We chose the TTTH1 electrophysiological endophenotype (electric potential FP1, far frontal left side channel) because the information supplied to Genetic Analysis Workshop participants regarding the COGA data indicated that microsatellite markers on chromosome 7 are linked to a QTL affecting normal variation in this phenotype. Linkage analyses were run at every 1-cM interval on chromosome 7 using multipoint estimates of IBD allele-sharing derived from the microsatellite marker data by the program LOKI [8,9]. Age at exam and maximum number of drinks consumed in a 24-hour period were included as covariates in the linkage analyses. COGA participants were not selected on the basis of the TTTH1 phenotype, hence no ascertainment correction was made. Subsequent to the linkage analysis, we used the single-nucleotide polymorphism (SNP) genotypes provided by Affymetrix and Illumina to conduct the QTLD test procedure in SOLAR, confining our analysis to that area of chromosome 7 showing evidence for linkage. For each SNP tested, we included a linkage component based on the short tandem repeat based multipoint IBDs for the integral centimorgan location nearest to the location of the SNP.
