(Note: Current Rosetta Inpharmatics employees are shown in boldface type.)

D.D. Shoemaker*, E.E. Schadt*, C.D. Armour, Y.D. He, P. Garrett-Engele, P.D. McDonagh, P.M. Loerch, A. Leonardson, P.Y. Lum, G. Cavet, L.F. Wu, S.J. Altschuler, S. Edwards, J. King, J.S. Tsang, G. Schimmack, J.M. Schelter, J. Koch, M. Ziman, M.J. Marton, B. Li, P. Cundiff, T. Ward, J. Castle, M. Krolewski, M.R. Meyer, M. Mao, J. Burchard, M.J. Kidd, H. Dai, J.W. Phillips, P.S. Linsley, R. Stoughton, S. Scherer & M.S. Boguski
*These authors contributed equally to this work..

Abstract

The most important product of sequencing a genome is a complete, accurate catalogue of genes and their products, primarily messenger RNA transcripts and their cognate proteins. Such a catalogue cannot be constructed by computational annotation alone; it requires experimental validation on a genome scale. Using 'exon' and 'tiling' arrays fabricated by ink-jet oligonucleotide synthesis, we devised an experimental approach to validate and refine computational gene predictions and define full-length transcripts on the basis of co-regulated expression of their exons. These methods can provide more accurate gene numbers and allow the detection of mRNA splice variants and identification of the tissue- and disease-specific conditions under which genes are expressed. We apply our technique to chromosome 22q under 69 experimental condition pairs, and to the entire human genome under two experimental conditions. We discuss implications for more comprehensive, consistent and reliable genome annotation, more efficient, full-length complementary DNA cloning strategies and application to complex diseases.

Downloading Data

The data and additional information supporting this paper are available in HTML, GEML file format, and text-delimited format.

View Data (opens new window)