Model-free linkage analysis: performance under real-world conditions.
The simulated data of the Genetic Analysis Workshop 12 problem set affords an ideal environment for testing real-world performance of model-free linkage analysis methods. To this end, we applied three different methods of model-free linkage analysis: mod scores [Hodge and Elston, Genet Epidemiol 11:329-42, 1994], maximized maximum lod score (MMLS) [Greenberg et al., Am J Hum Genet 63:870-9, 1998], and nonparametric linkage (NPL) scores [Whittemore and Halpern, Biometrics 50:118-27, 1994], as well as standard parametric linkage analysis to the detection of major gene 6 (MG6) using only the qualitative disease status data. Our results indicate that both mod scores and NPL scores perform well, even in the presence of an extremely complicated disease model. MMLS analysis did not perform well, except at the disease locus itself.
Barmada
M M
MM
Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Crabtree A300, 130 Desoto Street, Pittsburgh, PA 15261, USA.
O'Connell
J R
JR
D002874:Chromosome Mapping / Q000706:statistics & numerical data*; D002896:Chromosomes, Human, Pair 6; D004252:DNA Mutational Analysis; D005819:Genetic Markers / Q000235:genetics; D020022:Genetic Predisposition to Disease / Q000235:genetics*; D006801:Humans; D008126:Lod Score; D008957:Models, Genetic; D010641:Phenotype; D018709:Statistics, Nonparametric
D005819:Genetic Markers