Poster AGBT 2023

Integration of the ResolveOME™ multi-omics workflow with IDT xGen™ hybridization capture at single-cell resolution to obtain high quality exome data

Durga M. Arvapalli, Isai Salas-González, Benjamin Warlick, Viren Amin, Swetha D. Velivela, Katie Kennedy, Jamie Remington, Jeff Blackinton, Victor J. Weigman, Gary L. Harton, Jay A.A. West, Jon S. Zawistowski

Simultaneous examination of multiple -omic layers in single cells offers essential insights to decode the complexity of cancer and understand the pathophysiology of oncogenesis as well as tumor progression. ResolveOME™ amplification chemistry provides these insights through unified whole-genome and full-length transcriptome information from the same single cell. While whole genome sequencing (WGS) provides the complete complement of genomic elements for discovery, whole exome sequencing (WES) offers a cost-effective alternative while still providing the ability to ascertain the entirety of coding sequence.

Here we extend ResolveOME™ to a robust hybrid capture workflow to examine whole exomes. The core ResolveOME™ workflow is unification of template-switching single-cell RNAseq chemistry with ResolveDNA® whole genome amplification (WGA) technology, whereby the cDNA synthesized is separated from the genomic amplification fraction through affinity purification. The ResolveDNA® Library Preparation kit with enzymatic fragmentation was used to create libraries from the amplified genomic fraction. Prior to performing hybrid capture, low pass sequencing ensured high library complexity as assessed by the preseq algorithm. The libraries were pooled and enriched using the IDT xGen™ Exome Research Panel v2. The pool was 2X150 sequenced on an Illumina NextSeq 1000 instrument. The samples were downsampled to 40 million reads per library where analysis using BaseJumper™ software showed base coverage of 98% at 1X and 96% at 10X. The single-cell SNV calling metrics showed excellent precision and sensitivity of 99% and 92% respectively with robust allelic balance across single cells and with on + near target bases over 85%.

We demonstrated the successful coupling of the ResolveOME™ multi-omics workflow with IDT xGen™ Research Panel v2 hybridization capture of genomic libraries, providing the researcher a WES option in addition to WGS for maximizing cost and efficiency, with the key attributes of robust exomic metrics.