An encyclopedia of mouse genes (original) (raw)

• Letter
• Published: February 1999
• LaDeana Hillier1,
• Tamara Kucaba1,
• Melissa Allen1,
• Robert Barstead2,
• Catherine Beck1,
• Angela Blistain1,
• Maria Bonaldo3,
• Yvette Bowers1,
• Louise Bowles1,
• Marco Cardenas1,
• Ann Chamberlain1,
• Julie Chappell1,
• Sandra Clifton1,
• Anthony Favello1,
• Steve Geisel1,
• Marilyn Gibbons1,
• Njata Harvey1,
• Francesca Hill4,
• Yolanda Jackson1,
• Sophie Kohn1,
• Greg Lennon4,5,
• Elaine Mardis1,
• John Martin1,
• LeeAnne Mila4,
• Rhonda McCann1,
• Richard Morales1,
• Deana Pape1,
• Barry Person1,
• Christa Prange4,
• Erika Ritter1,
• Marcelo Soares3,
• Rebecca Schurk1,
• Tanya Shin1,
• Michele Steptoe1,
• Timothy Swaller1,
• Brenda Theising1,
• Karen Underwood1,
• Todd Wylie1,
• Tamara Yount1,
• Richard Wilson1 &
• …
• Robert Waterston1

Nature Genetics volume 21, pages 191–194 (1999)Cite this article

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Abstract

The laboratory mouse is the premier model system for studies of mammalian development due to the powerful classical genetic analysis1 possible (see also the Jackson Laboratory web site, http://www.jax.org/) and the ever–expanding collection of molecular tools2,3. To enhance the utility of the mouse system, we initiated a program to generate a large database of expressed sequence tags (ESTs) that can provide rapid access to genes4,5,6,7,8,9,10,11,12,13,14,15,16. Of particular significance was the possibility that cDNA libraries could be prepared from very early stages of development, a situation unrealized in human EST projects7,12. We report here the development of a comprehensive database of ESTs for the mouse. The project, initiated in March 1996, has focused on 5´ end sequences from directionally cloned, oligo–dT primed cDNA libraries. As of 23 October 1998, 352,040 sequences had been generated, annotated and deposited in dbEST, where they comprised 93% of the total ESTs available for mouse. EST data are versatile and have been applied to gene identification17, comparative sequence analysis18,19, comparative gene mapping and candidate disease gene identification20, genome sequence annotation21,22, microarray development23 and the development of gene–based map resources24.

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References

1. Brown, S.D.M. & Peters, J. Combining mutagenesis and genomics in the mouse—closing the phenotype gap. Trends Genet. 12, 433–435 (1996).
   Article CAS Google Scholar
2. Zambrowicz, B.P. et al. Disruption and sequence identification of 2,000 genes in mouse embryonic stem cells. Nature 392, 608– 611 (1998).
   Article CAS Google Scholar
3. Hicks, G.G. et al. Functional genomics in mice by tagged sequence mutagenesis. Nature Genet. 16, 338– 344 (1997).
   Article CAS Google Scholar
4. Milner, R.J. & Sutcliffe, J.G. Gene expression in rat brain. Nucleic Acids Res. 11, 5497– 5520 (1983).
   Article CAS Google Scholar
5. Putney, S.D., Herligh, W.D. & Schimmel, P. A new troponin T and cDNA clones for 13 different muscle proteins, found by shotgun sequencing. Nature 302, 718–721 (1983).
   Article CAS Google Scholar
6. Adams, M.D. et al. Complementary DNA sequencing: expressed sequence tags and the human genome project. Science 252, 1651 –1656 (1991).
   Article CAS Google Scholar
7. Adams, M.D. et al. Initial assessment of human gene diversity and expression patterns based upon 83 million nucleotides of cDNA sequence. Nature 377, 3–17 ( 1995).
   CAS PubMed Google Scholar
8. McCombie, W.R. et al. Caenorhabditis elegans expressed sequence tags identify gene families and potential disease gene homologues. Nature Genet. 1, 124–131 ( 1992).
   Article CAS Google Scholar
9. Waterston, R.H. et al. A survey of expressed genes in C. elegans. Nature Genet. 1, 114–123 (1992).
   Article CAS Google Scholar
10. Sasaki, T. et al. Toward cataloguing all rice genes: large–scale sequencing of randomly chosen rice cDNAs from a callus cDNA library. Plant J. 6, 615–624 ( 1994).
    Article CAS Google Scholar
11. Houlgatte, R. et al. The GenExpress index: a resource for gene discovery and the genic map of the human genome. Genome Res. 5, 272–304 (1995).
    Article CAS Google Scholar
12. Hillier, L. et al. Generation and analysis of 280,000 human expressed sequence tags. Genome Res. 6, 807– 828 (1996).
    Article CAS Google Scholar
13. Yamamoto, K. & Sasaki, T. Large–scale EST sequencing in rice. Plant Mol. Biol. 35, 135– 144 (1997).
    Article CAS Google Scholar
14. Nelson, P.S. et al. An expressed–sequence–tag database of the human prostate: sequence analysis of 1168 clones. Genomics 47, 12–25 (1998).
    Article CAS Google Scholar
15. Ajioka, J.W. et al. Gene discovery by EST sequencing in Toxoplasma gondii reveals sequences restricted to the Apicomplexa. Genome Res. 8, 18–28 (1998 ).
    Article CAS Google Scholar
16. Sasaki, N. et al. Characterization of gene expression in mouse blastocyst using single–pass sequencing of 3995 clones. Genomics 49, 167–179 (1998).
    Article CAS Google Scholar
17. Sutherland, H.F., Kim, U.J. & Scambler, P.J. Cloning and comparative mapping of the DiGeorge syndrome critical region in the mouse. Genomics 52, 37–43 (1998).
    Article CAS Google Scholar
18. Makalowski, W. & Boguski, M.S. Evolutionary parameters of the transcribed mammalian genome: an analysis of 2,820 orthologous rodent and human sequences. Proc. Natl Acad. Sci. USA 95, 9407–9412 (1998).
    Article CAS Google Scholar
19. Makalowski, W., Zhang, J. & Boguski, M.S. Comparative analysis of 1,196 orthologous mouse and human full–length mRNA and protein sequences. Genome Res. 6, 846–857 ( 1996).
    Article CAS Google Scholar
20. Scharf, J.M. et al. Identification of a candidate modifying gene for spinal muscular atrophy by comparative genomics. Nature Genet. 20, 83–86 (1998).
    Article CAS Google Scholar
21. Bailey, L.C. Jr, Searls, D.B. & Overton, G.C. Analysis of EST–driven gene annotation in human genomic sequence. Genome Res. 8, 362– 376 (1998).
    Article CAS Google Scholar
22. Jiang, J. & Jacob, H.J. EbEST: an automated tool using expressed sequence tags to delineate gene structure. Genome Res. 8, 268–275 (1998).
    Article Google Scholar
23. Schena, M. et al. Microarrays: biotechnology's discovery platform for functional genomics. Trends Biotechnol. 16, 301– 306 (1998).
    Article CAS Google Scholar
24. Schuler, G.D. et al. A gene map of the human genome. Science 274, 540–546 (1996).
    Article CAS Google Scholar
25. Bonaldo, M.F., Lennon, G. & Soares, M.B. Normalization and subtraction: two approaches to facilitate gene discovery. Genome Res. 6, 791– 806 (1996).
    Article CAS Google Scholar
26. Ewing, B., Hillier, L., Wendl, M. & Green, P. Basecalling of automated sequencer traces using PHRED I. Accuracy assessment. Genome Res. 8, 175–185 ( 1998).
    Article CAS Google Scholar
27. Ewing, B. & Green, P. Basecalling of automated sequencer traces using PHRED II. Error probabilities. Genome Res. 8,186–194 (1998).
    Article CAS Google Scholar
28. Suzuki, Y., Yoshitomo–Nakagawa, K., Maruyama, K., Suyama, A. & Sugano, S. Construction and characterization of a full length–enriched and a 5´–end enriched cDNA library. Gene 200, 149– 156 (1997).
    Article CAS Google Scholar
29. Lennon, G., Auffray, C., Polymeropoulos, M. & Soares, M.B. The I.M.A.G.E. Consortium: an integrated molecular analysis of genomes and their expression. Genomics 33, 151– 152 (1996).
    Article CAS Google Scholar
30. Sonnhammer, E.L. & Durbin, R. Analysis of protein domain families in Caenorhabditis elegans. Genomics 46, 200–216 (1997).
    Article CAS Google Scholar

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Acknowledgements

We thank all investigators who have donated libraries for sequencing; S. Tilghman for scientific guidance; S. Chissoe and S. Gorski for comments on the manuscript and useful discussion; G. Schuler, C. Tolstoshev and others at NCBI for assistance with databases; and the staff at Washington University Genome Center for technical support. Work by C.P. and G.L. was supported by the U.S. DOE under contract W–7405–Eng–48 to LLNL. Work at Washington University was funded by a grant from Howard Hughes Medical Institute.

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Authors and Affiliations

1. Washington University Genome Sequencing Center, 4444 Forest Park Boulevard, St. Louis, 63108, Missouri, USA
   Marco Marra, LaDeana Hillier, Tamara Kucaba, Melissa Allen, Catherine Beck, Angela Blistain, Yvette Bowers, Louise Bowles, Marco Cardenas, Ann Chamberlain, Julie Chappell, Sandra Clifton, Anthony Favello, Steve Geisel, Marilyn Gibbons, Njata Harvey, Yolanda Jackson, Sophie Kohn, Elaine Mardis, John Martin, Rhonda McCann, Richard Morales, Deana Pape, Barry Person, Erika Ritter, Rebecca Schurk, Tanya Shin, Michele Steptoe, Timothy Swaller, Brenda Theising, Karen Underwood, Todd Wylie, Tamara Yount, Richard Wilson & Robert Waterston
2. Oklahoma Medical Research Foundation, Program in Molecular & Cell Biology, 825 NE 13th Street, Oklahoma City, 73104, Oklahoma, USA
   Robert Barstead
3. The University of Iowa, Unit 41, 451 Eckstein Medical Research Building, Iowa City, 52242, Iowa, USA
   Maria Bonaldo & Marcelo Soares
4. The I.M.A.G.E. Consortium, Biology and Biotechnology Research Program, Lawrence Livermore National Laboratory, 7000 East Ave/L–452 Livermore, 94550, California, USA
   Francesca Hill, Greg Lennon, LeeAnne Mila & Christa Prange
5. GeneLogic, Inc. Genomics, 708 Quince Orchard Road, Gaithersburg, 20878 , Maryland, USA
   Greg Lennon

Authors

1. Marco Marra
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2. LaDeana Hillier
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3. Tamara Kucaba
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4. Melissa Allen
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5. Robert Barstead
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6. Catherine Beck
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7. Angela Blistain
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8. Maria Bonaldo
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9. Yvette Bowers
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10. Louise Bowles
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11. Marco Cardenas
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12. Ann Chamberlain
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13. Julie Chappell
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14. Sandra Clifton
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15. Anthony Favello
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16. Steve Geisel
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17. Marilyn Gibbons
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18. Njata Harvey
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19. Francesca Hill
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20. Yolanda Jackson
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21. Sophie Kohn
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22. Greg Lennon
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23. Elaine Mardis
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24. John Martin
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25. LeeAnne Mila
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26. Rhonda McCann
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27. Richard Morales
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28. Deana Pape
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29. Barry Person
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30. Christa Prange
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31. Erika Ritter
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32. Marcelo Soares
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33. Rebecca Schurk
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34. Tanya Shin
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35. Michele Steptoe
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36. Timothy Swaller
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37. Brenda Theising
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38. Karen Underwood
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39. Todd Wylie
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40. Tamara Yount
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41. Richard Wilson
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42. Robert Waterston
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Corresponding author

Correspondence toMarco Marra.

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Marra, M., Hillier, L., Kucaba, T. et al. An encyclopedia of mouse genes.Nat Genet 21, 191–194 (1999). https://doi.org/10.1038/5976

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• Received: 17 November 1998
• Accepted: 21 December 1998
• Issue Date: February 1999
• DOI: https://doi.org/10.1038/5976