Long-Read Sequencing Reveals Cancer-Driving Changes Missed by Conventional Testing

Cancer diagnosis often relies on identifying genomic alterations that influence tumor behavior and treatment selection. However, conventional short-read sequencing can miss complex DNA changes, leaving the underlying cause of genomic instability unresolved in some tumors. By reading longer stretches of the genome, long-read nanopore sequencing may help uncover these changes. New findings demonstrate this capability, revealing cancer-driving alterations that conventional methods failed to detect.

University of Michigan researchers incorporated long-read nanopore sequencing into Michigan’s Oncology Sequencing Program (MiOncoSeq), which launched in 2010 to analyze DNA and RNA from normal tissue and tumors for alterations that could guide treatment. The added technology reads thousands to tens of thousands of DNA letters in a single stretch, allowing researchers to examine complex changes and determine how they are arranged.

This capability can reveal whether one or both copies of a cancer-protective gene are disabled by complex DNA rearrangements or chemical modifications. It can also establish whether multiple mutations occur together on a single copy of a cancer-promoting gene, a configuration that may increase gene activity or contribute to drug resistance. 

In one arm of the study, researchers screened 768 patients with prostate, breast, or ovarian cancer and identified 46 tumors with genomic instability that conventional sequencing could not explain. Long-read sequencing resolved 32 of these cases by uncovering hidden alterations or chemical changes affecting cancer-protective genes.

In a broader analysis, the team screened 4,496 tumor samples from 3,688 MiOncoSeq patients, then used nanopore sequencing in selected cases to determine how mutations were arranged in genes including NOTCH1, PDGFRB, KIT, and PIK3CA. These findings were published in Cancer Discovery.

A separate study, published in the New England Journal of Medicine and involving University of Michigan collaborators, applied nanopore sequencing to a rare paraspinal tumor in a 3-year-old boy who had received gene therapy for Krabbe disease.

“Having a list of mutations doesn't always explain a tumor. We need to understand how these mutations are arranged, which conventional sequencing often cannot resolve,” said Arul Chinnaiyan, M.D., Ph.D., S.P. Hicks Professor of Pathology and Urology, director of the Michigan Center for Translational Pathology and a Howard Hughes Medical Institute investigator. 

“Gene therapy holds great promise, and understanding complications like this can help guide safer design. It is also important to monitor patients over the long term after they receive treatment,” added Dr. Chinnaiyan.

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