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Using the transcriptome to annotate the genome

Abstract

A remaining challenge for the human genome project involves the identification and annotation of expressed genes. The public and private sequencing efforts have identified 15,000 sequences that meet stringent criteria for genes, such as correspondence with known genes from humans or other species, and have made another 10,000–20,000 gene predictions of lower confidence, supported by various types of in silico evidence, including homology studies, domain searches, and ab initio gene predictions1,2. These computational methods have limitations, both because they are unable to identify a significant fraction of genes and exons and because they are unable to provide definitive evidence about whether a hypothetical gene is actually expressed3,4. As the in silico approaches identified a smaller number of genes than anticipated5,6,7,8,9, we wondered whether high-throughput experimental analyses could be used to provide evidence for the expression of hypothetical genes and to reveal previously undiscovered genes. We describe here the development of such a method—called long serial analysis of gene expression (LongSAGE), an adaption of the original SAGE approach10—that can be used to rapidly identify novel genes and exons.

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Figure 1: Schematic of LongSAGE method.
Figure 2: Expression analysis of candidate LS genes.

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Acknowledgements

We thank Kathy Romans for assistance with database searches, Jennifer Davis for statistical analyses, and Steve Madden, Kathy Klinger, Xiaohong Cao, and members of our laboratories for helpful discussions. This work was supported by NIH grant CA57345.

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Correspondence to Kenneth W. Kinzler or Victor E. Velculescu.

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Competing interests

K.W.K. received research funding from Genzyme Molecular Oncology (Genzyme). Under a licensing agreement between the Johns Hopkins University and Genzyme, the SAGE technology was licensed to Genzyme for commercial purposes, and B.V., K.W.K., and V.E.V. are entitled to shares of royalties received by the university from the sales of the licensed technology. The SAGE technology is freely available to academia for research purposes. K.W.K. and V.E.V. are consultants to Genzyme, and B.V. has consulted for Genzyme in the past. The university and researchers (B.V., K.W.K., and V.E.V.) own Genzyme stock, which is subject to certain restrictions under university policy. The terms of these arrangements are being managed by the university in accordance with its conflict of interest policies.

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Saha, S., Sparks, A., Rago, C. et al. Using the transcriptome to annotate the genome. Nat Biotechnol 20, 508–512 (2002). https://doi.org/10.1038/nbt0502-508

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