REPRESENTATIONAL APPROACHES TO GENOMIC ANALYSIS


Year of Award:
1999
Award Type:
R21
Project Number:
CA081674
RFA Number:
PAR-98-067
Technology Track:
Molecular & Cellular Analysis Technologies
PI/Project Leader:
WIGLER, MICHAEL H
Other PI or Project Leader:
N/A
Institution:
COLD SPRING HARBOR LABORATORY
In Phase One we will test if application of representational techniques can enable the development of high resolution, global genomic micro- arrays for measuring changes in gene copy number (amplification and deletion), loss-of-heterozygosity (LOH), and point mutation frequency in tumor DNA derived from biopsies. In particular, we will assay for these changes in low complexity representations (LCRs) of tumor and normal genomes. In Phase Two we will scale up the process of collecting LCR probes and their associated map positions. We will fabricate arrays of DNA probes using the conventional capillary arrayer format to achieve densities between 3,000 and 30,000 probes. These arrays will be tested under a variety of controlled and field test conditions to monitor their utility for detecting changes throughout the tumor genome. We will develop database and analysis tools so that the results of experiments can be readily accessed in a positionally ordered manner.