title: Computational analysis and experimental validation of tumor-associated alternative RNA splicing in human cancer.
abstract: A genome-wide computational screen was performed to identify tumor-associated alternative RNA splicing isoforms. A BLAST algorithm was used to compare 11,014 genes from RefSeq with 3,471,822 human expressed sequence tag sequences. The screen identified 26,258 alternative splicing isoforms of which 845 were significantly associated with human cancer, and 54 were specifically associated with liver cancer. Furthermore, canonical GT-AG splice junctions were used significantly less frequently in the alternative splicing isoforms in tumors. Reverse transcription-PCR experiments confirmed association of the alternative splicing isoforms with tumors. These results suggest that alternative splicing may have potential as a diagnostic marker for cancer.
authors.affiliation: Laboratory of Population Genetics, National Cancer Institute, National Institutes of Health, Gaithersburg, Maryland 20877,USA.
authors.forename: Zhining
authors.initials: Z
authors.lastname: Wang
authors.forename: H Shuen
authors.initials: HS
authors.lastname: Lo
authors.forename: Howard
authors.initials: H
authors.lastname: Yang
authors.forename: Sheryl
authors.initials: S
authors.lastname: Gere
authors.forename: Ying
authors.initials: Y
authors.lastname: Hu
authors.forename: Kenneth H
authors.initials: KH
authors.lastname: Buetow
authors.forename: Maxwell P
authors.initials: MP
authors.lastname: Lee
mesh_terms: D000465:Algorithms; D017398:Alternative Splicing; D019295:Computational Biology / Q000379:methods; D030561:Databases, Nucleic Acid; D020224:Expressed Sequence Tags; D005819:Genetic Markers / Q000235:genetics; D015894:Genome, Human; D006801:Humans; D008113:Liver Neoplasms / Q000235:genetics; D009369:Neoplasms / Q000235:genetics* / Q000378:metabolism; D015203:Reproducibility of Results; D020133:Reverse Transcriptase Polymerase Chain Reaction
chemical_list: D005819:Genetic Markers