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Updated: May 8, 2026

Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing
Published on: October 18, 2013
Identification of Somatic Variants in Cancer Genomes from Tissue and Liquid Biopsy Samples
Kiran Krishnamachari1, Hanaé Carrié1, Anders Jacobsen Skanderup2
1Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore.
Abstract:
Somatic variant detection is an important step in the analysis of cancer genomes for basic research as well as precision oncology. Here, we review existing computational methods for identifying somatic mutations from tissue as well as liquid biopsy samples. We then describe steps to run VarNet (Krishnamachari et al., Nat Commun 13:4248, 2022), a variant caller using deep learning, to accurately identify single nucleotide variants (SNVs) and short insertion-deletion (indels) mutations from next-generation sequencing (NGS) of tumor tissue samples.
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