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Comparative Study
. 2004 Oct;14(10B):2121-7.
doi: 10.1101/gr.2596504.

The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)

Daniela S Gerhard, Lukas Wagner, Elise A Feingold, Carolyn M Shenmen, Lynette H Grouse, Greg Schuler, Steven L Klein, Susan Old, Rebekah Rasooly, Peter Good, Mark Guyer, Allison M Peck, Jeffery G Derge, David Lipman, Francis S Collins, Wonhee Jang, Steven Sherry, Mike Feolo, Leonie Misquitta, Eduardo Lee, Kirill Rotmistrovsky, Susan F Greenhut, Carl F Schaefer, Kenneth Buetow, Tom I Bonner, David Haussler, Jim Kent, Mark Kiekhaus, Terry Furey, Michael Brent, Christa Prange, Kirsten Schreiber, Nicole Shapiro, Narayan K Bhat, Ralph F Hopkins, Florence Hsie, Tom Driscoll, M Bento Soares, Tom L Casavant, Todd E Scheetz, Michael J Brown-stein, Ted B Usdin, Shiraki Toshiyuki, Piero Carninci, Yulan Piao, Dawood B Dudekula, Minoru S H Ko, Koichi Kawakami, Yutaka Suzuki, Sumio Sugano, C E Gruber, M R Smith, Blake Simmons, Troy Moore, Richard Waterman, Stephen L Johnson, Yijun Ruan, Chia Lin Wei, S Mathavan, Preethi H Gunaratne, Jiaqian Wu, Angela M Garcia, Stephen W Hulyk, Edwin Fuh, Ye Yuan, Anna Sneed, Carla Kowis, Anne Hodgson, Donna M Muzny, John McPherson, Richard A Gibbs, Jessica Fahey, Erin Helton, Mark Ketteman, Anuradha Madan, Stephanie Rodrigues, Amy Sanchez, Michelle Whiting, Anup Madari, Alice C Young, Keith D Wetherby, Steven J Granite, Peggy N Kwong, Charles P Brinkley, Russell L Pearson, Gerard G Bouffard, Robert W Blakesly, Eric D Green, Mark C Dickson, Alex C Rodriguez, Jane Grimwood, Jeremy Schmutz, Richard M Myers, Yaron S N Butterfield, Malachi Griffith, Obi L Griffith, Martin I Krzywinski, Nancy Liao, Ryan Morin, Diana Palmquist, Anca S Petrescu, Ursula Skalska, Duane E Smailus, Jeff M Stott, Angelique Schnerch, Jacqueline E Schein, Steven J M Jones, Robert A Holt, Agnes Baross, Marco A Marra, Sandra Clifton, Kathryn A Makowski, Stephanie Bosak, Joel Malek; MGC Project Team
Comparative Study

The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)

Daniela S Gerhard et al. Genome Res. 2004 Oct.

Erratum in

  • Genome Res. 2006 Jun;16(6):804. Morrin, Ryan [corrected to Morin, Ryan]

Abstract

The National Institutes of Health's Mammalian Gene Collection (MGC) project was designed to generate and sequence a publicly accessible cDNA resource containing a complete open reading frame (ORF) for every human and mouse gene. The project initially used a random strategy to select clones from a large number of cDNA libraries from diverse tissues. Candidate clones were chosen based on 5'-EST sequences, and then fully sequenced to high accuracy and analyzed by algorithms developed for this project. Currently, more than 11,000 human and 10,000 mouse genes are represented in MGC by at least one clone with a full ORF. The random selection approach is now reaching a saturation point, and a transition to protocols targeted at the missing transcripts is now required to complete the mouse and human collections. Comparison of the sequence of the MGC clones to reference genome sequences reveals that most cDNA clones are of very high sequence quality, although it is likely that some cDNAs may carry missense variants as a consequence of experimental artifact, such as PCR, cloning, or reverse transcriptase errors. Recently, a rat cDNA component was added to the project, and ongoing frog (Xenopus) and zebrafish (Danio) cDNA projects were expanded to take advantage of the high-throughput MGC pipeline.

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Figures

Figure 1
Figure 1
Overlap of homologous human and mouse genes with representative MGC clones. Analyses were performed as described in Methods. There are 8412 human genes with mouse orthologs and 7808 mouse genes with human orthologs. The number of HomoloGene groups may include paralogous genes in addition to orthologous genes in 8% of the sets.
Figure 2
Figure 2
Progress of gene capture over time. The number of (A) human and (B) mouse full-ORF MGC clones and the number of genes represented by these clones over the lifetime of the project are shown. (Inset) The number of ESTs sequenced as a function of time. ESTs from prior data sets, including human and mouse cDNA libraries from the CGAP (Schaefer et al. 2001; Strausberg 2001, Strausberg et al. 2002a), were used to jump start the MGC project.
See this image and copyright information in PMC

References

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WEB SITE REFERENCES

    1. http://cgap.nci.nih.gov; Cancer Genome Anatomy Project.
    1. http://genome.ucsc.edu; UCSC Genome Browser.
    1. http://image.llnl.gov/image/html/vectors.shtml; complete sequence for each of the MGC vectors.
    1. http://mgc.nci.nih.gov; MGC.
    1. http://www.ebi.ac.uk/embl/indiex.html; chimpanzee.

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