Fig. 1

Assessment of genome-wide concordance of lc-WGS imputed genotypes in tissue versus blood of N = 10 patients. a, b Genome-wide concordance (Pearson correlation coefficient squared—y-axis) of allele dosages across all genotyped SNPs between blood and tissue as a function of their minor allele frequency (MAF, x-axis). Concordance was calculated for each individual and each filtering category including genotype imputation quality (a) with all genotypes shown in light green and high-quality genotypes (INFO > 80) in dark green, and copy number status of high-quality genotypes in tissue (b), from SNPs located in a region that was copy neutral (orange), gain (red) or loss (blue). For any given bin corresponding to a patient, MAF and filtering category had to have a minimum of 1000 SNPs to be included. Error estimates from 95% confidence intervals computed from 1000 bootstrapping iterations are indicated as shaded areas