Table 1.
Characteristics of six genes included in the assay.
Table 2.
Comparison of bench-top NGS platforms.
Table 3.
Sequencing and target capture performance metrics.
Figure 1.
a. The percentage of each gene that is captured and sequenced (at least one read) is shown for each platform (MiSeq in red, PGM in black), for 15 samples; Three genes were consistently fully sequenced. Coverage of KCNQ1 and KCNH2 was more variable: KCNQ1 and KCNE1 were fully covered in the best performing samples, while the best performance on KCNH2 covered >97% of the gene. b. Mean sequencing depth across each gene, for 15 samples. Quartiles are shown. There is significant intra- and inter- sample variability.
Table 4.
Sequencing coverage of each gene.
Figure 2.
Coverage of KCNQ1 and KCNH2 for the two platforms.
Mean depth of coverage for 15 samples is shown for two genes on a log scale. Regions of no coverage therefore have negative values. The blue lines indicate local GC content (calculated with a 50 bp sliding window). Regions consistently missed have high GC content, with similar patterns for both platforms. KCNQ1 exons 1 & 8 and KCNH2 exons 1, 4 & 12 are difficult to sequence. A cartoon of the exon structure is shown beneath each panel. Plus (+) and minus (-) denote gene strand. Plots for all genes are shown in Supporting Information Figure S5. a.) MiSeq b.) Ion Torrent PGM.
Table 5.
Detection of coding variants for each NGS platform.
Table 6.
Accuracy of variant calling for NGS platforms.