CRISPR Off-Target Analysis

CRISPR Off-Target Analysis

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CD Genomics, as one of the most competitive service providers in sequencing and data analysis, we use CRISPR technologies and advanced bioinformatics to help you explore the genetic information and decipher the essence of life. Our skills and experience in data analysis can meet customers' personalized data analysis needs.

Introduction of Genome-wide Assembly and Annotation

CRISPR-Cas systems, commonly employed for biological experiments, are RNA-directed endonucleases for genome engineering. While off-target effects can restrict this technology's effectiveness. These off-target sites lead from cleavage at analogous genomic areas that include mismatches, insertions, or deletions of one or more base pairs. To maximize the CRISPR-Cas9 system and guarantee that only intended sites are split, the detection of possible off-target sites is crucial.

Target region sequencing is a highly targeted method that allows researchers in particular genomic areas to evaluate genetic variation. The ultra-deep sequencing of PCR products (amplicons) facilitates the detection and classification of variants effectively. It enables the true on-target/off-target mutations of genome editing experimentation to be determined in conjunction with genome-wide off-target detection systems (GUIDE-seq, WGS) with high sensitivity and in a non-biased way.

In various fields, such as animal disease modeling, material science, genetically modified plant innovations, biofuel techniques, gene therapy, and drug development, the CRISPR system now offers significant potential. And identifying off-target sites in a highly sensitive and thorough manner continues to be a key problem.

The Bioinformatics Analysis That We Can Provide

In order to recognize CRISPR/Cas-induced on/off-target mutations via deep sequencing of PCR amplicons, CD Genomics has formed a cost-effective, high-throughput tactic. We give a one-stop alternative to reliably capture mutations caused by sequence-specific nucleases, based on years of experience in genome editing and off-target effect assessment. Our talented researchers will work closely with you to help you reach the goal of your studies.

CD Genomics delivers a robust method through deep sequencing of PCR amplicons to recognize CRISPR/Cas-induced on/off-target mutations (target region). From sample diagnosis, primer layout to amplicon sequencing, we offer a full service. Using various sequencing configurations, we can manage PCR amplicons of any size. You will be provided with all specific data about on/off-target mutations, along with verification of knockout/knockin alleles, evaluation of cutting utilization of sgRNAs, homozygous and heterozygous detection, verification of potential off-target sites. Focused on a particular project, our knowledgeable technical team will give a completely customized alternative.

Advantages of Pooled CRISPR Screen Analysis

Offers detailed genomic searches for off-target locations because of mismatches, deletions, and insertions

Provides experimental verification primers of anticipated off-target sites

Enables experimental testing using assays or deep sequencing of output-given prospective off-target sites:

Designs primers immediately to allow easy gel segregation of the uncleaved and cleavage bands

Consists of the genomic reference sequence for comparison to sequencing results

CD Genomics Pooled CRISPR Screen Analysis Pipeline

CD Genomics Pooled CRISPR Screen Analysis Pipeline

Bioinformatics Analysis Content

Analysis/Pipeline Details
Raw Data QC Gives a summary of SNPs and individuals filtered out from
Reference Alignment Classify similarity areas that may be the result of functional, structural, or evolutionary connections between the sequences
Validation of CRISPR Libraries Offer the CRISPR libraries themselves with verification using high-throughput sequencing
Analysis of predicted off-target loci Anticipate off-target loci for reading informative sequences

How It Works

CD Genomics is a high-tech company specializing in multiomic data analysis. We provide services such as project design, data analysis, and database construction. With a focus on developing breakthrough products and services, we are a pioneer in the biotechnology industry, serving researchers and partners worldwide.

How It Works

CD Genomics has over a decade of experience in sequencing and analysis. We can help you with your project from experimental data, through all analyses to intact report at competitive rates. If you have any questions about how we can help you, please get in touch. We look forward to working with you!


  1. Anderson KR, Haeussler M, Watanabe C, et al. CRISPR off-target analysis in genetically engineered rats and mice. Nature methods. 2018, 15(7).
  2. Wolt JD, Wang K, Sashital D, et al. Achieving plant CRISPR targeting that limits off‐target effects. The plant genome. 2016, 9(3).
  3. Cho SW, Kim S, Kim Y, et al. Analysis of off-target effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases. Genome research. 2014, 24(1).
* For Research Use Only. Not for use in diagnostic procedures.
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