Clinical OMICS

NOV-DEC 2017

Healthcare magazine for research scientists, labs, pathologists, hospitals, cancer centers, physicians and biopharma companies providing news articles, expert interviews and videos about molecular diagnostics in precision medicine

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16 Clinical OMICs November/December 2017 Diagnostics Ring in the New Rady Children's Hospital Introduces NovaSeq for Newborn Diagnoses by Kevin Davies O ver the past few years, Stephen Kingsmore has pio- neered the use of clinical next-gen sequencing for the diagnosis of babies admitted into the newborn intensive care unit (NICU). That expertise was honed at Children's Mercy Hospital in Kansas City, before Kingsmore moved in 2015 to the Rady Children's Hospital in San Diego. In a presentation at the American Society of Human Genet- ics annual conference, Kingsmore presented his vision for enhancing and expediting the pipeline, which he believes will become widely adopted at children's hospitals around the world. Kingsmore already holds the Guinness World Record for the fastest genetic diagnosis—26 hours—which was set using Illumina's HiSeq 2500 sequencing instrument (in rapid run mode). The push for rapid sequencing is a hallmark of the work of Kingsmore and his team at Rady Children's. "Dr. King- smore in a pioneer, especially in the field of rapid whole genome sequencing for critically ill children in the NICU/ PICU," said Martin Reese, founder, president, and CEO of computational genomics company Fabric Genomics, which provides a platform for clinical interpretation of variants to the hospital's program. "Very few doctors have the in-depth genetics training and deep knowledge of sequencing and interpreting disease-causing variants." About 5 percent of all newborns are admitted to the NICU. The ensuing diagnostic odyssey can be short or long. "Some babies will die. Others will be discharged without a diagnosis," said Kinsgmore. At the center of Kingsmore's vision is Illumina's latest sequencer, the NovaSeq 6000. The goal is "to obtain a diagnosis as rapidly as possible" which would enable "scalable, high-throughput analysis to be used at various hospitals around the world." In brief, the Rady pipeline uses natural language process- ing to extract information from the patient's medical record. This is converted into a standard vocabulary that enables pattern recognition to match against some 8,000 known genetic diseases, which are listed in rank order. Whole-genome sequencing is performed on the newborn and parents (if possible). For the most urgent cases, the new- born's genome is currently sequenced on the HiSeq 2500, which typically takes about 30 hours. The sequence data are fed into a rapid analysis pipeline using Edico Genome's DRAGEN processing platform and Fabric Genomics' Opal clinical variant platform for interpretation. "We can obtain a provisional diagnosis in two days if [the newborn is] sick enough to warrant that," Kingsmore said. Fuel the Vision The Rady team's experience with the first 42 cases in this paradigm "fuel the vision," said Kingsmore. Eighteen (40 Dr. Stepehn Kingsmore stands with a new NovaSeq 6000 and a flow cell at Rady Children's Hospital. E. Grafton / Rady Children's Institute for Genomic Medicine

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