# Assay Validation of Cell-Free DNA Shallow Whole Genome Sequencing To Determine 'Tumor Fraction' in Advanced Cancers

> **NIH NIH UH2** · BROAD INSTITUTE, INC. · 2020 · $214,899

## Abstract

PROJECT SUMMARY
The overarching goal of this research is to utilize a plasma-based genomic biomarker of cell-free DNA (cfDNA)
to guide therapy in metastatic breast and other cancers. In our approach, we use a cfDNA ‘ultra low pass
whole genome sequencing’ (ULP-WGS) assay with computational pipeline (ichorCNA) to determine the
amount of tumor DNA in circulation (‘tumor fraction’; TFx). Changes in TFx may serve as an early identifier for
patients responding – or failing to respond – to therapy and cfDNA ULP-WGS provides a cost-effective,
minimally-invasive approach to determine TFx. Our ULP-WGS cfDNA assay allows rapid, precise quantitation
of TFx from a single blood sample without prior knowledge of tumor mutations. While most liquid biopsy
approaches to date have focused on tracking known alterations or commonly mutated genes in cancer, our
approach is mutation agnostic and broadly applicable across advanced cancers.
This proposal developed through deep collaboration between three primary investigators working on concert
on the development and application of a cell-free DNA assay to guide prognosis and therapy in advanced
cancers. To date, we have performed the research version of this assay on over 3000 patients samples and, in
three publications to date, we demonstrate clinical utility in metastatic breast and prostate cancer as well as
multiple myeloma. We bring expertise in clinical breast cancer, sequencing assay development, and CLIA
sequencing at scale, with a strong track record of collaboration with multiple shared publications. All three PIs
are dedicated to the success of this proposal, with distinct yet complementary roles and responsibilities.
In this proposal, we will analytically validate our cfDNA ULP-WGS assay (UH2 portion) then establish clinical
validity and prospectively evaluate performance in therapeutic clinical trials (UH3 portion). In the UH2 portion,
we will determine the sensitivity and specificity of ULP-WGS using serial dilutions of patient samples, then
assess reproducibility, repeatability, and reportable range. We will then determine performance in the context
of ‘real world’ pre-analytic variability including blood collection tube type, amount of plasma, and detection
thresholds with respect to DNA input quantity. In the UH3 portion, we will establish clinical validity by
evaluating TFx in 700 clinical plasma specimens from patients with metastatic breast cancer then advance our
understanding of cfDNA by evaluating the association of TFx with patient response to therapy and survival
outcomes. Finally, we will evaluate ULP-WGS in two prospective therapeutic clinical trials of metastatic triple-
negative breast cancer, evaluating association with response to therapy.

## Key facts

- **NIH application ID:** 9976072
- **Project number:** 1UH2CA239105-01A1
- **Recipient organization:** BROAD INSTITUTE, INC.
- **Principal Investigator:** Viktor Adalsteinsson
- **Activity code:** UH2 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $214,899
- **Award type:** 1
- **Project period:** 2020-08-01 → 2022-07-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9976072

## Citation

> US National Institutes of Health, RePORTER application 9976072, Assay Validation of Cell-Free DNA Shallow Whole Genome Sequencing To Determine 'Tumor Fraction' in Advanced Cancers (1UH2CA239105-01A1). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/9976072. Licensed CC0.

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