Summary: Researchers developed a urine-based test utilizing whole genome sequencing to detect DNA fragments released by head and neck tumors. The test offers the potential for early detection of head and neck cancer, which lacks reliable screening methods.


  • The urine-based test detects ultra-short DNA fragments released by head and neck tumors that are often missed by conventional urine or blood-based tests, offering a novel approach to early cancer detection. 
  • The new study demonstrates the test’s ability to detect ctDNA in the urine of patients with breast cancer and acute myeloid leukemia, suggesting the potential for developing urine-based tests for a range of cancers.
  • Urine-based diagnostic assays offer advantages in convenience and patient compliance compared to blood-based assays. The self-collection of urine samples makes follow-up testing post-treatment more accessible for patients. 

Researchers from the University of Michigan Health Rogel Cancer Center created a urine-based test that detects pieces of DNA fragments released by head and neck tumors. The test could potentially facilitate early detection of this cancer type, which currently does not have a reliable screening method.

Urine Test Using Whole Genome Sequencing 

Using whole genome sequencing, the Rogel group showed that cell-free DNA fragments released by tumor cells, which are passed on from the bloodstream into urine through the kidneys, are predominantly ultra-short, with fewer than 50 base pairs. Given their small size, these fragments are likely to be missed using conventional urine or blood-based liquid biopsy tests in detecting circulating tumor DNA (ctDNA).

The research was led by Muneesh Tewari, MD, PhD, professor of hematology and oncology, J. Chad Brenner, PhD, associate professor of otolaryngology-head and neck surgery, and Paul L. Swiecicki, MD, associate medical director for the Oncology Clinical Trials Support Unit at Rogel. Initial results are published in JCI Insight.

“In this study we provide evidence to support the hypothesis that conventional assays do not detect ultrashort fragments found in urine, since they are designed to target longer DNA fragments. Our team used an unconventional approach to develop a urine test for HPV-positive head and neck cancer ctDNA detection,” says study co-first author and research specialist Chandan Bhambhani, Ph.D.

At-Home Urine Test

Still in the discovery phase, this mail-in test has already been distributed for research purposes to patients within a hundred-plus miles from Ann Arbor, allowing scientists to gather significant data on the efficacy of the at-home kit. Participants collect a urine sample and have it shipped back to the U-M laboratory, where the testing can be done to detect the presence or absence of head and neck cancer.

“One of the most remarkable outcomes of this study is that the test that has been developed has detected cancer recurrences far earlier than would typically happen based on clinical imaging. As such, these promising results have given us the confidence to broaden the scope of the study, seeking to expanding distribution even further,” says Brenner, co-senior author of the study.

Detecting Other Types of Cancer

While initial studies have focused on head and neck cancer, the paper also describes a new method that could be applied to expand the test to detect other cancers as well. For example, the authors show that the test can detect ctDNA in the urine of patients with breast cancer and acute myeloid leukemia. This suggests new opportunities to also study the application of urine-based testing for these additional cancers.

Further reading: Researcher Leads Development of Urine Test for Prostate Cancer Detection

“Many people are not aware that urine carries information about many different cancer types, although it is made in the kidneys. Our findings about the difference in ctDNA fragment sizes and the test we developed for HPV-positive head and neck cancer detection provide crucial information on how urine-based diagnostic assays can be developed for different cancers,” Bhambhani says. “Further, these types of tests are likely to have a much higher compliance in patients requiring follow-up testing post treatment, due to the convenience of self-collection of samples, when compared to blood-based assays.”