Agilent eBook - 3

Introduction

Q

uality control (QC) assessment is essential to the success
of all nucleic acid workflows. Without performing reliable
QC steps, the results of downstream applications can be
compromised, costing you precious time and resources. The Agilent
Fragment Analyzer and Femto Pulse systems, along with the Agilent
ProSize data analysis software, provide reliable sizing and quantification
of nucleic acid fragments and smears for various applications
including PCR, genomic DNA, and NGS library preparations. However,
as discussed in this book, certain practices can drastically improve
the consistency and accuracy of your results.
This collection of application notes provides the best practices utilized
by Agilent for reliable QC analysis and an in depth discussion about the
importance of sample quality control during library preparation.
The first application note, Best Quantification Practices with the Agilent
5200 Fragment Analyzer System, compares different mixing techniques
as well as the effects of no mixing on sample quantification. For best
measurement practices, it is important to choose the correct analysis
kit based on the type, size, and concentration of your specific sample,
while following the recommended sample mixing practices listed in the
kit's manual. Diluting the sample with the correct buffer also ensures
consistent, accurate results.
Reliable sizing of nucleic acids is just as essential as quantification
during quality control analysis. The second application note, Best Sizing
Practices with the Agilent 5200 Fragment Analyzer System, discusses
how to obtain the most accurate sizing on the Fragment Analyzer
systems. In particular, the differences between peak size and smear

size are examined. ProSize software automatically provides peak size,
which is ideal for fragments, while the ProSize Smear Analysis tab
provides an average size for smears based on the distribution of the
sample over the smear range designated by the user.
The use of independent quality metrics is another important practice
that is essential to the success of nucleic acid workflows. Quality
metrics remove individual scientists' biases during quality control
analysis. Agilent has developed metrics for both RNA and DNA
samples. These metrics, along with their uses, are discussed in the
final application note, Quality Metrics for Nucleic Acids with the Agilent
Fragment Analyzer and Femto Pulse Systems. Evaluating DNA, RNA
and genomic DNA quality and integrity is simplified with these quick
and user-friendly metrics. Their versatility allows them to be applied
to various samples from different organisms, providing reliable
assessment of nucleic acid quality and integrity. Following the
practices described in this collection will enable researchers to have
confidence in the outcomes of their downstream applications.
At the end of the book, Kyle Luttgeharm, PhD, discusses the importance
of sample QC during library preparation in his interview with GEN. Dr.
Luttgeharm is the product manager for the Agilent parallel CE instruments
and has extensive knowledge in this field. During the interview, he
addresses a few important topics when it comes to the QC analysis of
NGS libraries, that will help ensure successful sequencing results.
We hope you enjoy this book and all the best practices it contains. By
following these practices, you can improve your nucleic acid workflow
quality control analysis and achieve results you can be proud of.
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Agilent eBook

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