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LA Hospital Will Establish Core Facility, Implement Ion PGM to Study Childhood Cancers


By Monica Heger

The US Department of the Army has awarded $1.05 million to Timothy Triche, director of the center for personalized medicine at Children's Hospital Los Angeles, to develop a core facility to implement next-gen sequencing in the diagnosis and treatment of childhood cancers.

Triche told In Sequence via e-mail that the group will be using Life Technologies' newly launched Ion Torrent Personal Genome Machine, known as the Ion PGM (see story, same issue), and expects delivery of two of the machines by the end of the month.

The group will focus first on high-risk childhood cancers, specifically "bone and soft tissue sarcomas, which overall have less than 50 percent survival rates, compared with 80 percent overall survival for childhood cancer," Triche said.

In particular, the center will first study metastatic cancers, which have a 20 percent survival rate. Triche said that studying the highly malignant tumors will help in the overall understanding of metastatic cancer in children, "which will require mechanistic understanding and novel therapeutic approaches if improved outcomes are to be achieved."

Triche's group has collaborated with Helicos to study the childhood cancer Ewing's sarcoma in the past, and he said they will continue to use Helicos for "specific purposes, as we have amassed a large research database on that single-molecule sequencing technology and would like to remain consistent through the course of our current ongoing studies."

The team also plans to use Pacific Biosciences' single-molecule sequencing technology "through others who have established core capabilities with that technology."

The Ion PGM will be used for "targeted, clinically relevant studies, generally where the target or genomic region has been discovered by whole-genome methods," Triche said. Additionally, he said the system's fast turnaround time — two days start to finish, with just two hours of machine time — is "essential for clinical studies."

Because the group ultimately wants to develop diagnostic tools, Triche said he plans to seek CLIA and CAP certification for the new core facility, though that would likely be a year or two down the road.

In addition to sequencing technology, Triche said his team will also be using the NanoString nCounter technology, which measures gene expression, and can be used on many types of clinical samples, including FFPE samples.

The initial $1.05 million in funds will be used to purchase equipment, and to hire both a director and a research specialist technician, Triche said. Going forward, Triche said he hopes to secure additional funding to add more technology to the lab.

In addition to the $1.05 million grant, his team also has funding through another Department of Defense grant awarded to the Children's Oncology Group to study high-risk childhood cancers. Also, because the core facility will support both the children's hospital and the cancer center, funds will also come from grant-supported researchers who pay for services.

Have topics you'd like to see covered in In Sequence? Contact the editor at mheger [at] genomeweb [.] com.