Developing mutation signature extraction (MSE) for human tissues

The National Cancer Institute awarded Duke University $232,297 on September 3, 2026, under the Cancer Detection and Diagnosis Research program (CFDA 93.394) to develop mutation signature extraction (MSE) for normal human tissues.

The project develops a novel method to detect cancer-causing mutation signatures in normal tissues without requiring tissue culture or whole-genome sequencing. The approach uses mammalian maximum depth sequencing (MMDS) to deeply sequence targeted genomic regions, preserving patient genome privacy while identifying rare mutation signatures that could support cancer early detection and prevention. The work proceeds through four aims: determining which genomic region yields sufficient independent DNA fragments to capture mutation signatures; testing and optimizing MSE to reach required detection limits; validating the approach in human samples; and establishing a framework for clinical application.

The award recipient is Duke University's Office of Research Administration, located in Durham, North Carolina. The period of performance extends through August 31, 2029. The assistance type is Project Grant, a standard competitive award based on scientific merit and program relevance.

Abstract

(public) mutation signatures characteristic of human cancers are a product of mutagenic events leading to cancer- causing mutations that initiate or promote tumorigenesis. Therefore, screening for these signatures in normal tissues could aid in cancer early detection, prevention, and interception. These signatures have been captured by sequencing the genomes of multiple clones derived from adapting bronchial brushings to grow in tissue culture, or more recently, from surveying large portions of the genome from a variety of tissues by error-corrected sequencing. Unfortunately, the first approach is limited to those very few human tissues that can be cultured and is completely impractical in a clinical setting while the second approach does not provide genome privacy to the patient and is limited to the western european genome to differentiate bona fide mutations from naturally occurring single nucleotide polymorphisms. Thus, a new method is needed to detect mutation signatures that neither requires establishing tissues to grow in culture nor relies on sequencing large portions of the genome. In this regard, we demonstrate that deeply sequencing a single short region of genomic DNA by the novel mammalian maximum depth sequencing (mmds) assay can detect a mutation signature in the normal tissues of mice following a carcinogen exposure. Further, by increasing the amount of genomic DNA sequenced, we propose that mmds could also identify the rarer mutation signatures in normal human tissues. To achieve this goal, we propose to develop mutation signature extraction (MSE) for normal human tissues based on mmds in four aims. In aim 1 we will determine which region of the genome yields sufficient independent (barcoded) DNA fragments for MSE to capture enough mutations to derive a mutation signature. In aim 2, we will test and optimize as needed MSE to reach a detection limit required to detect the rare mutations of a mutation signature. In aim 3, we will test and optimize as needed MSE to detect the mutations comprising the mutation signature in cultured human bronchial epithelial cells exposed to a tobacco smoke carcinogen. Finally, in aim 4 we will evaluate the ability of MSE to detect the mutations of the signature characteristic of tobacco smoking in actual human bronchial brushings isolated from patients that smoke tobacco. Completion of these four aims will develop MSE to identify the mutations defining mutation signatures in human tissues, ultimately for use in cancer early detection, prevention, and interception.