Table 1.
Sequences and product sizes of PCR and qPCR primers.
Figure 1.
Comparison of five automated DNA extraction systems.
Illustration of relative DNA concentrations of samples 1–10 measured by the NanoDrop 2000c spectrophotometer (A) and Qubit 2.0 fluorometer (B). The concentrations of the Maxwell 16 extracts were set to 100% for each sample.
Figure 2.
Assessment of DNA quality obtained from each extraction method and impact on downstream applications.
(A) Electrophoretic pattern of DNA extracts 1, 3, 4 and 5 of each extraction method on a 1% agarose gel. Ladder indicates a 1 kb DNA ladder as molecular weight size marker (B) 201 bp, 404 bp and 614 bp amplified DNA fragments of the GAPDH gene for sample 1, 3, 4, 5, of each extraction method. + indicates a positive control and – a negative control. (C) 125–175 bp multiplex PCR product for sample 1, 3, 4 and 5 of each extraction method. + indicates a positive control and – a negative control.
Table 2.
Comparision of instrument prices and material costs per sample for five automated DNA extraction systems.
Figure 3.
Results of the five DNA quantification measurements.
Distribution of DNA concentrations of samples 1–16 measured by each of the five quantification method.
Figure 4.
Impact of DNA quantification methods on downstream applications.
(A) Electrophoretic pattern of 13 DNA extracts on a 1% agarose gel. (B) Amplified 275 bp fragment of the EGFR gene. 20 ng of sample DNA determined by each quantification method was used for PCR amplification. + indicates a positive control, - a negative control.
Figure 5.
Impact of DNA quantification methods on massively parallel sequencing.
(A) Mean amplicon coverage determined by in-house software for each sample, quantification method and amount of DNA used for multiplex PCR amplification. (B) Number of all variants called by in-house software for each sample, quantification method and starting material used.