Verifying expressed transcript variants by detecting and assembling stretches of consecutive exons

Tzu Hung Hsiao, Chien Hong Lin, Te Tsui Lee, Ji Yen Cheng, Pei Kuen Wei, Eric Y. Chuang, Konan Peck

Research output: Contribution to journalArticle

Abstract

We herein describe an integrated system for the high-throughput analysis of splicing events and the identification of transcript variants. The system resolves individual splicing events and elucidates transcript variants via a pipeline that combines aspects such as bioinformatic analysis, highthroughput transcript variant amplification, and high-resolution capillary electrophoresis. For the 14369 human genes known to have transcript variants, minimal primer sets were designed to amplify all transcript variants and examine all splicing events; these have been archived in the ASprimerDB database, which is newly described herein. A high-throughput thermocycler, dubbed GenTank, was developed to simultaneously perform thousands of PCR amplifications. Following the resolution of the various amplicons by capillary gel electrophoresis, two new computer programs, AmpliconViewer and VariantAssembler, may be used to analyze the splicing events, assemble the consecutive exons embodied by the PCR amplicons, and distinguish expressed versus putative transcript variants. This novel system not only facilitates the validation of putative transcript variants and the detection of novel transcript variants, it also semi-quantitatively measures the transcript variant expression levels of each gene. To demonstrate the system's capability, we used it to resolve transcript variants yielded by single and multiple splicing events, and to decipher the exon connectivity of long transcripts.

Original languageEnglish
Pages (from-to)e187
JournalNucleic acids research
Volume38
Issue number20
DOIs
Publication statusPublished - 2010 Nov

All Science Journal Classification (ASJC) codes

  • Genetics

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