In this figure, substitution and deletion errors are shown because, when the polyphony number is estimated, deletion errors can appear.
Combining results for both markers, we estimated deletion efficiency to be 7 ± 4 deletions per 1000 cells.
Our estimated deletion frequency for dinucleotides in LCL1261 cells is ≤ 10−4, which is lower than the deletion frequency observed in the fully MMR-deficient HCT116 cell line (Table 2).
Based on the failure or success of PCR amplification, the size and position of each deletion fragment was deduced and new primers spanning estimated deletion fragment were designed for straightforward amplification of pending test samples (see schematic diagram in Figure 2).
Estimated deletion-bearing genome proportions from qPCR results correlated positively with conventional PCR band scoring data (Spearman rank correlation = 0.74, P < 10-15) and revealed substantial among-isolate variation in ND5 deletion heteroplasmy levels.
*The "estimated deletions" were calculated by aligning the extended contigs (extended 10 kb on both sides of the identified novel contigs with HuRef genome as the reference) onto GRCh37 to find the distance between two broken sequences of each extended contigs.
A custom designed, clinically validated MitoMet® array CGH was used to estimate the deletion breakpoints and levels of heteroplasmy, followed by PCR/DNA sequencing to identify the exact breakpoints and deletion sizes (Figure S1 and Table S1).
To estimate the deletion rate, we used the maximum likelihood approach proposed by Petrov et al. [ 41, 42].
The cutoff level to estimate gene deletion(s) was determined by calculating the ratio of the TNFAIP3/CEP6 signal in the subject cells to that in the normal control cells in samples showing obvious deletions from sequence analysis.
However, by starting with a large number of 41 families, we could estimate the deletion process for 19 families, a large enough number to get an estimate that is representative of the genome.
