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
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 ResearchConceptsMitochondrial 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
2005
Identifying new candidate genes for hereditary facial paresis on chromosome 3q21–q22 by RNA in situ hybridization in mouse
van der Zwaag B, Burbach JP, Scharfe C, Oefner PJ, Brunner HG, Padberg GW, van Bokhoven H. Identifying new candidate genes for hereditary facial paresis on chromosome 3q21–q22 by RNA in situ hybridization in mouse. Genomics 2005, 86: 55-67. PMID: 15953540, DOI: 10.1016/j.ygeno.2005.03.007.Peer-Reviewed Original ResearchConceptsHereditary congenital facial paresisNew candidate genesMouse developmentCandidate genesSitu hybridizationTranscription-PCR analysisUndetectable expression levelsMouse embryogenesisPositional candidatesExpression analysisUbiquitous expressionGenesMeans of RNAExpression levelsGenetic defectsRNADisease familiesHybridizationCongenital cranial dysinnervation disordersExpressionFacial paresisCranial dysinnervation disordersEmbryogenesisChromosomesFamily
2004
Integrative Analysis of the Mitochondrial Proteome in Yeast
Prokisch H, Scharfe C, Camp DG, Xiao W, David L, Andreoli C, Monroe ME, Moore RJ, Gritsenko MA, Kozany C, Hixson KK, Mottaz HM, Zischka H, Ueffing M, Herman ZS, Davis RW, Meitinger T, Oefner PJ, Smith RD, Steinmetz LM. Integrative Analysis of the Mitochondrial Proteome in Yeast. PLOS Biology 2004, 2: e160. PMID: 15208715, PMCID: PMC423137, DOI: 10.1371/journal.pbio.0020160.Peer-Reviewed Original ResearchConceptsMitochondrial proteomeGenomic approachesPhenotype screeningGenome-wide approachesSubcellular localization studiesComplex mitochondrial disordersDifferent genomic approachesProtein interaction analysisYeast mitochondriaMitochondrial proteinsMitochondrial organellesProteomic approachProteome studiesAbundant proteinsExpression analysisCandidate genesExpression profilingIntegrative analysisMitochondrial functionLocalization studiesOrganellesMitochondrial disordersProteinSystematic identificationMass spectrometry