A mouse for every genethe Knockout Mouse Program KOMP mutagenesis project

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A mouse for every genethe Knockout Mouse Program
(KOMP) mutagenesis project
NIH/NCRR Council January 18, 2007

• Kent Lloyd
• University of California, Davis

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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.
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Since then, advances in DNA sequencing
technologies and throughput have provided
complete genome sequences for several commonly
used inbred strains of mice
FOR IMMEDIATE RELEASEWednesday, October 25, 2006
Mouse DNA To Aid Biomedical Research.
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
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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.
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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
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Fall of 2003 NIH convenes a Banbury conference
on Mouse Genome-Wide Targeted Mutagenesis to
discuss completing a knockout library of the
mouse genome.
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KOMP
2011 and beyond
2006-2011
Nature Genetics 200536, 921-924
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-Supported by 18 Categorical NIH Institutes, 1
Center, 1 Program, and 1 Office -Approximately
50million 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
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KOMP

• The Resource effort is composed of 3 distinct
  efforts
• Repatriation300 existing mutant lines not
  publicly available
• Acquisition360 selected from Deltagen and
  Lexicon
• Production...8000-13,500 DNA constructs,
  8000-8500 mutant ES cell clones, 500 mutant
  mice, and cryopreserved embryos

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2 Production grants
-Childrens Hospital Oakland Research Institute,
UC Davis, The Sanger Institute -Regeneron, Inc.
2 B6 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)
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CSD "null first" strategy
FRT
FRT
1
2
3
loxP
loxP
lacZ-tagged insertion allele
Cre recombinase
Flp recombinase
FRT
FRT
1
bgal
3
1
2
3
loxP
lacZ-tagged null allele (D exon)
pre-conditional allele (wild-type)
Cre recombinase
1
3
null allele (D exon, frameshift, NMD)
based on Testa et al., Genesis, 2004
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Regeneron "definitive null" strategy

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its a GLOBAL EFFORT
KOMP
EUCOMM (EUropean COnditional Mouse Mutagenesis)
Programme
(North American COnditional Mouse Mutagenesis)
Project
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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)...

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after 5 years.

• All mouse genes null
• Many genes conditional-ready
• Collections of both 129Substrain and B6 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

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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.