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Validation – The pivotal but rarely discussed step of genome editing

Written by Anja Brunner (Marketing Manager at Samplix)

Genome editing

Undoubtedly, advances in gene editing have allowed us to imagine a world where scientists can alter the genetic makeup of any living organism. More recently, however, the ease, speed, and precision of methods like CRISPR have made that vision tangibly real and surprisingly ubiquitous. For a couple hundred US dollars, anyone can buy a CRISPR editing kit online and make their very own strain of antibiotic-resistant bacteria on a kitchen counter.

The safety of genome editing and the recognition that CRISPR and other methods of excising and also inserting genetic material can leave unintended modifications have sparked conversations in research communities. The uncertainty is also fodder for headlines in the news. The attention is well-deserved, the discussion is essential.

Another side of the story, however, has been less conspicuous. Genome editing is also a powerful research tool. Today, precise genetic edits reveal the workings of complex organisms in unprecedented detail. In the near term, these editing techniques are specifically redefining how we explore the genome.


Whichever editing strategy a researcher uses – nuclease editors like CRISPR-Cas9 and TALEN or additive transgenesis – at some point they will have to ask: Did it work? At the very latest, when publishing findings based on knockout cell lines or transgenic mouse models, a reviewer will ask that question. Months of work specifically hinge on validating that an intended edit actually occurred, and nothing else.

Validation methods for genome editing range from simple and cost-effective mismatch detection assays to time-consuming whole genome sequencing. Choice is often based on the type of edit being scrutinised and the level at which the edit is evaluated, be it nucleotide sequence, DNA fragment length, or impact on protein expression. A typical experiment includes two or more validation methods to cover both genotypic and phenotypic assessments. Thus, that pivotal step of demonstrating edit validity, which is often described in a small and overlooked section of a research paper, is also a costly and time-intensive step. Choosing the right methods is decisive.   

Two additional criteria should inform the decision. First, scope. Does a method cover sufficiently large genomic stretches to detect very large unintended edits? Second, resolution. Does a method resolve complex insertion patterns and rearrangements? Can it reveal indels that affect only one allele?1

Time well spent

Weighing pros and cons of different methods along all four criteria – type of edit, level of evaluation, scope and resolution – can help ensure that time, effort, and budget committed to validating genomic edits is well spent and a catalyst to sharing research outcomes. Because nothing is more frustrating than a missing puzzle piece, that although unremarkable, can render the full picture of a research project incomplete and inconclusive.

With proper QC, editing will be transformative in genome research and expand the toolkit of science. It will also drive the development of further technologies – to delve deeper into life.

Join us for our upcoming webinar – ‘Gene Editing Quality Control – From Humanised Mice to Engineered Human Cells‘ on Thursday 4th March at 2PM GMT/3PM CET/9AM EST. This webinar brings you presentations and also live Q&A from two distinguished speakers focusing on gene editing quality control. Register now.


1 Thorarinn, B. et al. 2021. Verification of CRISPR editing and finding transgenic inserts by Xdrop® indirect sequence capture followed by short- and long-read sequencing.

Image by Arek Socha from Pixabay 

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