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

2. BIOINFORMATICS MPL Alternative splicing Form

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4. BIOINFORMATICS MPL 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

5. BIOINFORMATICS MPL 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

6. BIOINFORMATICS MPL  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.

7. BIOINFORMATICS MPL Results ASA 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%

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9. BIOINFORMATICS MPL  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)

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11. BIOINFORMATICS MPL 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

12. BIOINFORMATICS MPL  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

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14. BIOINFORMATICS MPL 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

15. BIOINFORMATICS MPL  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

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19. BIOINFORMATICS MPL 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.