Agilent 2019 - 23

Automated Nucleic Acid Sample Quality Control in NGS Workflows

Incoming gDNA QC

23

| GENengnews.com

A
[bp]

B
B4 C4 D4 E4

F4

G4 H4 A5 B5 C5 D5 E5

F5

G5 H5

400

48,500
15,000
7,000
4,000
3,000
2,500
2,000
1,500
1,200
900
600
400

300

200

100

250

900
1,200
1,500
2,000
2,500
3,000
4,000
7,000
15,000
48,500

600

400

DIN DIN DIN DIN DIN DIN DIN DIN DIN DIN DIN DIN DIN DIN DIN
2.9 4.9 3.9 3.1 2.6 1.5 4.4 4.4 3.2 3.6 2.5 2.3 3.3 3.7 3.5

250

0

100

100

Figure 2 shows a representative subset of the data
collected on the 4200 TapeStation system with the
Genomic DNA ScreenTape assay. gDNA samples
extracted from FPPE material are often of low
DNA integrity, but can still be sufficiently intact for
whole exome library preparation and successful
sequencing. Depending on the quality of the DNA
material, modified fragmentation protocols can be
applied for optimized results.

500

Sample intensity [FU]

To determine if the samples were suitable for
library preparation, a QC was performed at the
beginning for the batch of 88 gDNA samples
from FFPE tumor tissue by the High Throughput
Sequencing Unit. This initial QC includes
quantification and analysis with a 4200 
TapeStation system and the Genomic DNA
assay to determine DNA quality based on the
DNA integrity number (DIN). The DIN algorithm is
included in the 4200 TapeStation software, and
provides a numerical assessment of the DNA
sample by assigning a numerical score for DIN
from 1 to 10. A high DIN indicates highly intact
gDNA, and a low DIN a strongly degraded
gDNA sample.

Size (bp)

Figure 2. QC for gDNA extracted from FFPE tissue was performed by using the Agilent 4200 TapeStation system and the Agilent Genomic DNA
ScreenTape assay. A) The gel image of 15 samples with the determined DIN on bottom and the well on top of each lane are shown. B) An overlay of the
electropherograms of 15 samples. Both views enable to compare and visualize the integrity of the samples.



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Agilent 2019

Table of Contents for the Digital Edition of Agilent 2019

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