Sex confirmation. Sex identifiers were available for most of the liver samples obtained from the three study centers. We independently confirmed the sex of each individual providing a liver sample by two methods. First, we looked for expression of Y-specific genes in the liver gene expression based on three probes representing three distinct transcripts. Second, we scored heterozygosity of X-chromosome markers. We excluded any individual for which there was a discrepancy in any of the three measures of sex in order to ensure a coherent data set for analysis and that we had excluded as many potential cases of annotation or sample-handling errors as possible. For samples where sex was not noted in the records, we imputed the sex call if both the genotype and gene-expression data were concordant.
