A SIMPLE METHOD FOR ANALYZING MICROSATELLITE ALLELE IMAGE PATTERNS GENERATED FROM DNA POOLS AND ITS APPLICATION TO ALLELIC ASSOCIATION STUDIES

Allelic association studies provide the most powerful method for locat ing genes of small effect contributing to complex diseases and traits. However, in outbred populations, allelic association is usually maint ained only over distances of less than or equal to 1 cM. Therefore, sy stematic searches over large regions are costly. Here we present a met hod involving DNA pooling that can be used as a rapid preliminary scre en for allelic association with the most common class of polymorphic m arkers, single-sequence repeats. Patient and control samples are poole d separately, and markers are typed in the two pools. By use of primer s with fluorescent 5' ends, PCR products can be analyzed on an automat ed sequencing apparatus. Allele image patterns (AIPs) produced for the two groups are overlaid and differences in pattern area between pools computed. From this, a Delta AIP statistic is calculated from the dif ference in areas between the two AIPs expressed as a fraction of the t otal shared and nonshared area. AIPs of a range of different-sized poo ls were generated by computer simulation for markers with a range of a llele sizes and frequencies, Delta AIPs from pools and chi(2) values f or individual genotypings were compared, with both simulated and real data from microsatellite markers. The results demonstrated a high corr elation between Delta ATP and chi(2) values. Delta AIP analysis of rea l microsatellite data indicated the feasibility of using this method i n systematic searches for allelic association and generated a small nu mber of false positives but few false negatives. We conclude that Delt a AIP analysis of DNA pools can be used effectively and efficiently as a rapid screen for allelic association in case-control studies.