title: Comparison of novel and existing methods for detection of linkage disequilibrium using parent-child trios in the GAW12 genetic isolate simulated data.
abstract: A novel method for joint detection of association caused by linkage disequilibrium (LD) and estimation of both recombination fraction and linkage disequilibrium parameters was compared to several existing implementations of the transmission/disequilibrium test (TDT) and modifications of the TDT in the simulated genetic isolate data from Genetic Analysis Workshop 12. The first completely genotyped trio of affected child and parents was selected from each family in each replicate so that the TDT tests are valid tests of linkage and association, rather than being only valid as tests for linkage. In general, power to detect LD using the genome-wide scan markers was inadequate in the individual replicate samples, but the power was better when analyzing several SNP markers in candidate gene 1.
authors.affiliation: NIH/NHGRI, 333 Cassell Drive, Suite 2000, Baltimore, MD 21224, USA.
authors.forename: J E
authors.initials: JE
authors.lastname: Bailey-Wilson
authors.forename: A J
authors.initials: AJ
authors.lastname: Sorant
authors.forename: J D
authors.initials: JD
authors.lastname: Malley
authors.forename: S
authors.initials: S
authors.lastname: Presciuttini
authors.forename: R A
authors.initials: RA
authors.lastname: Redner
authors.forename: T A
authors.initials: TA
authors.lastname: Severini
authors.forename: J A
authors.initials: JA
authors.lastname: Badner
authors.forename: S
authors.initials: S
authors.lastname: Pajevic
authors.forename: R
authors.initials: R
authors.lastname: Jufer
authors.forename: A
authors.initials: A
authors.lastname: Baffoe-Bonnie
authors.forename: L
authors.initials: L
authors.lastname: Kao
authors.forename: B Q
authors.initials: BQ
authors.lastname: Doan
authors.forename: J L
authors.initials: JL
authors.lastname: Goldstein
authors.forename: T N
authors.initials: TN
authors.lastname: Holmes
authors.forename: D
authors.initials: D
authors.lastname: Behneman
authors.forename: D M
authors.initials: DM
authors.lastname: Mandal
authors.forename: T N
authors.initials: TN
authors.lastname: Turley
authors.forename: K A
authors.initials: KA
authors.lastname: Weissbecker
authors.forename: J
authors.initials: J
authors.lastname: O'Neill
authors.forename: E W
authors.initials: EW
authors.lastname: Pugh
mesh_terms: D000328:Adult; D000704:Analysis of Variance; D002648:Child; D002874:Chromosome Mapping / Q000706:statistics & numerical data; D005260:Female; D005819:Genetic Markers / Q000235:genetics; D020022:Genetic Predisposition to Disease / Q000235:genetics; D005838:Genotype; D006801:Humans; D015810:Linkage Disequilibrium; D008126:Lod Score; D008297:Male; D008957:Models, Genetic; D020641:Polymorphism, Single Nucleotide; D019655:Quantitative Trait, Heritable
chemical_list: D005819:Genetic Markers