Additional file 1 of Droplet digital PCR-based analyses for robust, rapid, and sensitive molecular diagnostics of gliomas
Creators: name: Wolter, Marietta
name: Felsberg, Jörg
name: Malzkorn, Bastian
name: Kaulich, Kerstin
name: Reifenberger, Guido
Publisher: name: figshare
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file1. Table S1 Overview of the primer and probe sequences used for the individual ddPCR assays in this study including both previously published and newly designed assays. Table S2 Commercially available assays used for ddPCR-based single nucleotide variant (SNV) and copy number variation (CNV) analyses of certain biomarkers. Table S3 Primers and probes used for ddPCR-based single nucleotide polymorphism (SNP) analysis on chromosomal arms 1p and 19q. Table S4 Primers and probes used for ddPCR-based SNP analysis on chromosome 10. Table S5 Thermocycler conditions used for ddPCR assays. Table S6 Sensitivity, specificity, accuracy, and precision of each ddPCR assay investigated in relation to the respective method used for validation. Table S7 Detection of IDH1 and IDH2 mutations using duplex and multiplex ddPCR assays. Table S8 Detection of BRAF V600E and BRAF V600K mutations using duplex ddPCR assays. Table S9 Detection of H3-3A p.K28M and H3-3A p.G35R mutations using duplex ddPCR assays. Table S10 Comparison of the experimentally detected mean allele frequency (AF) of deleted SNP loci on 1p and 19q versus the AF calculated from the mutant allele frequency (MAF) of TERTp (a) or IDH1/2 (b) mutations. Table S11 Comparison of the experimentally detected mean allele frequency (AF) of deleted SNP loci on chromosome 10 versus the AF calculated from the mutant allele frequency (MAF) of TERTp mutations. Table S12 Detection of the EGFRvIII variant using ddPCR as well as comparison of a commercially available PrimePCR™ ddPCR (a) and a self-designed (b) copy number assay for EGFR exon 28. Table S13 Determination of CDKN2A copy number in 66 glioma samples using a PrimePCR™ ddPCR CDKN2A copy number assay. Fig. S1 Detection of IDH1 and IDH2 hotspot mutations in FFPE DNA using ddPCR. Fig. S2 Sensitivity of ddPCR to detect IDH1 R132H (a), BRAF V600E (b) as well as H3-3A p.K28M (c.83A&gt;T) (c) and H3-3A p.G35R (c.103G&gt;A) (d) mutations in FFPE DNA. Fig. S3 Detection of BRAF V600E (a) and BRAF V600K (b) mutations in FFPE DNA using ddPCR. Fig. S4 Detection of H3-3A p.K28M and H3-3A p.G35R/V mutations in FFPE DNA using ddPCR. Fig. S5 Detection of the PRKCA D463H mutation in chordoid glioma FFPE tissue samples using ddPCR. Fig. S6 Analysis of copy number variations on chromosomal arms 1p and 19q in 15 glioma samples using ddPCR. Fig. S7 Loss of heterozygosity (LOH) on chromosomal arms 1p and 19q (a, b) as well as on chromosome 10 (c) detected by ddPCR-based SNP analysis. Fig. S8 Detection of BRAF duplication in 20 pilocytic astrocytomas by ddPCR analysis of UBN2 and BRAF copy number using the assay reported by Appay et al. [8]. Fig. S9 Job Report file of case 1 using the ARCHER® FusionPlex Panel and Archer Analysis software v6.2.7. Fig. S10 The general workflow for the ddPCR-based molecular diagnostics