Fig 1.
Visualization of all steps for (A) library preparation and (B) target capture until sequencing. An alternative approach for the number of PCR cycles and input amount is: ≥ 150 ng and ≤ 250 ng, 5 cycles; ≥ 25 ng and < 150 ng, 8 cycles; < 25 ng, 10 cycles.
Table 1.
Recommended input amount of DNA to library preparation.
Table 2.
Recommendation of number of PCR cycles depending on input amount.
Table 3.
Recommended number of PCR cycles after hybridization.
Fig 2.
Library concentrations for four library preparation strategies.
Yield in concentration (ng/μl) after library conversion for four different fragmentation and end-repair conditions; HyperPrep–no fragmentation, HyperPlus 6.5 min–fragmentation for 6.5 min, HyperPlus 12.5 min–fragmentation for 12.5 min, HyperPrep + HyperPlus–fragmentation for 12.5 min and extended end-repair. See S1 Table for data in a table format.
Fig 3.
Quality control data analysis for three library preparation strategies.
Analysis of quality control data for three different library preparation fragmentation and end-repair conditions; HyperPrep–no fragmentation, HyperPlus 12.5 min–fragmentation for 12.5 min, HyperPrep + HyperPlus–fragmentation for 12.5 min and extended end-repair. Mean insert size (A), duplication rate (B), median target coverage (C) and percent target bases 150X (D) in comparison to treatment conditions were investigated. Panel GMCKsolid4.1 was used. See S1 Table for data in a table format.
Fig 4.
Quality control data analysis for samples prepared with the combination protocol.
Five different samples (NA24143 (high molecular weight), HD798, HD799, HD803 (formalin-comprised) and HD777 (cfDNA)) at 10, 30, 50 and 250 ng input amounts were analyzed with the combination protocol (HyperPrep + HyperPlus–fragmentation for 17.5 min and extended end-repair). Data shows covered bases (percent target bases at 500 and 1000X, (A), duplication rate (B), as well as median target coverage (C) and mean insert size (D). Panel CG001 was used. See S2 Table for data in a table format.
Table 4.
Variants detected in the formalin-comprised control samples HD798, HD799 and HD803 prepared with the combination protocol.
Table 5.
Variants detected in the cfDNA control sample HD777 prepared with the combination protocol.