Scientists have identified a novel computer tool that aids in finding the genetic mistakes that underlie many cancers. Researchers are using the new algorithm to help identify the chromosomal rearrangements and DNA insertions or deletions unique to cancer.
The new computational method is known as CREST, short for Clipping Reveals Structure. Using CREST, researchers identified 89 new structural differences in the cancer genomes of five St. Jude patients with a subtype of acute lymphoblastic leukemia (ALL) known as T-lineage ALL.
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.
"CREST is significantly more accurate and sensitive than existing methods of finding structural variations in next-generation sequencing data. It finds differences between a patient's normal and cancer genomes other tools cannot find," said Jinghui Zhang, an associate member of the St. Jude Department of Computational Biology and the study's senior author.
"Similar tools miss up to 60 to 70 percent of these structural rearrangements in tumors. CREST ensures that scientists will be able to find important structural variations that play critical roles in tumor formation," Zhang added.
The study was recently published in the scientific journal Nature Methods.