Work

Somatic variant detection from multi-sampled genomic sequencing data of tumor specimens using the ith.Variant pipeline

Year: 2022

Type: article

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

Source: STAR Protocols

DOI: 10.1016/j.xpro.2022.101927

Authors: Nicole Maeser, Aziz Khan, Ruping Sun

Institutions: University of Minnesota, Masonic Cancer Center, Stanford Medicine, Stanford Cancer Institute, Stanford University

Language: English

Topic: Cancer Genomics and Diagnostics

Subfield: Cancer Research

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

SDG: Good health and well-being

Open Access status: gold

Estimated APC paid: $1,500