Fig. 3

Quality control (QC) of WGS data. a Using WGS data to perform QC on experimental samples. b Using shared variants between parental and daughter subclones to identify relationships between samples. Three scenarios are presented. The upper panel shows two histograms per experiment, with the total number of mutations per sample (horizontal histogram) and shared mutations between samples (vertical histogram, in decreasing order). Subclones and parental clones for each scenario are also noted. Subclones that share mutations are dotted black and connected with a line. The lower panel depicts hypothetical experiments. A red arrow indicates shared mutations between daughter subclones and parental clones. Scenario 1: all subclones are correctly derived from the same parental clone as they share mutations among themselves and with their designated parent, and also have unique mutations. Scenario 2: all subclones are derived from the same parental clone as they share high numbers of mutations among themselves but not with the sequenced parent. In this example, an incorrect parental clone (purple) has been sequenced. Scenario 3: subclones are derived from a mixed parental population. Not all subclones share a high number of mutations among themselves and with their sequenced parent. Subclones 1, 4, and 6 are likely from one lineage; subclones 2, 3, and 5 are from a different lineage. Note that clonal expansion for isolated daughter subclones is not depicted in the diagram for simplicity