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KIM DAE SOO

Oncogene. 2004 Apr. Identification of alternative spliced mRNA variants related to cancers by genome-wide ESTs alignment. KIM DAE SOO. Alternative splicing Form. Abstract. Alternative splicing of mRNAs by analysing the exon linkage relationship by alignment of ESTs to the genome sequence

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KIM DAE SOO

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  1. Oncogene. 2004 Apr Identification of alternative spliced mRNA variants related to cancers by genome-wide ESTs alignment KIM DAE SOO

  2. Alternative splicing Form MPL

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  4. Abstract • Alternative splicing of mRNAs by analysing the exon linkage relationship by alignment of ESTs to the genome sequence • Little effort has been made to investigate the relationship between cancers and alternative splicing • Alternative splicing assembler(ASA) • Of 4322 genes screened,3498(81%) were observed with at least one alternative splicing variants. • Using Fisher’s test, alternative splicing variants MPL

  5. Introduction • About 45% of the human EST sequence are derived from cancer cells. • Alternative splicing is an important mechanism in higher eukaryotes for producing proteomics complexity • Approximately 30-60% genes are alternative splicing as estimated by genomically aligned ESTs • Human could conceivably produce hundreds of thousands of different proteins by the estimated 35,000 genes • Alternative splicing of pre-mRNA is a versatile mechanism for regulating gene function at the post-transcription level MPL

  6. Alternative splicing defect as indicated by a survey of mutations in splicing junctions. • A total of 26812 alternative spliced variants from 4322 genes were included in the database • 2149 variants from 1827 genes were predicted as cancer associated. MPL

  7. ResultsASA was created to identify alternative splicing of human gene transcripts • 52 genes from alternative splicing database ,all having previously reported alternative splicing isoforms. • Only four EST hits were available on the average for these 6 genes ,202 EST hits could be found for the other 46 genes • ASA gives a false negative result of 12 %(about 88% of alternatively splicing genes) • SpliceNest,PALS,HASDB which have false negative rates of 15,35 and 38% MPL

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  9. EST sequences might be contaminated by genomic sequence, vector sequences and chimaeric cDNA clone • Randomly selected 82 splicing variants from 67 genes compared these variants with the NR db • 26%(21 out of 82) variants found at least one reported mRNA sequences • selected 13 variants ;RT-PCR (11 of 13 variants were confirmed by RT-PCR) MPL

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  11. Analysis of the alternative spliced variants and their tissue distribution in BASD • A total of 4322 reference sequences were screened and 3490(81%) reference sequences were predicted as alternative spliced ,producing 26,812 splicing variants. • On average six splicing variants were observed for each reference sequences. • 87% variants contained less then 16 EST ,and 58% were represented by the EST singletons. • If the singletons were excluded from the database, then only 66% genes were alternative spliced MPL

  12. A total of 6593 libraries were left and classified into 293 tissue types (NCBI EST data) • A sample of 127 random genes was used to analysis the tissue distribution of alternative splicing • Large fraction of splicing variants are tissue specific MPL

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  14. Identification of cancer-associated splicing variants • about 35% splicing variants were detected exclusively in cancer tissues • 29% were only detected in normal tissues • This implies that new splicing variants might be generated during carcinogenesis • This result supports the observation that during carcinogenesis not only is the expression profile affected but the splicing Patten MPL

  15. This 383 genes of variants will have a relatively higher confidence of cancer relationship. • About 85% cancer related variants had more than 16 ESTs • About 43% of cancer specific variants were related to more than two kinds of cancer types MPL

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  19. Discussion • We constructed BASD to search for splicing variants of gene transcripts especially those associated with cancer • These single EST supported variants in mining genomic information • Our work presents a genomic view of the relationship between cancer and alternative splicing. MPL

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