Four methods using identity by state (IBS) data from affected sib pair
s are compared for their ability to detect linkage between a diallelic
marker and disease. A joint null hypothesis of no linkage and no link
age disequilibrium between the marker and disease must be considered.
Two tests have undesirable properties in the case of linkage disequili
brium. Which of the other two tests has more power is dependent on the
presence or not of linkage disequilibrium. The procedure of choice wh
en possible is to type parents of affected sib pairs: the null hypothe
sis of no linkage can then be tested using identity by descent (IBD) v
alues from informative parents, and the null hypothesis of no marker a
ssociation with disease (linkage equilibrium) can be tested independen
tly using the marker allele frequencies in the affected sib pairs. (C)
1994 Wiley-Liss, Inc.