Gene targeting in embryonic stem cells has become the principal technology for manipulation of the mouse genome, offering unrivalled accuracy in allele design and access to conditional mutagenesis. To bring these advantages to the wider research community, large-scale mouse knockout programmes are producing a permanent resource of targeted mutations in all protein-coding genes. Here we report the establishment of a high-throughput gene-targeting pipeline for the generation of reporter-tagged, conditional alleles. Computational allele design, 96-well modular vector construction and high-efficiency gene-targeting strategies have been combined to mutate genes on an unprecedented scale. So far, more than 12,000 vectors and 9,000 conditional targeted alleles have been produced in highly germline-competent C57BL/6N embryonic stem cells. High-throughput genome engineering highlighted by this study is broadly applicable to rat and human stem cells and provides a foundation for future genome-wide efforts aimed at deciphering the function of all genes encoded by the mammalian genome. Knockout mice in which a specific gene is inactivated are central to the analysis of gene function. An important resource is reported here in the form of a high-throughput gene targeting pipeline that has already produced thousands of conditional mutations in the C57BL/6 embryonic stem-cell line, suitable for the creation of mutant mice for large-scale phenotyping programmes. The strategy is also applicable to rat and human stem cells and provides a foundation for deciphering the function of all genes encoded by the mammalian genome.

A conditional knockout resource for the genome-wide study of mouse gene function