We used ALSPAC GWAS estimates from the alcohol problems factor score to calculate polygenic scores for FinnTwin12 using the --score procedure in PLINK [38]. We computed a linear function of the number of score alleles an individual possessed weighted by the product of the sign of the SNP effect and the negative logarithm (base 10) of the associated GWAS p-value. This retains the same direction between calculated and original output values. Of the 2,450,300 autosomal SNPs that passed quality control in the ALSPAC sample, 2,221,783 (91%) were available in the FinnTwin12 sample.
