2024
Addendum: Points to consider in the reevaluation and reanalysis of genomic test results: A statement of the American College of Medical Genetics and Genomics (ACMG)
Reddi H, Avenarius M, Bean L, Best H, Guha S, Kang B, Scharfe C, Seifert B, Wakeling E, Committee A. Addendum: Points to consider in the reevaluation and reanalysis of genomic test results: A statement of the American College of Medical Genetics and Genomics (ACMG). Genetics In Medicine 2024, 26: 101100. DOI: 10.1016/j.gim.2024.101100.Peer-Reviewed Original Research
2023
Association of Maternal Age and Blood Markers for Metabolic Disease in Newborns
Xie Y, Peng G, Zhao H, Scharfe C. Association of Maternal Age and Blood Markers for Metabolic Disease in Newborns. Metabolites 2023, 14: 5. PMID: 38276295, PMCID: PMC10821442, DOI: 10.3390/metabo14010005.Peer-Reviewed Original ResearchMaternal ageAdvanced maternal ageBlood metabolic markersMaternal age groupsInborn metabolic disordersNeonatal outcomesSingleton infantsGestational ageClinical variablesMarker levelsBirth weightBlood levelsBlood markersRisk factorsAge-related differencesInfant sexMetabolic disordersMetabolic markersPotential confoundingMetabolic diseasesScreening markerAge groupsBlood collectionScreening panelHigh false positive rateNBSTRN Tools to Advance Newborn Screening Research and Support Newborn Screening Stakeholders
Chan K, Hu Z, Bush L, Cope H, Holm I, Kingsmore S, Wilhelm K, Scharfe C, Brower A. NBSTRN Tools to Advance Newborn Screening Research and Support Newborn Screening Stakeholders. International Journal Of Neonatal Screening 2023, 9: 63. PMID: 37987476, PMCID: PMC10660757, DOI: 10.3390/ijns9040063.Peer-Reviewed Original ResearchDigital assay for rapid electronic quantification of clinical pathogens using DNA nanoballs
Tayyab M, Barrett D, van Riel G, Liu S, Reinius B, Scharfe C, Griffin P, Steinmetz L, Javanmard M, Pelechano V. Digital assay for rapid electronic quantification of clinical pathogens using DNA nanoballs. Science Advances 2023, 9: eadi4997. PMID: 37672583, PMCID: PMC10482329, DOI: 10.1126/sciadv.adi4997.Peer-Reviewed Original ResearchConceptsMicrofluidic impedance cytometerDNA nanoballsLabel-free assayColorimetric readoutImpedance cytometerDigital assaysLoop-mediated isothermal amplificationCapillary-driven flowNanoballsDNA detectionStandalone deviceDNA/RNAIsothermal amplificationCompact systemNucleic acidsClinical pathogensPathogen identificationAccurate detectionRapid testReadoutDetectionNovel methodImpedanceContributions from medical geneticists in clinical trials of genetic therapies: A points to consider statement of the American College of Medical Genetics and Genomics (ACMG)
Peña L, Burrage L, Enns G, Esplin E, Harding C, Mendell J, Niu Z, Scharfe C, Yu T, Koeberl D, Committee A. Contributions from medical geneticists in clinical trials of genetic therapies: A points to consider statement of the American College of Medical Genetics and Genomics (ACMG). Genetics In Medicine 2023, 25: 100831. PMID: 37031408, PMCID: PMC11040261, DOI: 10.1016/j.gim.2023.100831.Peer-Reviewed Original ResearchNucleic Acid Quantification by Multi-Frequency Impedance Cytometry and Machine Learning
Kokabi M, Sui J, Gandotra N, Khamseh A, Scharfe C, Javanmard M. Nucleic Acid Quantification by Multi-Frequency Impedance Cytometry and Machine Learning. Biosensors 2023, 13: 316. PMID: 36979528, PMCID: PMC10046493, DOI: 10.3390/bios13030316.Peer-Reviewed Original ResearchA systems biology approach identifies the role of dysregulated PRDM6 in the development of hypertension
Gunawardhana K, Hong L, Rugira T, Uebbing S, Kucharczak J, Mehta S, Karunamuni D, Cabera-Mendoza B, Gandotra N, Scharfe C, Polimanti R, Noonan J, Mani A. A systems biology approach identifies the role of dysregulated PRDM6 in the development of hypertension. Journal Of Clinical Investigation 2023, 133: e160036. PMID: 36602864, PMCID: PMC9927944, DOI: 10.1172/jci160036.Peer-Reviewed Original ResearchConceptsDevelopment of hypertensionParallel reporter assaysRenin inhibitor aliskirenNeural crest-derived cellsRenin-producing cellsSystems biology approachRNA-seq analysisCell-specific disruptionCrest-derived cellsSmooth muscle cellsMuscle cell proteinsSystemic hypertensionBlood pressureWT miceAntihypertensive drugsBiology approachSuper enhancersFine mappingWT littermatesThird intronMultiple GWASCollagen depositionMouse aortaReporter assaysFate mappingValidation of a targeted metabolomics panel for improved second‐tier newborn screening
Mak J, Peng G, Le A, Gandotra N, Enns G, Scharfe C, Cowan T. Validation of a targeted metabolomics panel for improved second‐tier newborn screening. Journal Of Inherited Metabolic Disease 2023, 46: 194-205. PMID: 36680545, PMCID: PMC10023470, DOI: 10.1002/jimd.12591.Peer-Reviewed Original ResearchConceptsRecommended Uniform Screening PanelMethylmalonic acidemiaNewborn screeningOrnithine transcarbamylase deficiencySecond-tier assayDisease markersGlutaric acidemia type ILong-chain acyl-CoA dehydrogenase deficiencyScreen-positive casesUniform Screening PanelLong-chain acylcarnitinesSecond-tier testingFalse-positive casesSecond-tier testBlood spot samplesAcyl-CoA dehydrogenase deficiencyMetabolomics panelMetabolic disordersTargeted metabolomics analysisPositive casesMetabolite panelNBS programsDehydrogenase deficiencyLiquid chromatography-tandem mass spectrometryScreening panelP552: Improving DNA sequencing from dried blood spots for multi-tiered newborn screening
Gandotra N, Peng G, Tikhonova I, Storer C, Mak J, Wang G, Cowan T, Scharfe C. P552: Improving DNA sequencing from dried blood spots for multi-tiered newborn screening. Genetics In Medicine Open 2023, 1: 100599. DOI: 10.1016/j.gimo.2023.100599.Peer-Reviewed Original Research
2022
A multipurpose panel of microhaplotypes for casework
Kidd K, Pakstis A, Gandotra N, Scharfe C, Podini D. A multipurpose panel of microhaplotypes for casework. Forensic Science International Genetics Supplement Series 2022, 8: 202-204. DOI: 10.1016/j.fsigss.2022.10.035.Peer-Reviewed Original ResearchEmpirical haplotype calling and probabilistic interpretation of microhaplotype profiles
Standage D, Just R, Scharfe C, Gandotra N. Empirical haplotype calling and probabilistic interpretation of microhaplotype profiles. Forensic Science International Genetics Supplement Series 2022, 8: 265-267. DOI: 10.1016/j.fsigss.2022.10.057.Peer-Reviewed Original ResearchMetabolic diversity in human populations and correlation with genetic and ancestral geographic distances
Peng G, Pakstis AJ, Gandotra N, Cowan TM, Zhao H, Kidd KK, Scharfe C. Metabolic diversity in human populations and correlation with genetic and ancestral geographic distances. Molecular Genetics And Metabolism 2022, 137: 292-300. PMID: 36252453, PMCID: PMC10131177, DOI: 10.1016/j.ymgme.2022.10.002.Peer-Reviewed Original ResearchdbRUSP: An Interactive Database to Investigate Inborn Metabolic Differences for Improved Genetic Disease Screening
Peng G, Zhang Y, Zhao H, Scharfe C. dbRUSP: An Interactive Database to Investigate Inborn Metabolic Differences for Improved Genetic Disease Screening. International Journal Of Neonatal Screening 2022, 8: 48. PMID: 36135348, PMCID: PMC9504335, DOI: 10.3390/ijns8030048.Peer-Reviewed Original ResearchNewborn screeningMetabolite levelsUniversal newborn screeningUniform Screening PanelBlood metabolite levelsNew candidate markersGestational ageFalse-positive resultsBirth weightMetabolic disordersReference rangeInfluence of covariatesNutrition statusBlood collectionNBS programsScreening panelMetabolic conditionsDisease screeningCandidate markersMetabolic differencesNewbornsPositive resultsMetabolic analytesPopulation-Based Screening of Newborns: Findings From the NBS Expansion Study (Part One)
Brower A, Chan K, Williams M, Berry S, Currier R, Rinaldo P, Caggana M, Gaviglio A, Wilcox W, Steiner R, Holm IA, Taylor J, Orsini JJ, Brunelli L, Adelberg J, Bodamer O, Viall S, Scharfe C, Wasserstein M, Chen JY, Escolar M, Goldenberg A, Swoboda K, Ficicioglu C, Matern D, Lee R, Watson M. Population-Based Screening of Newborns: Findings From the NBS Expansion Study (Part One). Frontiers In Genetics 2022, 13: 867337. PMID: 35938011, PMCID: PMC9354846, DOI: 10.3389/fgene.2022.867337.Peer-Reviewed Original ResearchNewborn Screening Translational Research NetworkNewborn screeningPopulation-based newborn screeningPopulation-based screeningLife-saving interventionsSurvey of cliniciansState NBS programsEarly treatmentNBS programsNewbornsTranslational Research NetworkNumber of diseasesWorkshop of expertsUnited StatesResearch NetworkUniform panelStudy findingsScreeningCurrent practiceNationwide adoptionYearsCliniciansStudyDiseaseFindingsA multipurpose panel of microhaplotypes for use with STR markers in casework
Kidd KK, Pakstis AJ, Gandotra N, Scharfe C, Podini D. A multipurpose panel of microhaplotypes for use with STR markers in casework. Forensic Science International Genetics 2022, 60: 102729. PMID: 35696960, PMCID: PMC11071123, DOI: 10.1016/j.fsigen.2022.102729.Peer-Reviewed Original Research
2021
The population genetics characteristics of a 90 locus panel of microhaplotypes
Pakstis AJ, Gandotra N, Speed WC, Murtha M, Scharfe C, Kidd KK. The population genetics characteristics of a 90 locus panel of microhaplotypes. Human Genetics 2021, 140: 1753-1773. PMID: 34643790, PMCID: PMC8553733, DOI: 10.1007/s00439-021-02382-0.Peer-Reviewed Original ResearcheP037 Timing of newborn blood collection alters screening performance for metabolic disorders
Peng G, Tang Y, Gandotra N, Cowan T, Zhao H, Scharfe C. eP037 Timing of newborn blood collection alters screening performance for metabolic disorders. Molecular Genetics And Metabolism 2021, 132: s26. DOI: 10.1016/s1096-7192(21)00124-4.Peer-Reviewed Original ResearchMulti-frequency impedance sensing for detection and sizing of DNA fragments
Sui J, Gandotra N, Xie P, Lin Z, Scharfe C, Javanmard M. Multi-frequency impedance sensing for detection and sizing of DNA fragments. Scientific Reports 2021, 11: 6490. PMID: 33753781, PMCID: PMC7985362, DOI: 10.1038/s41598-021-85755-9.Peer-Reviewed Original ResearchConceptsTarget molecule bindsComplex biological samplesElectronic biosensorsNon-target materialsProbe selectivityAnalytical performanceMolecules bindBiological samplesReaction productsDifferent lengthsDNA moleculesDNA detectionMicrofluidic chipNonspecific bindingFmolElectronic signalsParamagnetic beadsImpedance sensorBeadsBiosensorDNA concentrationDNA fragmentsSelectivityProbePolymerase chain reaction productsTiming of Newborn Blood Collection Alters Metabolic Disease Screening Performance
Peng G, Tang Y, Cowan TM, Zhao H, Scharfe C. Timing of Newborn Blood Collection Alters Metabolic Disease Screening Performance. Frontiers In Pediatrics 2021, 8: 623184. PMID: 33553077, PMCID: PMC7854909, DOI: 10.3389/fped.2020.623184.Peer-Reviewed Original ResearchCarnitine transport defectBlood collectionMethylmalonic acidemiaIsovaleric acidemiaMarker levelsMetabolic disordersElevated marker levelsMetabolic marker levelsFalse-positive casesInborn metabolic disordersNewborn screening dataGestational ageClinical variablesBirth weightStandard groupFalse positive rateMetabolic changesDisease screeningHigh false positive rateEffect size analysisPhenylketonuriaScreening performanceAcidemiaCollection groupDisorders
2020
Massively parallel discovery of human-specific substitutions that alter enhancer activity
Uebbing S, Gockley J, Reilly SK, Kocher AA, Geller E, Gandotra N, Scharfe C, Cotney J, Noonan JP. Massively parallel discovery of human-specific substitutions that alter enhancer activity. Proceedings Of The National Academy Of Sciences Of The United States Of America 2020, 118: e2007049118. PMID: 33372131, PMCID: PMC7812811, DOI: 10.1073/pnas.2007049118.Peer-Reviewed Original ResearchConceptsHuman-specific substitutionsHuman-gained enhancersGenetic changesEnhancer functionEnhancer activityHuman-specific genetic changesHuman evolutionGene regulatory elementsBackground genetic variationAncestral functionRegulatory evolutionEnhancer assaysGenetic variationRegulatory elementsNeural stem cellsHuman traitsNovel activityNonadditive wayRegulatory activityStem cellsFunctional impactDifferential activityParallel discoveryEnhancerEvolution