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Research Teams at J. Craig Venter Institute and Ludwig Institute for Cancer Research Uncover New Chromosomal Alterations in Cancer Using Transcriptome Sequencing Approach
Date:1/27/2009

ROCKVILLE, Md. and NEW YORK, Jan. 27 /PRNewswire-USNewswire/ -- Researchers from the J. Craig Venter Institute (JCVI) and the Ludwig Institute for Cancer Research (LICR) have uncovered new genomic alterations that lead to gene fusions in a breast cancer cell line by using 454 Life Sciences sequencing technology. The work, led by Qi Zhao of JCVI and Otavia L. Caballero, of LICR, is being published the week of January 26 in the early online edition of the Journal of the Proceedings of the National Academy of Sciences (PNAS).

Previous studies have shown that gene fusions are key gene alteration events in the development and progression of many kinds of cancers. The discovery of the best known gene fusion, BCR-ABL, led to the development of Gleevec(R) for the treatment of chronic myelogenous leukemia and other cancers.

In this proof of concept study the researchers focused on the transcriptome, a subset of genes in the genome that code for proteins. It has long been known that cancers arise from various types of genomic changes in certain cells. Continued advances and cost efficiencies of next generation DNA sequencing technologies are enabling this more precise and detailed examination of changes in the human genome that could be directly involved in cancer.

The JCVI/LICR researchers began with a well-characterized breast cancer cell line, HCC1954 and performed high-throughput transcriptome sequencing. Previous studies on this cell line have uncovered certain types of genetic mutations and chromosomal abnormalities associated with breast cancer. By conducting the in-depth transcript sequencing in this study and comparing these data to the previous studies a clearer picture is emerging of all the expressed genes some of which present in altered forms in the cancer cell line.

The team began by generating more than half a million 454 reads of cDNA sequences. After extensive data
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SOURCE J. Craig Venter Institute
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