Biased evolutionary inferences from bulk tumor samples

ABSTRACT It is generally agreed that tumors are composed of multiple cell clones defined by different somatic mutations. Characterizing the evolutionary mechanisms driving this intratumor genetic heterogeneity (ITH) is crucial to improve both cancer diagnosis and therapeutic strategies. For that purpose, recent ITH studies have focused on qualitative comparisons of mutational profiles derived from bulk sequencing of multiple tumor samples extracted from the same patient. Here, we show some examples where the naive use of bulk data in multiregional studies may lead to erroneous inferences of the evolutionary trajectories that underlie tumor progression, including biased timing of somatic mutations, spurious parallel mutation events, and/or incorrect chronological ordering of metastatic events. In addition, we analyze three real datasets to highlight how the use of bulk mutational profiles instead of inferred clones can lead to different conclusions about mutational recurrence and population structure.