January 24, 2018 |
Scientists Dramatically Improve Method for Finding Genetic Alterations in Tumors
May 15, 2015  | 

Memphis, TN - St. Jude Children's Research Hospital scientists have developed a significantly better computer tool for finding genetic alterations that play an important role in many cancers but were difficult to identify with whole-genome sequencing. The findings appear today in the scientific journal Nature Methods.

The tool is an algorithm called CONSERTING, short for Copy Number Segmentation by Regression Tree in Next Generation Sequencing.

St. Jude researchers created CONSERTING to improve identification of copy number alterations (CNAs) in the billions of pieces of genetic information generated by next-generation, whole-genome sequencing techniques. CNAs involve the gain or loss of DNA segments. The alterations affect just a few or many hundreds of genes depending on the size of the DNA segments.

In this study, researchers showed CONSERTING identified such alterations with dramatically better accuracy and sensitivity than other techniques, including four published algorithms used to recognize CNA in whole-genome sequencing data. The comparison involved the normal and tumor genomes from 43 children and adults with brain tumors, leukemia, melanoma and the pediatric eye tumor retinoblastoma.

"CONSERTING has helped us harness the power of next-generation, whole-genome sequencing to better understand the genetic landscape of cancer genomes and lay the foundation for the next era of cancer therapy," said corresponding author Jinghui Zhang, Ph.D., a member of the St. Jude Department of Computational Biology. "In this study of the tumor and normal genomes of 43 patients, CONSERTING identified copy number alterations in children with 100 times greater precision and 10 times greater precision in adults." Continue>

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