Akshaya V Annapragada, Noushin Niknafs, James R White, Daniel C Bruhm, Christopher Cherry, Jamie E Medina, Vilmos Adleff, Carolyn Hruban, Dimitrios Mathios, Zachariah H Foda, Jillian Phallen, Robert B Scharpf, Victor E Velculescu
Genetic changes in repetitive sequences are a hallmark of cancer and other diseases, but characterizing these has been challenging using standard sequencing approaches. We developed a de novo kmer finding approach, called ARTEMIS (Analysis of RepeaT EleMents in dISease), to identify repeat elements from whole-genome sequencing. Using this method, we analyzed 1.2 billion kmers in 2837 tissue and plasma samples from 1975 patients, including those with lung, breast, colorectal, ovarian, liver, gastric, head and neck, bladder, cervical, thyroid, or prostate cancer...
March 13, 2024: Science Translational Medicine