Genome-wide allelotyping of medulloblstomas (Dr Steven Clifford)
3 year project with grant funding of £139,624
Jointly funded by SDBTT and Charlie’s Challenge
2001 - 2004
This project has now been completed:
Important insights have been produced into the genetic basis of medulloblastoma development. It has:
identified critical regions of frequent genetic abberrations in the tumour type
provided critical insights into the chromosomal mechanisms underlying genetic loss in this disease
defined and validated the methodology that would be required for the comprehensive characterisation of chromosomal defects in medulloblastoma.
It is anticipated that these finding will lead to four significant research publications over the coming year. These findings will be followed up with further studies aimed at:
further detailed mapping of the regions of frequent genetic abberration that have been detected
identification of critical genes lying within these regions
assessment of the clinical diagnosis and therapeutic potential of these findings.
The aim of this project is to carry out a genome-wide screen to assess the position, nature and frequency of chromosomal losses in medulloblastoma (MB), and to make a preliminary assessment of their clinical relevance. This will involve the allelotyping of polymorphic markers in a panel of MB tumour, and matched blood, DNA samples. Allelotyping will be carried out using PCR primers from a commercially available panel of 200 polymorphic microsatellite DNA markers.
The multiplexing and optimisation of all primers has now been completed utilising DNA samples from a panel of 11 MB cell lines. This represents the majority of MB cell lines described in the literature, which are widely used as the basis of genetic, biological and drug development studies in this disease. Each cell line was also analyzed by comparative genomic hybridization (CGH) and FISH analysis of isochromosome 17q, MYC and MYCN status, and these results were combined with, and compared to, the allelotyping results. These results thus represent an initial comprehensive genome wide survey of chromosomal defects in MBs, and have allowed the identification of novel and characteristic defects in this panel of cell lines, which may play a role in MB development. The majority of these were found at equivalent frequencies in cell lines to those reported in primary tumour samples. These MB cell lines therefore provide a valuable tool for the detailed mapping of chromosomal and genetic defects and the identification of critical genes in MB pathogenesis. Our data support the relevance of these cell lines as in vitro models of MB, and form a detailed genetic characterisation which will be valuable to ourselves and other groups undertaking studies on these cell lines.
The allelotyping of a panel of 30 primary MB tumour and matched blood DNA samples is now underway. It is anticipated that this part of the study will be completed by Summer 2004. Data will be compared with clinical and pathological data to establish any potential clinical relevance of common chromosomal losses identified. Furthermore, data will be combined with that obtained from cell lines (see above) to map the position of critical MB genes. Initial results have highlighted areas of common loss, which will be further investigated within this project if time permits.
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