Non-coding cancer driver candidates identified with a sample- and position-specific model of the somatic mutation rate

摘要

Cancers are diseases caused by changes in DNA sequences. Some changes occur in the protein-coding part of the DNA sequence, in other words, in the stretches of DNA that include the instructions to make a given protein. Other changes occur in the remaining parts of the DNA that do not code for proteins, which accounts for about 98% of the human genome. Modern technologies allow us to identify these DNA changes, but, up until recently, this has only been possible for the protein-coding part of the DNA. Many studies have thus analyzed DNA changes in the protein-coding part of the human genome, while the larger, non-coding part remains rather unexplored. Advances in technology means that large datasets are becoming available where changes in DNA sequences are identified across the entire genomes of a collection of cancer patients. However, it is not clear which of these DNA changes play a role in the development of cancer and which are neutral with no effect on cancer. Now, Juul et al. have developed a new method, named 'ncdDetect', to search the human genome and identify stretches of DNA that when changed give cancer cells an advantage and allow them to grow. Juul et al. refer to these DNA stretches as 'driver elements', and, after analyzing the genomes from 505 patients with cancer, they identified some known driver elements and some potentially new ones. For example, possible driver elements were found in non-coding parts of the DNA that regulate genes called SMUG1 and CD1A. Both of these genes encode proteins that had been linked to cancer in the past, but driver elements had not previously been described in the nearby non-coding regions. Juul et al. also found a number of possible driver elements that might be important to consider in the treatment of cancers. Importantly, not all the candidate driver elements identified with ncdDetect are true drivers. The changes in DNA vary greatly between different types of cancer and even between different cases of a single type of cancer. Understanding and describing this variation continues to be a challenge in identifying driver elements, and so Juul et al. plan to keep improving the method to make sure that the driver elements it identifies are all trustworthy.