Skip To The Main Content

PDA Glossary

PDA Glossary of Pharmaceutical and Biotechnology Terminology

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.

Browse Terms by Title


Browse Terms by TR #

  • Amplicon

    A segment of double stranded DNA formed as the product of polymerase chain reaction or other amplification based techniques such as TMA or NASBA. (TR50)

  • Annealing Temperature

    A temperature designed to allow primers to attach to single-stranded DNA or RNA to initiate amplification. The annealing temperature is usually kept a few degrees lower than the melting temperature of the primers to avoid non-specific amplification. See “Melting Temperature”. (TR50)

  • CFU: Genome Copy Ratio

    The relationship between the number of colony forming units counted on solid media and the number of genome copies measured using a method suitable for quantitative assessment of genomic DNA. (TR50)

  • Colony Forming Unit (CFU)

    One or more microorganisms that produce a visible, discrete growth entity on a semi-solid, agar-based microbiological medium. (TR22) (TR62)

    Visible outcome of growth of microorganisms arising from a single or multiple cells. (TR28)

    A single microorganism or an aggregate of many that forms a single discrete colony on solid agar media after suitable incubation. Colony forming units are used for bacterial titer (total bacteria load in a sample) determination on solid media. (TR50) (TR75)

  • Color Changing Unit (CCU)

    The quantity of mycoplasma contained in the highest dilution of a test article that produces a color change in a pH-sensitive liquid medium (typically containing phenol red) within a specified time of incubation, used for end-point determination of growth. (TR50)

  • Comparability Study

    An assessment of the similarities between the critical parameters and output results of two or more separate processes or methods. (TR50)

  • 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)

  • Extraction Control

    A known test article processed with a nucleic acid extraction procedure in order to ensure the proper extraction of nucleic acid. (TR50)

  • 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)

  • Fastidious strain (isolate)

    A population of microorganisms having complex nutritional requirements and thus difficult to cultivate. (TR50)

  • Genetic Marker

    A gene or DNA sequence within a chromosome which can be used for discrimination of one mycoplasma species or strain from another. (TR50)

  • Genome Copy (GC)

    An amount of nucleic acid equivalent to the genetic complement present in the genome of a single microorganism. (TR50)

  • Harvest Testing

    The screening of a biopharmaceutical bulk cell culture harvest for any adventitious contaminants, including mycoplasma, before further processing. (TR50)

  • 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)

  • 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)

  • In-vitro Transcribed RNA

    A RNA copy synthesized using a double-stranded DNA as template. The RNA polymerases of bacteriophage T7 or SP6 are usually used to perform the in-vitro transcription. (TR50)

  • Limit of Detection (LOD)

    The lowest concentration of microorganisms in a test sample that can be detected, but not necessarily quantified, under the stated experimental conditions. (TR33)

    The lowest amount of analyte in a sample that can be distinguished from the absence of analyte. (TR41)

    The lowest concentration of analyte that can be unambiguously detected in a sample. For qualitative and for quantitative NAT methods, this value is conventionally expressed as a 95% positive cut-off value, representing the target concentration detected in 95% of repeated tests using a certain assay. (TR50)

  • Limit Test

    A quantitative test designed to give a positive/negative response. Ideally, a limit test has a high degree of specificity and a low limit of detection. (TR50).

  • Magnetic Capture Hybridization (MCH)

    A purification method based on sequence-specific hybridization of labeled nucleic acid probes with targeted regions of test article nucleic acids, followed by magnetic bead capture. (TR50)

  • 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)

  • 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)

  • Mollicutes

    A class of bacteria which lack a cell wall. Mollicutes are small, typically about 0.1-0.5 &;mum in size, and vary in form (trivial name: mycoplasma) (TR50)

  • Negative Control

    A test article used to assess the performance of an assay in the known absence of a targeted microorganism or nucleic acid. Negative controls are used to minimize a risk of false positive results, which could occur due to non-specific signals. (TR50)

  • Nucleic Acid Amplification Technique (NAT)

    A method for detection, and in some cases, quantification of target organisms via detection of organism specific nucleic acid. PCR or polymerase chain reaction is a common NAT method that is based on amplification of targeted sequences using primers and specialized DNA polymerases. (TR50)

  • 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)

  • 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)

  • Occult Contamination

    A cell culture contamination not immediately apparent by visual inspection or other obvious indicators. (TR50)

  • 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)

  • Positive Control

    A test article used to assess the performance of an assay in the known presence of a targeted microorganism or nucleic acid. A positive control is used to monitor the performance of assay routinely and during validation. For culture-based assays, a live mycoplasma preparation must be used to show that the assay was run properly. NAT positive controls use a nucleic acid with the target sequence of interest. (TR50)

  • 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)

  • Psoralen

    A class of UV photoactivated chemicals able to covalently modify nucleic acids. Psoralens may be used to reduce contaminating nucleic acid in NAT reagents. (TR50)

  • 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)

  • Reference Standard

    A characterized biological material developed to monitor the performance of an assay. For example, the standards for NAT assays may be nucleic acid templates such as plasmids, genomic DNA, cellular or in vitro synthesized RNA. (TR50) The defining characteristics of a reference standard are:
    1) it is stable;
    2) it performs similarly (e.g., on dilution) to test materials in the assay; and
    3) it is homogeneous. (TR57)

    A reference standard, or reference material, is a substance prepared for use as the standard in an assay, identification, or purity test. It should have a quality appropriate to its use. It is often characterized and evaluated for its intended purpose by additional procedures other than those used in routine testing. For new drug substance reference standards intended for use in assays, the impurities should be adequately identified and/or controlled, and purity should be measured by a quantitative procedure. (TR63)

  • Reference Strain

    A well characterized, widely accepted preparation of viable organisms that is used to validate a microbiological assay. (TR50)

  • 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)

  • 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)

  • Specificity

    The ability of an analytical procedure to accurately measure or detect a target analyte in the presence of other components in the sample matrix. (TR50)

    The ability to assess unequivocally the analyte in the presence of components that may be expected to be present. Typically these might include impurities, degradants, matrix, etc. Lack of specificity of an individual analytical procedure may be compensated by other supporting analytical procedure(s). (TR57)

    The ability to detect a range of microorganisms, which demonstrate that the method is fit for its intended use. (TR33)

  • Targeted Species

    The range of species for which detection or analysis is aimed for by an assay method. (TR50)

  • Thermocycling

    Repetition of the PCR reaction steps of denaturing, annealing, and extension. Each step is characterized by different temperatures and reaction times. Some PCR methods combine the annealing and extension steps (i.e., two step PCR). (TR50)

  • Toll-like Receptor (TLR)

    A class of single membrane-spanning non-catalytic receptors that recognize structurally conserved molecules derived from microbes. They can activate immune cell responses when microbes have breached physical barriers such as the skin or intestinal tract mucosa. (TR50)

  • 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)

  • 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)

  • Transfectoma

    Cells expressing exogenous proteins or reporter genes, produced by the transfection of continuously growing cells with gene expression constructs. (TR50)

  • Validation Reference Standards

    Reference standard preparations used for method validations. (TR50)