Reproducibility of CRISPR-Cas9 methods for generation of conditional mouse alleles: a multi-center evaluation

  • Genome Biol. 2019 Aug 26;20(1):171. doi: 10.1186/s13059-019-1776-2.
Channabasavaiah B Gurumurthy  1  2 ,  Aidan R O'Brien  3  4 ,  Rolen M Quadros  5 ,  John Adams Jr  6 ,  Pilar Alcaide  7 ,  Shinya Ayabe  8 ,  Johnathan Ballard  6 ,  Surinder K Batra  9 ,  Marie-Claude Beauchamp  10 ,  Kathleen A Becker  11 ,  Guillaume Bernas  12 ,  David Brough  13 ,  Francisco Carrillo-Salinas  7 ,  Wesley Chan  10 ,  Hanying Chen  14 ,  Ruby Dawson  15 ,  Victoria DeMambro  11 ,  Jinke D'Hont  16  17 ,  Katharine M Dibb  18 ,  James D Eudy  19 ,  Lin Gan  20 ,  Jing Gao  4 ,  Amy Gonzales  6 ,  Anyonya R Guntur  11 ,  Huiping Guo  6 ,  Donald W Harms  5 ,  Anne Harrington  11 ,  Kathryn E Hentges  21 ,  Neil Humphreys  22 ,  Shiho Imai  23 ,  Hideshi Ishii  24 ,  Mizuho Iwama  8 ,  Eric Jonasch  25 ,  Michelle Karolak  11 ,  Bernard Keavney  26 ,  Nay-Chi Khin  4 ,  Masamitsu Konno  27 ,  Yuko Kotani  28 ,  Yayoi Kunihiro  28 ,  Imayavaramban Lakshmanan  9 ,  Catherine Larochelle  29 ,  Catherine B Lawrence  13 ,  Lin Li  30 ,  Volkhard Lindner  11 ,  Xian-De Liu  25 ,  Gloria Lopez-Castejon  31 ,  Andrew Loudon  32 ,  Jenna Lowe  4 ,  Loydie A Jerome-Majewska  10 ,  Taiji Matsusaka  23 ,  Hiromi Miura  33  34 ,  Yoshiki Miyasaka  28 ,  Benjamin Morpurgo  6 ,  Katherine Motyl  11 ,  Yo-Ichi Nabeshima  35 ,  Koji Nakade  8 ,  Toshiaki Nakashiba  8 ,  Kenichi Nakashima  8 ,  Yuichi Obata  8 ,  Sanae Ogiwara  36 ,  Mariette Ouellet  12 ,  Leif Oxburgh  11  37 ,  Sandra Piltz  15 ,  Ilka Pinz  11 ,  Moorthy P Ponnusamy  9 ,  David Ray  38 ,  Ronald J Redder  19 ,  Clifford J Rosen  11 ,  Nikki Ross  4 ,  Mark T Ruhe  39 ,  Larisa Ryzhova  11 ,  Ane M Salvador  7 ,  Sabrina Shameen Alam  10 ,  Radislav Sedlacek  40 ,  Karan Sharma  41 ,  Chad Smith  25 ,  Katrien Staes  16  17 ,  Lora Starrs  4 ,  Fumihiro Sugiyama  42 ,  Satoru Takahashi  42 ,  Tomohiro Tanaka  43 ,  Andrew W Trafford  18 ,  Yoshihiro Uno  28 ,  Leen Vanhoutte  16  17 ,  Frederique Vanrockeghem  16  17 ,  Brandon J Willis  39 ,  Christian S Wright  44 ,  Yuko Yamauchi  28 ,  Xin Yi  44 ,  Kazuto Yoshimi  28 ,  Xuesong Zhang  25 ,  Yu Zhang  30 ,  Masato Ohtsuka  33  34 ,  Satyabrata Das  45 ,  Daniel J Garry  46  47 ,  Tino Hochepied  16  17 ,  Paul Thomas  15 ,  Jan Parker-Thornburg  25 ,  Antony D Adamson  22 ,  Atsushi Yoshiki  8 ,  Jean-Francois Schmouth  12 ,  Andrei Golovko  6 ,  William R Thompson  44 ,  K C Kent Lloyd  39  47 ,  Joshua A Wood  39 ,  Mitra Cowan  48 ,  Tomoji Mashimo  28 ,  Seiya Mizuno  42 ,  Hao Zhu  30 ,  Petr Kasparek  40 ,  Lucy Liaw  11 ,  Joseph M Miano  20 ,  Gaetan Burgio  49
Affiliations
  • 1. Mouse Genome Engineering Core Facility, Vice Chancellor for Research Office, University of Nebraska Medical Center, Omaha, NE, USA. [email protected].
  • 2. Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA. [email protected].
  • 3. Transformational Bioinformatics, Health and Biosecurity Business Unit, CSIRO, North Ryde, Australia.
  • 4. Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, the Australian National University, Canberra, Australia.
  • 5. Mouse Genome Engineering Core Facility, Vice Chancellor for Research Office, University of Nebraska Medical Center, Omaha, NE, USA.
  • 6. Texas A&M Institute for Genomic Medicine (TIGM), Texas A&M University, College Station, TX, 77843, USA.
  • 7. Department of Immunology, Tufts University School of Medicine, Boston, USA.
  • 8. RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan.
  • 9. Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA.
  • 10. Departments of Anatomy and Cell Biology, Human Genetics and Pediatrics, Research Institute McGill University Health Center (RI-MUHC), Montreal, Canada.
  • 11. Maine Medical Center Research Institute (MMCRI), Scarborough, ME, USA.
  • 12. Transgenesis and Animal Modeling Core Facility, Centre de Recherche du Centre Hospitalier Universitaire de Montreal (CRCHUM), Montreal, Canada.
  • 13. Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, AV Hill Building, Oxford Road, Manchester, M13 9PT, UK.
  • 14. School of Medicine, Indiana University, Indianapolis, IN, 46202, USA.
  • 15. South Australian Health & Medical Research Institute and Department of Medicine, University of Adelaide, Adelaide, Australia.
  • 16. Transgenic Mouse Core Facility, VIB Center for Inflammation Research, Ghent, Belgium.
  • 17. Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.
  • 18. Unit of Cardiac Physiology, School of Medical Sciences, Manchester Academic Health Science Center, University of Manchester, Manchester, UK.
  • 19. High-Throughput DNA Sequencing and Genotyping Core Facility, Vice Chancellor for Research Office, University of Nebraska Medical Center, Omaha, USA.
  • 20. University of Rochester Medical Center, Rochester, NY, 14642, USA.
  • 21. Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK.
  • 22. Transgenic Unit Core Facility, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.
  • 23. Department of Basic Medicine, Division of Basic Medical Science and Molecular Medicine, School of Medicine, Tokai University, 143, Shimokasuya, Isehara, Kanagawa, 259-1193, Japan.
  • 24. Department of Medical Data Science, Osaka University Graduate School of Medicine, Suita, Japan.
  • 25. The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
  • 26. Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester and Manchester Heart Centre, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK.
  • 27. Department of Frontier Science for Cancer and Chemotherapy, Osaka University Graduate School of Medicine, Suita, Japan.
  • 28. The Institute of Experimental Animal Sciences, Osaka University Graduate School of Medicine, Suita, Japan.
  • 29. Centre de Recherche du Centre Hospitalier Universitaire de Montreal (CRCHUM), Montreal, Canada.
  • 30. Children's Research Institute Mouse Genome Engineering Core, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
  • 31. Manchester Collaborative Centre for Inflammation Research (MCCIR), School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK.
  • 32. Centre for Biological Timing, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.
  • 33. Center for Matrix Biology and Medicine, Graduate School of Medicine, Tokai University, Isehara, Kanagawa, 259-1193, Japan.
  • 34. Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, School of Medicine, Tokai University, 143, Shimokasuya, Isehara, Kanagawa, 259-1193, Japan.
  • 35. Laboratory of Molecular Life Science, Foundation for Biomedical Research and Innovation, Kobe, Japan.
  • 36. Department of Laboratory Animal Science, Support Center for Medical Research and Education, Tokai University, 143, Shimokasuya, Isehara, Kanagawa, 259-1193, Japan.
  • 37. Basic and Clinical Research, The Rogosin Institute, New York, USA.
  • 38. Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, OX37LE, UK.
  • 39. Mouse Biology Program, University of California, Davis, USA.
  • 40. Laboratory of Transgenic Models of Diseases and Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic.
  • 41. College of Osteopathic Medicine, Marian University, Indianapolis, IN, 46222, USA.
  • 42. Laboratory Animal Resource Center, University of Tsukuba, Tsukuba, Japan.
  • 43. Department of Gastroenterology and Metabolism, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan.
  • 44. School of Health and Human Sciences, Department of Physical Therapy, Indiana University, Indianapolis, IN, 46202, USA.
  • 45. Lillehei Heart Institute Regenerative Medicine and Sciences Program, University of Minnesota, Minneapolis, MN, USA.
  • 46. Paul and Sheila Wellstone Muscular Dystrophy Center, University of Minnesota, Minneapolis, MN, USA.
  • 47. Department of Surgery, School of Medicine, University of California, Davis, Davis, USA.
  • 48. McGill Integrated Core for Animal Modeling (MICAM), Montreal, Canada.
  • 49. Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, the Australian National University, Canberra, Australia. [email protected].
PMID: 31446895 DOI: 10.1186/s13059-019-1776-2
Abstract

Background: CRISPR-Cas9 gene-editing technology has facilitated the generation of knockout mice, providing an alternative to cumbersome and time-consuming traditional embryonic stem cell-based methods. An earlier study reported up to 16% efficiency in generating conditional knockout (cKO or floxed) alleles by microinjection of 2 single guide RNAs (sgRNA) and 2 single-stranded oligonucleotides as donors (referred herein as "two-donor floxing" method).

Results: We re-evaluate the two-donor method from a consortium of 20 laboratories across the world. The dataset constitutes 56 genetic loci, 17,887 zygotes, and 1718 live-born mice, of which only 15 (0.87%) mice contain cKO alleles. We subject the dataset to statistical analyses and a machine learning algorithm, which reveals that none of the factors analyzed was predictive for the success of this method. We test some of the newer methods that use one-donor DNA on 18 loci for which the two-donor approach failed to produce cKO alleles. We find that the one-donor methods are 10- to 20-fold more efficient than the two-donor approach.

Conclusion: We propose that the two-donor method lacks efficiency because it relies on two simultaneous recombination events in cis, an outcome that is dwarfed by pervasive accompanying undesired editing events. The methods that use one-donor DNA are fairly efficient as they rely on only one recombination event, and the probability of correct insertion of the donor cassette without unanticipated mutational events is much higher. Therefore, one-donor methods offer higher efficiencies for the routine generation of cKO animal models.

Keywords
CRISPR-Cas9; Conditional knockout mouse; Floxed allele; Homology-directed repair; Long single-stranded DNA; Machine learning; Mouse; Oligonucleotide; Reproducibility; Transgenesis.