Combined ResolveDNA® whole genome amplification with Twist Human Core Exome panel to generate high-quality human whole-exome data from single cells

Swetha D. Velivela1, Jon S. Zawistowski1, Isai Salas-González1, Viren Amin1, Victor J. Weigman1, Siyuan Chen2, Gary L. Harton1, Jason A.A. West1

  1. BioSkryb Genomics Inc, Durham, NC
  2. Twist Bioscience, South San Francisco, CA

Primary template-directed amplification (PTA) provides unprecedented genomic coverage and uniformity from single cells or low-input DNA, with high SNV calling sensitivity and minimal allelic dropout relative to existing methods. While assessment of the whole genome may be critical for some studies of single cells, other studies may aim to look exclusively at coding regions using whole-exome capture panels. This allows for a more cost-effective initial genomic survey of single cells. Here we report our success using the ResolveDNA WGA kit, based on PTA technology, combined with the Twist Human Core Exome hybrid capture panel (Twist Bioscience:PN:102025). ResolveDNA WGA combined with whole-exome sequencing of single cells will be a powerful tool to obtain high-quality exome data important for drug development & disease screening.

The Twist target enrichment panels yield highly uniform coverage due to the double-stranded nature of their probe set. We employed the Twist Human Core Exome panel (33Mb) to enrich Twist libraries derived from WGA products of GM12878 single cells using the ResolveDNA WGA kit. Following WGA and exome capture according to the manufacturers’ instructions, we sequenced (2) 8-plex pools on a NovaSeq 6000. The combined single-cell PTA protocol with the TWIST Human Core Exome panel achieved an average of 98% of the bases covered at 1x and 92% of the bases covered at 10X or higher, when downsampled to 40 million paired-end reads per library. We obtained robust coverage uniformity demonstrated by an average Fold 80 base penalty of 2.39, with a tight range between 2.29 and 2.76, as well by GC/AT dropout rate. This resulted in SNV calling sensitivity of 90% and 88% precision for these single cells.

Here we have shown the power of combining uniform single-cell whole genome amplification with whole-exome capture panels to allow reliable ascertainment of the exome, even at single-cell resolution. Coupling of these technologies has far-reaching potential in diverse applications including cancer, neurology, and preimplantation genetic testing.