DNF-467

Genomic DNA 50Kb Analysis Kit

High Sensitivity NGS Fragment Analysis Kit
500 Sample Genomic DNA 50Kb Analysis Kit

The Genomic DNA 50 Kb Analysis Kit is employed in the automated quality assessment of genomic DNA. Able to accurately size samples from 75 bp through 50 Kb, it is commonly employed as a quality check prior to downstream applications, such as whole genome sequencing. To simplify sample handling and preparation, a single 200X dilution of your sample is all that is required, further improving laboratory workflow.

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Components

500 Sample Kit
Genomic DNA Separation Gel 500 mL (DNF-270-0500)
Intercalating Dye 30 µL (DNF-600-U030)
5X 930 dsDNA Inlet Buffer 300 mL (DNF-355-0300)
5X Capillary Conditioning Solution 100 mL (DNF-475-0050)
HS Genomic DNA Diluent Marker Solution 240 mL (DNF-375-0120)
Extended Genomic DNA Ladder 15 µL (DNF-367-U050)
0.25X TE Rinse Buffer 125 mL (DNF-497-0125)
BF-25 Blank Solution 8 mL (DNF-300-0008)

Specifications

Specifications Description
Sample Volume Required 1 µL
Diluent Marker Volume Required 199 µL
DNA Sizing Range 75 bp – 48,500 bp
gDNA Concentration Range 25 ng/µL - 250 ng/µL input gDNA
(0.125 – 1.25 ng/µL final concentration after dilution)
gDNA Quantification Accuracy ± 30%
gDNA Quantification Precision 25% CV
Maximum gDNA Concentration 250 ng/µL
Total Electrophoresis Run Time 50 minutes (Short Array, 33-55)

Examples

The capability of the Genomic DNA 50 Kb Analysis Kit to accurately quantify and size genomic DNA samples is directly related to the Extended Genomic DNA Ladder. Accurate sizing and quantification is accomplished by the inclusion of a 48.5 Kb DNA fragment in the DNA ladder. Figure 1 shows a standard separation of the Extended Genomic DNA Ladder.

Figure 1
Figure 1. Extended Genomic DNA Ladder (DNF-367) separated on a Fragment Analyzer equipped with a Short Capillary Array (33-55) using the Genomic DNA 50 Kb Analysis Kit (DNF-467).

A separation of a standard genomic DNA sample is shown in Figure 2. An important feature in PROSize® for the rapid and efficient analysis of sample quality is the Genomic Quality Number (GQN). The GQN provides users with an adaptable measurement for sample quality. By manually setting a threshold for genomic DNA quality, users are able to define what good quality DNA is for their specific application. Genomic preparations vary in quality – based on myriad factors ranging from technique employed to source material – to a point that a fixed quality metric is limited in scope. In Figure 2, a threshold of 10 Kb (indicated by the dotted blue line) was set with a resulting GQN of 7.9. Allowing users to define, what they believe is, good quality DNA for their application enhances the versatility of this analysis.

Figure 1
Figure 2. A typical genomic DNA sample separated on a Fragment Analyzer equipped with a Short Capillary Array (33-55) using the Genomic DNA 50 Kb Analysis Kit (DNF-467). The sample had a GQN of 7.9 with a user-defined threshold of 10,000 Kb.

Additionally, the Genomic DNA 50 Kb Analysis Kit can be used to evaluate degraded samples, such as FFPE genomic DNA. The quality of FFPE samples are dependent on numerous factors including amount of time the sample was incubated in formalin and the physical size of the tissue sample. Figure 3 provides two examples of an FFPE genomic DNA sample. As the factors influencing DNA quality vary sample to sample, a common degradation pattern is not typical.

Figure 3a
Figure 3b
Figure 3. Two examples of an FFPE genomic DNA sample separated using the Genomic DNA 50 Kb Analysis Kit on a Fragment Analyzer fitted with a standard short capillary array (33-55).

The quantification precision and accuracy of the Genomic DNA 50 Kb Kit is shown in Figure 4. Samples were measured by a fluorometric instrument and Fragment Analyzer using this kit, with the measured concentrations for each instrument then plotted against each other. The graph clearly shows a near perfect one to one ratio, indicating that both methods produce equivalent measurements.

Figure 5
Figure 4. Fluorometric instrument concentration plotted against Fragment Analyzer concentration. The concentration values were obtained from the same samples.