# ERASE-Seq, an ultra-sensitive variant caller for liquid biopsy applications

> **NIH NIH R43** · FLUXION BIOSCIENCES, INC. · 2020 · $55,000

## Abstract

Abstract
Liquid biopsy tests based on cfDNA analysis have garnered a lot of interest, and show promise for being able
to determine the somatic mutational status of patients undergoing cancer treatment. For a significant fraction of
advanced stage patients, good agreement has been demonstrated between cfDNA and solid tumor variants.
Despite these exciting results, significant room for improvement remains. Even when using the leading cfDNA
CLIA test (Guardant Health) and testing advanced stage III and IV patients, about 30% of samples don’t have
sufficiently high prevalence variants to be detected. This leading test has demonstrated a detection limit of as
low as 0.3% allelic frequency (Guardant Health), but its specificity has only been demonstrated to be high
down to 2%. Sensitivity and specificity improvements will enable both test providers and individual genomic
test labs to routinely employ liquid biopsy tests across broad patient populations, and earlier in the disease
process.
The goal of this project is to develop a liquid biopsy workflow using ERASE-Seq, an ultra-sensitive somatic
variant caller. This is the first variant caller to make variant calls based on intersample data and a background-
aware model, which eliminates recurrent artifacts. A variant event matrix is assembled, containing the number
of occurrences in multiple sample and background runs for each variant. A statistical test then determines the
confidence score for presence of each variant over background, eliminating stochastic errors that contribute to
false positive calls.
The initial development and validation was performed using gDNA on a variety of different sequencing
technologies. High sensitivity detection of variants in sequencing data down to 0.1% allelic frequency was
shown, with no false positives detected across a full targeted somatic panel (>30kb). This performance is
superior to any molecular barcoding panels currently available and liquid biopsy CLIA tests for which sensitivity
and specificity data is available.
If successful, this grant will develop a universal tool for variant detection in cfDNA samples, providing order of
magnitude gains in sensitivity for a variety of different workflows and panels, without the added complications
associated with molecular barcodes. All users will have to do to use this tool is use the ERASE-Seq targeted
amplification kit and deliver fastq data to our ERASE caller software.

## Key facts

- **NIH application ID:** 10091631
- **Project number:** 3R43CA224894-01A1S1
- **Recipient organization:** FLUXION BIOSCIENCES, INC.
- **Principal Investigator:** CRISTIAN IONESCU-ZANETTI
- **Activity code:** R43 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $55,000
- **Award type:** 3
- **Project period:** 2018-09-10 → 2020-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10091631

## Citation

> US National Institutes of Health, RePORTER application 10091631, ERASE-Seq, an ultra-sensitive variant caller for liquid biopsy applications (3R43CA224894-01A1S1). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10091631. Licensed CC0.

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