KAPA Hyper Prep Kits
Shift your workflow into hyperdrive.
The KAPA HyperPrep Kit is a versatile, streamlined solution for DNA library preparation for Illumina® sequencing.
The novel one-tube chemistry, contain optimally formulated and evolved enzymes that enable higher yields of adapter-ligated library and lower amplification bias. This translates to higher library diversity, lower duplication rates and more uniform coverage, particularly for FFPE and low-input samples.
NEW! KAPA Dual-Indexed Adapter Kits are now available. For more information on KAPA Adapter Kits, scroll down to the Ordering section, or download the KAPA Adapter and Bead Calculator.
For Research Use Only. Not for use in diagnostic procedures.
Improve library yields and sequence quality
- Higher library yields translate to greater molecular complexity
- Fewer cycles of amplification with KAPA HiFi DNA Polymerase results in lower duplication rates and improved coverage
Create high-quality libraries from FFPE samples
- Generate high-quality libraries from 250 ng FFPE DNA or less*
- Significantly lower duplication rates and higher coverage*
Complete library construction in less than 3 hours
- One-tube workflow with minimal cleanup steps reduces overall time, and minimizes hands-on time
- Sample-to-library in <2 hours for PCR-free workflows, or <3 hours with amplification*
- Fewer handling steps lead to improved consistency and reproducibility
Improve performance with low-input samples
- Generate more sequence-quality library molecules without increasing adapter-dimers
- Increase yields without inducing size bias
*Data on file.
Are you sequencing low-input, FFPE or high quality DNA? RNA? Check out these Kapa NGS products to improve your workflow and results:
- Whole Genome Sequencing
- Whole Exome Sequencing
- Targeted Sequencing (custom panels)
- Amplicon Sequencing
Kits can be stored for up to 12 months at -20˚C.
Kits contain KAPA End Repair & A-Tailing Buffer, KAPA End Repair & A-Tailing Enzyme, KAPA Ligation Buffer, KAPA DNA Ligase, KAPA HiFi HotStart ReadyMix and KAPA Library Amplification Primer Mix
Compatible Platformllumina HiSeq, MiSeq, NextSeq and GAIIx
Starting MaterialFragmented DNA, cDNA, or PCR amplicons
Input Amount1 ng–1 µg
- Case Study
- Application Note
- Product Brochure
- Material Safety Data Sheet
- Technical Data Sheet
- Poster Note
- Whole-genome shotgun sequencing
- Targeted sequencing by solution hybrid selection (i.e. exome or custom capture using the SeqCap®EZ, Agilent SureSelect®, Illumina TruSeq™ or IDT xGen® Lockdown® Probes systems)
- Amplicon sequencing
- Methyl-seq (in combination with the KAPA HiFi Uracil+ Library Amplification ReadyMix)
This protocol has been validated for library construction from 1 ng–1 μg of appropriately fragmented dsDNA. However, libraries can be prepared from lower input amounts if the sample represents sufficient copies to ensure the requisite coverage and complexity in the final library.
- End repair and A-tailing, which produces end-repaired, 5′-phosphorylated, 3′-dA-tailed, dsDNA fragments
- Adapter ligation, during which dsDNA adapters with 3′-dTMP overhangs are ligated to 3′-dA-tailed library fragments
- Library amplification (optional), which employs high-fidelity, low-bias PCR to amplify library fragments carrying appropriate adapter sequences on both ends
The library construction process, from end repair and A-tailing to final, amplified library, can be performed in less than 3 hours, depending on experience and the number of samples being processed. If necessary, the protocol may be safely paused after completion of the post-ligation cleanup, or prior to post-amplification cleanup.
Adapter-ligated library may be stored at 4°C for one week, or at -20°C at least one month before amplification, target enrichment and/or sequencing. To avoid degradation, always store DNA in a buffered solution (10 mM Tris-HCl, pH 8.0), and minimize the number of freeze-thaw cycles.
- If you are performing a cleanup between shearing and end repair, shear in 10 mM Tris-HCl (pH 8 or 8.5) + 1 mMEDTA.
- If you are not performing a cleanup between shearing and end repair, shear in 10 mM Tris-HCl (pH 8 or 8.5) + 0.1 mMEDTA.
- Never shear DNA in water.
KAPA Dual- or Single-Indexed Adapters are recommended for use with KAPA HyperPrep Kits, except for methyl-seq applications. KAPA HyperPrep Kits are also compatible with non-indexed, single-indexed, and dual-indexed adapters that are routinely used in SeqCap EZ, Illumina TruSeq, Agilent SureSelect, and other similar library construction and target capture workflows. Custom adapters that are of similar design and are compatible with “TA-ligation” of dsDNA may also be used, remembering that custom adapter designs may impact library construction efficiency.
Ligation efficiency is robust for adapter-insert molar ratios from 10:1 to >200:1. The recommended adapter concentrations for different inputs are given in the table below. Note that high adapter-insert molar ratios are beneficial for low-input and challenging samples. When optimizing worfklows for DNA inputs ≤25 ng, it is recommended that two or three adapter concentrations be evaluated. Try the recommended concentration in the table, as well as one or two additional concentrations in the range that is 2 – 10 times higher.
|Input DNA||Adapter stock concentration||Adapter:insert
|1 μg||15 μM||10:1|
|500 ng||15 μM||20:1|
|250 ng||15 μM||40:1|
|100 ng||15 μM||100:1|
|50 ng||15 μM||200:1|
|25 ng||7.5 μM||200:1|
|10 ng||3 μM||200:1|
|5 ng||1.5 μM||200:1|
|2.5 ng||750 nM||200:1|
|1 ng||300 nM||200:1|
High Concentration (30 µM) KAPA Single-Indexed Adapter Kits are recommended for library construction from 10 ng – 1 µg inputs, whereas Low Concentration (1.5 µM) KAPA Single-Indexed Adapter Kits are recommended for inputs <10 ng. KAPA Dual-Indexed Adapters may be used for all inputs with the appropriate dilution. For assistance with adapter compatibility and ordering, please visit kapabiosystems.com/support.
Please refer to the KAPA Single-Indexed and Dual-Indexed Adapter Technical Data Sheets for information about barcode sequences, pooling, kit configurations, formulation, and dilution for different KAPA DNA and RNA library preparation kits and inputs.
KAPA Adapters undergo extensive qPCR- and sequencing-based functional and QC testing to confirm:
- optimal library construction efficiency
- minimal levels of adapter-dimer formation
- nominal levels of barcode cross-contamination
Library construction efficiency and adapter-dimer formatin are assessed in a low-input library construction workflow. The conversion rate achieved in the assay indicates library construction efficiency. This is calculated by measuring the yield of adapter-ligated library (before any amplification) by qPCR (using the KAPA Library Quantification Kit), and expressing this as a % of input DNA. To assess adapter-dimer formation, a modified library construction protocol— designed to measure adapter dimer with high sensitivity—is used.
Barcode cross-contamination is assessed by sequencing. Each adapter is ligated to a unique, synthetic insert of known sequence, using a standard library construction protocol. These constructs pooled and sequenced on a MiSeq. For every barcode, the number of reads (in the range of 115,000 – 500,000) associated with each insert is counted, and the total % correct inserts calculated. Contamination of any barcode with any other single barcode is guaranteed to be <0.25%. The total level of contamination for any barcode is typically in the range of 0.1 – 0.5%. This assay is unable to distinguish between chemical cross-contamination and adapter “cross-talk”, and measures the total number of incorrect inserts resulting from both phenomena.
No, follow the standard protocol to construct FFPE libraries for target capture. For WGS workflows, a size selection step will most likely be required.
The proportion of fragmented DNA that is successfully converted to adapter-ligated molecules decreases as input is reduced. When starting library construction (end repair and A-tailing) with >10 ng fragmented genomic DNA, 5%–35% of input DNA is typically recovered as adapter-ligated molecules. Workflows that contain additional bead-based cleanups or size selection prior to library amplification are likely to result in a lower yield of adapter-ligated molecules.
The novel, one-tube KAPA HyperPrep chemistry leads to less adapter-dimer formation and carry-over. A single bead-based cleanup after adapter ligation is sufficient to remove unused adapter and adapter dimer, even at the high adapter:insert molar ratios recommended for low-input applications. If necessary, a second post-ligation (or size selection step) cleanup may be included to remove all traces of unused adapter and adapter-dimer, especially for PCR-free workflows and/or when dual-indexed adapters are used.
If required, any commonly used size selection technique (e.g., the double-sided or an electrophoresis-based method) may be integrated in this protocol.
Size selection may be carried out at alternative points in the overall workflow, for example:
- prior to end repair of fragmented DNA,
- after the post-ligation cleanup, or
- after library amplification.
The standard KAPA HyperPrep protocol does not include size selection. Detailed protocols for double-sided size selection prior to library construction, after ligation or after library amplification may be found in Appendix 1 of the KAPA HyperPrep Technical Data Sheet.
KAPA HyperPrep Kits contain KAPA HiFi HotStart ReadyMix for library amplification. This contains the novel, B-family HiFi HotStart DNA Polymerase, which was evolved for low-bias, high-efficiency, high-fidelity PCR. KAPA HiFi has become the gold standard for NGS library amplification (1, 2, 3, 4).
- Oyola, S.O. et al. BMC Genomics 13, 1 (2012)
- Quail M.A. et al. Nature Methods 9, 10-11 (2012)
- Quail M.A. et al. BMC Genomics 13, 341 (2012)
- Ross, M.G. et al. Genome Biology 14: R51 (2013)
If cycled to completion (not recommended) a single 50 µL KAPA HiFi library amplification reaction can produce 8–10 µg of amplified library. To minimize over-amplification and associated undesired artefacts, the number of amplification cycles should be tailored to produce the optimal amount of amplified library required for downstream processes. This is typically in the range of 250 ng–1.5 µg of final, amplified library.
Quantification of adapter-ligated libraries prior to library amplification can greatly facilitate the optimization of library amplification parameters, particularly when a library construction workflow is first established or optimized. The amount of template DNA (adapter-ligated molecules) available for library amplification may be determined using the KAPA Library Quantification Kit. A simple algorithm can subsequently be used to theoretically predict the number of amplification cycles needed to achieve a specific yield of amplified library. A calculator that can be used for purpose is available on request from kapabiosystems.com/support.
The estimated number of amplification cycles for libraries prepared from different amounts of input DNA is given in the table below. The actual optimal number of amplification cycles may be 1–3 cycles higher or lower, depending on the sample type and size distribution of the input DNA.
|Input DNA1||Number of cycles required to generate:|
|100 ng||1 μg|
1Input into end repair and A-tailing reaction
If the amount of adapter-ligated library retrieved after the post-ligation cleanup is sufficient for the next process (e.g. direct sequencing), and the library molecules contain all the adapter motifs needed for that process, library amplification may be omitted. This further streamlines the workflow and reduces the overall library preparation time to <2 hours. The high conversion efficiency achievable with the KAPA HyperPrep Kit enables PCR-free workflows from as little as 100 ng input DNA. KAPA HyperPrep Kits without amplification reagents (KK8501, KK8503 and KK8505) are available for PCR-free workflows.
KAPA HyperPrep Kits contain a new, highly optimized Library Amplification Primer Mix, designed to eliminate or delay primer depletion during library amplification reactions performed with KAPA HiFi DNA polymerase. The primers in the mix are based on the P5 and P7 Illumina flow cell sequences, and are suitable for the amplification of libraries prepared with full-length adapters. User-supplied primer mixes may be used in combination with incomplete or custom adapters. Please contact firstname.lastname@example.org for guidelines on the formulation of user-supplied library amplification primers.
In library amplification reactions, primers are typically depleted before dNTPs. When DNA synthesis can no longer take place due to substrate depletion, subsequent rounds of DNA denaturation and annealing result in the separation of complementary DNA strands, followed by imperfect annealing to non-complementary partners. This presumably results in the formation of so-called “daisy chains” or “tangled knots”, comprising large assemblies of improperly annealed, partially double-stranded, heteroduplex DNA. These species migrate slower and are observed as secondary, higher molecular weight peaks during the electrophoretic analysis of amplified libraries.
Excessive library amplification can result in unwanted artifacts such as PCR duplicates, chimeric library inserts, amplification bias and heteroduplex formation. It is generally best to limit the extent of library amplification as much as possible, while ensuring that sufficient material is generated for QC and sequencing.
Library size distribution, and the absence of primer dimers and/or over-amplification products, should be confirmed by means of an electrophoretic method. KAPA Library Quantification Kits are recommended for qPCR-based quantification of libraries prior to pooling for target capture or sequencing. qPCR-based quantification of adapter-ligated libraries (prior to library amplification) is not routinely done, but can provide useful data for protocol optimization and troubleshooting.
The enzymes provided in this kit are temperature sensitive, and appropriate care should be taken during shipping and storage. KAPA HyperPrep Kits are shipped on dry ice or ice packs, depending on the country of destination. Upon receipt, immediately store enzymes and reaction buffers at -20°C in a constant-temperature freezer. When stored under these conditions and handled correctly, the kit components will retain full activity until the expiry date indicated on the kit label (12 months from the date of shipment).
Kit CodeRoche Cat. NoDescriptionKit SizeHow to buy
KAPA Single-Indexed Adapter Set A contains indices 2, 4, 5, 6, 7, 12, 13, 14, 15, 16, 18 and 19, whereas Set B contains indices 1, 3, 8, 9, 10, 11, 20, 21, 22, 23, 25, 27. All KAPA Single- and Dual-Indexed Adapter Kits contain KAPA Adapter Dilution Buffer. KAPA Dual-Indexed Adapter Kits also contain three additional sealing films to support multiple use.
Kit CodeRoche Cat. NoDescriptionKit SizeHow to buy