Identification of Parkinson's disease candidate genes using CAESAR and screening of MAPT and SNCAIP in South African Parkinson's disease patients

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dc.contributor.authorKeyser R.J.
dc.contributor.authorOppon E.
dc.contributor.authorCarr J.A.
dc.contributor.authorBardien S.
dc.date.accessioned2011-10-13T16:58:52Z
dc.date.available2011-10-13T16:58:52Z
dc.date.issued2011
dc.description.abstractAssuming that a significant cause of Parkinson's disease (PD) is genetic, genetic factors have been shown to account for <10% of all PD cases to date, and it is therefore necessary to identify novel genes. The aim of the present study was to identify PD candidate genes using a bioinformatic approach and to screen them for possible PD-causing mutations. The CAESAR (CAndidatE Search And Rank) program was used in the present study to identify and prioritize PD candidate genes. CAESAR ranks annotated human genes as candidates by using ontologies to semantically map natural language descriptions of the trait under investigation to gene-centric databases. Two of the candidates were selected and screened for mutations in 202 South African PD patients using the High-Resolution Melt (HRM) method. Samples exhibiting altered HRM profiles were sequenced. CAESAR generated a prioritized list of candidates including both known and novel PD genes. The MAPT and SNCAIP genes were selected for mutation screening from the list of ten highest scoring genes. Two novel missense (A91V and V635I), four synonymous and three intronic sequence variants were identified in MAPT. For SNCAIP, three novel missense (T383N, R606Q, N906H), one known (E709Q), four synonymous and one intronic sequence variant were found. A bioinformatic approach was used to aid in the identification and selection of PD candidate genes in a group of South African patients. Mutation screening of MAPT and SNCAIP identified novel sequence variants in both genes and further studies are necessary to determine their possible functional consequences. © Springer-Verlag 2011.
dc.description.versionArticle
dc.identifier.citationJournal of Neural Transmission
dc.identifier.citation118
dc.identifier.citation6
dc.identifier.citationhttp://www.scopus.com/inward/record.url?eid=2-s2.0-80051669351&partnerID=40&md5=6e660de4583b4a5ba35eba725ae52059
dc.identifier.issn3009564
dc.identifier.other10.1007/s00702-011-0591-z
dc.identifier.urihttp://hdl.handle.net/10019.1/16889
dc.subjectBioinformatic tools
dc.subjectCAESAR
dc.subjectMAPT
dc.subjectParkinson's disease
dc.subjectSNCAIP
dc.subjectalpha synuclein
dc.subjectamyloid precursor protein
dc.subjectbcl 2 like protein 1
dc.subjectbeta synuclein
dc.subjecthuntingtin
dc.subjectparkin
dc.subjectprotein bcl 2
dc.subjecttau protein
dc.subjecttyrosine 3 monooxygenase
dc.subjectubiquitin thiolesterase
dc.subjectubiquitin thiolesterase L1
dc.subjectunclassified drug
dc.subjectadult
dc.subjectarticle
dc.subjectbioinformatics
dc.subjectCandidate Search and Rank program
dc.subjectcomputer program
dc.subjectfemale
dc.subjectgene
dc.subjectgene mutation
dc.subjectgenetic database
dc.subjectgenetic screening
dc.subjecthigh resolution melting analysis
dc.subjecthuman
dc.subjectmajor clinical study
dc.subjectmale
dc.subjectmissense mutation
dc.subjectParkinson disease
dc.subjectpriority journal
dc.subjectSouth Africa
dc.subjectsynphilin 1 gene
dc.titleIdentification of Parkinson's disease candidate genes using CAESAR and screening of MAPT and SNCAIP in South African Parkinson's disease patients
dc.typeArticle
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