PDA Technical Glossary
PDA Technical Reports are highly valued membership benefits because they offer expert guidance and opinions on important scientific and regulatory topics and are used as essential references by industry and regulatory authorities around the world. These reports include terms which explain the material and enhance the reader’s understanding.
The database presented here includes the glossary terms from all current technical reports. The database is searchable by keyword, topic, or by technical report. Each definition provided includes a link to the source technical report within the PDA Technical Report Portal.
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Endpoint PCR
A classical PCR method based on repeated cycling of the reaction mixture between two or three temperatures (denaturing, annealing, and extension) with detection of the amplified product after reaction completion (e.g., by agarose gel electrophoresis). (TR50)
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Extraction Control
A known test article processed with a nucleic acid extraction procedure in order to ensure the proper extraction of nucleic acid. (TR50)
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Extraction Recovery
The efficiency of extraction of target analyte from a test matrix. It is usually measured as ratio (percentage) of analyte amount extracted from the matrix to that originally present in the matrix before extraction. (TR50)
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Genome Copy (GC)
An amount of nucleic acid equivalent to the genetic complement present in the genome of a single microorganism. (TR50)
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Hybridization
The formation of a double-stranded complex of complementary strands of nucleic acids (e.g., a primer and single-stranded DNA or RNA) (TR50)
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Internal Control
A reaction performed to provide confirmation of adequate performance of the NAT assay including preparation of nucleic acid, its amplification using appropriate amplification technology, and analysis of amplified products. An example is the amplification of a housekeeping gene from the production cell line which provides a positive signal even in the absence of contaminant DNA. (TR50)
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Matrix Spike Control
An internal control in which an amplifiable amount of nucleic acid is added to a test article to determine inhibition of the PCR. This addition is usually performed pre-extraction and should provide a weak signal 100% of the time. Also known as “interference control”. (TR50)
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Melting Temperature (Tm)
The calculated or observed temperature for a primer/nucleic acid mixture at which 50% of primer-binding sites are in single strand form. (TR50)
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Nucleic Acid Sequence Based Amplification (NASBA)
An isothermal amplification method targeting RNA in which amplifications of RNA occurs via DNA intermediates. Each of the DNA templates can make 100 to 1000 copies of RNA amplicons, potentially resulting in the production of greater than a billion amplicons. (TR50)
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Nucleic Acid Standard
A sample with a precisely measured content of specific nucleic acid. A nucleic acid standard can be serially diluted to assess the limit of detection of an NAT assay or to create a standard curve for Q-PCR to determine the concentration of target nucleic acid. (TR50)
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Plasmid
An extra-chromosomal DNA molecule in bacteria which is capable of replicating independently of the host chromosomal DNA. Plasmids are often used as positive controls for NAT assays. (TR50)
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Primer
A short synthetic single-stranded nucleic acid complementary to a specific sequence of a target gene, DNA or RNA. It usually serves to initiate the de novo synthesis of nucleic acid from a template. (TR50)
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Q-PCR Probe
A synthetic, chemically-labeled single-stranded nucleic acid complementary to a selected sequence within a DNA sequence to be amplified using forward and reverse primers in a Q-PCR reaction. A probe is typically labeled with both a fluorophor and quencher. The latter inhibits fluorescence until the quencher and fluorophore are separated by the exonuclease activity of DNA polymerase. (TR50)
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Reporter Gene
A coding sequence linked to a gene or promoter of interest. It is generally used to determine activation of the promoter or expression of the gene of interest in a cell or organism. (TR50)
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Reverse Transcriptase PCR (RT-PCR)
A technique for amplifying a defined segment of a RNA molecule. The RNA is first reverse-transcribed into complementary DNA (cDNA), followed by amplification of the cDNA using PCR. (TR50)
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Touchdown PCR
A technique to reduce appearance of non-specific amplicons in PCR reactions. The earliest cycles of a touchdown PCR method have high annealing temperatures. The annealing temperature is decreased in increments for subsequent cycles until a fixed point is reached. (TR50)
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Transcription-Mediated Amplification (TMA)
An isothermal NAT method that can amplify RNA or DNA targets a billion-fold in less than one hour. TMA technology uses two primers and two enzymes: RNA polymerase and reverse transcriptase. (TR50)