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

By D. Gerhard, L. Wagner, E. Feingold, C. M. Shenmen, L. Grouse, G. Schuler, S. L. Klein, S. Old, R. Rasooly, P. Good and 104 more. Genome Research, 2004

602 citations recorded by the source corpus.

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.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/3f475316f89b1a301db159071ad9354b89e9ccf8

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Citations in the corpus

The UCSC Genome Browser Database: 2008 update (2007, background): “Highlights of this year’s additions include a 28-species human-based vertebrate conservation annotation, an enhanced UCSC Genes set, and more human variation, MGC, and ENCODE data.”
Thousands of exon skipping events differentiate among splicing patterns in sixteen human tissues (2013, positive): “Annotation of alternative splicing has traditionally been based on cDNA (expressed sequence tags (EST), mRNA) sequence data from public repositories such as dbEST, RefSeq 10 , and the Mammalian Gene Collection 11 .”
Genome-wide characterization of transcriptional start sites in humans by integrative transcriptome analysis. (2011, background): “We first selected 16,080 nonredundant cDNAs from the MGC and FLJ collections whose 59-ends overlapped the TSCs (Supplemental Figs.”
The UCSC Genome Browser Database: update 2006 (2005, background): “Other areas of improvement are inclusion of RefSeq (13) mRNAs as initial candidates, pairing of proteins and mRNAs, coverage of splice isoforms, weighting of RefSeq and Mammalian Gene Collection (MGC) (14) genes and iden-tiﬁcation of coding DNA sequence (CDS) regions within mRNA sequences.”
The UCSC Genome Browser Database: update 2009 (2008, neutral): “Data in the GBD are updated regularly, including nightly updates of new mRNA submissions to GenBank (alignments of all new sequences to all assemblies), MGC (10) and consensus coding sequence (CCDS); weekly updates of EST data; and a complete realignment whenever GenBank releases a periodic update.”
EGASP: the human ENCODE Genome Annotation Assessment Project (2006, methodology): “The MGC transcripts (‘MGCGene’) and the CCDS transcripts (‘CCDSgene’) were 10% and 18% more specific at the transcript level, but had significantly lower sensitivity than the best EGASP method due to the incomplete nature of these sets at the time of the workshop.”
Control of developmental regulators by Polycomb in human embryonic stem cells. (2006, background): “, 2005), Mammalian Gene Collection (MGC) (Gerhard et al., 2004), Ensembl (Hubbard et al.”