eBook: Optimizing Results from Nucleic Acid Isolation - 26

Table 1. Summary table for the sources of nucleic acids available within various clinical biological sources, as well as the advantages
and disadvantages
Sample type Description

Fresh frozen
tissue block

After surgical excision,
tissues are snap-frozen
in liquid nitrogen. These
specimens are stored
in liquid nitrogen or
designated -150°C
freezers before use.

Following surgical
collection, tissue
samples are fixed in
Formalinformalin and paraffinfixed paraffin
embedded. They are the
embedded
most common source
(FFPE) block
of archived material
and stored at room
temperature.

Liquid
biopsy

A liquid biopsy is the
sampling and analysis
of non-solid tissue (e.g.,
blood). These samples
are routinely collected
and do not require
immediate processing
or storage.

Advantages and disadvantages
Advantages
* Rapid extraction process.
* Less time, effort, and expertise required for sample preparation.
* Samples are well suited for molecular biology assays.
* Range of standardized protocols and reagents for sample processing and nucleic acid isolation.
* Isolated nucleic acids are very high quality and concentration.
Disadvantages
* Invasive process to collect sample.
* Highly temperature sensitive.
* Large specialist equipment requirement for long-term storage.
* Collected samples need to be frozen as soon as possible following collection. Thawing
samples can lead to loss of sample and degradation of nucleic acids.
* Limited number of fresh frozen samples available in biobanks.
Advantages
* Extremely large biobanks with many historical samples.
* Very stable, allowing long-term, room temperature storage.
* Low cost of storage.
* FFPE preserves tissue structure, excellent for morphology studies.
* Large quantities of nucleic acids can be collected from FFPE blocks.
* Range of kits and reagents available to isolate nucleic acids.
Disadvantages
* Invasive process to obtain sample.
* Formalin is toxic and denatures proteins within the sample.
* Time consuming fixation and paraffin-embedding process.
* Nucleic acids are preserved poorly and can degrade, often requiring repair and amplification.
* Lack of standardization of FFPE protocol due to sample age(s) in biobanks.
* Variation in preparation due to collection at different times and locations by different personnel.
Advantages
* Minimally invasive and rapid process to collect diverse range of samples.
* Sample collection can be repeated at multiple time points (i.e., throughout treatment).
* Nucleic acids isolated are high quality.
* Nucleic acids are highly suitable for downstream molecular biology assays (e.g., NGS).
Disadvantages
* Ultra-low concentration of nucleic acids in each sample.
* High-fidelity reagents and expertise required to isolate, amplify, and measure nucleic acids.
* Reagents and systems are currently expensive.
* No standardized methodology for processing liquid biopsy.

eBook: Optimizing Results from Nucleic Acid Isolation

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