A mouse for every genethe Knockout Mouse Program

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A mouse for every gene…the Knockout Mouse Program (KOMP) mutagenesis project NIH/NCRR Council January

A mouse for every gene…the Knockout Mouse Program (KOMP) mutagenesis project NIH/NCRR Council January 18, 2007 Kent Lloyd University of California, Davis

The development of murine ES cell technologies in the late 80's marked the emergence

The development of murine ES cell technologies in the late 80's marked the emergence of knockout mice as an important animal surrogate for the study of human and animal disease, development, and behavior.

Since then, advances in DNA sequencing technologies and throughput have provided complete genome sequences

Since then, advances in DNA sequencing technologies and throughput have provided complete genome sequences for several commonly used inbred strains of mice: FOR IMMEDIATE RELEASE Wednesday, October 25, 2006 Mouse DNA To Aid Biomedical Researchers announced today that they have successfully resequenced the DNA of 15 mouse strains most commonly used in biomedical research. More than 8. 3 million single nucleotide polymorphisms (SNPs) were…

These accomplishments in both knockout technology and genomics have cleared the way for global

These accomplishments in both knockout technology and genomics have cleared the way for global efforts to assign function to the 20 -25, 000 transcribed genes in the mouse genome, by creating “a mouse for every gene”.

Over the last 15 years or so, these efforts have taken on a mostly

Over the last 15 years or so, these efforts have taken on a mostly “cottage-industry” approach, which have led to the generation of about 4000 gene-targeted knockouts and 7000 gene traps

Fall of 2003: NIH convenes a Banbury conference on “Mouse Genome-Wide Targeted Mutagenesis” to

Fall of 2003: NIH convenes a Banbury conference on “Mouse Genome-Wide Targeted Mutagenesis” to discuss completing a knockout library of the mouse genome.

KOMP 2011 and beyond… 2006 -2011 Nature Genetics 2005; 36, 921 -924

KOMP 2011 and beyond… 2006 -2011 Nature Genetics 2005; 36, 921 -924

KOMP -Supported by 18 Categorical NIH Institutes, 1 Center, 1 Program, and 1 Office

KOMP -Supported by 18 Categorical NIH Institutes, 1 Center, 1 Program, and 1 Office -Approximately $50 million awarded over 5 years -4 KOMP RFAs released beween 2005 and 2006 HG-05 -007: The completion of a comprehensive mouse knockout resource DA-06 -009: Development and improvement of inbred ES cell lines for use in generation of mouse mutants HG-05 -008: A data coordination center for the knockout mouse project (KOMP) RR-06 -005: Knockout mouse project (KOMP) repository

KOMP The Resource effort is composed of 3 distinct efforts: 1) “Repatriation“… 300 existing

KOMP The Resource effort is composed of 3 distinct efforts: 1) “Repatriation“… 300 existing mutant lines not publicly available 2) “Acquisition”… 360 selected from Deltagen and Lexicon 3) “Production“. . . 8000 -13, 500 DNA constructs, 8000 -8500 mutant ES cell clones, 500 mutant mice, and cryopreserved embryos

2 Production grants: -Children’s Hospital Oakland Research Institute, UC Davis, The Sanger Institute -Regeneron,

2 Production grants: -Children’s Hospital Oakland Research Institute, UC Davis, The Sanger Institute -Regeneron, Inc. 2 B 6 ES cell grants: -University of Pennsylvania, Philadelphia -Samuel Lunenfeld Research Institute of Mount Sinai Hospital in Toronto, Canada 1 Informatics grant: -The Jackson Laboratory, Bar Harbor, Maine 1 Distribution repository grant: -(pending, Spring 2007)

CSD "null first" strategy* FRT bgalneo 1 2 lox. P 3 lox. P lac.

CSD "null first" strategy* FRT bgalneo 1 2 lox. P 3 lox. P lac. Z-tagged insertion allele Cre recombinase Flp recombinase FRT 1 2 3 1 FRT bgalneo bgal 3 lox. P pre-conditional allele (wild-type) lac. Z-tagged null allele (D exon) Cre recombinase 1 3 null allele (D exon, frameshift, NMD) *based on Testa et al. , Genesis, 2004

Regeneron "definitive null" strategy .

Regeneron "definitive null" strategy .

it’s a GLOBAL EFFORT KOMP EUCOMM (“EUropean COnditional Mouse Mutagenesis) Programme (“North American COnditional

it’s a GLOBAL EFFORT KOMP EUCOMM (“EUropean COnditional Mouse Mutagenesis) Programme (“North American COnditional Mouse Mutagenesis) Project

The KOMP gene list: (www. knockoutmouse. org) Started with… · Step 1: Genes within

The KOMP gene list: (www. knockoutmouse. org) Started with… · Step 1: Genes within the NCBI Consensus CDS (CCDS) resource selected: · Step 2: CCDS genes in MGI with VEGA and Ensembl gene identifiers selected. · Step 3: Known trapped (IGTC), targeted, or to be mutated (EUCOMM) eliminated. Continues with… Community invited to nominate their favorite gene (www. knockoutmouse. org). . .

after 5 years…. • • • All mouse genes null Many genes conditional-ready Collections

after 5 years…. • • • All mouse genes null Many genes conditional-ready Collections of both 129 Substrain and B 6 ES cells Germplasm, embryos, ES cells, mice available Low cost to obtain No reach-through (academic research) Less need to use grant money to make mutant mice Available to biomedical research community Accessible around the world

KOMP products (mice, ES cells, embryos, data) will enable the study of disease, development,

KOMP products (mice, ES cells, embryos, data) will enable the study of disease, development, and behavior phenotypes with human homologues, relevant and appropriate to improving and enhancing the translation of basic science research to human (and animal!) patients…. Nature 2003; 422: 835