Clinicians and researchers at the University of Michigan have developed a pilot system to enable the use of high-throughput sequencing in the cancer clinic. They have shown that they can perform a broad, deep genomic analysis of patients with drug-resistant cancer, and based on that data, potentially match patients with clinical trials, all within 3 to 4 weeks.

As the price of sequencing drops, researchers see the potential for whole-genome analysis, rather than tissue type or small numbers of biomarkers, to guide treatment. But how to integrate the huge amount of data generated by whole-genome analysis into the clinic in a practical way is still an open question, says Sameek Roychowdhury, MD, PhD, a pathologist at the University of Michigan.

Roychowdhury and his colleagues performed whole-exome sequencing of tumor and normal tissue, and whole-genome and transcriptome sequencing of the tumor, in one patient with metastatic colorectal cancer and a second patient with malignant melanoma. They then convened a Sequencing Tumor Board (composed of clinicians, geneticists, bioinformatics experts, ethicists, and others) to match these patients to clinical trials based on the information obtained.

They showed that this process could be done within 4 weeks for $5,400 per patient—not including labor. Roychowdhury says this compares favorably to the price of genotyping products on the market today, which provide a more limited scope of information.

However, Roychowdhury notes that neither patient was eligible for any existing clinical trials. He hopes the results of the pilot study will help persuade researchers and agencies designing clinical trials to write their protocols in such a way that biomarkers—not just tumor type—can be incorporated into eligibility assessment. For example, the patient with colorectal cancer had several mutations, including CDK8 amplification, but was ineligible for a CDK8-inhibitor trial because it was designed for patients with ovarian cancer.

“How do you analyze these data to generate a therapy in a way that's clinically viable? That's completely up in the air,” comments Trey Ideker, PhD, chief of the genetics division at the University of California, San Diego School of Medicine. Studies like the one at Michigan are the only way to find out, he says. “This provides proof-of-principle for how this approach would work in the clinic.”

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