Variant calling from RNA-Seq data reveals allele-specific differential expression of pathogenic cancer variants.

Journal: Communications medicine
Published Date: May 28, 2025

Abstract

BACKGROUND: Genetic variants play a pivotal role in the initiation and progression of many diseases, including cancer. Detecting these variants is the first step in understanding their contribution to disease mechanisms. RNA sequencing (RNA-Seq) has become a crucial assay in cancer research, offering insights beyond those provided by DNA sequencing. This study introduces VarRNA, a novel method that utilizes RNA-Seq data to classify single nucleotide variants and insertions/deletions from tumor transcriptomes.

Authors

  • Audrey Bollas
    The Office of Data Sciences, The Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, USA.
  • Jeffrey Gaither
    The Office of Data Sciences, The Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, USA.
  • Kathleen M Schieffer
    The Steve and Cindy Rasmussen Institute for Genomic Medicine, The Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, USA.
  • Peter White
    Department of Pediatrics, Ohio State University, Columbus, Ohio; Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio.
  • Elaine R Mardis
    The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America; Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America; Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America; Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri, United States of America; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America.

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