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Rapid Whole-Genome Sequencing: Faster Diagnosis for Rare and Confounding Conditions

January 7, 2019

A collaborative effort between the UPMC Newborn Medicine Program, the Division of Medical Genetics at UPMC Children’s Hospital of Pittsburgh, and the Institute for Precision Medicine (IPM) — a collaborative effort between the University of Pittsburgh and UPMC — is providing rapid genomic testing for NICU patients who present with rare and difficult to diagnose conditions for which there may be an underlying genetic cause.

The UPMC Genome Center within the IPM, directed by Annerose Berndt, PhD, is providing rapid, low-cost, whole-genome sequencing to support clinical diagnostics and research initiatives, not only for NICU patients, but more broadly for cancer and immunotherapy research throughout UPMC and the University of Pittsburgh.

One of the first efforts of the UPMC Genome Center is examining the efficacy of whole-genome sequencing in critically ill infants admitted to the NICU at UPMC Children’s. Rapid, whole-genome sequencing may, in some cases, identify possible genetic-based diseases in an expedient manner.

Thomas Diacovo, MD, chief of the UPMC Newborn Medicine Program, is leading the NICU efforts at UPMC Children’s together with Jerry Vockley, MD, PhD, director of Medical Genetics at UPMC Children’s, and counterparts at the IPM, including Adrian Lee, PhD, on the NICU sequencing project.

“In addition to making a rapid diagnosis that can have profound implications on clinical care, “A crucially important aspect of any genetic profiling and sequencing program is helping families to understand the genetic information, its implications for the individual and family at-large, and how to interpret the information to make informed decisions for care and follow-up. This information has to be given in the appropriate context and with the necessary assistance to understand what it may mean for the patient and family,” says Dr. Diacovo.

UPMC Children’s Participates in New National Precision Medicine Clinical Trial

A new multicenter clinical trial sponsored by the National Center for Advancing Translational Sciences (NCATS) at the NIH is studying the use of rapid, targeted, next-generation sequencing technology to diagnose underlying genetic causes for disease in high-risk neonates.

Over a five-year period, the trial, led by researchers at Floating Hospital for Children at Tufts Medical Center, will enroll neonates who may have a variety of genetic disorders, but whose diagnoses were unable to be determined through the use of standard testing. The new study entails the conduction of whole-genome sequencing of the neonates, as well as a targeted examination of 1,722 genetic disorders known to afflict newborns.

The study will then compare the results between the targeted screening and the whole-genome sequencing to determine the viability of the targeted panel approach. UPMC Children’s is participating in the trial with Tufts Medical Center and four other institutions: Rady Children’s Institute for Genomic Medicine, Mt. Sinai Hospital, University of North Carolina at Chapel Hill, and Cincinnati Children’s Hospital.

“This study holds the promise of profound changes in how newborns are screened for life-threatening disorders, which is currently limited to a dozen conditions. For critically ill patients, time is of the essence and a diagnostic odyssey is out of the question. Many of these disorders will have treatments that may prevent or slow the progression of disease, but only if we know the cause and can find it quickly. That’s the promise of this trial,” says Dr. Diacovo.