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A comprehensive analysis of RNA sequences reveals macroscopic somatic clonal expansion across normal tissues

By Keren Yizhak, Francois Aguet, Jaegil Kim, Julian Hess, Kirsten Kubler, Jonna Grimsby, Ruslana Frazer, Hailei Zhang, Nicholas Haradhvala, Daniel Rosebrock, Dimitri Livitz, Xiao Li, Eila Arich-Landkof, Noam Shoresh, Chip Stewart, Ayelet Segre, Philip Branton, Paz Polak, Kristin Ardlie, Gad Getz

Posted 13 Sep 2018
bioRxiv DOI: 10.1101/416339

Cancer genome studies have significantly advanced our knowledge of somatic mutations. However, how these mutations accumulate in normal cells and whether they promote pre-cancerous lesions remains poorly understood. Here we perform a comprehensive analysis of normal tissues by utilizing RNA sequencing data from ~6,700 samples across 29 normal tissues collected as part of the Genotype-Tissue Expression (GTEx) project. We identify somatic mutations using a newly developed pipeline, RNA-MuTect, for calling somatic mutations directly from RNA-seq samples and their matched-normal DNA. When applied to the GTEx dataset, we detect multiple variants across different tissues and find that mutation burden is associated with both the age of the individual and tissue proliferation rate. We also detect hotspot cancer mutations that share tissue specificity with their matched cancer type. This study is the first to analyze a large number of samples across multiple normal tissues, identifying clones with genomic aberrations observed in cancer.

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