GENOMIC DNA continued
Figure 3 – Screenshot of the automatically launched analysis file for Genomic DNA ScreenTape by the 2200 TapeStation software. The gel image shows DNA-extracted FFPE samples from different tissues: lane 1, ladder; lanes 2 and 3, prostate; lanes 4–7, pancreas; lanes 8 and 9, endo- cervix; lanes 10 and 11, lung; lanes 12 and 13, kidney; lanes 14 and 15, bladder. (Data courtesy of Dr. Toumy Guettouche, Hussman Institute for Human Genomics, Genomics Core, University of Miami, FL.)
a
Figure 5 – The sample comparison function of the 2200 TapeStation soft- ware allows a direct comparison of multiple samples from multiple files to ensure consistent sample quality over time.
whether the sample analyzed was outside the recommended concentra- tion range (10 ng/µL–100 ng/µL).
The export function of the 2200 TapeStation software permits access to the gel images in .jpeg format. Figure 4 shows two exported gel images from breast tissue FFPE samples (Figure 4a) and human DNA extracted from FFPE blocks (Figure 4b). This gel image is superior to those generated by agarose gel and allows a visual check of the FFPE sample molecular weight and integrity. In contrast to an agarose gel, however, the image was generated in less than 2 min per sample with only a few minutes’ hands-on time and no exposure to harmful chemicals. In addition, the results generated are extremely reproducible due to the prepackaged and therefore standard- ized separation gel and buffers contained in the ScreenTape channels.
b
In addition to the gel image, the software provides sample electrophero- grams and the ability to compare profiles from multiple samples in multiple files (Figure 5). This feature is invaluable for comparing successful and unsuc- cessful samples from previous NGS or aCGH experiments to current sample preparations and extractions.
Conclusion The 2200 TapeStation system is a novel method for determining the con-
Figure 4 – a) Gel image export with optional sample well of DNA- extracted FFPE samples from breast tissue (courtesy of Dr. Toumy Guettouche). b) Gel image scaled to molecular weight range of human genomic DNA extracted from FFPE blocks (courtesy of Agilent Technologies, Uppsala, Sweden).
The data table details, as default, the start and end of the sample in base pairs as well as the molecular weight size of the peak maxima. Concentration details in ng/µL are also provided with an accurate determination of the double-stranded DNA in each sample. Additionally, the software will flag
centration, integrity, and molecular weight size of FFPE genomic DNA in one step using only 1 µL of starting material. The technology automates a manual, laborious process and reduces hands-on time and overall time to result from ~2 hr to less than 2 min per sample. The system analyzes genomic DNA in the concentration range of 10 ng/µL–100 ng/µL and has a sensitivity of 0.5 ng/µL. The Genomic DNA ScreenTape, combined with the 2200 TapeStation, offers speed, scaleability, and simplicity to the genomics researcher performing NGS and aCGH assays with FFPE samples.
Donna McDade Walker, Ph.D., is Product Marketing & Support Manager, Agilent Technologies UK Limited, 5 Lochside Ave., Edinburgh Park, Edin- burgh EH12 9DJ, U.K.; tel: +44 (0) 131 452 0715; e-mail:
donna.mcdade-
walker@agilent.com.
AMERICAN LABORATORY • 14 • SEPTEMBER 2013
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