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The goal of cancer genomics
is to identify mutations that drive tumorigenesis.
Clinically relevant mutations range in size
from point mutations to large structural alterations
such as duplications, deletions, inversions,
and translocations. Each acquired mutation potentially
affects gene structure and regulation, which
may influence a specific course towards malignancy
or present novel targets for new therapies.
However, effective genomic profiling of tumors
as a prognostic tool requires analysis that
comprehensively identifies a broad spectrum
of mutational structures. Because no commercial
platform meets this need, we decided to use
the optical mapping system for revealing structural
alterations that would likely escape detection
by cytogenetic techniques and hybridization
arrays. Oligodendroglioma has been selected
as a model for understanding the molecular basis
of how structural alterations influence the
clinical outcomes because a loss of heterozygosity
of 1p and 19q has been established as a predictor
of chemosensitivity in oligodendroglioma patients;
however, specific molecular candidates are lacking
despite analysis of these chromosomal regions
with traditional molecular and cytogenetic approaches.
I have aided further development of the optical
mapping system, allowing identification of over
1,000 alterations in 2 individual oligodendroglioma
biopsies, laying the basis for identification
of candidates that may elucidate the molecular
underpinnings of treatment efficacy associated
with cytogenetic observations.
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