Maximum likelihood haplotyping for general pedigrees. Human Heredity.pdf

1 MaximumLikelihoodHaplotyping forGeneralPedigrees Ma’ayanFishelson,NickolayDovgolevsky,puterScienceDepartment Technion,Haifa,Israel RunningTitle:MaximumLikelihoodHaplotyping CorrespondingAuthor:Ma’puterScienceDepartment,Technion, TechnionCity,Haifa32000,:+97248294895,Fax:+: ******@ Technion - Computer Science Department - Technical Report CS-2004-13 - 2004 2 Keywords:Haplotyping,LinkageAnalysis,Pedigree,superlink. Abstract Haplotypedataisvaluableinmappingdisease-susceptibilitygenes,especially eneralpedigrees,implementedinthenewestversion ,iclinkage ,tosupporte?cient haplotypinginlargerpedigrees,wehavealsoincorporatedanovelalgorithmfor work. presentexperimentalresultsforthenewalgorithmsonavarietyofrealandsemi- arti?cialdatasets,anduseoursoftwaretoevaluateMCMCapproximationsfor haplotyping. Technion - Computer Science Department - Technical Report CS-2004-13 - 2004 3 1 INTRODUCTION Haplotypedataisvaluableinmappingdisease-relatedgenes,plexdiseases(al.,1993;Littetal.,1994).Suchhaplotypedatade?nes binationeventsandconsequentlythesmallestintervalcon- usesofhaplotypingincludefamilybasedstatisticaltestssuchasTDT(Transmission DisequilibriumTest)whichrequirehaplotypedataasinput(EwensandSpielman,1995), orasameansfordetectinggenotypingerrors,whichareusuallyexpressedasanexcess binationevents(LinandSpeed,1997). Theinputdataforahaplotypingproblemcanbedividedintotwocategories:pedigree informationfrompopulationdataisoftenreconstructedusingsomeevolutionarymodel andisusuallyappliedtodatawithadensemapofmarkers(.,Stephensetal.,2001; Gus?eld,2002;