Table 1.
Targeted enrichment, included genomic regions.
Fig 1.
Overview of Bioinformatic workflows.
Schematic description of the utilized workflows MiSEQ Reporter 2.1.43 (Illumina inc), CLC Genomics Workbench 5.51 (CLCbio) and the in-house custom pipeline (ICP).
Table 2.
Detected mutations and patient characteristics
Table 3.
Read Mapping
Fig 2.
Results from the three different workflows; MSR; MiSEQ Reporter 2.1.43 (Illumina Inc), CLC; CLC Genomics Workbench 5.51 (CLCbio); and ICP, in-house custom pipeline. The proportion of reads mapped to the reference sequence and targeted bases respectively.
Fig 3.
Results from the three different workflows; MSR; MiSEQ Reporter 2.1.43 (Illumina Inc), CLC; CLC Genomics Workbench 5.51 (CLCbio); and ICP, in-house custom pipeline. The proportion of targeted reads that achieved X-fold coverage. Error bars represent +/- 2 standard deviations.
Table 4.
Variant calling
Table 5.
Sensitivity and specificity compared to Sanger Sequencing.
Fig 4.
Venn diagram of overlapping variants between the three workflows, total (all variants available at bases annotated for the 11 included genes) and non synonymous remaining variants after filtering synonymous variants with no calculated splice site disruption.
MSR; MiSEQ Reporter, CLC; CLC Genomics Workbench, and ICP; In-house custom pipeline.
Fig 5.
Venn diagram of overlapping variants between the two sequencing runs, total (all variants available at bases annotated for the 11 included genes) and non synonymous remaining variants after filtering synonymous variants with no calculated splice site disruption.
MSR; MiSEQ Reporter, CLC; CLC Genomics Workbench, and ICP; In-house custom pipeline.
Fig 6.
Chromatograms from automated Sanger sequencing as displayed in CLC Genomics Workbench 5.51 (CLCbio). NF1 variants available in germline DNA that were classified as pathogenic.