Custom ALL panel coverage and metrics of patient samples processed with the Tapestri platform for single-cell DNA sequencing. (A) The 110 genes included in the custom 305 amplicon ALL panel, which covers reported mutational hotspots (SNVs and small indels) in acute lymphoblastic leukemia. The text size is proportional to the number of amplicons per gene. The red color gradient is proportional to the number of reported mutations in previous sequencing studies that are covered by the panel amplicons of that gene. The number of reported mutations in ALL was according to the Pediatric Cancer Mutation (PeCan) and Catalogue of Somatic Mutations In Cancer (COSMIC) databases at the time of panel design. Genes with few reported mutations, 1 to 5, are denoted in gray. Details of the genomic regions covered in the custom ALL panel are in supplemental Table 3. (B) Total number of sequenced cells (i), average reads per amplicon per cell (ii), and average allele dropout rate (ADO, iii) per sample. Each point represents a sample (n = 25) from 1 of the 8 T-ALL patients. Median value is shown by a horizontal line. Detailed sample and sequencing metrics are in supplemental Table 2 and ADO details are in supplemental Table 5. (C) Bar plot with the distribution of sequencing reads across the 305 amplicons. Each bar represents an amplicon, and the height of the bar shows the average number of raw sequenced reads per cell (n = 25 samples). Amplicon name is shown for the 8 amplicons with highest coverage (left) and for the 16 lowest performing amplicons (right), which are below the minimum coverage of 10 reads (dashed red horizontal line). Amplicon coverage distribution per sample is in supplemental Table 4.