title: Development of DNA confirmatory and high-risk diagnostic testing for newborns using targeted next-generation DNA sequencing.
abstract: OBJECTIVE
  Genetic testing is routinely used for second-tier confirmation of newborn sequencing results to rule out false positives and to confirm diagnoses in newborns undergoing inpatient and outpatient care. We developed a targeted next-generation sequencing panel coupled with a variant processing pipeline and demonstrated utility and performance benchmarks across multiple newborn disease presentations in a retrospective clinical study.
  
  
  METHODS
  The test utilizes an in silico gene filter that focuses directly on 126 genes related to newborn screening diseases and is applied to the exome or a next-generation sequencing panel called NBDx. NBDx targets the 126 genes and additional newborn-specific disorders. It integrates DNA isolation from minimally invasive biological specimens, targeted next-generation screening, and rapid characterization of genetic variation.
  
  
  RESULTS
  We report a rapid parallel processing of 8 to 20 cases within 105 hours with high coverage on our NBDx panel. Analytical sensitivity of 99.8% was observed across known mutation hotspots. Concordance calls with or without clinical summaries were 94% and 75%, respectively.
  
  
  CONCLUSIONS
  Rapid, automated targeted next-generation sequencing and analysis are practical in newborns for second-tier confirmation and neonatal intensive care unit diagnoses, laying a foundation for future primary DNA-based molecular screening of additional disorders and improving existing molecular testing options for newborns.
authors.affiliation: Parabase Genomics, Boston, Massachusetts, USA.
authors.forename: Arindam
authors.initials: A
authors.lastname: Bhattacharjee
authors.affiliation: Parabase Genomics, Boston, Massachusetts, USA.
authors.forename: Tanya
authors.initials: T
authors.lastname: Sokolsky
authors.affiliation: Parabase Genomics, Boston, Massachusetts, USA.
authors.forename: Stacia K
authors.initials: SK
authors.lastname: Wyman
authors.affiliation: Omicia, Oakland, California, USA.
authors.forename: Martin G
authors.initials: MG
authors.lastname: Reese
authors.affiliation: Clinic for Special Children, Strasburg, Pennsylvania, USA.
authors.forename: Erik
authors.initials: E
authors.lastname: Puffenberger
authors.affiliation: Clinic for Special Children, Strasburg, Pennsylvania, USA.
authors.forename: Kevin
authors.initials: K
authors.lastname: Strauss
authors.affiliation: Clinic for Special Children, Strasburg, Pennsylvania, USA.
authors.forename: Holmes
authors.initials: H
authors.lastname: Morton
authors.affiliation: Department of Pediatric Newborn Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.
authors.forename: Richard B
authors.initials: RB
authors.lastname: Parad
authors.affiliation: 1] Parabase Genomics, Boston, Massachusetts, USA [2] Division of Genetics, Department of Pediatrics, Medical University of South Carolina, Charleston, South Carolina, USA.
authors.forename: Edwin W
authors.initials: EW
authors.lastname: Naylor
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods; D005820:Genetic Testing / Q000379:methods*; D014644:Genetic Variation; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006801:Humans; D007231:Infant, Newborn; D015997:Neonatal Screening; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D057188:Workflow