Abstract: | Microarray analysis using sets of known human genes provides a
powerful platform for identifying candidate oncogenes involved
in DNA amplification events but suffers from the disadvantage
that information can be gained only on genes that have been
preselected for inclusion on the array. To address this issue,
we have performed comparative genome hybridization (CGH) and
expression analyses on microarrays of clones, randomly selected
from a cDNA library, prepared from a cancer containing the DNA
amplicon under investigation. Application of this approach to
the BT474 breast carcinoma cell line, which contains amplicons
at 20q13, 17q22-21, and 17q22-23, identified 50 amplified and
expressed genes, including genes from these regions previously
proposed as candidate oncogenes. When considered together with
data from microarray expression profiles and Northern analyses,
we were able to propose five genes as new candidate oncogenes
where amplification in breast cancer cell lines was
consistently associated with higher levels of RNA expression.
These included the HB01 histone acetyl transferase gene at
17q22-23 and the TRAP100 gene, which encodes a thyroid hormone
receptor-associated protein coactivator, at 17q11-21. The
results demonstrate the utility of this microarray-based CGH
approach in hunting for candidate oncogenes within DNA
amplicons. |