Fig. 1

A multiplexed digital PCR assay to analyse HTT1a expression levels in human samples

A Schematic overview of assay positions within the 5’ region of the HTT gene. The cryptic polyA site is 7,327 bp into intron 1. Sequences are listed in Table 1. B Exemplary results of a chip-based, multiplexed digital PCR assay. HTT exon 2 transcripts (HTTex2) are shown on the x-axis and HTT1a transcripts on the y-axis. Wells with a positive signal for each assay are shifted towards larger values. Wells that did not contain a target transcript are shown in yellow. Wells that were only positive for either HTTex2 or HTT1a are shown in red or blue, respectively. Wells that contained both target transcripts are shown in green. C and D Samples had CAG sizes in the control (control), adult onset (HD) or juvenile-onset range (HD juvenile). C Comparison of the performance of individually run assays versus multiplexed assays in primary human lymphoblastoid cell lines. The same cDNAs were used for the comparisons. D Assessment of technical inter-chip variation. The same cDNA from human lymphoblastoid cell lines was run on multiple chips. The black line denotes the mean of the individual chips. Each stack represents a different cell line. Ratios were built by dividing the signal of HTT1a/HTT exon 2 for each chip and subsequently calculating the mean for each line.