A genome sequencing system for universal newborn screening, diagnosis, and precision medicine for severe genetic diseases

• Published in: American journal of human genetics Vol. 109; no. 9; pp. 1605 - 1619
• Main Authors: Kingsmore, Stephen F., Smith, Laurie D., Kunard, Chris M., Bainbridge, Matthew, Batalov, Sergey, Benson, Wendy, Blincow, Eric, Caylor, Sara, Chambers, Christina, Del Angel, Guillermo, Dimmock, David P., Ding, Yan, Ellsworth, Katarzyna, Feigenbaum, Annette, Frise, Erwin, Green, Robert C., Guidugli, Lucia, Hall, Kevin P., Hansen, Christian, Hobbs, Charlotte A., Kahn, Scott D., Kiel, Mark, Van Der Kraan, Lucita, Krilow, Chad, Kwon, Yong H., Madhavrao, Lakshminarasimha, Le, Jennie, Lefebvre, Sebastien, Mardach, Rebecca, Mowrey, William R., Oh, Danny, Owen, Mallory J., Powley, George, Scharer, Gunter, Shelnutt, Seth, Tokita, Mari, Mehtalia, Shyamal S., Oriol, Albert, Papadopoulos, Stavros, Perry, James, Rosales, Edwin, Sanford, Erica, Schwartz, Steve, Tran, Duke, Reese, Martin G., Wright, Meredith, Veeraraghavan, Narayanan, Wigby, Kristen, Willis, Mary J., Wolen, Aaron R., Defay, Thomas
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.09.2022; Elsevier
• Subjects: Child; clinical decision support; clinical utility; Critical Illness; diagnosis; diagnostic odyssey; gene therapy; genetic disease; Genetic Testing - methods; Humans; Infant, Newborn; Neonatal Screening - methods; newborn screening; orphan drug; Precision Medicine; rapid whole-genome sequencing; Retrospective Studies; sensitivity; specificity; UK Biobank; virtual management guidance; rapid whole-genome sequencing; gene therapy; diagnosis; diagnostic odyssey; orphan drug; virtual management guidance; clinical decision support; clinical utility; specificity; sensitivity; newborn screening; genetic disease; UK Biobank
• ISSN: 0002-9297; 1537-6605; 1537-6605
• DOI: 10.1016/j.ajhg.2022.08.003

Newborn screening (NBS) dramatically improves outcomes in severe childhood disorders by treatment before symptom onset. In many genetic diseases, however, outcomes remain poor because NBS has lagged behind drug development. Rapid whole-genome sequencing (rWGS) is attractive for comprehensive NBS because it concomitantly examines almost all genetic diseases and is gaining acceptance for genetic disease diagnosis in ill newborns. We describe prototypic methods for scalable, parentally consented, feedback-informed NBS and diagnosis of genetic diseases by rWGS and virtual, acute management guidance (NBS-rWGS). Using established criteria and the Delphi method, we reviewed 457 genetic diseases for NBS-rWGS, retaining 388 (85%) with effective treatments. Simulated NBS-rWGS in 454,707 UK Biobank subjects with 29,865 pathogenic or likely pathogenic variants associated with 388 disorders had a true negative rate (specificity) of 99.7% following root cause analysis. In 2,208 critically ill children with suspected genetic disorders and 2,168 of their parents, simulated NBS-rWGS for 388 disorders identified 104 (87%) of 119 diagnoses previously made by rWGS and 15 findings not previously reported (NBS-rWGS negative predictive value 99.6%, true positive rate [sensitivity] 88.8%). Retrospective NBS-rWGS diagnosed 15 children with disorders that had been undetected by conventional NBS. In 43 of the 104 children, had NBS-rWGS-based interventions been started on day of life 5, the Delphi consensus was that symptoms could have been avoided completely in seven critically ill children, mostly in 21, and partially in 13. We invite groups worldwide to refine these NBS-rWGS conditions and join us to prospectively examine clinical utility and cost effectiveness. [Display omitted] Because highly successful NBS has not kept pace with genome or therapeutic innovation, we adapted rWGS for comprehensive NBS. NBS-rWGS for 388 disorders had 99.7% specificity, 88.8% sensitivity, and could have avoided symptoms completely in seven of 2,208 critically ill infants, mostly in 21, and partially in 13.