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Data from: Bulk genotyping of biopsies can create spurious evidence for heterogeneity in mutation content

Citation

Kostadinov, Rumen; Maley, Carlo C.; Kuhner, Mary K. (2016), Data from: Bulk genotyping of biopsies can create spurious evidence for heterogeneity in mutation content, Dryad, Dataset, https://doi.org/10.5061/dryad.hf93c

Abstract

When multiple samples are taken from the neoplastic tissues of a single patient, it is natural to compare their mutation content. This is often done by bulk genotyping of whole biopsies, but the chance that a mutation will be detected in bulk genotyping depends on its local frequency in the sample. When the underlying mutation count per cell is equal, homogenous biopsies will have more high-frequency mutations, and thus more detectable mutations, than heterogeneous ones. Using simulations, we show that bulk genotyping of data simulated under a neutral model of somatic evolution generates strong spurious evidence for non-neutrality, because the pattern of tissue growth systematically generates differences in biopsy heterogeneity. Any experiment which compares mutation content across bulk-genotyped biopsies may therefore suggest mutation rate or selection intensity variation even when these forces are absent. We discuss computational and experimental approaches for resolving this problem.

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