NGS in CRISPR Genome Editing

CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) genome editing is a revolutionary method in which a programmable RNA targets a nuclease (eg, Cas9) to a specific location in the genome.^1,2 The speed, simplicity, and precision with which CRISPR-Cas9 technology enables genetic elements to be mutated, silenced, induced, or replaced has resulted in its widespread adoption in the global research community.

Next-generation sequencing (NGS) may be used at various stages of a genome editing workflow, from analyzing CRISPR off-target effects with whole-genome sequencing to confirming CRISPR knockouts and other edits with targeted sequencing. Follow-up studies can then be performed using applications such as methylation analysis and gene expression profiling with RNA sequencing, in order to assess the functional impact of a given gene edit.

Gene Editing Publication Review

See summaries of recent peer-reviewed gene editing research publications featuring Illumina NGS technology.

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Applications of CRISPR-Cas9 technology have been identified in the fields of basic and clinical research, therapeutics, drug development, agriculture, and the environment. Clinical research has shown potential utilization for CRISPR in such diseases as sickle cell disease, cancer, AIDS, Huntington’s disease, Duchenne muscular dystrophy, and more.

CRISPR genome editing allows researchers to create genetically modified cell lines and animal models with speed and precision. In addition to creating gene knockouts and gene knock-ins, researchers can use CRISPR technology to modulate gene expression via interference (CRISPRi) or activation (CRISPRa), without altering the genomic sequence. View the associated table to learn more.

Application	Required components	Examples
Knock-out	Disruption of function for a specific gene, can result from many different modifications	Cas9 (or Cas9 nickase); single (or dual) guide RNA (gRNA) introducing disruptive edits
Edit	Execution of a specific sequence modification at a specific genomic location	Cas9 (or Cas9 nickase); single (or dual) gRNA targeting the region where the edit should be made; repairing template
Interference (CRISPRi)	Reduction in expression of a gene without permanent modification of the genomic sequence	dCas9 or dCas9-repressor; gRNA(s) targeting promoter elements of target gene
Activation (CRIPSRa)	Increase in expression of a gene without permanent modification of the genomic sequence	dCas9 or dCas9-activator; gRNA(s) targeting promoter elements of target gene

CRISPR genome editing experiments result in mixed cell populations, with only a small subset carrying the desired edit. Researchers need to determine which cells have the desired CRISPR knockout or targeted mutation. Current methods to evaluate edits involve cleavage assays, PCR, Sanger sequencing, and NGS. View the associated table for additional information.

NGS is the only assay that provides both qualitative and quantitative information at high resolution across the full range of modifications, meets the needs of any throughput, and can be used to monitor off-target effects.⁷ NGS-based targeted sequencing provides a cost-effective solution for confirming CRISPR-induced edits by focusing on regions targeted for modification.

Learn more about targeted sequencing

Methods to Check Genome Editing On-Target Efficiency

Type of On-Target Assessment	Type of Identified Variation	Results	Information Content	Scale
Cleavage assay	Single mismatches and indels	Semi-quantitative	Low	Low to High throughput
PCR and RFLP	HDR insertions	Quantitative	Low	Low to High throughput
PCR	Deletions	Quantitative	Low	Low to High throughput
Sanger	All edits	Quantitative and Qualitative	High	Low throughput
NGS	All edits, genome-wide off-target effects	Quantitative and Qualitative	High	Low to High throughput

Successful implementation of CRISP/Cas9 technology should include strategies to identify and reduce off-target effects, or unintended modifications at sites other than the intended target. Computational methods to evaluate RNA specificity and predict off-target sites are commonly used during genome editing experiments.

Online tools and web-based algorithms are publicly available, as shown in the "Off-Target Analysis Tools" table. However, genome-wide analyses such as NGS-based whole-genome sequencing (WGS) are often necessary to discover off-target sites that may escape prediction algorithms.⁸

Learn more about WGS

Publicly Available Analysis Tools to Predict Off-Target Effects

Off-Target Analysis Tools	Website
Benchling	https://benchling.com
Broad GPP Portal	http://portals.broadinstitute.org/gpp/public
Cas-OFFinder	http://www.rgenome.net/cas-offinder
CROP-IT	http://cheetah.bioch.virginia.edu/AdliLab/CROP-IT/homepage.html
Deskgen	https://www.deskgen.com/landing
DNA 2.0 CRISPR gRNA Design Tool	https://www.dna20.com/products/crispr#4
E-CRISP	http://www.e-crisp.org/E-CRISP
EuPaGDT	http://grna.ctegd.uga.edu
GenScript gRNA Design Tool	http://www.genscript.com/gRNA-design-tool.html
MIT CRISPR Design Tool	http://crispr.mit.edu
ZiFiT	http://zifit.partners.org/ZiFiT

Genome-wide NGS approaches for detecting CRISPR off-target cleavage sites include cell-based assays (in live or fixed cells) as well in vitro assays. Each analysis method has both advantages and limitations; view the method comparison table to learn more.

Unbiased Methods to Analyze
Off-Target Effects

Method	Type	Description	Advantage	Limitation
IDLV capture (Integrase-defective lentiviral vector capture)	Cell-based (live cells)	Integration of IDLVs with a selectable marker into DNA double-strand break (DSB) sites, recovery of integration sites through LAM-PCR, high-throughput sequencing.	It can identify DSBs in living cells	Relatively insensitive
GUIDE-Seq (Genome-wide unbiased identification of DSBs enabled by sequencing)	Cell-based (live cells)	DSBs are tagged with double-stranded oligodeoxynucleotides (dsODNs), tag-specific amplification, high-throughput sequencing.	Simple, efficient, and precise, straightforward protocol, and availability of open-source software for data analysis	Possibly cytotoxic, not tested in vivo, sensitivity is limited and variable between cell types
HTGTS (High-throughput genome-wide translocation sequencing)	Cell-based (live cells)	Genome-wide 'prey' DSBs are detected and quantified via their translocation to a fixed 'bait' DSB. Bait-prey junctions are cloned, amplified by PCR, and sequenced.	Requires the delivery of only the editing complex and can potentially be used in vivo.	Relatively insensitive
BLESS (Breaks labeling, enrichment on streptavidin and next-generation sequencing)	Cell-based (fixed cells)	Isolation and fixation of treated cells, isolation and permeabilization of intact nuclei, in situ ligation of adapters to transient nuclease-induced DSBs, enrichment, high-throughput sequencing.	It has been used in tissues where Cas9 had been delivered in vivo, independent from endogenous DNA repair machinery	Technically challenging, only allows identification of DSBs present at a specific moment, cannot identify DSBs before permeabilization
Digenome-Seq (Digested genome sequencing)	In vitro	Isolation of genomic DNA from in vitro treated cells, ligation of sequencing adapters, whole-genome sequencing.	No limitations related to cell-based factors	Sequencing-inefficient, high background noise
CIRCLE-Seq (Circularization for in vitro reporting of cleavage effects by sequencing)	In vitro	Genomic DNA is sheared and circularized by intramolecular ligation. Undesired linear DNA molecules are degraded. Circular DNA molecules containing cleavage sites are re-linearized with the original CRISPR complex, releasing newly cleaved DNA ends for adaptor ligation, PCR amplification, and high-throughput sequencing.	No limitations related to cell-based factors	Time-consuming, challenging library prep
SITE-Seq (Selective enrichment and identification of tagged genomic DNA ends by sequencing)	In vitro	Genomic DNA is selectively tagged, enriched, sequenced, and mapped to a reference genome	Enables computational detection of cleavage sites	May require impractically high sequencing coverage to screen off-target sites
BLESS (Breaks labeling, enrichment on streptavidin and next-generation sequencing)	Cell-based (fixed cells)	Isolation and fixation of treated cells, isolation and permeabilization of intact nuclei, in situ ligation of adapters to transient nuclease-induced DSBs, enrichment, high-throughput sequencing.	It has been used in tissues where Cas9 had been delivered in vivo, independent from endogenous DNA repair machinery	Technically challenging, only allows identification of DSBs present at a specific moment, can't identify DSBs before permeabilization
Digenome-Seq (Digested genome sequencing)	In vitro	Isolation of genomic DNA from in vitro treated cells, ligation of sequencing adapters, whole-genome sequencing.	No limitations related to cell-based factors	Sequencing-inefficient, high background noise
CIRCLE-Seq (Circularization for in vitro reporting of cleavage effects by sequencing)	In vitro	Genomic DNA is sheared and circularized by intramolecular ligation. Undesired linear DNA molecules are degraded. Circular DNA molecules containing cleavage sites are re-linearized with the original CRISPR complex, releasing newly cleaved DNA ends for adaptor ligation, PCR amplification, and high-throughput sequencing.	No limitations related to cell-based factors	Time consuming, challenging library prep
SITE-Seq (Selective enrichment and identification of tagged genomic DNA ends by sequencing)	In vitro	Genomic DNA is selectively tagged, enriched, sequenced, and mapped to a reference genome	Enables computational detection of cleavage sites	May require impractically high sequencing coverage to screen off-target sites
UDiTaS (Uni-Directional Targeted Sequencing)	In vitro	Tagmentation of genomic DNA with a custom transposon followed by amplification with a sequence-specific 'anchor primer' and NGS	Enables simultaneous measurement of small indels and larger structural variations	Biases from primer binding or amplification may affect accuracy

Genome Editing and CRISPR-Cas9: Podcast Episode 32

Dr. Sam Sternberg of Columbia University discusses the biology and impact of CRISPR and gene editing.

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CRISPR-Cas9: Genome Engineering Made Simple

The Illumina Scientific Affairs team summarizes key publications on applications of CRISPR-Cas9 technology.

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Long Non-Coding RNAs and Cancer

Researchers discuss recent cancer-related lncRNA studies, from biomarker discovery to CRISPR- and siRNA-based approaches for silencing cancer-specific lncRNAs.

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Single-Cell RNA-Seq

Screen cell populations after CRISPR modification to determine the gene-regulatory impact of many genes in parallel in thousands of individual cells.

RNA Sequencing

Assess the impact of mutations on the transcriptome as a whole or on the expression of genes/gene families.

ChIP-Seq

Determine the impact of genome edits on DNA-protein binding.

Methylation Sequencing

Investigate the downstream impact of mutations on methylation status and chromatin remodeling.

NextSeq 2000 System

Groundbreaking benchtop sequencers allow you to explore new discoveries across a variety of current and emerging applications, with higher efficiency and fewer restraints.

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Illumina Stranded mRNA Prep

A simple, scalable, cost-effective, rapid single-day solution for analyzing the coding transcriptome leveraging as little as 25 ng input of standard (non-degraded) RNA.

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TruSeq ChIP Library Preparation Kit

Simple, cost-effective chromatin immunoprecipitation sequencing (ChIP-Seq) DNA library preparation, with master mixes and robust multiplex capabilities.

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TruSeq Methyl Capture EPIC Library Prep Kit

This kit combines next-generation sequencing with epigenetic insights to accelerate biomarker discovery and understand methylation’s role in gene regulation.

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In addition to high resolution on- and off-target assessment and functional analysis of CRISPR edits, NGS can be incorporated at additional stages of the CRISPR genome editing workflow.

During the initial design phase, resequencing of a locus or genome (for species that lack a reference genome) can aid in RNA selection. During the process of cloning CRISPR-Cas9/guide RNA constructs, resequencing of the resulting plasmids can provide rapid and high-confidence verification of the CRISPR delivery vectors, especially for high-throughput experiments with large plasmid libraries.

How NGS Fits into a CRISPR Genome Editing Workflow

Francis deSouza on Genomics, CRISPR, and the Future

Francis deSouza, President and CEO of Illumina, Inc., took the stage at Aspen Ideas: Health in Colorado to educate the audience on the impact genomics is having across healthcare, and the urgency in bringing its benefits to more people, more quickly.

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CEO Francis deSouza Speaks at Aspen Ideas: Health

Agrigenomics

The simplicity and low cost of CRISPR-Cas9 technology can extend gene editing in crops from large commodity species to a wider variety of agriculturally important species.

Learn more about agricultural genomics

Cancer Research

The speed and simplicity of CRISPR-Cas9 technology can facilitate development of cancer models and discovery of new immunotherapeutic targets and strategies.

Learn more about cancer research

Complex Disease Genomics

The precision of CRISPR-Cas9 genome editing technology can facilitate development of cell and animal models of human complex diseases to investigate disease pathology.

Learn more about complex disease research

Cell and Molecular Biology

The speed, simplicity, and low cost of CRISPR-Cas9 gene editing has revolutionized cell and molecular biology in the development of gene knockouts and transgenic models.

Learn more about cellular and molecular biology research

NGS Technology

Ultra-high throughput, scalability, and speed enable biological understanding never before possible.

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Publication Reviews

These summaries of peer-reviewed publications highlight how Illumina technology is furthering scientific research.

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References

Cong L, Ran F A, Cox D, et al. Multiplex genome engineering using CRISPR/Cas systems. Science. 2013;339:819-823.
Mali P, Yang L, Esvelt KM, et al. RNA-guided human genome engineering via Cas9. Science. 2013;339:823-826.
Maruyama T, Dougan SK, Truttmann MC, Bilate AM, Ingram JR, Ploegh HL. Increasing the efficiency of precise genome editing with CRISPR-Cas9 by inhibition of nonhomologous end joining. Nat Biotechnol. 2015;33:538-542.
Chu VT, Weber T, Wefers B, et al. Increasing the efficiency of homology-directed repair for CRISPR-Cas9-induced precise gene editing in mammalian cells. Nat Biotechnol. 2015;33:543-548.
Qi LS, Larson MH, Gilbert LA, et al. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell. 2013;152:1173-1183.
Cheng AW, Wang H, Yang H, et al. Multiplexed activation of endogenous genes by CRISPR-on, an RNA-guided transcriptional activator system. Cell Res. 2013;23:1163-1171.
Ran FA, Hsu PD, Wright J, Agarwala V, Scott DA, Zhang F. Genome engineering using the CRISPR-Cas9 system. Nat Protoc. 2013;8:2281-2308.
Tsai SQ, Joung JK. Defining and improving the genome-wide specificities of CRISPR-Cas9 nucleases. Nat Rev Genet. 2016;17:300-312.
Gabriel R, Lombardo A, Arens A, et al. An unbiased genome-wide analysis of zinc-finger nuclease specificity. Nat Biotechnol. 2011;29:816-823.
Tsai SQ, Zheng Z, Nguyen NT, et al. GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases. Nat Biotechnol. 2015;33:187-197.
Chiarle R, Zhang Y, Frock RL, et al. Genome-wide translocation sequencing reveals mechanisms of chromosome breaks and rearrangements in B cells. Cell. 2011;147:107-119.
Crosetto N, Mitra A, Silva MJ, et al. Nucleotide-resolution DNA double-strand break mapping by next-generation sequencing. Nat Methods. 2013;10:361-365.
Kim D, Kim S, Kim S, Park J, Kim JS. Genome-wide target specificities of CRISPR-Cas9 nucleases revealed by multiplex Digenome-seq. Genome Res. 2016;26:406-415.
Tsai SQ, Nguyen NT, Malagon-Lopez J, Topkar VV, Aryee MJ, Joung JK. CIRCLE-seq: a highly sensitive in vitro screen for genome-wide CRISPR-Cas9 nuclease off-targets. Nat Methods. 2017;14:607-614.

Accelerate CRISPR genome editing with next-generation sequencing

Analyze CRISPR off-target effects, confirm gene edits such as knockdowns, and study the functional impact of the edits

NGS in CRISPR Genome Editing

CRISPR Genome Editing Technology

Gene Editing Publication Review

Applications of CRISPR Genome Editing

Confirm CRISPR Knockouts and Other Edits

CRISPR Off-Target Analysis with NGS

Methods to Analyze Off-Target Effects

Featured CRISPR-Cas9 Genome Editing Content

Genome Editing and CRISPR-Cas9: Podcast Episode 32

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