Improvement In Detection Sensitivity Of Rare Disease Variants For Liquid Biopsy Testing

ID U-6390

Category Research Tools (Non-Tangible Property)

Subcategory

Researchers

Hunter Underhill

Brief Summary

Method for generating large family size cell-free DNA while maintaining and improving test sensitivity.

Problem Statement

Circulating tumor DNA and tumor-derived exosomes are becoming popular as non-invasive cancer diagnostic tools, termed “liquid” biopsy. Standard next-generation sequencing (NGS) DNA processing approaches enable broad identification of both known and unknown tumor-associated variants, including single nucleotide variants. However, even with the highest fidelity sequencing platforms, errors introduced at >0.1% limit identification of disease associated variants that occur at <1% frequency. This increases the risk of over-representation of false variants and diminishes the clinical relevance of such tests.

Technology Description

University of Utah researchers have developed a droplet digital PCR (ddPCR) approach for enhancing detection sensitivity. This ddPCR approach has the following proprietary intervening steps to enrich circulating tumor DNA: (1) high-throughput automated gel extraction to isolate subfractions of the mononucleosomal peak and (2) specific adapter sequences or molecular identifiers that allow grouping of PCR duplicates into “family sizes.”

Stage of Development

Design & Development

Benefit

Fraction preselection reduces sample complexity and yields larger PCR family sizes.
Compatible with downstream NGS.
Improved detection sensitivity of rare variant alleles in ddPCR.
Reduces false positives.

Publications

Underhill HR, Kitzman JO, Hellwig S, Welker NC, Daza R, et al. (2016) Fragment length of circulating tumor DNA. PLOS Genetics 12(7): e1006162. https://doi.org/10.1371/journal.pgen.1006162

Hellwig S, Nix DA, Gligorich KM, et al. (2018) Automated size selection for short cell-free DNA fragments enriches for circulating tumor DNA and improves error correction during next generation sequencing. PLoS One 13(7):e0197333. https://doi.org/10.1371/journal.pone.0197333

IP

Publication Number: US-2019-0106737-A1
Patent Title: Size-Selection of Cell-Free DNA for Increasing Family Size During Next-Generation Sequencing
Jurisdiction/Country: United States
Application Type: Non-Provisional