Array Comparative Genomic Hybridization of Malignant Gliomas
It has been known for many years that malignant tumors have chromosome losses that contribute to their malignancy. In recent years, considerable research effort has been directed at identifying the one common region of deletion that occurs within specific tumor types in order to identify the actual gene(s) involved in the transformations. Traditionally, loss of heterozygosity mapping, using polymorphic markers and genotype information, and comparative genomic hybridization (CGH), utilizing normal metaphase chromosomes as the template upon which differentially labeled test and control samples are hybridized, have been used to identify chromosomal rearrangements. However, these approaches have proven to be relatively time consuming and have low resolution when identifying aberrant chromosomal regions.
The project outlined here describes the development of high-resolution, chromosome specific, CGH arrays for the detection of chromosomal deletions and amplifications in neurological neoplasia. High-resolution array CGH will allow for very rapid and accurate (100-200 kilobase) characterization of chromosomal rearrangements within a large number of tumors. High-resolution genome-wide coverage, on a per-chromosome basis, will be achieved by utilizing complete, overlapping, minimum-tile path clones that were generated by the Human Genome Project in its production of highly accurate genomic sequence.
The research project contains four basic aims:
- The generation of genome-wide 1Mb, chromosome- and region-specific high-resolution CGH arrays, including the purification of minimum-tile path DNA and production of amino-linked DOP-PCR products;
- The characterization of the arrays by testing with differentially labeled normal DNAs as well as known deletions and amplifications;
- The characterization of clinically defined brain tumor types (glioblastoma multiforme, oligoastrocytoma and oligodendroglioma) by high-resolution CGH hybridization to determine exact regions of chromosomal rearrangement and therefore the putative disease-causing genes within them;
- Investigate the use of high-resolution CGH arrays as a diagnostic tool for predicting the responsiveness of oligodendrogliomas to chemotherapeutic treatment that are associated with known chromosome deletions.