@article {Elrick2021.10.06.463037, author = {Hillary Elrick and Kevin A. Peterson and Joshua A. Wood and Denise G. Lanza and Elif F. Acar and Lydia Teboul and Edward J. Ryder and Shinya Ayabe and Marie-Christine Birling and Adam Caulder and Francesco Chiani and Gemma F. Codner and Brendan Doe and Graham Duddy and Alessia Gambadoro and Marina Gertsenstein and Alba Gomez-Segura and Leslie O. Goodwin and Cunxiang Ju and Petr Kasparek and Ruairidh King and Daekee Lee and Ho Lee and Lauri G. Lintott and Zhiwei Liu and Isabel Lorenzo and Matthew Mackenzie and Susan Marschall and Peter Matthews and Mark Ruhe and Luis Santos and John R. Seavitt and Claudia Seisenberger and Hannah Wardle-Jones and Brandon J. Willis and Jie Zhang and Jing Zhao and Fei Zhou and David J. Adams and Allan Bradley and Robert E. Braun and Francesco J. DeMayo and Mary E. Dickinson and Xiang Gao and Yann H{\'e}rault and Martin Hrabe de Angelis and K. C. Kent Lloyd and Ann-Marie Mallon and Fabio Mammano and Colin McKerlie and Terrence Meehan and Helen Parkinson and Ramiro Ramirez-Solis and Radislav Sedlacek and Je Kyung Seong and William C. Skarnes and Damien Smedley and Masaru Tamura and Sara Wells and Jacqueline K. White and Wolfgang Wurst and Atsushi Yoshiki and International Mouse Phenotyping Consortium and Stephen A. Murray and Jason D. Heaney and Lauryl M. J. Nutter}, title = {The production of 4,182 mouse lines identifies experimental and biological variables impacting Cas9-mediated mutant mouse line production}, elocation-id = {2021.10.06.463037}, year = {2021}, doi = {10.1101/2021.10.06.463037}, publisher = {Cold Spring Harbor Laboratory}, abstract = {The International Mouse Phenotyping Consortium (IMPC) is generating and phenotyping null mutations for every protein-coding gene in the mouse1,2. The IMPC now uses Cas9, a programmable RNA-guided nuclease that has revolutionized mouse genome editing3 and increased capacity and flexibility to efficiently generate null alleles in the C57BL/6N strain. In addition to being a valuable novel and accessible research resource, the production of \>3,300 knockout mouse lines using comparable protocols provides a rich dataset to analyze experimental and biological variables affecting in vivo null allele engineering with Cas9. Mouse line production has two critical steps {\textendash} generation of founders with the desired allele and germline transmission (GLT) of that allele from founders to offspring. Our analysis identified that whether a gene is essential for viability was the primary factor influencing successful production of null alleles. Collectively, our findings provide best practice recommendations for generating null alleles in mice using Cas9; these recommendations may be applicable to other allele types and species.Competing Interest StatementThe authors have declared no competing interest.}, URL = {https://www.biorxiv.org/content/early/2021/10/06/2021.10.06.463037}, eprint = {https://www.biorxiv.org/content/early/2021/10/06/2021.10.06.463037.full.pdf}, journal = {bioRxiv} }