A pedigree partitioning approach to quantitative trait loci mapping of IgE serum level in the GAW12 Hutterite data

We present a semi-automatic method that uses principles from factor analysis to subdivide large pedigrees into smaller, non-overlapping sub-pedigrees. Application of our method to the Genetic Analysis Workshop 12 Hutterite pedigree yielded 12 sub-pedigrees that were used to carry out a genome-wide linkage scan for IgE serum level in SOLAR. Two-point analyses resulted in strong evidence for linkage to two marker loci on chromosome 1, D1S3723 (lod = 3.70) and D1S534 (lod = 3.58). Multipoint analysis resulted in a maximum lod of 4.58 on chromosome 1 at 143 cM. After extending the two pedigrees that contributed the most evidence for linkage, the maximum lod score decreased to 4.18, with most of the evidence for linkage due to a single large sub-pedigree.