Computational Genomics Tools for Copy-Number Fluctuations in Prostate Cancer
Final rept. 1 Nov 2004-31 Oct 2005
NEW YORK UNIV NY
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The goal of this research was to produce a large, useful, open-access database of lesions in prostate cancer, organized in terms of segments of aberrant copy numbers for subsequent automated statistical analysis. The authors aimed to make this data base easily searched, so that users could find those genes likely to be causally related to the disease. They hoped to maximize the utility of the data base by optimizing the following factors cost, availability, efficiency, quality, and ease of use. In summary, the authors have made significant and visible progress towards the following three goals 1 developed new statistical methods to improve the detection of abnormal lesions, define confidence in the detected lesions, and localize putative genes involved in the cancer 2 created a data base with improved statistical significance and with an enhanced human-computer interface so that users can effortlessly maneuver through the data to draw conclusions and 3 created the foundations to build two important bridges to future work. The first bridge is a novel statistical algorithm to combine the genomic data with whole genome data for SNP and other markers for instance, indicating LOH. The second bridge is better low-level background correction software that makes the genomic data usable without too many expensive biological replicates. They now have software based on redescription that allows one to easily combine the genomic data with gene-expression data.
- Genetic Engineering and Molecular Biology
- Medicine and Medical Research
- Computer Programming and Software