Beware the IDES

Beware the IDESResearchers at the Stanford University School of Medicine have devised a way to significantly raise the sensitivity of a technique to identify and then sequence DNA from cancer cells that circulate in a person’s blood, with the hope that such “liquid biopsies” of easily-obtained blood samples could eventually replace the need to surgically obtain tumor tissue for study.

This new approach works by identifying errors that occur when tumor DNA is captured from the blood and prepared for sequencing.  Removing these errors from the sequencing results will allow researchers to more accurately find true cancer-associated mutations from even miniscule amounts of starting material.  Researchers say that this means they’ll be able to detect the presence of specific mutations in the cancer DNA that could help to drive treatment choices or detect the presence of residual cancer, getting us closer to reducing the need for invasive biopsies to identify tumor mutations or track response to therapies.

Even without treatment, cancer cells are constantly dividing and dying, releasing DNA into the bloodstream.  Learning to identify and read these and pick out the one in 1,000 or one million that come from a cancer could help clinicians quickly and noninvasively monitor the presence and volume of a tumor, a patient’s response to therapy and even how the tumor mutations evolve over time in the face of treatment or other selective pressures.  Researchers termed their new, two-pronged approach “integrated digital error suppression”, or IDES.  This builds upon a method called CAPP-Seq that was previously designed to capture very small amounts of tumor DNA from the blood.

IDES builds upon CAPP-Seq by addressing an inherent technical limitation: an inability to accurately sequence very small quantities of DNA.  Before any sequencing can be attempted, many copies need to be made of each double-stranded DNA fragment, in a process known as amplification, during which time the chance of introducing an error in the sequence becomes higher and higher.  Researchers, therefore, needed a way to determine whether mutations identified during the sequencing process came from the tumor or were introduced during the sequencing process.  They used “bar codes” that uniquely mark each original molecule to tag circulating double-stranded DNA molecules.  Since the strands of original DNA fit together, it’s possible to predict the sequence of one strand from the other.  Bar codes therefore allowed the researchers to match up the two strands and work from there.

Since it eliminates more false positives without sacrificing true positives, the researchers say that their technique is a significant advance.  Tagging top DNA molecules allows them to keep track of which molecules have been faithfully reproduced during the sequencing process.  The bar-coding approach was then combined with a computer algorithm meant to scan data and flag any possible trouble spots.  This combination allowed the researchers to filter out common sequencing mistakes far more efficiently than either technique used on its own.

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