Figure 4 - uploaded by Sudhir Kumar
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A simple tree used in explaining PP computation. xi is a base in the single-cell sequence, yi is a base in the ancestral sequence, and bi refers to a branch length.
Source publication
Motivation: Tumor sequencing has entered an exciting phase with the advent of single-cell techniques that are revolutionizing the assessment of single nucleotide variation (SNV) at the highest cellular resolution. However, state-of-the-art single-cell sequencing technologies produce data with many missing bases (MBs) and incorrect base designations...
Contexts in source publication
Context 1
... this example, cells from the same clones (the same color) generally cluster together, but identical cells of a clone can show extensive observed sequence divergence (e.g., brown cells in Fig. 2a and 3a). Given this ini- tial cell phylogeny and the initial cell sequences, we estimate PP of each possible base assignment at each position in a cell sequence. This compu- tation is explained by considering a set of four sequences (Fig. 4). In this tree, x1 to x3 represent the nucleotides at a given position in the tumor cell sequence; x4 is the wild-type base from the normal cell ...
Context 2
... together, but identical cells of a clone can show extensive observed sequence divergence (e.g., brown cells in Fig. 2a and 3a). Given this initial cell phylogeny and the initial cell sequences, we estimate PP of each possible base assignment at each position in a cell sequence. This computation is explained by considering a set of four sequences (Fig. 4). In this tree, x1 to x3 represent the nucleotides at a given position in the tumor cell sequence; x4 is the wild-type base from the normal cell ...
