title: HaploShare: identification of extended haplotypes shared by cases and evaluation against controls.
abstract: Recent founder mutations may play important roles in complex diseases and Mendelian disorders. Detecting shared haplotypes that are identical by descent (IBD) could facilitate discovery of these mutations. Several programs address this, but are usually limited to detecting pair-wise shared haplotypes and not providing a comparison of cases and controls. We present a novel algorithm and software package, HaploShare, which detects extended haplotypes that are shared by multiple individuals, and allows comparisons between cases and controls. Testing on simulated and real cases demonstrated significant improvements in detection power and reduction of false positive rate by HaploShare relative to other programs.
authors.affiliation: Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, 21 Sassoon Rd., Pokfulam, Hong Kong. jonsonfox@gmail.com.|Department of Psychiatry, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong. jonsonfox@gmail.com.
authors.forename: Dingge
authors.initials: D
authors.lastname: Ying
authors.affiliation: Department of Psychiatry, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong. pcsham@hku.hk.|Centre for Genomic Sciences, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong. pcsham@hku.hk.
authors.forename: Pak Chung
authors.initials: PC
authors.lastname: Sham
authors.affiliation: State Key Laboratory for Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong. dsmithhk@gmail.com.
authors.forename: David Keith
authors.initials: DK
authors.lastname: Smith
authors.affiliation: Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, 21 Sassoon Rd., Pokfulam, Hong Kong. zhanglu295@gmail.com.
authors.forename: Lu
authors.initials: L
authors.lastname: Zhang
authors.affiliation: Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, 21 Sassoon Rd., Pokfulam, Hong Kong. lauylung@hkucc.hku.hk.
authors.forename: Yu Lung
authors.initials: YL
authors.lastname: Lau
authors.affiliation: Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, 21 Sassoon Rd., Pokfulam, Hong Kong. yangwl@hku.hk.|Centre for Genomic Sciences, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong. yangwl@hku.hk.
authors.forename: Wanling
authors.initials: W
authors.lastname: Yang
mesh_terms: D000465:Algorithms; D044466:Asian People / Q000235:genetics; D016022:Case-Control Studies; D019295:Computational Biology; D005189:False Positive Reactions; D056726:Genetic Association Studies / Q000379:methods*; D006239:Haplotypes; D006627:Hirschsprung Disease / Q000175:diagnosis / Q000235:genetics; D006801:Humans; D009154:Mutation; D020641:Polymorphism, Single Nucleotide; D012680:Sensitivity and Specificity