At Fluxion, we’re passionate about delivering cell-based and cell-free solutions that facilitate the transformation of research discoveries into new ways to diagnose and treat patients. By characterizing molecular and cellular mechanisms of disease, Fluxion’s platforms help bridge the translational medicine gap, enabling rapid advances in disease research, drug discovery, and the development of diagnostic tests.
Inter-sample digital processing improves sensitivity and specificity of variant calling; results superior to molecular barcoding approaches
Alameda, Calif. -- Fluxion Biosciences announced today the publication of peer-reviewed research on its ERASE-Seq™ bioinformatics solution. The paper, titled “ERASE-Seq: Leveraging Replicate Measurements To Enhance Ultralow Frequency Variant Detection In NGS Data”, was published in PLOS One on April 9 and is co-authored by researchers at Illumina and Swift Biosciences. Data presented demonstrates that ERASE-Seq provides variant-calling performance superior to competitive sequencing approaches at the very low allele frequencies (to 0.1% and below) required for liquid biopsy samples, with DNA input quantities as low as 20ng.
Liquid biopsies offer the potential to improve treatment of cancer by providing affordable, non-invasive detection of actionable cancer mutations from a blood sample. However, the relative abundance of cancer DNA in blood is extremely low, below the sensitivity threshold of standard sequencers. Approaches such as molecular barcodes have resulted in improved performance; however, high sensitivity and, importantly, high specificity have been difficult to achieve at allele frequencies between 0.1-0.5%. This is a critical region for somatic cancer variant detection in liquid biopsies, and data presented here demonstrate that ERASE-Seq provides superior results compared to competitive approaches, whether the sample type is genomic DNA from cells or fragmented cell-free DNA (ctDNA) from plasma.
“Fluxion’s ERASE-Seq bioinformatics solution utilizes statistical processing and background modeling to reduce both systematic (repeated) errors as well as random errors (noise), without the need for molecular barcodes (unique molecular IDs, or UMIs)”, states Cristian Ionescu-Zanetti, PhD, CTO.
“ERASE-Seq works by comparing sample technical replicates to a well-characterized background noise model that is developed for each targeted NGS panel. This approach allows true variants to be accurately detected at very low levels where other techniques, such as molecular barcoding, show high numbers of false positives”, stated Bioinformatics Director Nick Kamps-Hughes, PhD. “ERASE-Seq provides levels of sensitivity normally only associated with droplet digital PCR (ddPCR), an analytical technique that is considered the gold standard for sensitivity. However, ERASE-Seq offers the ability to test for thousands of variants in a single sample, where ddPCR is limited to only a few variants per test.”
Results of the study include targeted sequencing of gDNA and ctDNA samples using the following panels: Spotlight 59 (Fluxon), TruSight Tumor 15 (Illumina), and Accel-Amplicon 56G (Swift Biosciences). ERASE-Seq is available as a cloud-based or locally-installed software solution. The PLOS One paper is available for download via the PLOS One website.