RARE Daily

PacBio and GeneDx and UW Launch Collaboration to Study Long-Read Whole Genome Sequencing for Neonatal Diagnosis

August 7, 2023

Rare Daily Staff

PacBio and GeneDx said they have entered into a research collaboration with the University of Washington to study the capabilities of HiFi long-read whole genome sequencing to increase diagnostic rates in pediatric patients with genetic conditions.

“Through this work, we move closer to our vision of creating a world where no family spends years on a diagnostic odyssey trying to understand the underlying genetic cause of their child’s disease or wondering whether future children will also be afflicted,” said Christian Henry, president and CEO of PacBio.

GeneDx will perform WGS sequencing and analysis of samples from 350 people including 120 enrolled in the SeqFirst WGS study at Seattle Children’s Hospital, as well as their biological parents—duos and trios—as available. Both short- and long-read WGS will be performed as researchers explore whether novel variants not previously accessible via short-read sequencing technologies may underlie certain genetic conditions.

Conventional care for children with rare diseases is often empirical, imprecise, and only modestly effective—leaving substantial room for improvement and innovation. The “promise” of more precise, and by inference, better care, begins with accurate genetic diagnoses. SeqFirst is a project that tests whether whole genome sequencing of children with suspected developmental differences at point-of-diagnosis, as opposed to conventional diagnostic evaluations, will lead to earlier, more rapid diagnoses, reduce costs of these diagnoses, and improve therapeutic outcomes. SeqFirst, sponsored by GeneDx and in part funded by the Brotman Baty Institute, is a hub for genomic research and precision medicine, and a collaboration among three Seattle research institutions—UW Medicine, Seattle Children’s Hospital, and Fred Hutchinson Cancer Center.

“Long-read sequencing is a potential approach for interrogating whole human genomes and the novel variants inaccessible with short-read sequencing,” said Mike Bamshad, SeqFirst principal investigator, professor and chief of genetic medicine in the Department of Pediatrics at the University of Washington School of Medicine and Seattle Children’s Hospital.

GeneDx will use the PacBio Revio sequencing system to perform all long-read WGS sequencing and analysis for this study. The study intends to determine whether the increased accuracy, read-length and methylation insights offered by the Revio system will enable collaborators to better explore–and potentially increase–diagnostic yield. Aggregate sequencing data including novel variants and their frequencies identified through this study will be contributed to the Consortium of Long Read Sequencing (CoLoRS) database to advance scientific understanding of variant prevalence and classification.

PacBio has previously partnered with Google to implement the deep learning method DeepConsensus on the Revio system and improve long-read whole genome sequencing performance with DeepVariant. Google has expanded upon this earlier technical collaboration to contribute funding for this research study.

“These collaborations will allow us to realize goals from the origin of Google Health—for AI to find real applications in healthcare to help with critical and complex cases,” said Greg Corrado, head of health AI at Google. “By contributing to solutions for the most complex cases and the least served communities, we believe we can demonstrate the usefulness and importance of such technologies in better health outcomes.”

Photo: Christian Henry, president and CEO of PacBio.

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