Multiplex gene sequencing and metabolomics analysis from newborn dried blood spots to improve screening and diagnosis of metabolic disorders.
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Principal Investigator: Curt Scharfe Organization: YALE UNIVERSITY Fiscal Year: 2024 Award: $478,960 Funding agency: Eunice Kennedy Shriver National Institute of Child Health and Human Development Abstract: Newborn screening (NBS) using tandem mass spectrometry (MS/MS) has transformed our ability to identify and provide early, lifesaving treatment to infants with inborn errors of metabolism. While MS/MS screening identifies most affected babies, it is accompanied by frequent false-positive results that require collecting blood and urine samples for additional confirmatory testing. While DNA sequencing has become an important part of confirmatory testing, newborn dried blood spots (DBS) yield only small and highly variable DNA amounts. There is an urgent need for a more efficient second-tier NBS approach for confirming all screen-positive cases directly from the DBS cards collected at birth. This is especially critical for infants at risk for metabolic disease in their first weeks of life. The overall objective of this proposal is to combine novel DNA sequencing and mass spectrometry technology to diagnose inborn metabolic disorders from DBS, and to demonstrate the clinical feasibility of this approach for second-tier screening. To achieve this objective, the following specific aims will be pursued: (1) Develop multiplex gene sequencing (RUSPseq) and 10X linked-read sequencing for rapid genetic diagnosis without the need for additional parental testing; (2) Develop mass spectrometry (Q-TOF/LC-MS) and Random Forest (RF) machine learning to identify novel metabolic markers, which will be integrated in a novel second-tier screening panel to separate true and false-positive cases; and (3) Demonstrate clinical and translational feasibility of this approach to more rapidly identify both true and false-positive cases. We will work with the public NBS program and NBSTRN’s Pilot Research and Implementation workgroup to translate this combined approach into second-tier NBS. These outcomes will have significant impact by reducing diagnostic delays and uncertainties, and by reducing iterative testing rounds and the cost associated with them, thereby reducing the burden on the healthcare system as well as patients and their families. Terms: <0-4 weeks old><Adoption><Affect><Archives><Assay><Bioassay><Biochemical><Biochemical Genetics><Biological Assay><Birth><Blood><Blood Reticuloendothelial System><Blood Volume><CFTR><CFTR Protein><California><Chemicals><Clinical><Compound Q><Cystic Fibrosis Transmembrane Conductance Regulator><DNA><DNA seq><DNA sequencing><DNAseq><Data><Data Analyses><Data Analysis><Deoxyribonucleic Acid><Detection><Diagnosis><Diagnostic><Differentation Markers><Differentiation Antigens><Differentiation Markers><Dryness><Early Diagnosis><Ethnic Group><Ethnic People><Ethnic Population><Ethnic individual><Ethnicity People><Ethnicity Population><Exclusion><Family><Genes><Genetic><Genetic analyses><Goals><Haplotypes><Health Care Systems><Healthcare Systems><Hereditary Metabolic Disorder><Hospitals><Inborn Errors of Metabolism><Infant><Intervention><Intervention Strategies><Laboratories><Letters><Life><Link><Machine Learning><Marker Antigens><Mass Photometry/Spectrum Analysis><Mass Spectrometry><Mass Spectroscopy><Mass Spectrum><Mass Spectrum Analyses><Mass Spectrum Analysis><Measurement><Metabolic><Metabolic Diseases><Metabolic Disorder><Metabolic Marker><Methods><NGS Method><NGS system><Neonatal Screening><Newborn Infant><Newborn Infant Screening><Newborns><Outcome><Parents><Parturition><Patients><Phase><Physicians><Pilot Projects><Recommendation><Research><Risk><Running><Sampling><Sensitivity and Specificity><Spottings><Symptoms><Technology><Testing><Thesaurismosis><Time><Translating><Translations><Trichosanthin><Trust><Uncertainty><Urine><Variant><Variation><Work><alpha-Trichosanthin><carrier status><clinical phenotype><cost><cystic fibrosis transmembrane regulator><data interpretation><doubt><early detection><ethnic subgroup><ethnicity group><genetic analysis><genetic approach><genetic diagnosis><genetic disorder diagnosis><genetic strategy><improved><inborn metabolism disorder><interventional strategy><machine based learning><member><metabolism disorder><metabolism measurement><metabolomics><metabonomics><multi-ethnic><multiethnic><new approaches><new marker><new technology><newborn child><newborn children><newborn screening><next gen sequencing><next generation sequencing><nextgen sequencing><novel><novel approaches><novel biomarker><novel marker><novel strategies><novel strategy><novel technologies><parent><pilot study><random forest><screening><screening panel><screening program><screenings><tandem mass spectrometry><translation><web tool><web-based tool>