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Tree reliability was evaluated by sample concordance factors (CFs).
In the comparison of video counts, the sample concordance correlation coefficient was 0.997 (p < 0.001).
When measuring agreement between the two investigators, the sample concordance correlation coefficient for audio counts was 0.998 (p < 0.001).
Assays included duplicates and laboratory controls, which showed sample concordance of 99.93%, genotype call rate of 99.7%.
In the comparison of video counts, the sample concordance correlation coefficient was 0.997 with 95% lower confidence bound of 0.991 (p < 0.001).
For the comparison of investigator 1's video counts to the corresponding audio counts, the sample concordance correlation coefficient was 0.968 (p = 0.026).
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Here, we report the results of that study which followed SWGDAM guidelines and includes data for: species specificity, sensitivity, stability, precision, reproducibility and repeatability, case-type samples, concordance, stutter, DNA mixtures, and PCR-based procedures.
Computing inter-sample concordance rates at each base provides yet another way to highlight sequencing errors.
Then we eliminated about 20-30% of SNPs in the 4-plexes as unconfirmed using inter-sample concordance checks between technical replicates (see Additional file 1 and Additional file 2: Table S12).
We further recommend, if cost allows, to duplicate samples (which is easily performed in a multiplexed experiment) and validate computed SNPs by inter-sample concordance checks between these technical replicates.
As no intra-sample concordance results are available, the question whether these differences are because of a true discordance between primary tumour and metastases or rather due to an intra-sample variability (i.e., variability (a) between different areas within the same sample because of biological heterogeneity (Al-Mulla et al, 1998 ) or (b) to technical reproducibility) remains unanswered.
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