2020
Ethnic 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 screening
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 toolsMSeqDR
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
2010
Identification of rare DNA variants in mitochondrial disorders with improved array-based sequencing
Wang W, Shen P, Thiyagarajan S, Lin S, Palm C, Horvath R, Klopstock T, Cutler D, Pique L, Schrijver I, Davis RW, Mindrinos M, Speed TP, Scharfe C. Identification of rare DNA variants in mitochondrial disorders with improved array-based sequencing. Nucleic Acids Research 2010, 39: 44-58. PMID: 20843780, PMCID: PMC3017602, DOI: 10.1093/nar/gkq750.Peer-Reviewed Original ResearchConceptsDNA variantsFunctional DNA variantsMitochondrial DNA maintenanceRare DNA variantsSecond-generation sequencing technologiesNovel rare variantsSanger capillary sequencingSynergistic genetic effectsNuclear candidate genesDNA maintenanceRare variantsGenomic variationSequencing technologiesRare heterozygous variantsCandidate genesGenetic effectsFalse discovery rateMitochondrial disordersCapillary sequencingSequence verificationGenesNovel statistical methodSequencingDiscovery rateHeterozygous variants
2009
Mapping Gene Associations in Human Mitochondria using Clinical Disease Phenotypes
Scharfe C, Lu HH, Neuenburg JK, Allen EA, Li GC, Klopstock T, Cowan TM, Enns GM, Davis RW. Mapping Gene Associations in Human Mitochondria using Clinical Disease Phenotypes. PLOS Computational Biology 2009, 5: e1000374. PMID: 19390613, PMCID: PMC2668170, DOI: 10.1371/journal.pcbi.1000374.Peer-Reviewed Original ResearchMeSH KeywordsChromosome MappingComputer SimulationDNA, MitochondrialGenetic Predisposition to DiseaseHumansMitochondrial DiseasesModels, GeneticQuantitative Trait LociConceptsMitochondrial disease genesDisease genesMitochondrial genesMost mitochondrial proteinsMitochondrial disease phenotypesGene network analysisDisease phenotypePhenotypic featuresGenotype-phenotype relationsNuclear genesHuman mitochondriaMitochondrial proteinsCharacteristic interaction patternsPhenotypic dataCandidate genesMitochondrial systemDifferent genesSimilar phenotypeGene associationsGenesFunctional interactionMitochondrial disordersClinical disease phenotypeSimilarity valuesPhenotype
2006
MitoP2: the mitochondrial proteome database—now including mouse data
Prokisch H, Andreoli C, Ahting U, Heiss K, Ruepp A, Scharfe C, Meitinger T. MitoP2: the mitochondrial proteome database—now including mouse data. Nucleic Acids Research 2006, 34: d705-d711. PMID: 16381964, PMCID: PMC1347489, DOI: 10.1093/nar/gkj127.Peer-Reviewed Original ResearchConceptsMitochondrial proteinsSystematic genome-wide studiesMitochondrial proteome databaseNovel mitochondrial proteinGenome-wide studiesSystems biology approachOrthologous proteinsMolecular functionsBiology approachProteome databaseRare mitochondrial diseaseMitochondrial diseasePhenotype screeningMitochondrial dysfunctionReference proteinProteinMitochondriaMouse dataMitoP2ProteomicsIntegration of dataYeastGenesSpeciesPathway
2002
Systematic screen for human disease genes in yeast
Steinmetz LM, Scharfe C, Deutschbauer AM, Mokranjac D, Herman ZS, Jones T, Chu AM, Giaever G, Prokisch H, Oefner PJ, Davis RW. Systematic screen for human disease genes in yeast. Nature Genetics 2002, 31: 400-404. PMID: 12134146, DOI: 10.1038/ng929.Peer-Reviewed Original ResearchConceptsMitochondrial proteinsNuclear-encoded mitochondrial proteinsGenomic map positionFunctional genomic studiesHuman disease genesGene expression analysisHuman mitochondriaYeast deletionHuman orthologGenomic studiesMap positionHuman genesSystematic screenFunctional screenStrain fitnessExpression analysisDisease genesHuman disordersMitochondrial diseaseHigh similarityMitochondrial respirationHeritable diseaseMitochondrial functionGenesProtein
2001
Frequency of mitochondrial transfer RNA mutations and deletions in 225 patients presenting with respiratory chain deficiencies
Jaksch M, Kleinle S, Scharfe C, Klopstock T, Pongratz D, Müller-Höcker J, Gerbitz KD, Liechti-Gallati S, Lochmuller H, Horvath R. Frequency of mitochondrial transfer RNA mutations and deletions in 225 patients presenting with respiratory chain deficiencies. Journal Of Medical Genetics 2001, 38: 665. PMID: 11584044, PMCID: PMC1734743, DOI: 10.1136/jmg.38.10.665.Peer-Reviewed Original ResearchMeSH KeywordsAdolescentAdultChildChild, PreschoolDNA Mutational AnalysisElectron TransportFemaleGene FrequencyGenetic VariationGenotypeHumansInfantInfant, NewbornMaleMiddle AgedMitochondria, MuscleMitochondrial DiseasesMuscle, SkeletalMutationPhenotypePolymorphism, GeneticRNARNA, MitochondrialRNA, TransferSequence DeletionConceptsMitochondrial transfer RNA (mt-tRNA) mutationsAdult patientsRespiratory chain deficiencyDistinct neurological syndromesChain deficiencyNeonatal groupPediatric groupClinical symptomsNeurological syndromeIndex patientsPathogenic mitochondrial DNA mutationsPatientsPathogenic relevanceMitochondrial DNA mutationsSkeletal musclePathogenic mutationsMuscle DNARNA mutationsMitochondrial disordersG mutationSkeletal muscle DNADeficiencyDetection rateDNA mutationsRC deficiency