Avoid PCR bias to reveal unintended on-target and off-target rearrangements using the Xdrop® workflow
Our team has detected unintended edits in a CRISPR-Cas9 engineered cell line. Apart from the more known off-target effects, on-target unexpected outcomes can be more frequent than previously thought. Watch this talk.
Using the Xdrop or Xdrop Sort workflow with the appropriate sequencing, you can investigate genome editing related to any kind of genetic engineering, from gene therapy to more traditional transgenic integrations.
“Xdrop has allowed us to examine a highly complex genomic and molecular interaction induced by our CRISPR/Cas9 deletion. At present, the Xdrop approach is the most suitable for our application.” Keyi Geng, Karolinska Institutet, Sweden
As CRISPR-based technologies gain traction in sensitive applications of genome editing and genetic engineering, verifying the presence of (un)intended modifications has become crucial. Standard PCR approaches for validation focus only on the immediate vicinity of the edit site. Xdrop is different.
Xdrop allows scrutinizing ~100 kb around the edit sites by enabling targeted sequencing of long DNA fragments. Automated and designed with an easy workflow that is accessible to any lab, Xdrop can reveal unintended modifications where standard PCR methods can’t.
Using Xdrop, we enriched long fragments of DNA isolated from isogenic human cell lines CRISPR-engineered to differ at two single-nucleotide positions on Exon 4 of the APOE gene.
Focusing on two of those cell lines with (supposedly) homozygous haplotypes ε3/ε3 and ε2/ε2, we used Indirect Sequence Capture to sort out single molecules of interest based on the presence of a short sequence (Detection Sequence) ~2 kb upstream of the edit sites.
These molecules were then amplified by droplet MDA and prepared for sequencing on Oxford Nanopore (ONT) and Illumina (ILL) instruments. In both sequencing approaches, enrichment was roughly 200x for a 100 kb region and as high as ~1000x for a 10 kb region centered on the Detection Sequence and including the edit sites. Targeted enrichment was achieved using a single primer set and only 10 ng of input DNA.
See the Application Note below for a graphical representation of the sequencing depth.
Although the edit accuracy, integrity and haplotype of the two cell lines had been assessed by PCR and Sanger sequencing, we uncovered an unintended insertion of a co-transfection plasmid immediately downstream from the edit sites. The insert affected only one haplotype in both cell lines, expanding the primer distance for the edit assessment from 227 bp to >3.5 kb.
The expansion prevented amplification of the affected allele and therefore, the standard PCR-based assessment only detected the unaffected haplotype. Because both cell lines seemed homozygous as expected after editing, the failed amplification went unnoticed.
The Indirect Sequence Capture of long DNA molecules and the single-molecule amplification of Xdrop ensured the discovery of the unwanted insertion.
DNA microinjection into single-cell embryos has been used to create transgenic animal models for nearly 30 years. Suprisingly, because injected transgenes insert randomly, the exact insertion site and pattern is unknown for numerous animal lines.
Here as well, Xdrop has proven helpful. Targeted enrichment with Xdrop followed by long-read sequencing identified the unexpected insertion of a Pax8-CreERT2 sequence into chromosome 1 of a transgenic mouse line developed by the U.S. National Cancer Institute. The data showed that the modification event resulted in a 96.5 kb deletion and a triple insertion of the construct in series with variable truncations and insertions at the borders (see figure).
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