How DRAGEN is being used by research and clinical genomics customers

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Application Case Study

Clinical Genomics

The Customer

HudsonAlpha has created one of the world’s first end-to-end genomic medicine programs to diagnose rare disease. HudsonAlpha Institute for Biotechnology is a genomic science and applications nonprofit organization. It is both a high-volume genomic data producer serving hundreds of academic, clinical, and commercial clients’ needs and a global scientific collaborator valued for its genomic data analysis and interpretation to solve some of the most pressing questions in cancer, undiagnosed disease, neuro-psychiatric disorders, immune-mediated disease, agriculture, and public health.

The Genomic Services Laboratory (GSL) was established in 2009 by Dr. Shawn Levy and is the hub for nearly all sequencing activity at HudsonAlpha. This unique facility leverages front-line genomic research tools for HudsonAlpha’s scientists and extends them to global academic institutions as well as commercial clients.

To date, the GSL has supported more than 1,800 projects and sequenced over 84,000 samples. These projects have been in collaboration with colleagues from HudsonAlpha and from hundreds of laboratories around the world. Data produced in the GSL have revealed the genetic causes of more than 10 inherited diseases and is contributing to the understanding of complex disorders such as autism, ALS, bipolar disorder, schizophrenia, diabetes and other diseases.

The Challenge

The speed with which data is produced is typically far greater than the speed with which it can be analyzed. After buying a HiSeq X Ten from Illumina, data ouput at the lab tripled with 15,000 human genomes coming down the pipeline every year. The analysis required to turn BCL files received as output HiSeq sequencers into the more useful variant call format (VCF) was lagging behind.

The GSL director, Shaw Levy recognized the need for a tool that could analyze this data rapidly and enable them to arrive at insights that could inform patient care sooner and unveil genetic causes of inherited diseases faster while simultaneously helping advance our understanding of complex genetic disorders.

The Solution

The 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. The DRAGEN genome pipeline includes highly optimized algorithms for BCL conversion (the company claims to do the BCL to FASTQ conversion in 12 minutes), 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.

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 available in a pre-configured server that facilitates easy integrated into next-generation sequencing bioinformatics workflows.

DRAGEN is currently used in Levy’s Genomic Services Laboratory, as well as in its newly established Clinical Services Laboratory, which performs 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.

The Results

The installation of the Dragen processor has allowed HudsonAlpha to phase out the servers that used to support its data analysis activities. A single DRAGEN processor is able to analyze the 15,000 human genomes generated by the institute’s HiSeq X Ten sequencing system, manufactured by Illumina Inc.

“Our collaboration has completely transformed the way we process whole-genome data.” HudsonAlpha GSL Director Shawn Levy said in a statement. “Our average time from completing chemistry on the sequencer to a VCF file being available is 40 minutes,” Levy has found that a single DRAGEN system will keep up with an Illumina X10 when processing a genome every 40 minutes.

Levy credits the system with preserving HudsonAlpha’s ability to meet its commitments. “The implementation of that DRAGEN card and the speed with which we’re able to do it completely saved our ability to deliver genomes on the timescale we were promising,” Levy said.