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Development of systematic exon trapping for gene identification in genomic DNA

Objective

- To develop and improve the prototype exon trapping system.
- To use the improved systems to systematically identify and isolate genes from 2.5Mb of sequenced genomic clones on chromosome 22.
- To extensively evaluate and assess gene identification in sequenced genomic clones using computer based programmes and cDNA selection methods versus our improved exon trapping systems.

Isolation of genes within the human genome is critical to our understanding of the structural, functional and organisational aspects of the genome. Current estimations of the total number of transcribes sequences (genes) in the human genome lie in the order of 75,000. A number of different strategies including genomic sequencing and computer based gene prediction have been employed in an attempt to identify genes in genomic clones in a systematic fashion. However, with the exception of exon trapping, none of these strategies offer a comprehensive method for systematic identification of genes in cloned and sequenced genomic DNA. Consequently, it has been estimated that as many as 10-40% of genes may go undetected.

Exon trapping approaches offer the best potential for systematic gene identification. However, current exon trapping systems suffer from several limitations prohibiting large scale systematic use. The project partners have addressed these limitations and have developed improved prototype systems for exon trapping These systems offer significant advantages over existing exon trapping approaches. The objectives of this project are to develop and improve these systems to allow rapid, efficient and high throughput exon trapping, to apply and evaluate these improved systems for systematic identification of genes in sequenced and cloned genomic DNA. Specifically, the partners will a) improve the prototype exon trapping systems to allow rapid, efficient and high throughput systematic identification of genes in cloned and sequenced genomic DNA, b) use the improved prototypes to systematically identify and isolate genes from 2.5Mb of sequenced genomic clones on chromosome, c) extensively evaluate and assess gene identification in sequenced genomic clones using computer based programmes and cDNA selection methods with exon trapping approaches.

Successful implementation of this project will make a substantial contribution to human genome research since this proposal offers the means to systematically and efficiently identify the large number of genes in genomic DNA that will not be identified by genome sequencing or cDNA selection / sequencing approaches

Coordinator

UNIVERSITY COLLEGE CORK, NATIONAL UNIVERSITY OF IRELAND, CORK
Address
Lee Maltings, Prospect Row
30 Cork
Ireland

Participants (2)

GENOME RESEARCH LTD.
United Kingdom
Address
The Wellcome Trust Genome Campus Hinxton
CB10 1SA Saffron Walden
Rijksuniversiteit Leiden
Netherlands
Address
72,Wassenaarseweg
2333 AL Leiden