high confidence SNVs simultaneously. eWGA can  be used to identify CNVs in single tumor cells with the highest resolution around 250kb. Besides, eMDA is compatible with targeted enrichment methods such as exome capture. The overall performance of eWGA makes it an ideal choice for single cell whole genome amplification.

  Yusi Fu, the first author of this paper, is a graduate student of BIOPIC at Peking University. This work is supported by NSF China.

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