A two-step process was used to find loci contributing to the qualitative di
sease phenotype in the Genetic Analysis Workshop (GAW) 12 simulated data. T
he first step used parametric linkage analysis with a limited number of dom
inant and recessive models to detect linkage to chromosomal regions. Subseq
uently, a subset of the simulated biallelic sequence polymorphisms was used
for transmission/disequilibrium tests and to build haplotypes to fine map
the disease-predisposing polymorphism(s). A haplotype, strongly associated
with the disease phenotype whose proximal end was within 39 base pairs of t
he functional allele for simulated major gene 6, was identified in the isol
ated population. (C) 2001 Wiley-Liss, Inc.