title: Rule-based induction method for haplotype comparison and identification of candidate disease loci.
abstract: There is a need for methods that are able to identify rare variants that cause low or moderate penetrance disease susceptibility. To answer this need, we introduce a rule-based haplotype comparison method, Haplous, which identifies haplotypes within multiple samples from phased genotype data and compares them within and between sample groups. We demonstrate that Haplous is able to accurately identify haplotypes that are identical by descent, exclude common haplotypes in the studied population and select rare haplotypes from the data. Our analysis of three families with multiple individuals affected by lymphoma identified several interesting haplotypes shared by distantly related patients.
authors.affiliation: Research Programs Unit, Genome-Scale Biology, and Institute of Biomedicine, Biochemistry and Developmental Biology, University of Helsinki, Haartmaninkatu 8, Helsinki, FIN-00014, Finland. sampsa.hautaniemi@helsinki.fi.
authors.forename: Sirkku
authors.initials: S
authors.lastname: Karinen
authors.forename: Silva
authors.initials: S
authors.lastname: Saarinen
authors.forename: Rainer
authors.initials: R
authors.lastname: Lehtonen
authors.forename: Pasi
authors.initials: P
authors.lastname: Rastas
authors.forename: Pia
authors.initials: P
authors.lastname: Vahteristo
authors.forename: Lauri A
authors.initials: LA
authors.lastname: Aaltonen
authors.forename: Sampsa
authors.initials: S
authors.lastname: Hautaniemi