Edico Genome announced that its Dragen Bio-IT processor has been integrated into HudsonAlpha Institute for Biotechnology’s next-generation sequencing workflow, thereby increasing the throughput of the sequencing facility and eliminating the need for expensive servers.
A single Dragen processor is able to analyse the 15,000 human genomes generated by the Institute’s HiSeq X Ten sequencing system, manufactured by Illumina Inc. As part of the Dragen integration, HudsonAlpha developed a front-end management system to enable robust and automated transfer of data from a collection of sequencers to the processor, and automated reporting of results at the conclusion of the analysis.
Dragen is currently utilised in HudsonAlpha’s high-volume Genomic Services Laboratory, as well as in its newly established Clinical Services Laboratory, which performs mix levy 1280 whole genome sequencing for patients with medical conditions. The processor also is used in HudsonAlpha’s Clinical Sequencing Exploratory Research (CSER) consortium project, initiated by the National Human Genome Research Institute (NHGRI) and the National Cancer Institute (NCI) and uses exome sequencing to diagnosis children with developmental delays.
“Our purchase of an Illumina HiSeq X Ten sequencing system more than tripled the number of whole genomes we are sequencing to just over 15,000 per year, and we recognised we needed a tool that could analyse this data rapidly and enable us to arrive at insights that could inform patient care sooner,” said Shawn Levy, Ph.D., director of the HudsonAlpha Genomics Service Laboratory.
“Dragen’s ability to analyse genomic data rapidly while also reducing costs will enable us to unveil genetic causes of inherited diseases faster, while simultaneously helping advance our understanding of complex genetic disorders. Our average time from completing chemistry on the sequencer to a VCF file being available is 40 minutes. Our collaboration has completely transformed the way we process whole-genome data.”
Added Pieter van Rooyen, Ph.D., chief executive officer of Edico Genome, “HudsonAlpha’s implementation of Dragen is a great example of the benefits that Dragen can confer to high-volume genomics labs. We continue to see high demand for our Dragen platform from many different players in the genomics field that have a need for fast and cost-effective data analysis, including clinical labs, sequencing centers, large and small companies and academic institutions.”
Dragen is the first processor designed for genomic applications, and is able to analyse a whole human genome (30x coverage) from FASTQ to variant call format (VCF) in under 28 minutes, compared to over 14 hours using standard software. Dragen’s speed has been further extended to the time-consuming step immediately prior, BCL to FASTQ, completing this conversion in only 12 minutes compared to many hours using standard algorithms.
The Dragen genome pipeline includes highly optimised algorithms for BCL conversion, compression, mapping, alignment, sorting, duplicate marking, haplotype variant calling and joint genotyping, and the reconfigurable processor can be loaded with additional pipelines, such as RNAseq, methylome, microbiome and cancer. Dragen is available in a pre-configured server that is easily integrated into next-generation sequencing bioinformatics workflows. The supporting workflow that Dr. Levy’s lab has developed will be freely available to academic labs.
HudsonAlpha Institute for Biotechnology is a genomic science and applications nonprofit organisation.
Edico Genome, developer of the world’s first next-generation sequencing Bio-IT processor, Dragen, is helping usher in the new era of precision medicine by enabling customised treatments and data-driven insights tailored to the individual.