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Updated: Nov 26, 2025

Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing
Published on: October 18, 2013
A validated lineage-derived somatic truth data set enables benchmarking in cancer genome analysis
Megan Shand1, Jose Soto2, Lee Lichtenstein2
1Broad Institute of Harvard and MIT, Cambridge, MA, USA. mshand@broadinstitute.org.
Abstract:
Existing cancer benchmark data sets for human sequencing data use germline variants, synthetic methods, or expensive validations, none of which are satisfactory for providing a large collection of true somatic variation across a whole genome. Here we propose a data set, Lineage derived Somatic Truth (LinST), of short somatic mutations in the HT115 colon cancer cell-line, that are validated using a known cell lineage that includes thousands of mutations and a high confidence region covering 2.7 gigabases per sample.
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