# A highly sensitive linear amplification based DNA methylation profiling technique for clinical cancer research

> **NIH NIH R33** · UNIVERSITY OF CHICAGO · 2022 · $421,166

## Abstract

PROJECT SUMMARY
Validating highly sensitive molecular analysis approaches that can fully exploit precious clinical specimens will
transform cancer research and clinical applications. Tissue biopsy is the gold standard for cancer diagnosis
and has been the primary source of clinical biospecimens in cancer research. However, one of the biggest
challenges in basic and clinical cancer research is the frequent lack of sufficient amount of tumor materials
from biopsy for multi-omics research (e.g., parallel RNA and DNA-based profiling) after diagnostic procedures,
thus limiting progress in systems biology. As such, the ability to conveniently sample bodily fluids, including
circulating cell-free DNA (cfDNA) from plasma, offers great promise for enabling highly-sensitive, minimally-
invasive, cost-efficient cancer diagnostic methods, and facilitating screening of high-risk populations and
patient monitoring. However, cfDNA typically exists in extremely low quantity (e.g., a few nanograms from
several mL of blood). Cancer-derived cfDNA is expected to constitute an even smaller portion of the already
scarce cfDNA. To accelerate and enhance cancer biology and clinical applications, this R33 aims to validate a
novel technology for profiling DNA methylation, i.e., 5-methylcytosines (5mC), which contributes to cancer
pathobiology, is reflected in patient-derived cfDNA, and has been integrated in several FDA-approved tests.
Given the prevalence of 5mC in the human genome, its roles in gene regulation, and high chemical stability,
validating a novel 5mC technology in nanogram or sub-nanogram-level DNA materials offers promising
opportunities for various applications in cancer research that have been limited by technology that can utilize
limited clinical samples. Specifically, we developed the T7-Linear Amplification based Bisulfite Sequencing
(LABS-seq) that integrates a specially-designed bisulfite conversion procedure with the next-generation
sequencing (NGS) for sensitively and unbiasedly detecting 5mC in nanogram or sub-nanogram-level DNA
materials (e.g., 100 pg). Our preliminary results demonstrated the technical robustness of the LABS-seq and
the feasibility of using this innovative technology to identify cancer-specific 5mC changes in cfDNA. In this R33,
we will rigorously validate the LABS-seq technique using banked tumor tissues/cells and plasma cfDNA
samples from 250 patients with diverse cancer types and 50 frequency-matched healthy controls as well as
longitudinal samples from 200 prospectively recruited cancer patients. In Aim 1, we will validate the LABS-seq
in genomic DNA (gDNA) from tumor tissues/cells to detect cancer type-specific epigenetic alterations. In Aim 2,
we will validate the LABS-seq in cfDNA for the detection of cancer and longitudinal changes. Upon completion
of this project, we will provide a highly sensitive, cost-efficient, transformative epigenetic approach applicable
to both gDNA and cfDNA, opening up opportunities for resear...

## Key facts

- **NIH application ID:** 10413620
- **Project number:** 1R33CA269100-01
- **Recipient organization:** UNIVERSITY OF CHICAGO
- **Principal Investigator:** BRIAN C-H CHIU
- **Activity code:** R33 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $421,166
- **Award type:** 1
- **Project period:** 2022-06-08 → 2025-05-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10413620

## Citation

> US National Institutes of Health, RePORTER application 10413620, A highly sensitive linear amplification based DNA methylation profiling technique for clinical cancer research (1R33CA269100-01). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10413620. Licensed CC0.

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