Precision medicine promises to turn the medical framework on its head. Rather than only testing therapies to determine whether they are safe and effective for ‘most’ before they are available to ‘all,’ precision medicine applies technology to big data to investigate whether therapies will be effective, and, almost as important, will not be effective, for the individual.
The hope is that with tailored, ‘personalized medicine’— another common name for precision medicine — patients will respond to targeted therapies, and patients will avoid (more often) all too common onerous, often damaging treatment regimens. The reason this is so important is that diseases are unique to the individual; diseases progress differently in different people, and treatments that are effective for one person may fail altogether for another.
What if we had a barcode unique to each of us that would determine exactly what therapy might work? Well it turns out there is such a barcode called DNA (and its closely related friend RNA). Precision medicine increasingly is leveraging advances in big data to analyze large amounts of genomic data and apply the understanding gained to individual diseases and treatment. For hundreds of years the engine of medicine has been the clinical trial, which asks the central question of, what is effective for ‘most’ people. Genomic data, and the technology developed to compute, analyze and understand this data, is becoming the engine of medicine going forward.
Sixteen years ago the human genome was first assembled and published on the internet by leading researchers at UC Santa Cruz (David Haussler and Jim Kent of the nascent Genomics Institute)— and we all thought, ‘voila’, but alas timing is everything in life. Using genomics to help guide therapy in a patient is not new. What is new is the vision to share and consolidate all the cancer genomic data so everyone can share the scientific and technical knowledge for the benefit of each new patient. By many measure we are now at a point of understanding more and more of that code on a monthly basis, and it’s accelerating. Building on the publishing of the human genome, UC Santa Cruz’ Genomics Institute is pursuing several initiatives in precision medicine particularly for childhood cancer and adult breast cancer.
Ongoing initiatives
At the Treehouse Childhood Cancer Initiative, researchers are identifying potential treatments for children with cancer who would otherwise have no therapeutic options. They do this through precision medicine, leveraging large genomic databases. Treating cancer—and particularly cancer in children—is a problem of genomic data analysis as much as medicine. Using a precision medicine approach, researchers and their computer engineering counterparts deploy technologies to gain genomic insights from large datasets of genomic material. Treehouse has a database of 11,000+ tumor gene expression profiles—publicly available to researchers everywhere—against which it compares a child’s tumor. At the bottom of this process are algorithms mathematically similar those that Amazon uses to find products you may like based on those you’ve purchased. By finding other tumors, Treehouse can gather clues as to what is going wrong with the cells, and using different automated analyses of big data clinical trials and FDA drug approvals, can determine whether promising therapies exist. This allows the team to discover actionable individualized leads for treatment possibilities for kids who, most often, have run out of possibilities.
Eventually by sharing data and outcomes from patients worldwide researchers will have vast information about the effectiveness of therapies and risks of disease across individual characteristics. Precision medicine not only leads to information when the disease has progressed, but it also can point to individual vulnerabilities to inform life choices. Innovations in breast cancer research, reaped by precision medicine, offer good examples. One of the most well-known of these is BRCA—a ‘mistake’ in our ability to repair DNA replication errors. Two genes, BRCA1 and BRCA2, have over 20k different ‘variants.’ Some are harmless, but others increase your lifetime risk of cancer to almost 70 percent. Today, finding out whether you have one of these is very easy—for $250 you can spit in a cup and 10 days later learn your BRCA variants are. However, more often than is comfortable, the variant discovered is unknown, or rather the implications of it are unknown. Using precision medicine computational approaches, there is a worldwide effort to transform the ‘unknown’ to ‘known’.
This model can apply to all cancers, and eventually to all diseases. A new initiative known as the Cancer Gene Trust is working to generalize the virtuous cycle that the BRCA Exchange began. The Cancer Gene Trust is gathering information about all tumors and, as in Treehouse, advocating for the sequencing of tumors. By paving the path for the genomic information on the tumor to be ‘exhausted’ in real time from the clinic into a global database, a virtuous cycle is made possible. Every patient’s data cannot only be used to the good of the patient, but can be added to an ever-expanding database of information, to help the next patients, and then the next.
