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Comparison of Novel and Existing Methods for Detection of Linkage Disequilibrium Using Parent‐Child Trios in the GAW12 Genetic Isolate Simulated Data
Author(s) -
Bailey-Wilson J.E.,
Sorant A.J.M.,
Malley J.D.,
Presciuttini S.,
Redner R.A.,
Severini T.A.,
Badner J.A.,
Pajevic S.,
Jufer R.,
Baffoe-Bonnie A.,
Kao L.,
Doan B.Q.,
Goldstein J.L.,
Holmes T.N.,
Behneman D.,
Mandal D.M.,
Turley T.N.,
Weissbecker K.A.,
O'Neill J.,
Pugh E.W.
Publication year - 2001
Publication title -
genetic epidemiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.301
H-Index - 98
eISSN - 1098-2272
pISSN - 0741-0395
DOI - 10.1002/gepi.2001.21.s1.s378
Subject(s) - linkage disequilibrium , transmission disequilibrium test , linkage (software) , replicate , genetics , genetic association , biology , single nucleotide polymorphism , genetic linkage , tag snp , snp , disequilibrium , computational biology , statistics , gene , genotype , mathematics , medicine , ophthalmology
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. © 2001 Wiley‐Liss, Inc.