Fig. 3

Assessing the specificity of HTT ddPCR assays. a HD cell lines used; D—differentiation. b Scheme of HTT transcript with marked CAG repeat tract (green triangle) and SNP variants identified in HD cell lines (red arrows—SNPs used in ddPCR assays; black arrows—other identified SNPs); light orange box—UTRs. Table presents all SNP variants identified in analyzed HD cell lines. Bolded SNPs were selected to be targets for ddPCR assays and they will be hereinafter referred to as HTT_SNP2, HTT_SNP5, and HTT_SNP7 in the text. CDS—coding sequence, ∆—deletion. RefSNP number according to the Single Nucleotide Polymorphism Database (dbSNP). c Results from ddPCR analysis of HTT_SNP2 assay specificity performed on seven samples with predefined ratios of WT/MUT plasmids (samples: I—100% WT and 0% MUT; II—90% WT and 10% MUT; III—75% WT and 25% MUT; IV—50% WT and 50% MUT; V—25% WT and 75% MUT; VI—10% WT and 90% MUT; VII—0% WT and 100% MUT). Precise values are indicated on WT/MUT bars ± poisson error. d Percentage ratio of HTT WT allele obtained with ddPCR HTT_SNP7 assay using gDNA from indicated HD cell lines. Three biological replicates were performed. These data are presented as means ± SD