AFFECTED SIB PAIR IDENTITY BY STATE ANALYSES

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.