title: At least two well-spaced samples are needed to genotype a solid tumor.
abstract: 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.
authors.affiliation: Department of Preventive Medicine, University of Southern California Keck School of Medicine, Los Angeles, CA, USA.
authors.forename: Kimberly
authors.initials: K
authors.lastname: Siegmund
authors.affiliation: Department of Pathology, University of Southern California Keck School of Medicine, 1441 Eastlake Avenue , NOR2424, Los Angeles, CA, 90033, USA. dshibata@usc.edu.
authors.forename: Darryl
authors.initials: D
authors.lastname: Shibata
mesh_terms: D015179:Colorectal Neoplasms / Q000235:genetics* / Q000473:pathology; D056915:DNA Copy Number Variations / Q000235:genetics; D059472:Exome / Q000235:genetics; D018740:Genetic Heterogeneity; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D009154:Mutation / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D018401:Sample Size
keywords: Colorectal cancer; Exome sequencing; Mutation topography; Tumor heterogeneity