The rhAmpSeq CRISPR Analysis System allows quick and accurate quantification of CRISPR-Cas edits. Our proprietary RNAse H2-dependent PCR technology generates amplicon libraries for targeted sequencing on Illumina® NGS platforms. The system also includes an advanced but accessible cloud-based data analysis pipeline for quantification of on- and off-target edits.
Create highly multiplexed amplicon sequencing panels for your targets of interest.
Rapid, cost-effective library preparation for rhAmpSeq CRISPR targeted sequencing. The rhAmpSeq CRISPR Library Kit also comes with analysis credits to enable data processing and quantification of editing events via the rhAmpSeq CRISPR Analysis Tool. Each analysis credit allows for the analysis of up to 500 targets for one, indexed sample.
Easily prepare and combine rhAmpSeq libraries onto a single sequencing run for maximum efficiency.
The rhAmpSeq CRISPR Analysis System enables singleplex or multiplex analysis of CRISPR edits by next generation sequencing (NGS) in less than a week. Our custom design tool ensures maximal compatibility between the target primers. The rhAmpSeq CRISPR Library Kit prevents primer-dimer amplification during the two simple PCR steps required for sequencing on any Illumina platform (Figure 2). The system provides access to an intuitive data analysis tool that generates publication quality figures without the need for advanced bioinformatics expertise.
Figure 2. The rhAmpSeq CRISPR Analysis System provides robust on-target rate and uniform coverage with no primer-dimer amplicons. (A) The workflow for targeted enrichment via amplification with the rhAmpSeq CRISPR Analysis System generates NGS-ready libraries in two straightforward PCR steps. (B) The rhAmpSeq CRISPR on-target rate represents the fraction of reads from expected targets in the rhAmpSeq CRISPR Panel relative to all mapped reads from the library. In this experiment, genomic DNA samples (Coriell) were amplified with a 19-, 282-, and 994-plex rhAmpSeq CRISPR Panel with 10 and 50 ng of input DNA. All panels were highly specific giving on-target mapping rates of >98%. (C) The uniformity of target amplification in a 990-plex is shown. In this experiment, 95% of all targets give coverage that is >0.2X of the mean coverage depth of the entire panel. (D) DNA-only primers compared to rhAmp primers show an accumulation of primer dimers in this 35-plex reaction with unblocked DNA primers, while no primer-dimers are observed when using end-blocked, RNaseH2-cleavable, rhAmp primers.
High uniformity and specificity with rhAmpSeq CRISPR Panels allow for interrogation of on- and off-target editing in a single library prep with PCR amplification as represented below using the popular AAVS1 “safe harbor” site (Figure 3). All 28 empirically identified off-target sites can be verified when Cas9 is constitutively expressed in HEK293 cells. Using ribonucleoprotein (RNP) delivery of the Cas9/guide complex in conjunction with Alt-R™ S.p. HiFi Cas9 Nuclease V3 dramatically reduces off-target editing.
Figure 3. High uniformity and specificity with rhAmpSeq CRISPR Panels allow for interrogation of on- and off-target editing in a single library prep with PCR amplification. HEK293 cells constitutively expressing S.p. Cas9 nuclease were electroporated with 10 µM AAVS1-targeting Alt-R sgRNA. Alternatively, standard HEK293 cells were electroporated with 4 µM Alt-R wild-type (WT) or HiFi Cas9 Nuclease complexed to the AAVS1 sgRNA (at a 1:1.2 protein to gRNA ratio), including 4 µM Alt-R Cas9 Electroporation Enhancer using the Amaxa™ Nucleofector™ 96-well Shuttle™ System (Lonza). gDNA was isolated and amplified using a custom rhAmpSeq CRISPR Panel containing amplicons for the on-target and 28 of the top off-target sites identified by GUIDE-Seq. Amplicon sequencing on the Illumina MiSeq (v2 chemistry, 150 bp paired-end reads) was performed and analyzed using the rhAmpSeq CRISPR Analysis Tool. (A) The histogram of panel coverage shows 100% of assays have read coverage depth that is >0.2X of the mean read coverage depth for all assays in the panel, indicating highly uniform enrichment via amplification. (B) Fragment analysis of final panels in duplicate shows the expected fragment sizes of 300–400 bp with no primer dimers present. (C) NHEJ editing for the on-target locus (Assay 1) and off-target loci (Assays 2-29) is reported using an untreated control for background subtraction. Background editing was <0.2% for all assays in this panel.
The rhAmpSeq CRISPR Analysis System offers access to the rhAmpSeq CRISPR Analysis Tool, which enables robust detection of low-frequency insertion/deletions (indels) (Figure 4).
Powered by NGS, the rhAmpSeq CRISPR Analysis System offers more accurate annotation of genomic edits than Sanger deconvolution, particularly at low editing frequencies (Figure 5).
Figure 5. Next generation sequencing (NGS) is more accurate than Sanger deconvolution for annotating genome editing, especially at low editing frequencies. On-target editing levels for guide RNAs (gRNAs) targeting the RAG1 and RAG2 loci in CD34+ hematopoietic stem/progenitor cells (HSPCs) quantified by NGS are compared to Sanger deconvolution methods (TIDE/ICE). gRNAs were delivered in multiple formats (IVT sgRNA, 2-part system, 2-part system with XT modifications, and synthetic sgRNA) and multiple RNP concentrations (1 µM, 2 µM, 4 µM) for each gRNA in triplicate (n=72 samples per analysis method). The comparisons of editing frequencies are shown in (A) linear and (B) log scale. Sanger deconvolution methods generally underestimate editing frequency and are unreliable at editing frequencies <10%. (Results adapted from Shapiro et al. 2020.)
While the rhAmpSeq CRISPR Analysis System is designed for multiplex analysis of on- and off-target editing, it also performs exceptionally well on batch analysis for single amplicon designs. Its analyses of on-target editing have high concordance with traditional workflows but offer a more simplified and cost-effective workflow, supporting high-throughput screening applications (Figure 6).
Figure 6. The rhAmpSeq CRISPR system supports a robust, complete workflow for high-throughput, batch single amplicon design and analysis for on-target editing. (A) A batch of single amplicon assays (n=96) were designed using the rhAmpSeq Design Tool or Primer3 (primers spaced >20 bp from the cut site with 130 bp design space) with default parameters, and the features/design success rates were compared. The rhAmpSeq Design Tool was more supportive than Primer3 to batch primer design. (B) Primers designed by Primer3 were synthesized as DNA-only primers, while primers designed by the rhAmpSeq Design Tool were synthesized as end-blocked, RNaseH2-cleavable rhAmp primers. DNA-only or rhAmp primers were used to amplify CRISPR-edited gDNA samples from HEK293 cells using either Q5® Hot Start High-Fidelity 2x Master Mix (NEB) or rhAmpSeq Master Mix. (C) NGS libraries from each combination of design/amplification were prepared and sequenced on an Illumina MiSeq system (2x150) and analyzed using the rhAmpSeq CRISPR Analysis Tool. Editing (% indels) concordance demonstrates that editing quantification between the two assay design strategies is equivalent.
One of the many intuitive features of the rhAmpSeq CRISPR Analysis System is the ability to display editing outcomes from up to 384 samples simultaneously on a single display, allowing easy comparison between multiple experimental parameters (Figure 7).
Genome editing outcomes are challenging to analyze. It is therefore essential that a trustworthy data analysis tool is used. When challenged with a dataset containing pre-determined editing events, the rhAmpSeq CRISPR Analysis System generates more accurate analyses than alternative systems (Figure 8).
Figure 8. CRISPAltRations demonstrates superior accuracy for annotating HDR events derived from CRISPR genome editing. CRISPAltRations is the analysis platform behind the rhAmpSeq CRISPR Analysis Tool. CRISPResso2 and CRISPAltRations were compared using a synthetic dataset (n=91 sites) for their ability to accurately determine the percentage of events derived from (A) perfect HDR, (B) imperfect HDR (HDR event with any unintended mutations), (C) wild type, and (D) NHEJ at all edited sites (w=window size).
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