Principle of cell lineage reconstruction. (A) Inferred tree of lineage relationships and genotypes of the first two postzygotic divisions, as well as the arithmetical rules of variant allele frequencies (VAFs) of mosaic mutations used for the lineage reconstruction. The red and black numbers represent independently arising mutations that were first fixed and subsequently inherited, respectively. Pie charts represent example contributions of the early embryonic cell to the adult samples. (B) Overall experimental procedure for reconstruction of lineages. (C,D) Examples of the arithmetical relationship of VAFs of mosaic mutations in individual tissues of a mouse (mouse ID: ConC31). Mutations that show the same frequency in all tissues are considered co-occurring. The sum of the VAFs of the two mutation groups is indicated by the black line. The sum of the average VAF of mutations #2, #19, and #33A (VAF#2/19/33A) and the average VAF of mutations #28 and #33C (VAF#28/33C) equals 50%, indicating the first cell cleavage after a fertilized egg (B). The sum of VAF#14/41 and VAF#51/80 is equal to the VAF#2/19/33A, indicating the subsequent cell division after the first cell cleavage (C). Other examples are shown in Supplemental Figure S1.
