Article Figures & Data
Figures
- Fig. 1. Overview of the work flow used for the DNA-quality assay.
(A), An aqueous phase containing DNA extracted from paraffin-embedded tissues and PCR reagents is compartmentalized into droplets before thermocycling. (B), The mixture contains 2-color TaqMan® probes [FAM (excitation λ, 494 nm; emission λ, 522 nm) and VIC (excitation λ, 528 nm; emission λ, 554 nm)] at 2 concentrations (0.16 μmol/L and 0.2 μmol/L) to identify 4 kinds of DNA according to size (C, D). arb., Arbitary.
- Fig. 2. dPCR-quality assay applied to human genomic DNA samples of various length.
(A), Distribution of fragment lengths in the samples as determined by gel electrophoresis. (B–F), Analysis of human genomic DNA fragmented to mean sizes from 170 bp to 570 bp. (G), Distributions of amplifiable DNA as measured by dPCR (data points) and standard capillary electrophoresis (dashed lines).
- Fig. 3. dPCR-quality assay as applied to different quantities of human genomic DNA.
Human genomic DNA fragmented to a mean size of 400 bp and different quantities of the DNA test sample as analyzed with the multiplex dPCR-quality assay.
- Fig. 4. DNA-quality assay comparison of fragmented DNA and FFPE samples.
(A), Control sample corresponding to genomic DNA fragmented to 230 bp. A sample of relatively high quality (B), a medium-quality sample (C), and a severely degraded sample of low quality (D). arb., Arbitrary.
- Fig. 5. Analysis of DNA extracted from 12 FFPE lung adenocarcinoma samples with the 4-plex DNA-quality assay.
Results are expressed as the fraction of amplifiable DNA (calculated from the expected occupancy in droplets for a 3-kb fragmented sample for the 78-, 159-, 197- and 550-bp clusters). Black arrows indicate samples selected for sequencing.
Tables
- Table 1. DNA-quality assay results for the analysis of 12 patient DNA samples extracted from FFPE lung adenocarcinoma tissuesa
Sample no. Fragment-size cluster 78-bp Cluster, % 159-bp Cluster, % 197-bp Cluster, % 550-bp Cluster, % 1 5.8 7.0 0.6 0.4 0.7 0.7 0.2 0.3 2 2.9 2.9 0.3 0.2 0.3 0.3 ND 0.2 3 6.3 6.5 ND ND 0.7 0.8 0.5 0.1 4 9.2 9.6 0.7 0.9 0.8 0.8 ND 0.2 5 3.9 3.8 0.1 0.1 0.4 0.3 ND 0.1 6 3.5 3.0 ND ND 0.3 0.6 0.2 ND 7 4.0 3.7 0.1 ND 0.4 0.4 ND ND 8 0.9 1.0 ND ND ND 0.1 ND ND 9 4.8 4.8 0.2 0.1 0.3 0.2 0.2 0.2 10 3.0 2.8 ND ND 0.5 0.3 ND ND 11 9.0 11.2 0.6 0.1 1.0 1.0 0.5 0.4 12 0.1 ND ND ND ND ND ND ND ↵a The results of 2 separate experiments are shown for each sample. The results are expressed as the percentage of expected amplifiable DNA calculated for a nondegraded sample (see main text). Rows in boldface correspond to the samples selected for sequencing analysis. ND, no droplets for the cluster.
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