A novel computational method for finding regions with copy number abnormalities in cancer cells

Mentors: Manuel Garber and Mike Zody

Cancer can result from mutations that delete tumor suppressor genes or activate oncogenes. Types of mutations that can activate oncogenes include amplifications and chromosomal rearrangements known as translocations. Raw data produced from microarray hybridization experiments can reveal the number of copies of each chromosomal region in a tumor cell. Abnormal copy numbers may indicate that cancer-promoting mutations have occurred in certain chromosomal regions.

Vivek designed a computer program to identify pairs of chromosomal regions with a high correlation of copy number in cancer cells. Using his program to analyze data from colorectal cancer cells, Vivek found several pairs of chromosomal regions that had highly correlated reductions in copy number. Vivek and his mentors hypothesized that the deletion of these pairs of partner genes together may promote cancerous cell growth more than the deletion of either of them alone.

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Vivek, a senior at Chestnut Hill’s Beaver Country Day School, wrote a computer program to identify copy number abnormalities in cancer cells.


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