Exon Boundary Tags (EBTs) for Human Functional Genome Annotation

DESCRIPTION (provided by applicant): The Human Genome Project has brought the field of functional genomics to the forefront of biological and pharmaceutical research. However, deciphering the function(s) of each gene in a high throughput format is complicated by alternative splicing and post- translational modifications of proteins. Serial Analysis of Vector Integration (SAVI(r)) is a patented method for high-throughput acquisition of genome-wide functional exons and gene expression profiling by sequencing only a certain length of each exon boundary as Exon Boundary Tag (EBT) after retroviral gene trapping. Since the EBTs generated will be proportioned to the copy numbers of corresponding mRNA molecules or alternative transcripts, quantification of acquired EBTs can reflect the transcription level for gene expression profiles between different treatments or cell types, such as cancer vs. normal cells, for pharmaceutical developments. Preliminary studies demonstrate the feasibility of generating unique data in this research field with a high potential for functional genome annotation, cDNA collection and exon/splice-specific microarray design. The study we are proposing here is a high-throughput acquisition of genome- wide functional exons by sequencing only a certain length of each exon boundary to assemble open reading frames for functional genome annotation and gene expression profiling.