Fig 1.
Workflow for the FFPE tissues.
Three SEER RTRs selected cases that would likely meet the study criteria from their database. Cases were screened for histology/morphology, tumor nuclei content, and necrotic cell content to select cases meet the study criteria. The RTRs screened 30 or 31 cases; one RTR did not keep track of the number of cases they screened. Each RTR selected and sent 20 cases that met study criteria to the lab. One case was excluded from analyses due to incomplete information regarding storage time. 59 cases were considered for subsequent analyses. DNA was successfully extracted from 58 cases. WES was successful on 53 of the cases.
Table 1.
FFPE specimens selected for analysis.
Table 2.
Pathology review results of FFPE tissues for serous ovarian adenocarcinoma received at the NCI lab.
Table 3.
DNA quantity and quality metrics by storage time of specimen.
Fig 2.
Association between specimen storage time and the Q129/41 ratio.
The solid line indicates the estimated linear relationship between age and Q129/41 ratio. The shaded area denotes pointwise 95% confidence intervals of the conditional mean. Cases successful through the entire WES workflow (DNA extraction through WES sequencing) are denoted as circles (N = 53); unsuccessful cases are denoted as X’s (N = 6).
Fig 3.
Association between specimen storage time and final library size in base pairs.
Specimens that failed sequencing do not have library size values and are indicated by x. The solid line indicates the estimated linear relationship between storage time and library size (N = 59). The shaded area denotes pointwise 95% confidence intervals for the conditional means. Cases successful through the entire WES workflow (DNA extraction through WES sequencing) are denoted as circles (N = 53); unsuccessful cases are denoted as X’s (N = 6). Failed assays were not used to estimate the linear trend.
Table 4.
Whole Exome Sequencing QC metrics by duration of specimen storage.
Fig 4.
Association between specimen storage time and average read depth.
The solid line indicates the estimated linear relationship between age and average read depth. The shaded area denoted pointwise 95% confidence intervals of the conditional mean. Cases successful through the entire WES workflow (DNA extraction through WES sequencing) are denoted as circles (N = 53); unsuccessful cases are denoted as X’s (N = 6). Failed assays were not used to estimate the linear trend.
Table 5.
Success of whole exome assay by formalin-fixed paraffin-embedded specimen storage time.
Table 6.
Success of whole exome assays by SEER Registry sites.