KAPA HyperPrep Kits

Figure 1. KAPA HyperPrep Kits enable higher library construction efficiency. Conversion rates for libraries prepared for target capture from different amounts of Covaris-sheared human genomic DNA, using the KAPA HyperPrep or competitor library construction kits. Libraries were prepared according to manufacturer’s instructions. Input DNA was quantified by Qubit, whereas the qPCR-based KAPA Library Quantification Kit was used to determine KAPA HyperPrep and TruSeq Nano library yields after adapter ligation. Conversion rates for NEBNext libraries cannot be measured directly with the KAPA Library Quantification Kit and were derived from post-amplification yields.

Figure 2. KAPA HiFi introduces minimal amplification bias and offers high coverage uniformity. GC bias plots for libraries prepared for whole-genome shotgun sequencing of bacteria with extreme genomic GC content (Clostridium, 29% GC and Bordetella, 68% GC). Libraries were prepared with the KAPA HyperPrep Kit from 100 ng or 1 ng DNA, Covaris-sheared to an average size of ~200 bp; and sequenced without amplification, or after amplification with KAPA HiFi. Minimal amplification bias was introduced by KAPA HiFi, despite a relatively high number of PCR cycles (12 cycles for Clostridium and 13 cycles for Bordetella). Paired-end sequencing (2 x 300 bp) was performed on an Illumina MiSeq, and data analyzed using Picard.

Figure 4. KAPA HyperPrep Kits enable improved coverage depth for FFPE samples. Key sequencing metrics for libraries prepared from 100 ng of FFPE DNA for target capture, using either the KAPA HyperPrep Kit or TruSeq Nano DNA Sample Prep Kit (Illumina). Captures were performed with the SeqCap EZ Comprehensive Cancer Design (4 Mb) according to the manufacturer’s instructions, with the exception that the number of pre-capture amplification cycles for each library type was optimized based on post-ligation yields (10 cycles for KAPA HyperPrep vs. 14 cycles for TruSeq Nano DNA libraries). All libraries were amplified for 13 cycles after capture. More efficient library construction and less PCR bias with the KAPA HyperPrep Kits resulted in higher library complexity prior to capture, lower duplication rates, and improved coverage. Sequencing (2 x 75 bp) was performed on an Illumina HiSeq 2500. Sequencing reads were down-sampled to ~14 million per library prior to analysis with Picard.