The strong effect of the indel on gene expression, and the finding that it was common to eight individuals with the higher risk haplotype of OPRK1, led us to examine its potential association with alcoholism. We genotyped 1914 individuals in 219 European American families in which at least three first-degree relatives were alcohol dependent. Genotyping was by PCR amplification followed by size determination of the fragments on agarose gels (Fig. 3). The reference sequence was the major allele. The allele with the indel (the net 830 bp insertion) was the minor allele, with a frequency of 28% in these families; genotypes were in Hardy–Weinberg equilibrium. The indel was in high LD (as measured by D′) with all of the SNPs we had previously genotyped (17) (data not shown). However, owing to differences in allele frequencies, the indel had only a low correlation (r2) with many of the SNPs (Fig. 4).
