An Improved Chromosomal Comparative Genomic Hybridization (CGH) Microarray for the Detection of Cancer Associated Genome Amplification and Deletion Events
Description of Invention:
The progression and therapeutic response of cancer is closely associated with chromosomal instability (i.e. genomic amplifications and deletions). The most widely used technique to detect these small changes in the genome is CGH. CGH utilizes nucleic acid hybridization to oligonucleotide features corresponding to specific, predetermined regions of the genome to detect DNA copy number changes. Due to the size of the human genome, it is necessary to have high-density features to detect small amplification and deletion events within the genome.
The current invention is based on a CGH microarray with oligonucleotide features that provides a high-density coverage. More specifically, the inventors have used 60-mer oligonucleotide features within a previously shown set of 36 tumor associated genes/genomic regions and have successfully detected small changes in DNA copy number with high density coverage (1 feature per 400bp). Furthermore, the inventors have used a fade-out design for coverage of the flanking regions and cover the remainder of the genome at an average density of 1 feature per 100kb.
Applications:
CGH microarray can be used to detect small regions of genomic instability within cancer associated genes, while larger events can also be detected with similar efficacy.
Gene amplification and deletion profiles of patient samples can be used in diagnosis and therapeutic decision making.
Advantages:
Easy to use, CGH microarray technique, based on current technology.
Technology detects small changes in tumor associated genomic instability more efficiently than current available technologies.
The average coverage of Agilent oligoarray is 1 per 35kb of human genome, while the average coverage of the currently described technology is 1 per 400bp.
Developmental Status:
The technology is ready for use.
Benefits:
More than 600,000 cancer deaths are estimated to occur in 2007. Efficient diagnosis and informed decision making will aid in improved clinical management of cancer. This technology can rapidly diagnose cancer and thus help in proper clinical management leading to improved overall survival and quality of life of patients suffering from cancer. The current in-vitro diagnostics market is valued at $30 billion dollars and expected to grow.
