11
Universal
Probe Reagents for Detection and Quantitation of RNA Splicing—Callida
Genomics Inc., 750 N. Pastoria Avenue, Sunnyvale,
CA 94085; 408-739-2353
Dr.
Snezana Drmanac, Principal Investigator, snezana@sbhgenomics.com
Dr.
Radoje Drmanac, Business Official, rade@sbhgenomics.com
DOE
Grant No. DE-FG02-05ER84275
Amount:
$749,146
The
number of genes in the genome of higher organisms is relatively small; however,
the protein complexity arising from these genes has been shown to be much
higher. In part, this is due to
alternative splice variants that are created during the processing of gene
transcripts. The formation of gene
splice variants has implications for human disease (for example, in cancer
susceptibility) and also for medical diagnostics, drug development, and
bioengineering. However, there are
hundreds of thousands of exons for each higher organism, which imposes a
technical problem of generating millions of exon-specific detection reagents.
This project will advance gene splice variant detection and quantitation
by utilizing a small library of a few thousand universal-probe reagents and
universal-probe microarrays, sufficient to analyze any gene from any organism.
In Phase I, efficient assay designs and
analysis software were developed, and accurate exon detection was demonstrated
on 11 genes. Accurate exon detection
was also demonstrated on pools of 10 cDNA clones representing 10 distinct genes.
Over 300 cDNA clones (~1Mb of DNA) from 6 human tissues were efficiently
analyzed using this new splice variant analysis method.
Phase II will develop fully functional prototypes and user-friendly
protocols, and perform end-user-directed testing of: (1)
pre-made probe pools for human genes; (2) on-demand probe pools for gene mixes
and genes from other organisms; and (3) a universal set of labeled probe pools
for multiplex detection of DNA clones or amplicons longer than 100 bp. The
technical goal is to provide novel or improved chips, probe reagents, assay
kits, and software, underlying all three products.
Commercial Applications and other Benefits as
described by the awardee: Pre-made or easy made-on-demand-labeled
gene probe cocktails, combined with universal 6-mer microarrays, would have many
research and diagnostic applications, including fundamental studies of gene
expression control, organism development and evolution, understanding disease
susceptibility and progression such as in cancer, drug development for gene
expression control, and agricultural and industrial research. An
additional benefit involves the isolation of rare and complex splice variants
for protein expression, without an expensive long gene synthesis process.