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Series GSE6274

Query DataSets for GSE6274

Status

Public on Mar 01, 2007

Title

GAPF profiles from HFF2 and Colo320DM cells

Organism

Homo sapiens

Experiment type

Genome variation profiling by array

Summary

Amplification of large chromosomal regions (gene amplification) is a common somatic alteration in human cancer cells and often is associated with advanced disease. A critical event initiating gene amplification is a DNA double strand break (DSB), which is immediately followed by the formation of a large DNA palindrome. Large DNA palindromes are frequent and non-randomly distributed in the genomes of cancer cells and facilitate further increase in copy number. Although the importance of the formation of large DNA palindromes as a very early event in gene amplification is widely recognized, it is not known 1) how a DSB is resolved to form a large DNA palindrome; and 2) whether any local DNA structure determines the location of large DNA palindromes. We show here that intra-strand annealing following a DNA double-strand break leads to the formation of large DNA palindromes and that DNA inverted repeats in the genome determines the efficiency of this event. Furthermore, in human Colo320DM cancer cells, a DNA inverted repeat in the genome marks the border between amplified and non-amplified DNA. Therefore, an early step of gene amplification is a regulated process that is facilitated by DNA inverted repeats in the genome.
Keywords: cancer vs. normal sample comparison

Overall design

Genomic DNA samples from HFF2 and Colo320DM cells were collected and taken through the GAPF procedure. Their GAPF profiles were analyzed using Affymetrix HGU 133A arrays, and the differentially hybridized genes were determined to be significant according to a FDR<0.05

Contributor(s)

Tanaka H, Cao Y, Bergstrom DA, Kooperberg C, Tapscott SJ, Yao M

Citation(s)

17242211

Submission date

Nov 14, 2006

Last update date

Aug 10, 2018

Contact name

Yi Cao

E-mail(s)

[email protected]