CHICAGO (GenomeWeb) – A program to bring rapid genomic testing to 12 of 13 neonatal intensive care units in Australia and all six pediatric ICUs has received ethics approval and should begin recruiting patients in the next two weeks, according to one of its leaders.
The Australian Genomics Health Alliance-sponsored program, called Acute Care Genomics, aims to collect 250 DNA samples from critically ill infants and children, then return genomic test results in as little as five days. It will be the first nationwide effort in Australia involving rapid gene-based diagnosis of rare disease, organizers said.
Today, Victorian Clinical Genetics Services (VCGS), the laboratory and clinical genetics arm of the Murdoch Children's Research Institute near Melbourne, Australia — and one of the two testing sites for the program — announced a technology deal with Edico Genome to support Acute Care Genomics. VCGS said it began using Edico's Dynamic Read Analysis for Genomics (DRAGEN) Bio-IT platform in January for fast analysis of sequencing data.
"Testing is limited to pediatric cases in intensive care at one of the member hospitals where there is a strong suspicion of an underlying genetic condition," Sebastian Lunke, who heads translational genomics at VCGS, explained via email.
"Diagnosing children and newborns in the NICU and PICU is a race against the clock. While NGS is known to be a rich diagnostic tool, lengthy turnaround times have prevented its use in this setting," Edico Genome President and CEO Pieter van Rooyen said in a statement.
"Shrinking NGS analysis times enables potentially life-altering results and corresponding treatments to be received as quickly as possible while increasing labs' capacity, enabling more patients to benefit from NGS," van Rooyen added.
For the Acute Care Genomics program, VCGS is splitting the work with Genome.One, a sequencing-based diagnostics startup from the Garvan Institute of Medical Research. Sydney-based Genome.One is getting cases from the Australian states of New South Wales and Queensland, Lunke said, while hospitals in Victoria and South Australia are referring tests to VCGS.
The program seems off to a good start. "We have already successfully processed a handful of pilot samples here at VCGS using DRAGEN technology, all in under 70 hours from sample receipt to fully accredited clinical report," Lunke told GenomeWeb. That beats the five-day goal by 50 hours.
VCGS initially is focusing on clinical germline whole-exome sequencing, but Lunke said the Melbourne center is "investigating and evaluating" other capabilities of the Edico technology for the future, including RNA analysis. "There is no doubt in my mind that the DRAGEN will also play a central role in our future endeavor to achieve accreditation for WGS," Lunke said.
To prepare for the Acute Care Genomics launch, VCGS tested DRAGEN Bio-IT for six months. The system met the institution's requirements for speed and accuracy of germline analysis, as well as for precision in processing of clinical samples, according to Lunke. During the test phase, VCGS integrated the DRAGEN platform into its existing pipeline automation system and its clinically accredited analysis workflows.
There are no current plans to integrate with other information systems at VCGS, though Edico on Monday announced a partnership with InterSystems to link genomics and electronic health records workflows.
VCGS chose a local installation of DRAGEN rather than a cloud option. "This was done to adhere with Australian privacy laws, but also to increase analysis speeds," Lunke said. "As it stands, DRAGEN can process data quicker than we could upload and download it to and from the cloud."
An Edico representative likened the Australian partnership to one Edico has with the Rady Children's Institute for Genomic Medicine in San Diego. That organization uses Illumina STAT-seq rapid WGS tests to help diagnose and treat critically ill newborns.
Indeed, Lunke said he turned to Rady Children's Institute for Genomic Medicine President and CEO Stephen Kingsmore for advice while evaluating technology for Acute Care Genomics.
"Stephen Kingsmore's recommendation of the [Edico] platform was a key factor in our decision to trial the system. Indeed it is fair to say that his work was part of what inspired us to embark on the Acute Care Genomics journey in the first place," said Lunke, who made the long trip to visit Rady last year.
VCGS has also been looking to bring genomics into the prenatal space. In late 2014, the center signed a deal with Illumina to develop noninvasive prenatal tests using Illumina sequencers.
While VCGS is among the few genetic labs in the Southern Hemisphere to have NIPT for whole-chromosome analysis, Lunke said that there is "no overlap" between this work and the new Edico partnership at present.