Researchers at St. Jude have invented an improved method for amplifying the genomes of single cells which they have termed Primary Template-Directed Amplification (PTA) that improves uniformity, reproducibility and genome recovery. In addition, this method produces shorter amplicons which will allow the addition of cellular barcodes, enabling massively parallel amplification of genomes of single cells that recently became possible for single-cell RNA-seq (http://www.cell.com/abstract/S0092-8674(15)00549-8).
This discovery can be used in research labs to study the clonal heterogeneity and drug resistance of cancer samples. The protocol is easy to carryout, can be implemented in a highly parallel manner, and reduces the cost of sequencing per cell. Widespread interest in the cancer research community (like Drop-Seq for single-cell RNA-seq) is expected.
This type of single-cell whole genome amplification can also be used to screen embryos for preimplantation genetic diagnoses and to study the roles of mosaicism in human disease. The researchers anticipate single-cell DNA sequencing will be incorporated into clinical cancer diagnostics, as it is more sensitive than standard sequencing methods and has the ability to identify clonal populations by segregating mutations into the same cells.
This new method has specific advantages compared to current approaches used to amplify the genomes of single cells:
a.) PCR-based methods (DOP-PCR) are uniform but recover <40% of the genome,
b.) Isothermal Methods (Multiple Displacement Amplification or MDA) recover >80% of the genome but are extremely non-uniform so high depth of sequencing is needed to call variants.
c.) hybrid methods (MALBAC, PicoPlex) perform intermediate between the two (improved uniformity but with only 50-60% genome recovery).
Amplify, genome, Primary Template-Directed Amplification (PTA), genetic diagnoses, cancer diagnostics.
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