We used a new version of GENEHUNTER [6], which has recently been released to deal with SNP markers. Even with these recent enhancements, the complete Affymetrix map with 578 markers on chromosome 7 still surpassed the memory capacity of our systems. We therefore constructed three separate maps consisting of the first 289 markers, the last 289 markers and 289 markers from the middle of chromosome 7. The composite map consisted of the first two-thirds of the first set, the middle two-thirds of the middle set and the last two-thirds of the last set. This ensures that all markers in the composite map have at least some multipoint support from flanking markers. Once the chromosome was divided, the data files could be loaded. Some of the large pedigrees created prohibitive computational time requirements. We set the MAXBITS = 16 option in GENEHUNTER to allow it to automatically remove individuals from the pedigrees to reduce the large pedigrees to manageable form. In almost every case only unaffecteds were trimmed.
