Rapid WGS at OICR supports COMPASS pancreatic cancer trial

Recent publication in Clinical Cancer Research describes rapid genomic profiling at OICR.

Genomic profiling of advanced pancreatic cases yields actionable mutations

In March, a team led by Dr. Kyaw Aung published a paper showing results from the first 62 paired whole genomes and transcriptomes sequenced at OICR as part of the COMPASS clinical trial. The team is proud to be supporting this initiative with an impressive median time from biopsy to report of 35 days. Within that time frame, the median time for sequencing to reporting was just 28 days!

High priority projects like COMPASS create a sense of urgency and bring the entire Genomics and GSI team together to ensure that the flow in the lab is as seamless as possible. One particularly remarkable case in the summer of 2016 was a young patient in his mid-20’s which the clinical team wanted to expedite. This case led several of us to ask how data could be generated as fast as possible and critically examine our overall lab processes to eliminate sources of delay.

One of the areas of lag we identified was the period between data coming off sequencers and the QC sign-off process. in most NGS labs, sequencing QC metrics are automatically generated using tools like FastQC and can pre-set thresholds can be relied on to identify problem samples. For many of our projects using clinical samples, such as COMPASS, default thresholds work as a guideline but sample variability creates the need for someone to review reports in the context of each sample and decide whether to continue with analysis or request the lab to conduct additional sequencing. Implementing additional communication processes ended up helping us improve turnaround times for COMPASS and other projects across the lab.

About the author

Paul Krzyzanowski is the Director of Genome Technology Translation at OICR and can be found on Twitter @pmkrzyzanowski.

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