& PERFORMANCE SUPERIOR SPEED · 125 100 75 50 25 0 KAPA HyperPrep TruSeq® Nano DNA Kits Conversion...
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Data on file. For Research Use Only. Not for use in diagnostic procedures. SUPERIOR SPEED & PERFORMANCE Benefits • Superior speed and convenience • Lower duplication rates and higher sequencing coverage • Improved performance with low-input samples • High-quality library construction from FFPE samples • PCR-free workflows • Qualified automation methods The KAPA HyperPrep Kit provides a streamlined, versatile library preparation solution that significantly reduces library preparation time. The novel, single-tube chemistry offers improvements to library construction efficiency, particularly for challenging samples such as FFPE and cell-free DNA. KAPA HyperPrep Kits Shift your workflow into hyperdrive
Transcript of & PERFORMANCE SUPERIOR SPEED · 125 100 75 50 25 0 KAPA HyperPrep TruSeq® Nano DNA Kits Conversion...
Data on file.For Research Use Only. Not for use in diagnostic procedures.
SUPERIOR SPEED& PERFORMANCE
Benefits• Superior speed and convenience
• Lower duplication rates and higher sequencing coverage
• Improved performance with low-input samples
• High-quality library construction from FFPE samples
• PCR-free workflows
• Qualified automation methods
The KAPA HyperPrep Kit provides a streamlined, versatile library preparation solution that significantly reduces library preparation time. The novel, single-tube chemistry offers improvements to library construction efficiency, particularly for challenging samples such as FFPE and cell-free DNA.
KAPA HyperPrep KitsShift your workflow into hyperdrive
2Data on file.For Research Use Only. Not for use in diagnostic procedures.
Superior speed and convenienceThe streamlined, one-tube KAPA HyperPrep protocol offers rapid turnaround times, with minimal hands-on time. • Complete library construction in less than 3 hours
• Library amplification may be omitted for PCR-free workflows
• Bead-based size selection steps can be incorporated to achieve the appropriate final library fragment-size distribution
Industry-leading yields and sequencing qualityConversion rate, defined as % input DNA converted to sequenceable, adapter-ligated library, is a key library construction metric which ultimately determines library diversity and quality.• Achieve higher library yields across a
range of input DNA and sample types
• Fewer amplification cycles for downstream processing, result in lower duplication rates and higher sequence coverage
• Achieve successful library construction with challenging samples and PCR-free workflows
KAPA Hyper Prep KitTotal time: 2.75 hours
End Repair & A-tailing
Adapter Ligation
Library Amplification
Bead Cleanup
Bead Cleanup
NEBNext® Ultra Library Prep Kit
Total time: 3 hours
End Repair & A-tailing
Adapter Ligation
USER Excision
Library Amplification
Bead Cleanup
Bead Cleanup
Illumina® TruSeq® Nano DNA Sample Prep Kit
Total time: 6 hours
End Repair
A-tailing
Adapter Ligation
Library Amplification
Bead Cleanup
Size Selection
Bead Cleanup
(optional)
Conversion rates for libraries prepared for target capture from different amounts of Covaris-sheared 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 using the KAPA Library Quantification Kit and were derived from post-amplification yields.
DNA Input
40
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5
01 μg 100 ng 10 ng
KAPA HyperPrep
TruSeq Nano DNA KitsNEBNext Ultra
Con
vers
ion
(%)
Conversion rate comparison
3Data on file.For Research Use Only. Not for use in diagnostic procedures.
Minimal amplification bias• In workflows where
amplification is required, KAPA HiFi introduces minimal amplification bias, resulting in more uniform sequence coverage
• Kits without an amplification module are available for PCR-free workflows
High-quality library construction from FFPE samples• Lower duplication rates and high sequence coverage enables improved detection
of low-frequency mutations
• More unique adapter-ligated library fragments from low-quality sample types translate to higher library diversity
GC bias plots for libraries prepared for whole-genome shotgun sequencing of bacteria with extreme genomic GC content. 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 HotStart ReadyMix. Sequencing (2 x 300 bp) was performed on an Illumina® MiSeq® instrument and data analyzed using Picard.
Library diversity
KAPA HyperPrep
TruSeq Nano DNA
25
20
15
10
5
0Uni
que
mol
ecul
es (
x 10
6 )
19.5
6.4
Clostridium_100ng_Covaris_NoClean_Hyper_NoAmp.bam.null GC Bias Plot Total clusters: 239,377, Aligned reads: 458,669
GC% of 100 base windows
Frac
tion
of n
orm
alize
d co
vera
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Mea
n ba
se q
ualit
y0 20 40 60 80 100
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2.0
010
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Clostridium
Frac
tion
of n
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ed c
over
age
Mea
n ba
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% GC for 100 bp windows
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Clostridium_1ng_Covaris_NoClean_Hyper_Amp.bam.null GC Bias Plot Total clusters: 233,138, Aligned reads: 444,053
GC% of 100 base windows
Frac
tion
of n
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alize
d co
vera
ge
Mea
n ba
se q
ualit
y
0 20 40 60 80 100
0.0
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1.0
1.5
2.0
010
2030
40Total Clusters: 233,138
Aligned Reads: 444,053
Total Clusters: 239,377
Aligned Reads: 458,669
GC bias plotsBordetella_100ng_Covarls_NoClean_Hyper_NoAmp.bam.null
GC Blas Plot
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0.0
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1.0
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2.0
GC% of 100 base windows
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tion
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orm
alize
d co
vera
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010
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GC% of 100 base windows
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Bordetella_1ng_Covaris_NoClean_Hyper_Amp.bam.null GC Bias PlotTotal clusters: 312,391, Aligned reads 580,794
Mea
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ualit
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100 ng PCR-free 1 ng amplified
Borde
tella
Total Clusters: 312,391
Aligned Reads: 508,794
Total Clusters: 319,787
Aligned Reads: 600,235
Frac
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over
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% GC for 100 bp windows
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Sequencing metrics for libraries prepared from 100 ng 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. Sequencing (2 x 75 bp) was performed on an Illumina HiSeq® instrument. Sequencing reads were down-sampled to ~14 million per library prior to analysis with Picard.
Duplication rates
KAPA HyperPrep
TruSeq Nano DNA
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20
15
10
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0
(%)
9.7
19.5
Conv
ersio
n (%
)
Sequence coverage depth150
125
100
75
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KAPA HyperPrep
TruSeq® Nano DNA Kits
Con
vers
ion
(%)
% Bases at 10X
97.5 97.1
% Bases at 20X
96.2 94.2
% Bases at 30X
94.489.2
% Bases at 50X
87.7
71.3
% Bases at 100X
56.4
24.6
Normalized Coverage Windows at GC% Base Quality at GC%
Published by:
Roche Sequencing Solutions, Inc.4300 Hacienda DrivePleasanton, CA 94588
sequencing.roche.com
Data on file.For Research Use Only. Not for use in diagnostic procedures.KAPA and SeqCap are trademarks of Roche. All other product names and trademarks are the property of their respective owners. ©2017 Roche Sequencing Solutions, Inc. All rights reserved. SEQ100003 A038 02/17
Improved performance with low-input samples• Generate more diverse libraries from limited amounts of input DNA
• High adapter:insert molar ratios can be used to increase library construction efficiency
Ordering information
Roche Cat. No. KAPA Code Description Kit Size
07962312001 KK8500 KAPA HyperPrep Kit with Library Amplification 8 rxn
07962347001 KK8502 KAPA HyperPrep Kit with Library Amplification 24 rxn
07962363001 KK8504 KAPA HyperPrep Kit with Library Amplification 96 rxn
07962339001 KK8501 KAPA HyperPrep Kit, PCR-free 8 rxn
07962355001 KK8503 KAPA HyperPrep Kit, PCR-free 24 rxn
07962371001 KK8505 KAPA HyperPrep Kit, PCR-free 96 rxn
Competitor
0.18
Library diversity Duplication rates
Library diversity and duplication rates for libraries prepared from 2 ng of cell-free DNA. Libraries were constructed with the KAPA HyperPrep Kit or a competitor kit optimized for low-input library construction, according to manufacturer’s instructions. Standard ligation parameters were used. KAPA HyperPrep libraries were prepared with a range of adapter:insert molar ratios. Sequencing (2 x 150 bp) was performed on an Illumina® MiSeq® instrument and data analyzed using Picard.
Conv
ersio
n (%
)
HyperPrep (60:1)
HyperPrep (300:1)
HyperPrep (1000:1)
Competitor
3
2
1
0
x10
8 mol
ecul
es
1.521.74
2.64
1.85
Conv
ersio
n (%
)
HyperPrep (60:1)
HyperPrep (300:1)
HyperPrep (1000:1)
0.25
0.20
0.15
0.10
0.05
0.00
(%)
0.210.18
0.17
