The UNM Cancer Center will be among a small number of sites worldwide to receive one of the first 20 units of the next-generation ion proton genome sequencer.
Genome sequencers help researchers discover the exact sequence of an individual’s DNA, which carries the instructions for protein manufacture inside a cell. The instructions are encoded in the DNA bases, or rungs of the DNA ladder-like structure. If these instructions go awry, the proteins that the cell builds may not function properly, and improperly functioning proteins can sometimes lead to cancer.
Whole genome sequencers in use today are quite expensive, so cancer researchers often narrow their focus. “Right now we typically sequence the one and a half million bases in the regions that are typically involved in cancer,” said Jeremy Edwards, associate professor of molecular genetics and microbiology and chemical engineering at the UNM Cancer Center. “With the ion proton, we will be able to routinely sequence the entire human genome, not just a small panel of cancer genes. That’s a great advantage.”
Existing whole genome sequencers can take two weeks to sequence an entire genome at a price of around $10,000. The new ion proton genome sequencer will be able to sequence the entire human genome of 3 billion bases in half a day for $1,000. This faster sequencing means Edwards can rapidly analyze an entire genome and use this technology in the clinic. Comparison of the entire genome from cancerous and noncancerous cells from the same individual could be used to define cancer treatment, a process known as precision medicine.
“We know there are variations in the genome because they’re what make us different from each other,” Edwards said. The 3 billion bases in the human genome typically have millions of polymorphisms – significant differences – that are recognized variations between individuals. But a cancer genome has approximately 10 mutations that could be playing a role in the cancer. It is a computational challenge to find these driver mutations and devise a therapy to treat the cancer.
Determining an individual’s specific variations and the differences between cancerous and noncancerous cells in the same person will enable researchers and clinicians to individualize that person’s treatment even further by linking mutations to their corresponding protein. “If we know where the mutations are, we can find out which ones are causing protein changes, what the protein changes are, and where they are,” Edwards said. “Then we can determine what we can do to help this person. What drugs are available to target this protein?” Sometimes, no drug that affects the protein in question is available, but there may be a drug that affects another part of the same chemical process within the cell. In the end, it’s possible to recommend a precise treatment for the individual.
Precision medicine is still in its infancy. Only clinical labs can be used to dictate treatments for patients in the U.S., and they are monitored much more closely than research labs. However, clinicians can use data from research labs like Edwards’ as long as they conduct their own investigation. The patient still benefits, but it’s a longer process. “The really big goal right now,” Edwards said, “is to bring this technology into the clinic to improve people’s treatments.”