Ontario Institute for Cancer Research (OICR) researchers in Canada, together with international collaborators, have invented a technique to avoid a major problem with common laboratory techniques and improve the sensitivity of important cancer tests. The findings, published online on March 2, 2017 in Nature Protocols, describe a process by which the sensitivity of DNA sequencing can be improved. The technology, called SiMSen-Seq, could aid in detecting the recurrence of cancers, catching possible disease relapses faster than current methods and improving patient outcomes. The new article is titled “Simple Multiplexed PCR-Based Barcoding of DNA for Ultrasensitive Mutation Detection by Next-Generation Sequencing.” To sequence DNA, scientists often use a technique called polymerase chain reaction (PCR) to increase the amount of DNA available from a sample. However, PCR can introduce mistakes that can limit researchers' ability to detect real mutations in the original DNA molecules. To track the original molecules in a sample, molecular tags called DNA barcodes are added. This technique is essential for sensitive detection of mutations but can lead to other errors, as components of the tags can interfere with each other and affect the final results. "We created a DNA barcode with a hairpin structure that opens up to be read when heated and contracts when cooled. This allows us to 'hide' the barcode and analyze more patient DNA fragments in a single reaction," said Dr. Paul Krzyzanowski, Program Manager of OICR's Genome Technologies Program. Dr. Krzyzanowski led the development of the analysis pipeline software used in SiMSen-Seq. This software flags errors in sequencing results and corrects them computationally.
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