Accurate somatic variant calling performance using Avidity Sequencing with Burning Rock OncoScreenTM Plus panel

Abstract

BackgroundNext-generation sequencing (NGS) comprehensive genomic profiling panels provide targeted genome-wide detection of the somatic variant landscape of various cancer types. Recently, an innovative sequencing technology, Avidity Sequencing from Element Biosciences, has emerged to provide economical option for mid-throughput sequencing, with high quality (Q40). AimsThe aim of this study was to evaluate the performance characteristics of AVITI sequencing by avidity on detection of somatic variants from reference samples, and to compare the variant detection concordance between AVITI and NovaSeq sequencing platforms by evaluating the variant callings of 518 cancer-related genes using Burning Rocks OncoScreenTM Plus panel. MethodsContrived commercial reference control samples (harboring known variants) and clinical Formalin-Fixed Paraffin-Embedded tissue (FFPE) samples were examined to evaluate the variant detection performance of two sequencing platforms, with respects to Single Nucleotide Variant (SNV), Insertion-Deletion (Indel), Structure Variant (SV/Fusion), Copy Number Variation (CNV), Microsatellite Instability (MSI), and Tumor Mutation Burden (TMB). Variant specific QC metrics were developed to evaluate sequencing-level and variant calling level accuracy. All samples were processed utilizing the OncoScreenTM Plus assay, including library preparation and bioinformatics post sequencing data analysis. ResultsThe OncoScreenTM Plus assay is compatible with the AVITI system. Samples prepared with the OncoScreenTM Plus panel and sequenced on the AVITI system has successfully detected cancer related variants including SNV/Indels, SV/Fusion, CNVs, MSIs, and TMB, which were highly concordant with reference controls. In addition, the AVITI system produced a higher overall quality score, index assignment rate, mean target coverage, and lower optical duplication rate AVITI than NovaSeq system. ConclusionThe new sequencing technology Avidity from AVITI system can be applied seamlessly to current high-performance targeted oncology assays to reliably identify somatic variants in a flexible and cost-effective manner.