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Applications

How DRAGEN is being used by research and clinical genomics customers

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Application Case Study

NICU Diagnostics

The Customer

The Center for Pediatric Genomic Medicine at Children’s Mercy Hospital in Kansas City, established in 2011, is among the first of its kind with a pediatric focus. The center provides clinical genomic services and is an epicenter for genomic research with a focus on sequencing and analysis of rare inherited diseases in children. Dr Stephen Kingsmore, the founding director, pioneered rapid genome sequencing to diagnose critically ill infants with suspected genetic disease.

The Challenge

Rapid (Whole Genome Sequencing) WGS is imperative in light of growing evidence of its utility in acute care, such as in diagnosis of genetic diseases in very ill infants where there is likely only a narrow time window for interventions. Early diagnosis can be life-saving. For some, it highlights a nutrient that the baby can’t break down because of certain genetic mutations, and changing the newborn’s diet can reverse the symptoms and stop further damage to the baby’s health. The sooner such diagnoses can be made, the less potential long term harms the infant suffers.

The Solution

Sequence data were generated with Illumina RTA 1.12.4.2 & CASAVA-1.8.2, aligned to the human reference GRCh37.p5 using GSNAP [22], and nucleotide (nt) variants were detected and genotyped with the Genome Analysis Tool Kit [23] (GATK, versions 1.6. and 3.2). Sequence analysis used FASTQ, bam, and VCF files. Variants were annotated with the Rapid Understanding of Nucleotide variant Effect Software (RUNES, v3.3.5)

The DRAGEN pipeline operates on a single-server hybrid hardware/software platform, with a dual Intel Xeon central processing units (CPUs), and a custom Peripheral Component Interconnect Express (PCIe) board with a field-programmable gate array (FPGA) and 32 GB of Dynamic random-access memory (DRAM) attached directly via four double data rate type three synchronous dynamic random-access memory DDR3 SDRAM channels. Critical compute-intensive functions of the pipeline are performed by custom massively parallel FPGA logic for maximum speed, while other functions run in optimized multi-threaded software on the Xeon cores, for maximum flexibility. A parallel (redundant array of independent disks, RAID 0) Solid State Drive (SSD) file system provides the I/O bandwidth necessary to feed the processing pipeline, and FPGA compress/decompress engines maintain throughput to and from compressed file formats.

DRAGEN uses a hash table index of a reference genome to map many overlapping seeds from each read to exact matches in the reference. After mapping, reads are sorted by reference position; PCR or optical duplicates are optionally flagged. An initial sorting phase operates on aligned reads returning from the FPGA. Final sorting and duplicate marking commences when mapping completes; these operations overlap variant calling when the latter is requested, and add almost zero time to the FASTQ-to-VCF pipeline.

The DRAGEN variant caller runs mostly in highly optimized software, for maximum flexibility of the algorithms. Only stable, compute-intensive operations are accelerated by FPGA engines. DRAGEN implements multi-threaded parallelism in a single pass over the whole reference genome, without launching multiple caller processes on various subsets of the reference. A single call to the DRAGEN executable runs the entire pipeline from FASTQ to VCF, for the whole genome. Mapping/alignment is done in one pass over the reads, and all steps of variant calling (in addition to read sorting and duplicate marking) run simultaneously in a software/hardware pipeline emitting VCF results.

Causative variants were identified primarily with Variant Integration and Knowledge INterpretation in Genomes (VIKING) software. By allowing dynamic filtering of variants based on variables such as individual clinical

features, diseases, genes, assigned ACMG-type pathogenicity category, allele frequency, genotype, and inheritance pattern, VIKING assists in identification of a differential diagnosis.

The Results

WGS with a 26-h time from blood sample to provisional diagnosis, was achieved by the acceleration of several components. Significant time-savings were achieved with Edico Genome’s DRAGEN processor. The time taken for sequence alignment, variant detection, and genotyping was reduced from approximately 15 h in gapped alignment, and variant calling with CASAVA v1.8.2 (Illumina), to approximately 40 min with the novel DRAGEN aligner and variant caller.

By using current technology and reducing the number of technicians needed to operate the device and analyze the data, DRAGEN could lower the cost of genetic sequencing from about $3 million to $6,500 per test

Researchers at Children’s Mercy Kansas City found that more than half of 35 critically ill infants undergoing a rapid whole-genome sequencing test received a genetic diagnosis, and almost two-thirds of those diagnosed saw a change in their clinical management, suggesting clinical utility of the test for selected patients.

“This technology is even more powerful in terms of its impact on the care of these babies than we expected,” says Dr. Stephen Kingsmore, now president of the Rady Pediatric Genomics and Systems Medicine Institute at Rady Children’s Hospital in San Diego. “Fully 60% of babies being tested are getting a diagnosis.” He added that he was pleasantly surprised that not only was the speed of DRAGEN unprecedented, but so was the accuracy. “We want to empower NICUs all around the country so babies in 2015 and 2016 can see the benefits of this,” he says.