Association of posterior p-values of S.A.G.E. SIBPAL proportion-IBD and Haseman-Elston statistics for ACTHR112

Derek Gordon1*, Stephen J. Finch2, Adam L. Jacobs1, Nancy R. Mendell2, Richard M. Single3, Thomas G. Marr1
1 Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
2 SUNY at Stony Brook, Stony Brook, New York
3 St. Olaf College, Northfield, Minnesota
* Correspondence to Derek Gordon, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724

Genetic Epidemiology, 14(6), 629-634 (1997)

Abstract

A common practice among researchers performing linkage studies is the use of equal allele frequencies as input when reporting p-values from computer linkage programs such as S.A.G.E. SIBPAL. Our results, using 5,000 sets from a uniform- prior distribution of allele frequencies, showed that such input may be problematic. Further, we found that the S.A.G.E. SIBPAL test for proportion of alleles shared identical by descent among concordantly affected sib pairs showed a greater percentage of significant p-values with decreasing parental genotype information (Table III), while the S.A.G.E. SIBPAL Haseman-Elston test produced significant p-values comparatively less frequently (Table IV).