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Updated: Aug 15, 2025
Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing
Published on: October 18, 2013
Somatic variant detection from multi-sampled genomic sequencing data of tumor specimens using the ith.Variant
Nicole Maeser1, Aziz Khan2, Ruping Sun1
1Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA.
Abstract:
A common technique for uncovering intra-tumor genomic heterogeneity (ITH) is variant detection. However, it can be challenging to reliably characterize ITH given uneven sample quality (e.g., depth of coverage, tumor purity, and subclonality). We describe a protocol for calling point mutations and copy number alterations using sequencing of multiple related clinical patient samples across diverse tissue, optimizing for sensitivity with specificity. The ith.Variant pipeline can be run on single- or multi-region whole-genome and whole-exome sequencing. For complete details on the use and execution of this protocol, please refer to Sun et al. (2017).1.
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