Abstract

Glioblastoma multiforme (GBM) are aggressive brain tumors found in the nervous system of humans. Derived from glia such as astrocytes, oligodendrocytes and Schwannn cells, glioblastomas can develop throughout the nervous system, but are most commonly found in the brain. Prognosis following glioblastoma diagnosis is often very grim; only 3-5% of patients diagnosed with glioblastoma live beyond 36 months, therefore early detection and proper treatment are imperative. Scientists have studied the genetic factors linked to GBM development in humans and model organisms and determined a number of glioblastoma GOI. Many of the glioblastoma GOI have been previously identified as oncogenes such as MET, PDGFR and EGFR, or tumor suppressor genes such as PTEN, NF1 and p53 whose expression has been altered.

In this study, glioblastoma GOI query sequences from humans, canines, mice and rats were aligned with associated chromosome sequences amongst these species in order to determine how conserved GOI sequences were across genomes. Using a combination of BLAST algorithms such as NCBI's BLASTn and Blast-Off, which was written for the purpose of this study, both the gapless and optimized gapped alignments of each GOI sequence against the subject chromosome sequence were determined and scored. Across all 3 model organisms, there was relatively low gapless sequence conservation, however scores often improved drastically with the introduction of gaps and extensions. There were only 3 human GOI that showed higher than 10% gapless alignment when queried against the subject chromosome sequences: CHIC2, MET and MYCN. The most highly conserved GBM GOI sequences were MET, EGFR and MYCN; all 3 sequences were at least 15% conserved across more than 1 model organism. It is unknown what functional regions may be located within the conserved gene sequences, however identification of these conserved regions may help scientists better understand genetic changes associated to glioblastoma.

Library of Congress Subject Headings

Glioblastoma multiforme--Genetics; Brain--Tumors--Diagnosis; Human genome

Publication Date

12-3-2014

Document Type

Thesis

Student Type

Graduate

Degree Name

Bioinformatics (MS)

Advisor

Gary R. Skuse

Advisor/Committee Member

Larry Buckley

Advisor/Committee Member

Jean A. Douthwright

Comments

Physical copy available from RIT's Wallace Library at RC280.B7 K37 2014

Campus

RIT – Main Campus

Plan Codes

BIOINFO-MS

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