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Researchers improve method for finding genetic mistakes that fuel cancer
Date:6/12/2011

nd sometimes signal problems in sequencing data. Other analytic methods discard soft clips. But in developing CREST, researchers used the soft clips to precisely identify sites of chromosomal rearrangement or where pieces of DNA are inserted or deleted.

"CREST marks the first use of soft clips to identify fusion proteins," Zhang said, referring to hybrid proteins made when genomic rearrangements fuse pieces of two genes. The resulting proteins can disrupt normal cellular controls and lead to the unchecked cell division that marks cancer.

Using CREST, researchers found 110 structural variations in the five T-ALL genomes, including 89 that scientists validated using other laboratory methods. The results were better than the percentage found using other analytic tools.

When researchers used CREST to search for structural variations in the published whole-genome sequence of melanoma cells, they found 50 previously unidentified variations. Researchers went on to validate 18 of the 20 newly found variations selected for confirmatory testing.

"With the incorporation of CREST, we now can augment the existing approaches we have developed at Washington University to better detect and analyze important structural variants in human cancers," said co-author Li Ding, Ph.D., a geneticist and assistant director of medical genomics at Washington University's Genome Institute.


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Contact: Summer Freeman
summer.freeman@stjude.org
901-595-3061
St. Jude Children's Research Hospital
Source:Eurekalert

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