The University of Michigan’s Oncology Sequencing Program, known as MiOncoSeq, analyzes DNA and RNA from patients’ tumors and healthy tissue to find genetic alterations that can inform treatment. Two new studies from the team, one published in Cancer Discovery and another in the New England Journal of Medicine, show how adding long-read nanopore sequencing to that process can surface genetic changes that conventional sequencing methods overlook entirely.
Long-read sequencing makes it possible to see how complex genetic changes are arranged relative to each other, something conventional methods often can’t resolve. As Arul Chinnaiyan, senior author on both papers, put it: “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.” Since most genes exist in two copies, one from each parent, this arrangement matters: nanopore sequencing can reveal whether one or both copies of a cancer-protective gene have been disabled through complex rearrangements or chemical changes, or whether several mutations have stacked up on a single copy of a cancer-promoting gene in ways that boost its activity or fuel drug resistance.
In one part of the Cancer Discovery study, the team screened 768 patients with prostate, breast or ovarian cancer and found 46 tumors showing signs of genomic instability that conventional sequencing couldn’t explain; long-read sequencing resolved 32 of those by uncovering hidden alterations or chemical modifications in protective genes. A broader screen of 4,496 tumor samples from 3,688 MiOncoSeq patients used nanopore sequencing in select cases to map how mutations were arranged in genes including NOTCH1, PDGFRB, KIT and PIK3CA, work the team says can clarify why some patients develop drug resistance and inform treatment decisions. The approach also caught an inherited risk a commercial multigene panel had missed: a woman with a strong family history of breast and ovarian cancer, who had tested negative on that panel, was found through nanopore sequencing of a blood sample to carry a disease-causing insertion in BRCA2, a DNA-repair gene—a finding the researchers hope could help guide genetic counseling for relatives in similar unexplained cases.
The second study traced a rare tumor that appeared beside the spine of a 3-year-old boy 26 months after he received gene therapy for Krabbe disease, an inherited disorder affecting the protective coating of nerve cells. The therapy, delivered after a stem cell transplant, used a modified virus to supply a working copy of the gene missing in Krabbe disease. Nanopore sequencing showed that a fragment of that viral DNA had inserted into the GLI1 gene, carrying genetic switches that drove abnormally high GLI1 activity capable of promoting tumor growth. At the time of the report, the child had no tumor-related symptoms and was being monitored with repeat imaging. “Gene therapy holds great promise, and understanding complications like this can help guide safer design,” Chinnaiyan said. “It is also important to monitor patients over the long term after they receive treatment.”
Long-read sequencing makes it possible to see how complex genetic changes are arranged relative to each other, something conventional methods often can’t resolve. As Arul Chinnaiyan, senior author on both papers, put it: “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.” Since most genes exist in two copies, one from each parent, this arrangement matters: nanopore sequencing can reveal whether one or both copies of a cancer-protective gene have been disabled through complex rearrangements or chemical changes, or whether several mutations have stacked up on a single copy of a cancer-promoting gene in ways that boost its activity or fuel drug resistance.
In one part of the Cancer Discovery study, the team screened 768 patients with prostate, breast or ovarian cancer and found 46 tumors showing signs of genomic instability that conventional sequencing couldn’t explain; long-read sequencing resolved 32 of those by uncovering hidden alterations or chemical modifications in protective genes. A broader screen of 4,496 tumor samples from 3,688 MiOncoSeq patients used nanopore sequencing in select cases to map how mutations were arranged in genes including NOTCH1, PDGFRB, KIT and PIK3CA, work the team says can clarify why some patients develop drug resistance and inform treatment decisions. The approach also caught an inherited risk a commercial multigene panel had missed: a woman with a strong family history of breast and ovarian cancer, who had tested negative on that panel, was found through nanopore sequencing of a blood sample to carry a disease-causing insertion in BRCA2, a DNA-repair gene—a finding the researchers hope could help guide genetic counseling for relatives in similar unexplained cases.
The second study traced a rare tumor that appeared beside the spine of a 3-year-old boy 26 months after he received gene therapy for Krabbe disease, an inherited disorder affecting the protective coating of nerve cells. The therapy, delivered after a stem cell transplant, used a modified virus to supply a working copy of the gene missing in Krabbe disease. Nanopore sequencing showed that a fragment of that viral DNA had inserted into the GLI1 gene, carrying genetic switches that drove abnormally high GLI1 activity capable of promoting tumor growth. At the time of the report, the child had no tumor-related symptoms and was being monitored with repeat imaging. “Gene therapy holds great promise, and understanding complications like this can help guide safer design,” Chinnaiyan said. “It is also important to monitor patients over the long term after they receive treatment.”