FEATURE GENOMIC MEDICINE 025
level, and genetic testing will become as automated and routine as any other test. The biggest challenge is that our ability to sequence genes has advanced faster than our ability to process the information. Every individual who has his or her whole genome sequenced will have hundreds or even thousands of single nucleotide polymorphisms, and today we don’t know what the vast majority of them mean. We’re sequencing genes much faster than we can understand them. We face other critical challenges to develop appropriate quality control and proficiency testing mechanisms. Although it seems counterintuitive, laboratories are also struggling
with how to report the information in a useful format. In all those reams of data, which findings are relevant? If we give a treating physician a long report on the patient’s abnormal genes in a raw format without highlighting the important abnormalities or clearly explaining their significance, we have not provided clinically useful information.
DATA STORAGE ISSUES The amount of data storage that would be required to store everybody’s genetic information would be incredible, perhaps beyond today’s computing capacity. When you multiply the billions of base pairs in the human genome with the number of people in just the US, it’s a staggering amount of data. Some people predict that sequencing technology will become so cheap that, rather than try and store the genetic information, we’ll just re-analyze the patient’s DNA as needed.
WHEN TO JUMP IN? The technology platforms for genetic testing will change rapidly over the next decade and it’s impossible to predict at this point what technologies will survive and flourish. Ten years ago classic Sanger sequencing was the only technology. Today there are many, with more on the way, and no one knows which technologies will survive. Knowing when it is the right time for your laboratory to adopt one of the technologies is entirely dependent on the clinical needs in your area. When my cardiologists ask for a pharmacogenetic analysis to find out which patients are abnormal Plavix metabolizers, they must wait for a send-out test that takes a minimum of three days. If the cardiologist is placing the stent that very morning, he or she wants an answer faster. That kind of clinical pressure will lead laboratories to begin doing analyses closer to home, where we can get faster turnaround times. If a technology is available to provide the service we need, it will be adopted, but we need technologies that can be used in a routine clinical lab. We’re not there yet.
SPECIMEN INTEGRITY Fortunately, DNA samples are fairly stable, but when it comes to analysis of RNA or small molecules, change is extremely rapid, and a surgical specimen might need to be processed within five to ten minutes to preserve the metabolic pathways. Using proper collection and preservation techniques is extremely critical whether you do a test in-house or send it out.
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