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Two Children's Hospitals Plan to Move into Clinical Whole-Genome Sequencing with Ion Proton

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Two children's hospitals — the Hospital for Sick Children in Toronto and Boston Children's Hospital — are launching new initiatives to incorporate next-generation sequencing into their clinical workflow.

Both hospitals recently announced agreements with Life Technologies to co-develop sequencing workflows on the Ion Proton machine.

Stephen Scherer, who will co-direct the new Centre for Genetic Medicine at SickKids hospital, told Clinical Sequencing News that incorporating sequencing into the pediatric setting makes sense because nearly 70 percent of the patients admitted to children's hospitals have some form of genetic disorder. Indeed, pediatric hospitals such as the Children's Hospital of Philadelphia and the Children's Hospital of Wisconsin have been among the earliest adopters of next-gen sequencing in the clinical arena.

Currently, when patients are admitted, they undergo a range of testing, from microarray-based tests to karyotyping and single-gene tests, and sometimes all three, Scherer said.

However, "whole-genome sequencing, in theory, should be able to replace all of those tests," said Scherer. "The time seems to be right now to move whole-genome sequencing into the clinical research realm," he added.

Scherer said that researchers within the hospital have already been outsourcing whole-genome sequencing to both Complete Genomics and BGI to "get a handle on how to deal with whole-genome sequence datasets. …But, ultimately, we want to do this in-house."

Scherer said that four Ion Proton machines will be installed in the center in July. The center will first run the Proton I chip for exome sequencing, but plans to shift to whole genomes on the Proton II chip when it becomes available at the end of the year.

The machines will also be validated within a CLIA-certified and CAP-accredited laboratory.

The long-term goal is to make whole-genome sequencing the initial technology used for all patients admitted to the hospital — about 10,000 per year. Depending on patient consent, the sequence data could then be used for both diagnostic purposes and clinical research, Scherer said.

Scherer said he envisions that all samples will be handled in the same way, whether for clinical or research purposes, with genomes being sequenced on the Proton in the CLIA lab, and the data ending up "where it will have the most impact," whether that is for a research study or directly to the family.

As an initial project over the next year, the group will sequence autism exomes and genomes. The autism samples will be the same that are currently being sequenced by researchers led by Scherer at the SickKids' Center for Applied Genomics.

The team is in the midst of a 1,000-patient autism exome sequencing study. Scherer said that these same samples will be sequenced on the Proton, which will serve both to validate the technology for clinical use and also to look for new findings.

Scherer said that these autism samples are frequently re-assessed with new technology when it is brought into the lab, and the samples have now undergone extensive testing on microarrays and next-gen sequencing.

The Center for Applied Genomics at SickKids, which Scherer also directs, is the main genomics research center at the hospital and is currently equipped with the Illumina HiSeq 2000, Life Technologies' SOLiD and Ion Torrent PGM machines, and Roche's 454 GS FLX.

Scherer said the group chose the Proton for the new clinical center because it wanted a technology that would "get us to the right place" with regards to clinical sequencing. The Proton "met our requirements with respect to time to do the experiment, sequence capacity, and cost."

Boston Children's Hospital also plans to bring in the Ion Proton and develop clinical sequencing protocols in collaboration with Life Tech. Like SickKids, the hospital is building out a CLIA certified and CAP accredited sequencing facility.

Officials from Boston Children's Hospital declined to comment, but David Margulies, director of the Gene Partnership Program at the hospital, said in a statement that the collaboration is an "important first step toward providing informed, personalized care for patients whose conditions are difficult to treat."

Additionally, "the development of an optimized laboratory infrastructure will support our mission of providing the highest quality, innovative and cost effective care to our patients," he added.

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