GENETIC TESTING

New Speed Record Set for Genome Analysis

Anew world record was set for fastest analysis of 1,000 genomes on Oct. 19. The achievement was a collaboration between Children’s Hospital of Philadelphia (CHOP) and Edico Genomics (San Diego, Calif.). The milestone, achieved in just under two and a half hours, brings precision medicine one step closer to mainstream clinical practice, the participants say.

The 1,000 deidentified research samples were curated to reflect the composition of CHOP’s Center for Applied Genomics (CAG) biobank. The samples represent common complex disorders and rare single-gene diseases. Results from the rapid analysis will be utilized by the CAG with the hope of uncovering genetic links to common childhood diseases, including asthma, autism, diabetes, epilepsy, obesity, schizophrenia, pediatric cancer, and other rare diseases.

"The speed of this technology in processing vast amounts of raw data in a matter of minutes will allow us to deliver actionable results in hours—an important capability as we go forward in realizing the benefits of precision medicine for children and families," says Hakon Hakonarson, M.D., Ph.D., director of CAG in a statement.

The title was presented onsite by an official Guinness World Records adjudicator, and will be granted upon publication of the results in a peerreviewed journal. Analysis began with the streaming of the 1,000 data files in standard FASTQ format from Amazon Simple Storage Service (S3) to 1,000 Amazon EC2 F1.2xlarge instances, which deployed the DRAGEN Genome Pipeline. The pipeline entailed mapping, aligning, sorting, duplicate marking, and haplotype variant calling. The process ended when a variant call format file was delivered back to a secure Amazon S3 bucket.

Edico’s pipeline has been used to set another Guinness World Record: the 26-hour diagnostic genome conducted by Stephen Kingsmore and his colleagues at the Center for Pediatric Genomic Medicine at Children’s Mercy in Kansas City.

Takeaway: With dramatic decreases in the time to process and interpret whole genomes, whole-genome sequencing results may be returned in time for critical clinical decision-making.

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