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Comparative Study
, 14 (10B), 2121-7

The Status, Quality, and Expansion of the NIH Full-Length cDNA Project: The Mammalian Gene Collection (MGC)

Daniela S GerhardLukas WagnerElise A FeingoldCarolyn M ShenmenLynette H GrouseGreg SchulerSteven L KleinSusan OldRebekah RasoolyPeter GoodMark GuyerAllison M PeckJeffery G DergeDavid LipmanFrancis S CollinsWonhee JangSteven SherryMike FeoloLeonie MisquittaEduardo LeeKirill RotmistrovskySusan F GreenhutCarl F SchaeferKenneth BuetowTom I BonnerDavid HausslerJim KentMark KiekhausTerry FureyMichael BrentChrista PrangeKirsten SchreiberNicole ShapiroNarayan K BhatRalph F HopkinsFlorence HsieTom DriscollM Bento SoaresTom L CasavantTodd E ScheetzMichael J Brown-steinTed B UsdinShiraki ToshiyukiPiero CarninciYulan PiaoDawood B DudekulaMinoru S H KoKoichi KawakamiYutaka SuzukiSumio SuganoC E GruberM R SmithBlake SimmonsTroy MooreRichard WatermanStephen L JohnsonYijun RuanChia Lin WeiS MathavanPreethi H GunaratneJiaqian WuAngela M GarciaStephen W HulykEdwin FuhYe YuanAnna SneedCarla KowisAnne HodgsonDonna M MuznyJohn McPhersonRichard A GibbsJessica FaheyErin HeltonMark KettemanAnuradha MadanStephanie RodriguesAmy SanchezMichelle WhitingAnup MadariAlice C YoungKeith D WetherbySteven J GranitePeggy N KwongCharles P BrinkleyRussell L PearsonGerard G BouffardRobert W BlakeslyEric D GreenMark C DicksonAlex C RodriguezJane GrimwoodJeremy SchmutzRichard M MyersYaron S N ButterfieldMalachi GriffithObi L GriffithMartin I KrzywinskiNancy LiaoRyan MorinDiana PalmquistAnca S PetrescuUrsula SkalskaDuane E SmailusJeff M StottAngelique SchnerchJacqueline E ScheinSteven J M JonesRobert A HoltAgnes BarossMarco A MarraSandra CliftonKathryn A MakowskiStephanie BosakJoel MalekMGC 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.

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.

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.

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