Wednesday, November 29, 2017
Fastest time to analyze 1,000 human genomes: world record set by the Children's Hospital of Philadelphia
Philadelphia, PA, USA -- The Children's Hospital of Philadelphia(CHOP) and Edico Genomeused the DRAGEN pipeline to process 1,000 whole pediatric genomes in two hours and twenty-five minutes, thus setting the new world record for Fastest time to analyze 1,000 human genomes , according to the World Record Academy .
Photo: Using Edico Genome's DRAGEN pipeline on 1,000 Amazon EC2 F1 instances, the Children's Hospital of Philadelphia (CHOP) and Edico Genome set a new scientific world standard in rapidly processing whole human genomes. ( enlarge photo )
CHOP used the DRAGEN pipeline to process 1,000 whole pediatric genomes in two hours and twenty-five minutes. The feat set the set the World Record title for Fastest time to analyze 1,000 human genomes.
The demonstration used a pediatric cohort of 1,000 whole genomes from the Center for Applied Genomics (CAG), a specialized Center of Emphasis at CHOP. The de-identified samples were chosen to reflect the composition of the entire biobank and represent the most common complex disorders and rare single-gene diseases.
FASTQ files were moved from Amazon S3 buckets into the EC2 F1.2xlarge instances, which use Xilinx Virtex UltraScale+ field programmable gate arrays (FPGAs).
The DRAGEN pipeline consisted of mapping, aligning, sorting, duplicate marking, and haplotype variant calling and ended when a variant call format (VCF) file was delivered back to a secure Amazon S3 bucket.
"Today's speed test is a culmination of two years of collaboration between CAG and Edico Genome, including beta-testing their product in our center," said Hakon Hakonarson, M.D., Ph.D., director of CAG at CHOP in a press release.
"We utilize DRAGEN as part of our genomic workflow to achieve our mission of translating basic research findings to medical innovations. 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."
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