Whole Exome Sequencing QC metrics by duration of specimen storage.

Final Library Size (bp): This QC metric represents the peak size from BioAnalyzer electropherogram traces of the final exome library from each sample using the Agilent BioAnalyzer High Sensitivity DNA kit.
% Target Covered at 20x: The percentage of all target bases achieving 20X or greater read depth. This metric measures the efficiency of the exome capture. DNA samples with poor quality samples tend to have lower % target covered.
Average Read Depth: Average read depth in the target region.
Percent Duplication: Percent of reads originating from same fragment of the library. These duplicated reads may indicate bias originating from sample quality, library amplification etc. DNA samples with poor quality samples tend to have higher percent duplication.
Ti/Tv Ratio: This is ratio of transitions (single nucleotide substitutions with the same type of nucleotide, e.g., pyrimidine to pyrimidine (C<>T) or purine to purine (A<>G)) to transversions (single nucleotide substitutions with the different type of nucleotide, i.e., pyrimidine to purine or vice versa (A<>T etc.). FFPE DNA samples tend to have higher Ti/Tv ratio due to chemical crosslink and modification.
CI = confidence Interval. Overall means and standard deviations for quality measures and by storage time, differences per 10 years of storage and 95% confidence intervals estimated by linear regression on continuous time. P-values are for Wald tests of time coefficients in regression models. A slope of zero indicates no association with specimen storage time. P-values are not adjusted for multiple comparisons.
Whole Exome Sequencing QC metrics by duration of specimen storage.