Microarray analysis unmasked two siblings with pure hereditary spastic paraplegia shared a run of(4)

Microarray analysis unmasked two siblings with pure hereditary spastic paraplegia shared a run of homozygosity region onchromosome 3q28–q29

W.Yuetal./JournaloftheNeurologicalSciences359(2015)351–355353

oftime,heshowedslurredspeechandmildfootdrop.Hecanwalkwiththehelpofwalkingaidswhenarrivedatourhospital.Neurologicexam-inationofthetwopatientsrevealedweaknessandspasticityinthelowerlimbswithpositivepyramidaltractsigns(hypertonicityofthelowerlimbs,markedbilateralankleclonusandbilateralBabinskisigns),pescavusandplantarhypermyotonia.Noneofthemdisplayedabnormalitiesonelectroencephalography(EEG).Theirbrainswerealsonormalbasedonmagnetic-resonanceimaging(MRI).Atthetimeofrecentvisit,theeldersisterwascon nedtobedwithmalnutritionandamyotrophy,whichmightbepartiallyascribedtodisuseatrophy.Nystagmuswasobservedinbothpatients.ThedetailedinformationissummarizedinTable1.Bothofthemwereclassi edaspureHSPbytwoexperiencedneurologists(Dr.Q-LSongandDr.JSu).ExceptforIII-1andIII-2,otherindividualsfromthisfamilyarenormalinclinicalmanifestationsandauxiliaryexaminations.

3.3.Mutationanalysis

Whole-exomesequencingwasperformedontheIII-1,III-2andII-6.Theresultscovered93%ofthetargetregionwiththemedianreaddepth(102×,100×and81×),26,033SNPsand258indelswereidenti ed.SinceHSPwasassumedtobeaveryrareconditionandnoclinicalsig-ni cantmutationinknownHSPgeneswasdetected,weexcludedheterozygouschanges,changesnotsharedbytheaffectedsiblingsandhomozygouschangesconsistentwiththeirmother.Tenhomozygousvariationswithafrequencyofb1%indbSNP138wereidenti ed,twoofwhichwerein5′UTRregionsandonewasintheintronicregion.Thefrequencyofthesethreevariantsrangedfrom0.1to0.4%referencedinthedbSNP138(rs185421189,rs147536472andrs191327348).NoneofthemwaslikelypathogenicsincetheydidnotaffectsplicesitesthroughpredictionbytheHumanSplicingFinder(HSF).Thesevenre-mainingvariantswerelocatedinexoncodingsequences,threeofthemweremissensevariantsinC3orf43,CRLF1andKIR3DL1genespreviouslyreportedinthedbSNP138,HapMap,and1,000GenomesDatabase(rs118152136,rs117193413andrs150084719respectively),theywerepredictedasbenignbySIFTandPolyphen2predictionpro-grams.Theremainingweresynonymousmutations,twoofwhichhadfrequency0.5%indbSNP138(rs35480846,rs139525246),andwerepredictedtobenon-pathologicbyHSF.Theothertwonovelsynony-mousvariant,oneofwhichlocatedatthe rstexonoftheMUC4gene(c.G10605C),theotherwasavariantintheFBXO45genec.33CNT.However,theywerebothpredictednottoaffectadjacentsplicesitesoractivatecrypticsplicesites.