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Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing
Published on: October 19, 2013
Prospects for cancer genetics
1Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
Abstract:
A number of distinct strategies have been used over the past two decades to uncover the genes involved in tumorigenesis. Their use raises the questions of whether we will require novel approaches in order to continue the progress of cancer genetics. Retrovirus mediated transduction of proto-oncogenes and transfection of tumour associated oncogenes are both inefficient ways of uncovering oncogenes, each being encumbered by technical obstacles that limit their utility. Improvements in the gene transfer strategy may yield a host of new oncogenes. New cloning techniques may have a role here as well as in revealing the existence of genes that are amplified in tumour cell genomes. The major technique for uncovering novel tumour suppressor genes--detection of loss of heterozygosity--is also limited in its sensitivity to detecting genes that are lost in large numbers of tumours. The techniques for uncovering these genes through analysis of pedigrees in which mutant versions of these genes are passed through the germline are encumbered by issues of penetrance and the complexities associated with the inheritance of polygenic traits. In both instances, improvements in data acquisition and analysis will reveal tumour suppressor genes that have proved elusive until now. Over the next decade, we will learn much about how the defects in another apparatus--that responsible for the maintenance of genomic integrity--contribute to cancer susceptibility. Beyond these genes lie yet others about which we seem to know little at present--those that induce the last stages of cancer including invasiveness and metastasis. These will represent an entirely new cohort of genes to be uncovered over the next decade.
Insights
Discovering cancer-related genes requires novel approaches. Current methods for identifying oncogenes and tumor suppressor genes have limitations, necessitating advancements in gene transfer and genomic analysis for future cancer genetics progress.
Area of Science:
- Cancer genetics
- Molecular oncology
- Genomic instability
Background:
- Over the past two decades, various strategies have been employed to identify genes implicated in tumorigenesis.
- Existing methods for oncogene and tumor suppressor gene discovery face technical limitations and inefficiencies.
Purpose of the Study:
- To address the limitations of current gene discovery techniques in cancer genetics.
- To explore novel approaches for identifying oncogenes, tumor suppressor genes, and genes involved in cancer progression.
Main Methods:
- Review of existing strategies including retrovirus-mediated transduction, gene transfection, and loss of heterozygosity detection.
- Discussion of potential improvements in gene transfer, cloning techniques, and data analysis for gene discovery.
- Consideration of germline mutation analysis and its challenges (penetrance, polygenic traits).
Main Results:
- Current methods for oncogene and tumor suppressor gene identification are inefficient and limited in sensitivity.
- Improvements in gene transfer, cloning, and data analysis are expected to reveal new oncogenes and tumor suppressor genes.
- Future research will focus on genes involved in genomic integrity maintenance and those driving cancer invasiveness and metastasis.
Conclusions:
- Novel approaches and technological advancements are crucial for continued progress in cancer genetics.
- Understanding genes related to genomic integrity and metastasis will be a key focus in the next decade.
- Further research is needed to uncover the full spectrum of genes contributing to cancer development and progression.
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