2023
Digital 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 ResearchValidation 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 panel
2022
Metabolic 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 ResearchA 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 Research
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 discoveryEnhancerEvolutionEthnic variability in newborn metabolic screening markers associated with false‐positive outcomes
Peng G, Tang Y, Gandotra N, Enns GM, Cowan TM, Zhao H, Scharfe C. Ethnic variability in newborn metabolic screening markers associated with false‐positive outcomes. Journal Of Inherited Metabolic Disease 2020, 43: 934-943. PMID: 32216101, PMCID: PMC7540352, DOI: 10.1002/jimd.12236.Peer-Reviewed Original ResearchMeSH KeywordsAcyl-CoA Dehydrogenase, Long-ChainAmino Acid Metabolism, Inborn ErrorsBiomarkersBrain Diseases, MetabolicCaliforniaCongenital Bone Marrow Failure SyndromesEthnicityFalse Positive ReactionsFemaleGestational AgeGlutaryl-CoA DehydrogenaseHumansInfant, NewbornLipid Metabolism, Inborn ErrorsMaleMitochondrial DiseasesMuscular DiseasesNeonatal ScreeningOrnithine Carbamoyltransferase Deficiency DiseaseTandem Mass SpectrometryConceptsMetabolic marker levelsOrnithine transcarbamylase deficiencyMethylmalonic acidemiaClinical variablesMarker levelsBlack infantsMetabolic markersBlood metabolic markersDiverse newborn populationGlutaric acidemia type 1False-positive screensLong-chain acyl-CoA dehydrogenase deficiencyEthnicity-related differencesNewborn screening programsFalse-positive casesInborn metabolic disordersAcyl-CoA dehydrogenase deficiencySingleton babiesGestational ageBirth weightScreening programMetabolic disordersNewborn populationInfluence of ethnicityMetabolic screeningValidation of novel forensic DNA markers using multiplex microhaplotype sequencing
Gandotra N, Speed WC, Qin W, Tang Y, Pakstis AJ, Kidd KK, Scharfe C. Validation of novel forensic DNA markers using multiplex microhaplotype sequencing. Forensic Science International Genetics 2020, 47: 102275. PMID: 32305739, PMCID: PMC10131188, DOI: 10.1016/j.fsigen.2020.102275.Peer-Reviewed Original ResearchConceptsSingle nucleotide polymorphismsMH lociMultiplex sequencingNovel single nucleotide polymorphismsSmall DNA amountsSingle MiSeq runMultiple single nucleotide polymorphismsHigher effective numberBiogeographic variationDNA markersGenomic sequencesNovel lociGenome ProjectDNA amountMiSeq runDifferent world populationsNucleotide polymorphismsLociSequencingMicrohaplotypesEffective numberDiverse range
2018
Elevated methylmalonic acidemia (MMA) screening markers in Hispanic and preterm newborns
Peng G, de Fontnouvelle CA, Enns GM, Cowan TM, Zhao H, Scharfe C. Elevated methylmalonic acidemia (MMA) screening markers in Hispanic and preterm newborns. Molecular Genetics And Metabolism 2018, 126: 39-42. PMID: 30448007, PMCID: PMC6361520, DOI: 10.1016/j.ymgme.2018.11.006.Peer-Reviewed Original ResearchConceptsMarker levelsBirth weightMethylmalonic acidemiaPreterm birthHispanic infantsBlack infantsLow birth weightPreterm birth rateFalse-positive casesPreterm newbornsGestational ageFalse-positive resultsHigh prevalenceDiagnostic proceduresInfantsNon-HispanicsBirth rateNewbornsPredictive covariatesAcidemiaCombining newborn metabolic and DNA analysis for second-tier testing of methylmalonic acidemia
Peng G, Shen P, Gandotra N, Le A, Fung E, Jelliffe-Pawlowski L, Davis RW, Enns GM, Zhao H, Cowan TM, Scharfe C. Combining newborn metabolic and DNA analysis for second-tier testing of methylmalonic acidemia. Genetics In Medicine 2018, 21: 896-903. PMID: 30209273, PMCID: PMC6416784, DOI: 10.1038/s41436-018-0272-5.Peer-Reviewed Original ResearchConceptsScreen-positive newbornsMethylmalonic acidemiaMMA patientsPathogenic variantsNewborn screeningNewborn metabolic screeningLikely pathogenic variantsSecond-tier testingFalse-positive casesInborn metabolic disordersMMA casesHealthy controlsHispanic ethnicityMetabolic disordersMetabolic screeningPatientsDiverse multiethnic populationsMultiethnic populationMolecular findingsBlood spotsUnknown significanceFalse-positive outcomesNBS programsClinical performanceScreening panel
2016
Acylcarnitine Profiles Reflect Metabolic Vulnerability for Necrotizing Enterocolitis in Newborns Born Premature
Sylvester KG, Kastenberg ZJ, Moss RL, Enns GM, Cowan TM, Shaw GM, Stevenson DK, Sinclair TJ, Scharfe C, Ryckman KK, Jelliffe-Pawlowski LL. Acylcarnitine Profiles Reflect Metabolic Vulnerability for Necrotizing Enterocolitis in Newborns Born Premature. The Journal Of Pediatrics 2016, 181: 80-85.e1. PMID: 27836286, PMCID: PMC5538349, DOI: 10.1016/j.jpeds.2016.10.019.Peer-Reviewed Original ResearchMeSH KeywordsBiomarkersCaliforniaCarnitineCohort StudiesConfidence IntervalsEnterocolitis, NecrotizingFemaleFollow-Up StudiesGestational AgeHumansIncidenceInfant, NewbornInfant, PrematureIntensive Care Units, NeonatalMaleMultivariate AnalysisNeonatal ScreeningOdds RatioReproducibility of ResultsRetrospective StudiesRisk AssessmentVulnerable PopulationsConceptsModel development cohortValidation cohortAcylcarnitine levelsAcylcarnitine profilesNeonatal intensive care unitAbnormal fatty acid metabolismRetrospective cohort studyTotal parenteral nutritionDevelopment of NECIntensive care unitRisk stratification modelNewborn screening resultsDisease prevention strategiesLog unit increaseFatty acid metabolismCohort studyNecrotizing enterocolitisParenteral nutritionPreterm birthCare unitDevelopment of diseaseBirth weightBiologic surrogatesFree carnitineNewborn screeningNext-Generation Molecular Testing of Newborn Dried Blood Spots for Cystic Fibrosis
Lefterova MI, Shen P, Odegaard JI, Fung E, Chiang T, Peng G, Davis RW, Wang W, Kharrazi M, Schrijver I, Scharfe C. Next-Generation Molecular Testing of Newborn Dried Blood Spots for Cystic Fibrosis. Journal Of Molecular Diagnostics 2016, 18: 267-282. PMID: 26847993, PMCID: PMC4816703, DOI: 10.1016/j.jmoldx.2015.11.005.Peer-Reviewed Original ResearchMeSH KeywordsCosts and Cost AnalysisCystic FibrosisCystic Fibrosis Transmembrane Conductance RegulatorDNA Copy Number VariationsDNA PrimersDried Blood Spot TestingGenetic TestingHigh-Throughput Nucleotide SequencingHumansInfant, NewbornMultiplex Polymerase Chain ReactionNeonatal ScreeningQuality ControlReproducibility of ResultsSensitivity and SpecificityConceptsMultiplex next-generation sequencingCost-effective assayHigh-throughput screeningLengthy turnaround timeNewborn Dried Blood SpotsAmplification methodUnique designSample processingGenomic DNAMolecular assaysHigh costTurnaround timeGenetic diseasesBlood spotsCFTR analysisComplete concordanceDried Blood SpotsSingle runAssaysScreen-positive newbornsCostDetection
2015
A Rapid, High-Quality, Cost-Effective, Comprehensive and Expandable Targeted Next-Generation Sequencing Assay for Inherited Heart Diseases
Wilson KD, Shen P, Fung E, Karakikes I, Zhang A, InanlooRahatloo K, Odegaard J, Sallam K, Davis RW, Lui GK, Ashley EA, Scharfe C, Wu JC. A Rapid, High-Quality, Cost-Effective, Comprehensive and Expandable Targeted Next-Generation Sequencing Assay for Inherited Heart Diseases. Circulation Research 2015, 117: 603-611. PMID: 26265630, PMCID: PMC4568077, DOI: 10.1161/circresaha.115.306723.Peer-Reviewed Original ResearchConceptsHeterozygous single nucleotide polymorphismsCongenital heart disease genesThousands of mutationsHeart disease genesShelf kitsRegulatory sequencesNext-generation sequencingSingle nucleotide polymorphismsCardiac developmentDisease genesGenomic DNATargeted Next-Generation Sequencing AssayCardiac genesGenesSequencing runPowerful new toolHigh-throughput detectionNucleotide polymorphismsSequencing assaysMutationsMiR-499Polymorphic regionDNA mutation detectionGermline variantsNext-generation sequencing assay
2014
Mitochondrial Disease Sequence Data Resource (MSeqDR): A global grass-roots consortium to facilitate deposition, curation, annotation, and integrated analysis of genomic data for the mitochondrial disease clinical and research communities
Falk M, Shen L, Gonzalez M, Leipzig J, Lott M, Stassen A, Diroma M, Navarro-Gomez D, Yeske P, Bai R, Boles R, Brilhante V, Ralph D, DaRe J, Shelton R, Terry S, Zhang Z, Copeland W, van Oven M, Prokisch H, Wallace D, Attimonelli M, Krotoski D, Zuchner S, Gai X, participants: M, Bale S, Bedoyan J, Behar D, Bonnen P, Brooks L, Calabrese C, Calvo S, Chinnery P, Christodoulou J, Church D, Clima R, Cohen B, Cotton R, de Coo I, Derbenevoa O, Dunnen J, Dimmock D, Enns G, Gasparre G, Goldstein A, Gonzalez I, Gwinn K, Hahn S, Haas R, Hakonarson H, Hirano M, Kerr D, Li D, Lvova M, Macrae F, Maglott D, McCormick E, Mitchell G, Mootha V, Okazaki Y, Pujol A, Parisi M, Perin J, Pierce E, Procaccio V, Rahman S, Reddi H, Rehm H, Riggs E, Rodenburg R, Rubinstein Y, Saneto R, Santorsola M, Scharfe C, Sheldon C, Shoubridge E, Simone D, Smeets B, Smeitink J, Stanley C, Suomalainen A, Tarnopolsky M, Thiffault I, Thorburn D, Van Hove J, Wolfe L, Wong L. Mitochondrial Disease Sequence Data Resource (MSeqDR): A global grass-roots consortium to facilitate deposition, curation, annotation, and integrated analysis of genomic data for the mitochondrial disease clinical and research communities. Molecular Genetics And Metabolism 2014, 114: 388-396. PMID: 25542617, PMCID: PMC4512182, DOI: 10.1016/j.ymgme.2014.11.016.Peer-Reviewed Original ResearchConceptsWeb portalData resourcesLocus-specific databasesAnnotation tracksData analysis needsResearch communityAnalysis toolsUnique identifier systemsCentral web portalMitochondrial diseaseCustom annotation tracksUser-friendly fashionData analysis toolsGenomic data analysisUser interrogationData of relevanceDataset curationData sharingData visualizationIdentifier systemVariant pathogenicity assessmentCentralized knowledgeAnalysis needsOntology toolsMSeqDRA functional screen for copper homeostasis genes identifies a pharmacologically tractable cellular system
Schlecht U, Suresh S, Xu W, Aparicio AM, Chu A, Proctor MJ, Davis RW, Scharfe C, St Onge RP. A functional screen for copper homeostasis genes identifies a pharmacologically tractable cellular system. BMC Genomics 2014, 15: 263. PMID: 24708151, PMCID: PMC4023593, DOI: 10.1186/1471-2164-15-263.Peer-Reviewed Original ResearchConceptsRespiratory growthFunctional screenCopper homeostasis genesHomozygous diploid deletionIntracellular copper concentrationList of genesComplex cellular systemsDeletion strainHomeostasis genesCopper homeostasisLow vacuolar pHDirect regulatorRespiratory defectsDifferent genesAerobic organismsIron uptakeFunctional linkMendelian disordersGenesCellular systemsGrowth mediumVacuolar pHHomeostasis resultsGenetic originHuman health
2013
Rare variant detection using family-based sequencing analysis
Peng G, Fan Y, Palculict TB, Shen P, Ruteshouser EC, Chi AK, Davis RW, Huff V, Scharfe C, Wang W. Rare variant detection using family-based sequencing analysis. Proceedings Of The National Academy Of Sciences Of The United States Of America 2013, 110: 3985-3990. PMID: 23426633, PMCID: PMC3593912, DOI: 10.1073/pnas.1222158110.Peer-Reviewed Original Research
2012
Forward Chemical Genetics in Yeast for Discovery of Chemical Probes Targeting Metabolism
St.Onge R, Schlecht U, Scharfe C, Evangelista M. Forward Chemical Genetics in Yeast for Discovery of Chemical Probes Targeting Metabolism. Molecules 2012, 17: 13098-13115. PMID: 23128089, PMCID: PMC3539408, DOI: 10.3390/molecules171113098.Peer-Reviewed Original ResearchConceptsChemical geneticsChemical probesCellular metabolismDominant model organismChemical genetic screeningForward chemical geneticsHigh-throughput phenotypicDrug target identificationNormal cellular metabolismNew chemical probesHigher eukaryotesExperimental tractabilityModel organismsYeast SaccharomycesCellular processesIdeal organismNew druggable targetsMolecular biologyYeastDruggable targetsGeneticsDiseased statesOrganismsGenetic screeningMetabolismSRMA: an R package for resequencing array data analysis
Zhang N, Xu Y, O'Hely M, Speed TP, Scharfe C, Wang W. SRMA: an R package for resequencing array data analysis. Bioinformatics 2012, 28: 1928-1930. PMID: 22581181, PMCID: PMC3389772, DOI: 10.1093/bioinformatics/bts286.Peer-Reviewed Original Research
2011
High-quality DNA sequence capture of 524 disease candidate genes
Shen P, Wang W, Krishnakumar S, Palm C, Chi AK, Enns GM, Davis RW, Speed TP, Mindrinos MN, Scharfe C. High-quality DNA sequence capture of 524 disease candidate genes. Proceedings Of The National Academy Of Sciences Of The United States Of America 2011, 108: 6549-6554. PMID: 21467225, PMCID: PMC3080966, DOI: 10.1073/pnas.1018981108.Peer-Reviewed Original ResearchConceptsGenome informationCandidate genomic regionsCopy number differencesHigh GC contentPadlock probesMolecular diagnosticsSingle nucleotide changeExon-level resolutionDisease candidate genesMitochondrial genesGenomic regionsSequence captureOrnithine transcarbamylase deficiencyGC contentOTC geneCandidate genesDNA variantsExon captureGenomic DNANucleotide changesSample processingStructural variantsGenesSequence verificationDNA samples