False positive rates in a genomic screen for complex quantitative traits

We conducted a genomic screen for genes associated with Q1, Q2, and Q3 in 239 nuclear pedigrees from replicate 115, Problem Set 2A. We compared false positive (FP) and true positive (TP) rates for three significance levels and two map densities. Using the 2 cM genetic map and alpha = 0.05 produced the most FP but detected the greatest number of major genes. Following up only 31 plateaus (two or more adjacent markers with significant results) from the 2 cM screen eliminated some FP, but failed to detect MG3 for Q3. Multipoint analysis reduced the number of priority regions from 31 to seven; only two of these regions were TP. Replication of the two-point analysis of plateau markers in replicate 80 detected all of the genes associated with Q1 and Q2, but not Q3. Multipoint analysis in replicate 80 failed to replicate any genes associated with Q1, Q2, or Q3, but "replicated" two FP regions. While FP may be reduced by decreasing map density, considering only plateaus for follow up and decreasing significance levels, such adjustments may also fail to detect weak TP. Multipoint analysis and replication in independent data sets may not be reliable methods of distinguishing FP from TP.