The generation and utilization of a cancer-oriented representation of the human transcriptome by using expressed sequence tags

The Human Cancer Genome Project/Cancer Genome Anatomy Project Annotation Consortium, The Human Cancer Genome Project Sequencing Consortium

Research output: Contribution to journalArticle

Abstract

Whereas genome sequencing defines the genetic potential of an organism, transcript sequencing defines the utilization of this potential and links the genome with most areas of biology. To exploit the information within the human genome in the fight against cancer, we have deposited some two million expressed sequence tags (ESTs) from human tumors and their corresponding normal tissues in the public databases. The data currently define ≈23,500 genes, of which only ≈1,250 are still represented only by ESTs. Examination of the EST coverage of known cancer-related (CR) genes reveals that < 1% do not have corresponding ESTs, indicating that the representation of genes associated with commonly studied tumors is high. The careful recording of the origin of all ESTs we have produced has enabled detailed definition of where the genes they represent are expressed in the human body. More than 100,000 ESTs are available for seven tissues, indicating a surprising variability of gene usage that has led to the discovery of a significant number of genes with restricted expression, and that may thus be therapeutically useful. The ESTs also reveal novel nonsynonymous germline variants (although the one-pass nature of the data necessitates careful validation) and many alternatively spliced transcripts. Although widely exploited by the scientific community, vindicating our totally open source policy, the EST data generated still provide extensive information that remains to be systematically explored, and that may further facilitate progress toward both the understanding and treatment of human cancers.

Original languageEnglish (US)
Pages (from-to)13418-13423
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume100
Issue number23
DOIs
StatePublished - Nov 11 2003

ASJC Scopus subject areas

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    The Human Cancer Genome Project/Cancer Genome Anatomy Project Annotation Consortium, & The Human Cancer Genome Project Sequencing Consortium (2003). The generation and utilization of a cancer-oriented representation of the human transcriptome by using expressed sequence tags. Proceedings of the National Academy of Sciences of the United States of America, 100(23), 13418-13423. https://doi.org/10.1073/pnas.1233632100