At least two well-spaced samples are needed to genotype a solid tumor

BACKGROUND: Human cancers are often sequenced to identify mutations. However, cancers are spatially heterogeneous populations with public mutations in all cells and private mutations in some cells. Without empiric knowledge of how mutations are distributed within a solid tumor it is uncertain whether single or multiple samples adequately sample its heterogeneity. METHODS: Using a cohort of 12 human colorectal tumors with well-validated mutations, the abilities to correctly classify public and private mutations were tested (paired t-test) with one sample or two samples obtained from opposite tumor sides. RESULTS: Two samples were significantly better than a single sample for correctly identifying public (99 % versus 97 %) and private mutations (85 % versus 46 %). Confounding single sample accuracy was that many private mutations appeared “clonal” in individual samples. Two samples detected the most frequent private mutations in 11 of the 12 tumors. CONCLUSIONS: Two spatially-separated samples efficiently distinguish public from private mutations because private mutations common in one specimen are usually less frequent or absent in another sample. The patch-like private mutation topography in most colorectal tumors inherently limits the information in single tumor samples. The correct identification of public and private mutations may aid efforts to target mutations present in all tumor cells. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12885-016-2202-8) contains supplementary material, which is available to authorized users.