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A novel PTA technology captures more than 95% of the genomes of single cells, providing more uniform, accurate, and reproducible single-cell analysis data.
On Dec. 1, 2020, BioSkryb, a developer of genomic amplification technologies, reported the release of foundational data demonstrating that primary template-directed amplification (PTA) has a superior ability to accurately and uniformly amplify the genomes of single cells. The data was released on bioRxiv, the preprint server, prior to publication.
Whole genome amplification (WGA) is required for low-input DNA and single-cell analysis, and single-cell approaches are critical for tackling difficult biological questions involving genomic heterogeneity. Current WGA technologies and methods for single-cell or low-input DNA analysis, however, only cover a fraction of the genome, have a limited capacity to detect genetic variation in each cell, and suffer from significant biases, experimental artifacts, and poor reproducibility. The new data show that PTA can overcome these limitations as well as provide high-quality, scalable analysis of single-cell genomic heterogeneity. Having access to this analysis can enable new insights into human disease at the cellular level and empower high-resolution diagnostics for cancer, gene-editing, and other applications, BioSkryb stated in a company press release.
Furthermore, the PTA technology accurately calls genomic variants within tissues, one cell at a time, and reproducibly captures more than 95% of the genomes of those cells in a more controlled and accurate manner than existing approaches. According to the data released, PTA can be reliably used to call copy number variation in primary cancer cells and genome-wide variant detection in gene-edited cells. The technology can enable the feasibility of performing single-cell evaluations of biopsies from cancer and gene-edited tissues.
The PTA technology has been made a part of BioSkryb’s ResolveDNA kits, which contain all the enzymes and reagents needed for whole genome amplification from single cells or ultra-low DNA inputs. The kits employ a unique set of nucleotides to prevent recopying of the amplification products, which results in less errors and higher, more uniform coverage of the genome. The PTA technology also enables the attachment of cell barcodes to the resultant products for pooling and downstream analysis.
“We developed PTA to accurately and efficiently decipher genetic diversity at the cellular level so that we can better detect, understand, and treat disease,” said Charles Gawad, MD, PhD, inventor of the PTA technology, cofounder of BioSkryb, and associate professor at Stanford University, in the press release. “These data show that PTA amplifies the genomes of single cells with high coverage breadth and uniformity in a reproducible manner to significantly improve variant calling of all types. The ability of PTA to enable highly accurate genetic information at single-cell resolution could uncover new drug targets for cancer and neurological diseases as well as identify CRISPR off-target activity to monitor the safety and fidelity of gene editing.”
“Chuck and I cofounded BioSkryb to ensure researchers had access to the most advanced DNA analysis technologies, so it’s especially exciting to see the superior performance of PTA over current methods and to be able to make it commercially available through our ResolveDNA kits,” said Jay West, PhD, CEO, and cofounder of BioSkryb, in the press release. “Existing whole genome amplification methods uncover a fraction of the genomic information, but now with ResolveDNA, researchers can explore new places in the genome and be confident in the quality of the sequencing data at those sites.”