eBook: Optimizing Results from Nucleic Acid Isolation - 8

notable exceptions are formalin-fixed paraffin-embedded (FFPE) samples and blood collection cards.

racks and stations, microplate stacking, etc. with
robotic systems. Advantages of automation include consistent protocol repetition and handsoff time for lab personnel to attend to other tasks.
Automated systems for nucleic acid extraction automation fall into two categories: multiple-purpose
automation platforms and systems dedicated to
nucleic acid extraction.

Worldwide archives of FFPE tissues with associated
clinical histories represent a highly valuable source
of material for biomedical research. However, the
formalin fixation process, originally conceived to
preserve microscopic detail at the multi-cellular
level, is damaging to nucleic acids. The process of
nucleic acid extraction is further complicated by
the requirement of de-paraffinizing samples to release cells for analysis.

Many makers of multi-functional benchtop robotic
systems have worked out hardware control software that automates protocols found in the user
guides of nucleic acid extraction kits. In addition to
the general advantages of automation, these versatile systems allow the possibility of integrating
a nucleic acid extraction protocol with the downstream application for which the extracted material
is intended. Referring to the company's benchtop
automation product, Bruce Jamieson of Hudson
Robotics said, "The SOLO system supports extracted DNA normalization with an OD plate reader. We
can attach a thermal cycler on the deck and do PCR.
We've automated full NGS library prep processes,
and we just competed a successful validation of the
Lucigen NGS kits."

Kits for nucleic acid extraction from FFPE samples
represent an active area of product development,
which will ultimately enable large retrospective
studies. Recently, a research group conducted a
rigorous comparison of seven commercial kits for
the extraction of nucleic acids from FFPE samples.
While all but one of the kits tested were of the
"spin-column" variety, there were greater differences among the kits relative to de-paraffinization
methods, functional capture surfaces, and buffer
compositions. The study, published this year in Plos
One, found "variable quantity, quality, and performance of the isolated nucleic acids extracted by the
kits tested. In the open-access article, the authors
provided useful information to enable researchers
to select the "optimal procedure" for a given sample
type and intended downstream application.

Dedicated devices for nucleic acid extraction take
up less space and are tightly linked and optimized
for use with a limited number of kits. Makers expand the capabilities of these systems by developing compatible new kits and protocols.

Blood collection cards are composed of plain filter
paper, or the same paper treated with a chemical
mixture for biomolecule preservation. Preserved
blood samples spotted onto the cards can be stored
for lengthy periods of time or else transported at
ambient temperature until the extraction process
is performed.

Special applications
Typically, cell collection and lysis are carried out as
immediately prior to the purification steps detailed
above as possible in order to minimize loss of nucleic acid yield or quality due to degradation. Two

8


https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0197456

eBook: Optimizing Results from Nucleic Acid Isolation

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eBook: Optimizing Results from Nucleic Acid Isolation - 1
eBook: Optimizing Results from Nucleic Acid Isolation - Contents
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