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Yong-Jie Lu, MD, PhD

Joshue Schiffman, MD

Yong-Jie Lu of Queen Mary, University of London and Colleen Elso of the Walter and Eliza Hall Institute of Medical Research discuss a groundbreaking method for rapidly identifying chromosome rearrangements and precisely mapping breakpoints

Researchers at Queen Mary, University of London have developed a new technique that combines three previously available technologies to quickly and precisely identify DNA rearrangements associated with tumor formation and

growth. This new approach, which utilizes M-FISH, high-resolution karyotyping, and exon array analysis, may help researchers identify critical candidate genes and genetic markers and better understand the role of complex genetic changes in human cancers.

Traditionally, researchers have used techniques such as g-banding karyotyping and 24-color fluorescence in situ hybridization (FISH) analysis to identify sections of a chromosome that diff between tumor cells and normal cells. However, these techniques are limited in their resolution and cannot pinpoint exactly where in the DNA sequence the changes occur or how they change gene expression.

We used the 500K SNP arrays in combination with M-FISH for chromosome rearrangement because it gave us a resolution 1,000 times higher than traditional karyotyping and 20 times higher than FISH mapping using BACs.

The researchers at Queen Mary, University of London, led by Dr. Yong-Jie Lu, were the first to combine a 24-color FISH analysis, called M-FISH, with high-density microarray analysis using the GeneChip® Mapping 500K Array Set for high-resolution karyotyping. "We used the 500K SNP arrays in combination with M-FISH for chromosome rearrangement because it gave us a resolution 1,000 times higher than traditional karyotyping and 20 times higher than FISH mapping," said Dr. Lu, a senior lecturer in Medical Oncology at the Institute of Cancer, Barts and the London School of Medicine and Dentistry, Queen Mary, University of London.

Using this technique and in-house analysis software dubbed GOLF (Genome-Oriented Laboratory Filing system) to identify genomic copy number changes and define breakpoints, the team precisely defined the breakpoints of 27 translocations in three prostate cancer cell lines. They also identified 29 internal deletions, changes that can also lead to gene fusions.

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