1. A B C
Supplementary Figure 1 - Assessment of performance of FFPE DNA in QC qPCR and Infinium assay
QC qPCR values, SNP call rates and LRR variance were used to assess suitability of DNA from FFPE samples for DNA restoration and Infinium SNP array analysis and data quality. Overall, DNA samples producing lower QC values yielded high SNP call rates (A; linear regression R2 = ; nonparametric Spearman correlation P value = ) and reduced LRR variance (B; linear regression R2 = ; nonparametric Spearman correlation P value ). LRR Variance also correlated with SNP call rates (C; linear regression R2 = ; nonparametric Spearman correlation P value < ).
Note – annotation of data points in A: DNA from the same case are highlighted with the same symbol; filled in symbols used to denote DNA samples from autopsy cases; open symbols denote DNA from recent surgical cases; symbols with cross denote DNA samples from surgical cases ~20 years old.