Genomic DNA Quality Control Analysis

Genomic DNA Quality Control Analysis

First isolated in the mid-1800s, genomic DNA (gDNA) comprises of the chromosomal DNA of an organism. It contains all an organism’s biological information to direct its cellular function, which is also passed on to the next generation.

The gDNA sequence carries information organized in genes and other discrete genetic elements, which researchers can access by isolating genetic material and sequencing or manipulating it. This access is regulated by the genome’s organization or structure, and chemical and physical modifications to the DNA, including the associated binding of small molecules and proteins. Genomic analysis helps scientists better understand the functions, interactions, and regulation of specific genes that control the development of an organism.

Whether your research application uses next-generation sequencing (NGS), gene editing, cloning, or genotyping, beginning your experiments with high-quality, high-integrity DNA helps ensure robust results.

Agilent offers a portfolio of solutions for gDNA quality analysis, including instruments, reagent kits, and software to enable you to successfully assess DNA size, integrity, and concentration. Achieve reliable results with automation and scalable throughput.

Genomic DNA Quality Control Analysis you can rely on

Molecular biologists and geneticists employ many applications that require gDNA and high-quality DNA samples to generate reliable, robust results. Assessment of sample quality is important.

The Agilent Automated Electrophoresis portfolio includes a range of instruments that offer advantages in terms of throughput scalability, sensitivity, speed, and resolution. Read on to find out how you can conduct superior assessment of intact gDNA, including accurate qualification, sizing, and quantification.

Increase Throughput with Fragment Analyzer Systems

Agilent’s Fragment Analyzer systems provide you with robust gDNA analysis solutions to fit any throughput need – from 12 samples in about one hour, to over 2,400 samples in 24 hours.

There are two kits designed to analyze gDNA:

• The Genomic DNA 50 kb kit (p/n DNF-467) provides confident assessment of gDNA smears through 60 kb. A single 200-fold dilution greatly simplifies sample preparation, conserving researcher time.
• The HS Genomic DNA 50 kb kit (p/n DNF-468) offers sizing of gDNA smears through 60 kb, for lower concentration samples.

GQN: An Empirical Assessment of Quality

Agilent’s fragment analysis solutions allow for easy and empirical assessment of gDNA quality with a dynamic quality metric. ProSize data analysis software calculates a Genomic Quality Number (GQN) for the gDNA smear as a value between 0 and 10, simplifying comparison of quality.

Smear Analysis To Improve Accuracy And Precision

Agilent’s fragment analysis solutions also support specific analysis of concentration and size (bp) of gDNA smears within a user-defined sizing range. The Smear Analysis function provides researchers with the accuracy and precision demanded by downstream applications.

Simplified Electrophoresis with Agilent TapeStation systems

High-quality input gDNA samples are essential for downstream applications, such as NGS.

The TapeStation systems offer easy and fast automated electrophoretic separations of genomic DNA. This is supplemented by the Genomic DNA ScreenTape assay (p/n 5067-5365 and 5067-5366), which provides accurate quantitation and reliable quality analysis of up to 96 samples from 200 through 60,000 bp in less than two minutes per sample.

The TapeStation software provides an an automated and objective quality score, the DNA integrity number (DIN). The DIN ranges from 1 to 10 and indicates the quality of a gDNA sample by assessing its distribution across the entire sizing range. A lower DIN correlates to more degraded sample, while a high DIN would indicate a good quality sample, allowing researchers to make more informed decisions.

Detailed information and accurate sizing of gDNA

For applications that require more detailed information and accurate DNA sizing above 60 kb, such as long read sequencing, the Femto Pulse system is ideal. A meticulously designed optical detection platform with unprecedented sensitivity, the Femto Pulse system is flexible enough to handle any workflow scenarios. The Genomic DNA 165 kb kit (p/n FP-1002) uses pulsed-field capillary electrophoresis, to size high molecular weight gDNA smears through an unprecedented 165 kb, in about 1.5 hours.

Additionally, the ProSize data analysis software tools used with the Fragment Analyzer systems can be used with the large gDNA smears analyzed on the Femto Pulse system. This provides you with even more detailed information about high molecular weight samples.

Sensitive Analysis of Degraded and FFPE gDNA

gDNA that has been fragmented or degraded – for instance, formalin-fixed, paraffin-embedded (FFPE) gDNA – presents unique challenges for QC analysis. Quality scoring of FFPE gDNA and degraded gDNA is complex, often requiring researchers to make a best guess when using conventional agarose gel electrophoresis.

For instance, gDNA extracted from FFPE tissue often undergoes shearing and cross-linking with proteins and other molecules, frequently resulting in a complex and convoluted separation profile. Agilent’s range of automated electrophoresis systems, including the Fragment Analyzer, TapeStation, and Femto Pulse systems enable researchers to extract reliable results even from FFPE gDNA.

While FFPE gDNA generally has a lower integrity, knowing the quality of the sample can allow a user to modify certain workflows for these samples. For example, fragmentation conditions could be adapted based on a sample’s initial integrity. Agilent’s fragment analysis and Femto Pulse solutions allow for accurate assessment of FFPE gDNA quality and integrity with two metrics: the Genomic Quality Number, and the DNA integrity number.

The ProSize data analysis software calculates a Genomic Quality Number (GQN) for the gDNA smear as a value between 0 and 10, enabling an empirical quality scoring strategy. The Genomic DNA ScreenTape assay for the TapeStation systems provides an objective measurement of DNA integrity through the DNA integrity number (DIN).

Discover Agilent’s comprehensive portfolio of Genomic DNA (gDNA) Analysis Kits

Agilent offers several instrument-based solutions for the effective and reliable analysis of gDNA. The Fragment Analyzer, TapeStation, and Femto Pulse systems, with the appropriate assays and reagent kits, provide superior analysis with unmatched resolution and sizing capabilities.

Instrument	Part Number	Reagent Kit Name	Sizing Range	Quantitative Range	Quality Metric
Fragment Analyzer systems	DNF-467-0500	Genomic DNA 50 kb kit	75 to 60,000 bp	25 to 250 ng/µL	GQN
	DNF-468-0500	HS Genomic DNA 50 kb kit	75 to 60,000 bp	0.3 to 12 ng/µL	GQN
TapeStation systems	5067–5365 5067-5366	Genomic DNA ScreenTape Genomic DNA reagents	200 to >60,000 bp	10 to 100 ng/µL	DIN
Femto Pulse system	FP-1002-0275	Genomic DNA 165 kb kit	1,300 to 165,000 bp	Fragment: 5 to 500 pg/µL Smear: 0.3 to 30 pg/µL	GQN

Read more about gDNA analysis in our application notes.

Assessment of Genomic DNA Quality with the Agilent 5200 Fragment Analyzer System

The Agilent 5200 Fragment Analyzer offers effortless analysis of genomic DNA (gDNA) with the Genomic DNA 50 kb Kit and the HS Genomic DNA 50 kb Kit.

Genomic DNA Sizing and Quality Control on the Agilent Femto Pulse System

Separation of HMW gDNA, providing accurate, reproducible sizing and quality control using the Agilent Femto Pulse System.

Genomic DNA Extractions Compared with the Agilent Femto Pulse System

The Agilent Femto Pulse system is the only automated system capable of replacing overnight PFGE analysis of HMW gDNA in only 70 minutes, saving time and money.

Quality Assessment of Genomic DNA for Biobanking Samples with the Agilent Femto Pulse System

The Agilent Femto Pulse System is the only instrument capable of replacing pulsed-field gel electrophoresis for the analysis of high molecular weight (HMW) gDNA.

Use of the Agilent 4200 TapeStation System for Sample Quality Control in the Whole Exome Sequencing workflow at the German Cancer Research Center (DKFZ)

QC steps including quantification and qualification of the DNA, and can be done with the 4200 TapeStation System.

Retrospective Quality Analysis of DNA Samples from the Heidelberg CardioBiobank

This Application Note demonstrates the use of the Agilent 4150 TapeStation system as a quality control (QC) tool to analyze DNA samples stored at the Heidelberg CardioBiobank (HCB).