Table 1.
Data for FFPE blocks.
Table 2.
Overview of nucleic acids extracted with the different extraction kits from commercial vendors.
Fig 1.
Yield and amplifiability of extracted DNA and RNA.
(A) Average total amount of DNA. (B) Average total amount of RNA. (C) Amplifiable DNA quantified with the FFPE QC kit from Illumina. (D) Amplifiable RNA quantified with the PreSeq QC assay from ArcherDx. The average total amount and average delta Ct values for the different samples and extraction methods are shown. The standard deviation is shown as vertical bars. Methods with significant differences in yield are marked as connected with horizontal bars (p < 0.05). Samples with Ct values > 45 were censored giving a delta Ct of 21, shown as #.
Table 3.
Yield of final DNA HTS libraries obtained using DNA extracted with different extraction kits.
Fig 2.
Variants identified in the samples extracted with different DNA extraction methods.
(A-D) Venn diagram showing the distribution of variants between DNA extraction methods in four different FFPE samples, SARC1-4. Variants were detected by MuTect and Strelka, using an artificial control as normal. The data was filtered on exonic variants with allele frequency > 5% and coverage > 100x, being present at < 1% in the normal population (ExAC database).
Table 4.
Complexity of final DNA HTS libraries represented by duplication rates of downsized libraries.
Table 5.
Yield of Archer FusionPlex Sarcoma Assay libraries obtained using RNA extracted with different extraction kits.
Table 6.
Fusion detection in Archer FusionPlex Sarcoma Assay libraries with total number of unique reads and down-sampled number of reads for each sarcoma sample separately.