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

TLDR

The MGC project aims to create a publicly available, full‑ORF cDNA collection for every human and mouse gene, and to shift from random to targeted strategies to capture remaining transcripts. The project initially used random clone selection from diverse tissue libraries guided by 5′‑ESTs, followed by high‑accuracy sequencing and algorithmic analysis, and has expanded to rat, frog, and zebrafish using a high‑throughput pipeline. The collection now includes over 11,000 human and 10,000 mouse full‑ORF clones of very high sequence quality, though some may contain missense variants from experimental artifacts.

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.