MPSE identifies newborns for whole genome sequencing within 48 h of NICU admission.

Journal: NPJ genomic medicine
Published Date: Jun 12, 2025

Abstract

Identifying critically ill newborns who will benefit from whole genome sequencing (WGS) is difficult and time-consuming due to complex eligibility criteria and evolving clinical features. The Mendelian Phenotype Search Engine (MPSE) automates the prioritization of neonatal intensive care unit (NICU) patients for WGS. Using clinical data from 2885 NICU patients, we evaluated the utility of different machine learning (ML) classifiers, clinical natural language processing (CNLP) tools, and types of Electronic Health Record (EHR) data to identify sick newborns with genetic diseases. Our results show that MPSE can identify children most likely to benefit from WGS within the first 48 h after NICU admission, a critical window for maximally impactful care. Moreover, MPSE provided stable, robust means to identify these children using many combinations of classifiers, CNLP tools, and input data types-meaning MPSE can be used by diverse health systems despite differences in EHR contents and IT support.

Authors

  • Bennet Peterson
    Department of Biomedical Informatics, University of Utah, Salt Lake City, UT, USA.
  • Edwin F Juarez
    Rady Children's Institute for Genomic Medicine, San Diego, CA, USA.
  • Barry Moore
    Department of Human Genetics, Utah Center for Genetic Discovery, University of Utah, Salt Lake City, UT, USA.
  • Edgar Javier Hernandez
    Department of Human Genetics, Utah Center for Genetic Discovery, University of Utah, Salt Lake City, UT, USA.
  • Erwin Frise
    Fabric Genomics Inc., Oakland, CA, USA.
  • Jianrong Li
    College of Food Science and Technology, Bohai University, Jinzhou, China.
  • Yves Lussier
    Department of Biomedical Informatics, University of Utah, Salt Lake City, UT, USA.
  • Martin Tristani-Firouzi
    Division of Pediatric Cardiology (M.T.-F.), University of Utah School of Medicine, Salt Lake City.
  • Martin G Reese
    Fabric Genomics Inc., Oakland, CA, USA. mreese@fabricgenomics.com.
  • Sabrina Malone Jenkins
    Division of Neonatology, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT, USA.
  • Stephen F Kingsmore
    Rady Children's Institute for Genomic Medicine, San Diego, CA, USA.
  • Matthew N Bainbridge
    Rady Children's Institute for Genomic Medicine, San Diego, CA, USA.
  • Mark Yandell
    Eccles Institute of Human Genetics (M.Y.), University of Utah, Salt Lake City.

Keywords

No keywords available for this article.

External Resources

Popular Topics
Recent Journals