Enabling genome engineering

On January 27th Kornel Labun successfully defended his PhD thesis with the title:  “In silico design and analysis of targeted genome editing with CRISPR”.

CRISPR-Cas systems have revolutionized genome editing in recent years. Scientists all over the world want to use CRISPR in their systems, but are often held back by the lack of tools to design experiments in their model organism. To help researchers conduct their experiments, Kornel developed CHOPCHOP, which over the last few years has become one of the most cited and used tools for CRISPR guide RNA design in the world. Under Kornel’s direction CHOPCHOP has evolved to become a multi-functional tool for a large range of CRISPR-dependent experiments. 

After a CRISPR experiment has been performed, there is also a need for data analysis and validation of the induced changes. For this, Kornel developed another tool: ampliCan, an R package that enables thousands of gene changes to be performed in parallel. It has a number of functionalities such as automated normalization and accurate estimation of editing efficiencies. In benchmarks ampliCan outperformed all other comparable tools.

Both of these tools were developed with the idea that CRISPR experiments should be easily accessible to everyone without requiring a deep understanding of the mechanics. At the same time, expert users should be able to tweak and adjust the settings for their particular use-cases. The hope is that these tools will facilitate the implementation of the CRISPR technology for biologists and enable them to use this amazing technology to make breakthroughs in the future.

Publications:

CHOPCHOP v3: expanding the CRISPR web toolbox beyond genome editing
K Labun, TG Montague, M Krause, YN Torres Cleuren, H Tjeldnes, E Valen
Nucleic Acids Research 47 (W1), W171-W174

Accurate analysis of genuine CRISPR editing events with ampliCan
K Labun, X Guo, A Chavez, G Church, JA Gagnon, E Valen
Genome Research 29 (5), 843-847

CHOPCHOP v2: a web tool for the next generation of CRISPR genome engineering
K Labun, TG Montague, JA Gagnon, SB Thyme, E Valen
Nucleic Acids Research 44 (W1), W272-W276