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PCR & Gene Amplification Glossary & taxonomy

Evolving terminologies for evolving technologies
Questions? Revisions? Comments?
Mary Chitty MSLS
Last revised July 03, 2019

What are the odds we'll be able to amplify dinosaur DNA? See Jurassic Park and PCR

Technologies  term index   Related glossaries include Combinatorial libraries & synthesis,   Labels, Signaling & Detection, Microarrays,  PCR is a key technology for, and an important tool for molecular diagnostics and Sequencing   Biology Gene definitions,    DNA,   Sequences, DNA & beyond 

Agglutination-PCR (ADAP): an ultrasensitive solution-phase method for detecting antibodies.[1] Antibodies bind to and agglutinate synthetic antigenDNA conjugates, enabling ligation of the DNA strands and subsequent quantification by qPCR. Like other Immuno-PCR (IPCR) detection methods[2][3] ADAP combines the specificity of antibody-antigen recognition and the sensitivity of PCR. ADAP detects zepto- to attomoles of antibodies in 2 μL of sample with a dynamic range spanning 5–6 orders of magnitude. For example, ADAP allows to detect anti-thyroglobulin autoantibodies from human patient plasma with a 1000-fold increased sensitivity over an FDA-approved radioimmunoassay. ADAP also allows to simultaneously detect multiple antibodies in one experiment, much more than ELISA or radioimmunoassay. Wikipedia accessed 2018 Nov 8

Amplified Fragment Length Polymorphism Analysis: The detection of RESTRICTION FRAGMENT LENGTH POLYMORPHISMS by selective PCR amplification of restriction fragments derived from genomic DNA followed by electrophoretic analysis of the amplified restriction fragments.  MeSH 2008

ASO probe (Allele Specific Oligo): The sequence of the oligo is designed in such a way to allow/ inhibit hybridization in the spot where the mutant (resistant) allele differs from the wild type (susceptible) allele. [Schlwindlein]

absolute quantification: To express true value, scientists (including the author) have been using absolute quantification … it does not appear to be a good fit for gene quantification, and thus the use of this terminology should be discouraged … at this low level, a probability rather than an absolute number defines the true copy number value for a given sample.  Francois. Ferré “Key issues” Gene Quantification Birkhauser 1998

Attempts to state the number of copies of a specific RNA per cell or unit mass of tissue.  Requires a number of extra conditions and treatments that relative quantification does not.  WM Freeman et al “Quantitative RT-PCR: Pitfalls and Potential” Biotechniques 26: 112-125 Jan 1999 Related term: relative quantification.

Agglutination-PCR (ADAP): an ultrasensitive solution-phase method for detecting antibodies.[1] Antibodies bind to and agglutinate synthetic antigenDNA conjugates, enabling ligation of the DNA strands and subsequent quantification by qPCR. Like other Immuno-PCR (IPCR) detection methods[2][3] ADAP combines the specificity of antibody-antigen recognition and the sensitivity of PCR. ADAP detects zepto- to attomoles of antibodies in 2 μL of sample with a dynamic range spanning 5–6 orders of magnitude. For example, ADAP allows to detect anti-thyroglobulin autoantibodies from human patient plasma with a 1000-fold increased sensitivity over an FDA-approved radioimmunoassay. ADAP also allows to simultaneously detect multiple antibodies in one experiment, much more than ELISA or radioimmunoassay. Wikipedia accessed 2018 Nov 8

amplicon: In molecular biology, an amplicon is a piece of DNA or RNA that is the source and/or product of amplification or replication events. It can be formed artificially, using various methods including polymerase chain reactions (PCR) or ligase chain reactions (LCR), or naturally through gene duplication. In this context, amplification refers to the production of one or more copies of a genetic fragment or target sequence, specifically the amplicon. As it refers to the product of an amplification reaction, amplicon is used interchangeably with common laboratory terms, such as "PCR product." Wikipedia accessed 2018 Feb 26

amplification: Narrower terms: gene amplification, kinetic PCR, kinetic RT- PCR, LCR, microamplification, NASBA, nested PCR, nucleic acid amplification, protein amplification, RNA amplification, transcript mediated amplification, target amplification; signal amplification; RNA amplified antisense RNA;   

amplimer:  A piece of DNA formed as the products of natural or artificial amplification events, as in a polymerase chain reaction. Wiktionary

anneal:  to be capable of combining with complementary nucleic acid by a process of heating and cooling. Meriam Webster

branched DNA bDNA: Direct detection of target sequences by hybridization with a branched DNA probe and target specific oligonucleotides. Alkaline phosphatase- conjugated oligonucleotides, complementary to the branched DNA complex, are detected using a chemiluminescent substrate. Whereas PCR amplifies target sequences, the bDNA assay amplifies signal. Urdea, M.S. et al. Clinical Chemistry 35, 1571, 1989 Promega

branched DNA signal amplification assay: A molecular probe technique that utilizes branched DNA (bDNA) as a means to amplify the hybridization signal. One end of the bDNA molecule is designed to bind a specific target, while the other end of the bDNA molecule contains many branches of DNA that are designed to bind a probe used for signal detection. MeSH, 2001

capture probe: Phage or antibody probes that bind proteins in a sample such that their relative expression levels can be detected. Broader term: probe; Related term: reporter probe

competitive hybridization: Another critical feature of most microarrays is that different samples (often two - control and sample) can be hybridized, competitively, to the same array. This competitive hybridization is possible because fluorescent dyes with different emission spectra can be used on different samples, allowing samples tagged with the various dyes to be discriminated in imaging.  Related term: competitive PCR. 

competitive PCR cPCR: During the last few years, many efforts have been made to provide suitable controls to convert PCR to a quantitative method ... One group [of methods] relies on external calibration ... among [these] the competitive PCR methods (cPCR) are the most robust and reliable.  They are based on a co- amplification of the target DNA (sample) with a homologous or heterologous DNA standard (competitor) which competes with the sample template DNA for the same set of PCR primers. S Rupf, K. Eschrich,  "Quantification of bacteria by competitive polymerase chain reaction" American Laboratory: 44-  46, July 2000

An internal control, close in composition to the target nucleic acid, competes with the latter for reagents (such as common primers) in the same reaction tube … represents the prototype for the so- called end- point quantitative methods, in which quantification is based on the amount of amplified material (amplicon) obtained at the last amplification cycle. F. Ferré "Key issues" in Gene Quantification Birkhauser 1998  Related terms competitive RT-PCR; competitive immunoassay Labels, signaling & detection

competitive RT-PCR: Should be that - a competition between a known amount of a template and an unknown target. This method avoids difficulties created by differences in the efficiency of the PCR reaction itself with different template/ primer sets. A competitive template binds the same primers but has been altered in some way (small deletions, point mutation) to provide a product that is distinguishable from the target itself. [Laura De Francesco, "Taking the Measure of the Message" The Scientist 12[23]: 20, Nov. 23, 1998]     Compare non-competitive RT-PCR

digital PCR dPCR:  Remains an important technology to have in diagnostic labs, and as more groups add and use this technology, novel applications continue to emerge.

dMIQE guidelines: Minimum Information for Publication of Quantitative Digital PCR Experiments guidelines.

DNA amplification: See gene amplification, PCR  

DNA probes: Species- or subspecies-specific DNA (including COMPLEMENTARY DNA; conserved genes, whole chromosomes, or whole genomes) used in hybridization studies in order to identify microorganisms, to measure DNA- DNA homologies, to group subspecies, etc. The DNA probe hybridizes with a specific mRNA, if present. Conventional techniques used for testing for the hybridization product include dot blot assays, Southern blot assays, and DNA :RNA hybrid- specific antibody tests. Conventional labels for the DNA probe include the radioisotope labels 32P and 125I and the chemical label biotin. The use of DNA probes provides a specific, sensitive, rapid, and inexpensive replacement for cell culture techniques for diagnosing infections. MeSH, 1989

end-point: The traditional measurements of product … analyze the reaction after it is completed can be accomplished through the use of fluorescent intercalating dyes or through measurement of  incorporated radioactivity by autoradiography or phosphor imaging … Southern blots or fluorescence detection are also used. A third type uses solid- state approaches in which a bound enzyme produces fluorescence or luminescence. Finally, several laboratories measure the production of amplification products following resolution by HPLC or capillary electrophoresis. WM Freeman et al. "Quantitative RT-PCR: Pitfalls and Potential" Biotechniques 26: 112-125 Jan 1999 Compare real time.

FISH Fluorescence In Situ Hybridization: A type of IN SITU HYBRIDIZATION in which target sequences are stained with fluorescent dye so their location and size can be determined using fluorescence microscopy. This staining is sufficiently distinct that the hybridization signal can be seen both in metaphase spreads and in interphase nuclei. MeSH, 1993  Broader terms: hybridization, in situ hybridization ISH. Narrower term: chromosome painting  Related term: Labels, signaling & detection  fluorescence  

gene amplification: An increase in the number of copies of a specific gene in an organism. This can lead to the production of a corresponding protein at elevated levels. IUPAC Compendium

A selective increase in the number of copies of a gene coding for a specific protein without a proportional increase in other genes. It occurs naturally via the excision of a copy of the repeating sequence from the chromosome and its extrachromosomal replication in a plasmid, or via the production of an RNA transcript of the entire repeating sequence of ribosomal RNA followed by the reverse transcription of the molecule to produce an additional copy of the original DNA sequence. Laboratory techniques have been introduced for inducing disproportional replication by unequal crossing over, uptake of DNA from lysed cells, or generation of extrachromosomal sequences from rolling circle replication. MeSH, 1980  
Broader term: nucleic acid amplification Narrower term: PCR Related terms branched DNA, LCR, NASBA, nested PCR, OLA, PNA, target amplification  Narrower terms: kinetic PCR, real- time PCR; Related term: Assays & screening quantitative assays
Gene Quantification,
Technical Univ. Munich, Germany

heteroduplex analysis:  A method of detecting gene mutation by mixing PCR- amplified mutant and wild- type DNA followed by denaturation and reannealing. The resultant products are resolved by gel electrophoresis, with single base substitutions detectable under optimal electrophoretic conditions and gel formulations. Large base pair mismatches may also be analyzed by using electron microscopy to visualize heteroduplex regions. MeSH, 1999

hot-start: PCR reaction in which a necessary component for polymerization (polymerase, magnesium, nucleotides, etc.) is withheld from the reaction until all other components achieve a temperature exceeding the annealing temperature of the primers.  This process minimizes amplification artifacts associated with low temperature extension of misprimed oligonucleotides. C.R. Newton et. al. Nucleic Acids Research 17: 2503, 1989. Promega

1. The formation of stable duplexes of two DNA and/ or RNA (complementary) strands via Watson- Crick base pairing used for locating or identifying nucleotide sequences and to establish the effective transfer of nucleic acid material to a new host. 2. The formation of a novel diploid organism either by sexual processes or by protoplast fusion. IUPAC Biotech

A chemical reaction in which single-stranded DNA or RNA molecules combine to form double-stranded complexes, including, for example, the famous DNA double helix. The reaction obeys the usual base-pairing rules, sometimes called Watson- Crick base pairing, in which adenine (A) binds to thymine (T) (or uracil [U], in the case of RNA), and cytosine (C) binds to guanine (G). Binding occurs through the formation of hydrogen bonds between the paired bases, which are much weaker than the covalent bonds that bind the elements of each strand. 
Narrower terms: active hybridization,  competitive hybridization, in situ hybridization ISH, passive hybridization. Related terms: anneal, stringency; Microarrays blotting

hybridization stringency: The percentage of nucleotides which must match on two unrelated single- stranded nucleic acid molecules before they will base pair with each other to form a duplex, given a certain set of physical and chemical conditions. The hybridization stringency is used to determine when a hybridization probe and a target nucleic acid will come together, and can be set by the researcher by varying the conditions. In general, if the percentage of matching nucleotides is lower than 70 percent, the two single- stranded nucleic acid molecules are considered nonhomologous and any hybridization is considered nonstringent. Life Sciences Dictionary   Broader term: stringency

immuno-PCR: Techniques that combine nucleic acid amplification with an antibody-based assay can dramatically increase the sensitivity of conventional immunoassays. This review summarizes the methodology and applications of one such protein detection technique that has been used for the past 23 years—the immuno-polymerase chain reaction (usually referred to as immuno-PCR or IPCR). The key component of an immuno-PCR is a DNA–antibody conjugate that serves as a bridge to link the solid-phase immunoreaction with nucleic acid amplification. The efficiency of immuno-PCR enables a 10- to 109-fold increase in detection sensitivity compared with that of ELISA. Advancements in immuno-PCR have included improvements of production of the DNA–antibody conjugate, assay formats, and readout methods. As an ultrasensitive protein assay, immuno-PCR has a broad range of applications in immunological research and clinical diagnostics. Immuno-PCR: An ultrasensitive immunoassay for biomolecular detection,  Jinming Lia Lunan Wanga  Analytica Chimica Acta Volume 910, 3 March 2016, Pages 12-24

in situ hybridization ISH: A technique that localizes specific nucleic acid sequences within intact chromosomes, eukaryotic cells, or bacterial cells through the use of specific nucleic acid-labeled probes. MeSH, 1993

Using labeled (radioactive or fluorescent) nucleic acid probes - allows researchers to quantify levels of specific mRNAs within a cell.  From the Latin "in place".  Narrower terms: FISH, primed in situ labeling; Related term comparative genomic hybridization;  Broader term: hybridization  

Jurassic Park and PCR:
Although GenBank lacks dinosaur DNA, fragments of genomes past can be found here. A practical limit of about 100,000 years currently applies to the age of recoverable DNA samples. Beyond this limit, hydrolysis of the phosphate backbone of the DNA and oxidative damage to the bases that make up the DNA sequence become too great to allow for efficient PCR amplification. This is why deposition of significant amounts of dinosaur sequence (age > 65 million years) in GenBank is unlikely to occur in the near future. However, many DNA sequences arising from extinct organisms and ancient genomes [including from a Neanderthal, the late Neolithic "Iceman", Egyptian mummies, woolly mammoths, a quagga, a moa and medieval French rabbits] are in the database today, and the number is expected to grow as technology for the extraction and amplification of aged DNA progresses.  "DNA Sequences from Times Past in GenBank" NCBI News, Spring 1999 Sequences

kinetic RT-PCR: Direct use of amplification kinetics to quantify RNA without the use of a standard. Started as an attempt to avoid the long development times of standard construction and the problems of designing, storing and accurately quantifying the standard itself. ... never been widely used, recent advances in detection methods suggest that this concept has the greatest potential for future quantitative RT-PCR development. WM Freeman et al “Quantitative RT- PCR: Pitfalls and Potential” Biotechniques 26: 112- 125 Jan 1999

LCR Ligase Chain Reaction: A DNA amplification technique based upon the ligation of OLIGONUCLEOTIDE PROBES. The probes are designed to exactly match two adjacent sequences of a specific target DNA. The chain reaction is repeated in three steps in the presence of excess probe: (1) heat denaturation of double- .stranded DNA, (2) annealing of probes to target DNA, and (3) joining of the probes by thermostable DNA ligase. After the reaction is repeated for 20- 30 cycles the production of ligated probe is measured.  MeSH, 2001

miniaturization, PCR: We will create a single, integrated platform where PCR primers are synthesized in tandem, and PCR amplification is initiated by the release of the PCR primers, and progress of the PCR reactions is monitored in Real-Time. Furthermore, such reactions will be multiplexed in a high-throughput device with sub-microliter reaction volumes, and will allow at least 1536 PCR reactions to be performed and monitored in parallel. PCR Miniaturization, Genome Technology Center, Stanford Univ School of Medicine, 2007 

molecular beacons: single-stranded oligonucleotide hybridization probes that form a stem-and-loop structure. The loop contains a probe sequence that is complementary to a target sequence, and the stem is formed by the annealing of complementary arm sequences that are located on either side of the probe sequence. A fluorophore is covalently linked to the end of one arm and a quencher is covalently linked to the end of the other arm. Molecular beacons do not fluoresce when they are free in solution. However, when they hybridize to a nucleic acid strand containing a target sequence they undergo a conformational change that enables them to fluoresce brightly Public Health Research Institute New Jersey Medical School - Rutgers, The State University of New Jersey. 

multiplex: A sequencing approach that uses several pooled samples, greatly increasing sequencing speed. DOE

In general, primer- extension technologies are amenable to high- throughput applications and automation, yet only very low levels of multiplexing are possible. Higher multiplexing can be accomplished by combining primer- extension technology with microarray technology.  

Originally a math term meaning multiple, later a 19th century telecommunications term, dating from the telegraph. Oxford English Dictionary 

NASBA Nucleic Acid Sequence Based Amplification: Use Self Sustained Sequence Based Amplification MeSH entry term 2001

non-competitive RT-PCR: The native signal is unaltered by the standard. An increasing series of standard amounts is co- amplified with equal amounts of total experimental RNA; however, this occurs under conditions in which there is no competition for the components in the PCR. The quantification is therefore estimated on a linear scaled graph. The amount of standard signal is plotted against the native signal. When the lines intersect, they reach the equivalence point, and quantification is achieved. .. Generally some estimate of the amount of native signal must be made before deciding on the standard amounts, because they are designed to differ by only one log above and below the native. WM Freeman et al “Quantitative RT- PCR: Pitfalls and Potential” Biotechniques 26: 112-125 Jan 1999 Compare competitive RT- PCR.

nucleic acid amplification: Narrower terms:  DNA amplification, gene amplification, PCR, RNA amplification.

nucleic acid amplification techniques:
Laboratory techniques that involve the in-vitro synthesis of many copies of DNA or RNA from one original template MeSH, 2001

nucleic acid probes: Nucleic acid which complements a specific mRNA or DNA molecule, or fragment thereof; used for hybridization studies in order to identify microorganisms and for genetic studies. MeSH, 1989

Nucleic Acid Testing NAT:  Nucleic Acid Testing (NAT) - FDA   Dec 28, 2017 - Nucleic Acid Testing (NAT) for. Human Immunodeficiency. Virus Type 1 (HIV-1) and. Hepatitis C Virus (HCV): Testing, Product Disposition, and. Donor Deferral and Reentry. Guidance for Industry for plasma testing

PCR and NGS-Based Molecular Diagnostics March 14-15, 2019 San Francisco, CA Program |   Advances Techniques and Tools for Precision Medicine Advances in molecular diagnostics technologies have sparked innovation, expanded research capabilities, and enhanced clinical diagnostics. Cambridge Healthtech Institute’s 6th Annual PCR and NGS-Based Diagnostics symposium puts an emphasis on the NGS and PCR technologies that drive precision medicine and showcases how they are being used to alter clinical outcomes. This event will provide a comprehensive look at integrating molecular diagnostics solutions for biomarker discovery and development, point-of-care, companion diagnostics, and infectious disease.  See also Polymerase Chain Reaction
PNA Peptide Nucleic Acid: DNA analogs containing neutral amide backbone linkages composed of aminoethyl glycine units instead of the usual phosphodiester linkage of deoxyribose groups. Peptide nucleic acids have high biological stability and higher affinity for complementary DNA or RNA sequences than analogous DNA oligomers. MeSH, 1999

PNA probes (peptide nucleic acid) : Made of PNA rather than DNA, attempts to address the intrastrand hybridization problem. A Marshall & J Hodgson “DNA chips: an array of possibilities” Nature Biotechnology 16 (1): 27- 31 Jan 1998

Polymerase Chain Reaction PCR: A laboratory technique to rapidly amplify pre- determined regions of double- stranded DNA. Generally involves the use of a heat stranded DNA polymerase. IUPAC Bioinorganic

In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double- stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult to isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships. MeSH, 1991

Originally described in 1984 by Kary B. Mullis, who shared the Nobel Prize for Chemistry for this invention in 1993, PCR enables the amplification of specific nucleotide sequences through the use of a DNA polymerase. The sequence to be amplified is identified through the use of synthetic oligonucleotides that are complementary to the two terminal regions of the targeted sequence. 
Broader terms: gene amplification, nucleic acid amplification and detection; Related terms: polymerase, primers, RT-PCR; Narrower term: Q-PCR 

PCR and multiplex PCR: Guide and troubleshooting, Octavian Henegariu, Yale Univ., US  
Polymerase Chain Reaction (PCR) JumpStation
, Horizon Press, UK

polymerase DNA or RNA: Any enzyme that catalyzes the formation of DNA or RNA from deoxyribonucleotides or ribonucleotides. ORD  Narrower term: Taq polymerase

primed in situ labeling: A technique that labels specific sequences in whole chromosomes by in situ DNA chain elongation or PCR (polymerase chain reaction).   MeSH, 1999

primer- DNA: Short sequences (generally about 10 base pairs) of DNA that are complementary to sequences of messenger RNA and allow reverse transcriptases to start copying the adjacent sequences of mRNA. Primers are used extensively in genetic and molecular biology techniques. MeSH, 1994

A molecule that initiates the synthesis of a larger molecule. For example, a short synthetic piece of DNA serves as a primer to initiate template- directed DNA synthesis in PCR. NHLBI
Narrower term: primer extension. Related term probes primer dimer: 
Artifacts, non- target amplification products, caused by homologies within primers.

primer extension: A method of SNP detection.

probes: A specific DNA or RNA sequence which has been labelled by radioactivity, fluorescence labels or chemiluminescence labels and which is used to detect complementary sequences by hybridization techniques, such as blotting or colony hybridization. IUPAC Compendium

Biomolecular probes used "to measure the presence or concentration of biological molecules, biological structures, microorganisms, etc. by translating a biochemical interaction at the probe surface into a quantifiable physical signal. MeSH "biosensing techniques", 1999

Devices which use detector molecules to detect, investigate, or analyze other molecules, macromolecules, molecular aggregates, or organisms. MeSH "molecular probe techniques", 1991
Related terms: oligonucleotide primers, target. Narrower terms: capture probes, ASO probes, molecular beacons, nucleic acid probes, PNA probes, padlock probes, RNA, probes; Narrower [or equivalent?] terms: DNA probes, hybridization probes, Labels, signal & detection See also probes
Microarrays  discussing the ambiguities of probe and target designations.

quantitative PCR: A valuable technology used for diagnostics of diseases such as cancer and infectious diseases, and for the detection of bacterial, fungal and viral pathogens. The introduction of novel technology platforms such as digital PCR, high-throughput platforms and improvements in automation and standardization may provide useful tools for diagnosis, prognosis and therapeutic evaluations for both the pharmaceutical industry and the medical community to move the application of qPCR to the next level.  Despite recent attention focused on this technique, quantitation is an old idea- almost as old as PCR itself. "Quantitative PCR has been happening all along," says François Ferré, who heads the gene quantification company Althea Technologies. In the early 1990s, for example, Michael Piatak, Ferré, and others used quantitative PCR to show that HIV viral loads - the degree of infection - in patients' blood were higher than previously thought (3, 4). "Even back in 1989, at meetings focused on PCR, quantitation was a hot topic," Ferré says .. As genes are located, their functions need to be determined, and studies of gene expression become the focus. "The next dimension of research is to figure out what is expressed and how much and when," says Mike Lucero, product marketing manager for PCR at Perkin- Elmer. "That is just as basic as knowing what the DNA sequence is." .. When many researchers say "quantitative PCR", they mean kinetic or real-time PCR. Analytical Chemistry News & Features, March 1, 1999 191A-195A

Intended either to determine the number of copies of a given nucleic acid sequence, or more generally to determine the relative abundance of two sequences. J Peccoud and C Jacob "Statistical Estimations of PCR Amplification Rates" in F. Ferré Gene Quantification Birkhauser 1998  Related terms: absolute quantification, gene quantification, QRT- PCR, relative quantification, relative QRT- PCR

quantitative RT-PCR QRT-PCR: Has evolved into a widely used tool for sensitive detection and quantitation of low- abundance RNA species. As the focus of genomic research is shifting from the location of genes towards functional genomics there is a growing demand for techniques capable of accurately quantitating differences in mRNA levels in different settings. J. Stenman et al. Supplement to: Accurate determination of relative messenger RNA levels by RT-PCR" Nature Biotechnology supp 17: 720- 722 July 1999

The RT step is the source of most of the variability in a quantitative RT-PCR experiment. The final step in  QRT- PCR is the detection and quantification of amplification products. Inherently an indirect method of measurement. WM Freeman et al "Quantitative RT-PCR: Pitfalls and Potential" Biotechniques 26: 112-125 Jan 1999  Related term: differential display Expression, genes & beyond

Random Amplified Polymorphic DNA Technique RAPD: Technique that utilizes low stringency polymerase chain reaction (PCR) amplification with single primers of arbitrary sequence to generate strain specific arrays of anonymous DNA fragments. RAPD technique may be used to determine taxonomic identity, assess kinship relationships, analyze mixed genome samples, and create specific probes. MeSH, 1996

real time PCR: [Russell] Higuchi and co- workers [at Roche] developed a system in which PCR products can be detected in real time, meaning that the accumulation of PCR products could be visualized at each cycle using an intercalating dye, such as ethidium bromide, an ultraviolet source, and a CCD camera … also referred to as "kinetic PCR". F. Ferre Gene Quantification Birkhauser 1998

Real-time determinations monitor the reaction in the thermal cycler as it progresses …offers the potential for improved quantification. The errors in sample manipulation for end- point quantification are minimized and a great deal more information about the PCR is obtained from the data points for each cycle. WM Freeman et al "Quantitative RT- PCR: Pitfalls and Potential" Biotechniques 26: 112-125 Jan 1999  Compare end-point Related terms: kinetic PCR, kinetic RT-PCR

relative quantification: The fact that relative quantification is perceived as poor quantitative information has led to the false impression that it is essential to publish copy numbers to increase the credibility of the results. …methods capable of relative quantitation can provide extremely valuable quantitative information. The quantitative power of such methods will be directly proportional to the extent of their dynamic ranges and to the tightness of their precision.  F. Ferre “Key issues” in Gene Quantification Birkhauser 1998

Determines the changes in steady-state expression of a gene. For the purposes of the vast majority of investigators, relative quantification is adequate. Semi- quantitative is sometimes used as a synonym for relative quantification; however, it is not an optimal term because of the confusion it causes and its imprecise nature.  WM Freeman et al “Quantitative RT-PCR: Pitfalls and Potential” Biotechniques 26: 112-125 Jan 1999
Related term: absolute quantification

relative quantitative RT-PCR: Uses an internal standard to monitor each reaction and allow comparisons between different reactions to be made. To do this, a second set of primers is incorporated into the reaction for an invariant, housekeeping message. The difficulty here is matching the level of the internal message to that of the target so that one reaction doesn't dominate ... Finally, purely exogenous standards (template plus primer) may be added to the reaction, which can give a signal against which the unknown can be compared, providing a relative estimate of the amount of a target species. Laura De Francesco, "Taking the Measure of the Message" The Scientist 12[23]:20, Nov. 23, 1998  

Reverse Transcriptase PCR: See RT-PCR.

reverse transcriptases: Enzymes found in retroviruses that can synthesize complementary single strands of DNA from an mRNA sequence as template. They are used in genetic engineering to produce specific cDNA molecules from purified preparations of mRNA. IUPAC Compendium Related term: RT-PCR

Rolling Circle Amplification RCA: The derivative from of rolling circle replication has been successfully used for amplification of DNA from very small amounts of starting material.[1] This amplification technique is named as Rolling circle amplification (RCA). Different from conventional DNA amplification techniques such as polymerase chain reaction (PCR), RCA is an isothermal nucleic acid amplification technique where the polymerase continuously adds single nucleotides to a primer annealed to a circular template which results in a long concatemer ssDNA that contains tens to hundreds of tandem repeats (complementary to the circular template).[11]  Wikipedia accessed 2018 Feb 26  
Broader term: Rolling  circle replication

RT-PCR Reverse Transcriptase Polymerase Chain Reaction: A variation of the PCR technique in which cDNA is made from RNA via reverse transcription. The resultant cDNA is then amplified using standard PCR protocols. MeSH, 1999

A method for assessing gene expression, detecting low copy number mRNA transcripts, and generating complementary DNAs (cDNAs) for cloning. [Aileen Constans "Lab Consumer Reverse Psychology" Scientist 14 (7): 29 Sept 4, 2000]   Narrower term: competitive RT- PCR  Related terms: Expression gene & protein

SBH Sequencing by Hybridization: A novel DNA sequencing technique in which an array (SBH chip) of short sequences of nucleotides (probes) is brought in contact with a solution of (replicas of) the target DNA sequence. A biochemical method determines the subset of probes that bind to the target sequence (the spectrum of the sequence), and a combinatorial method is used to reconstruct the DNA sequence from the spectrum. Franco Preparata, Eli Upfel, Samuel Health, Sequencing by Hybridization, Brown Univ. 1999

self-sustained sequence replication: An isothermal in-vitro nucleotide amplification process. The process involves the concomitant action of a RNA- DIRECTED DNA POLYMERASE, a ribonuclease (RIBONUCLEASES), and a DNA- DIRECTED RNA POLYMERASE to synthesize large quantities of sequence- specific RNA and DNA molecules. MeSH, 2001

signal amplification methods:  Increasing the amount of signal per unit of target for better detection. Because of the minute scale of hybridization, and the small amounts of target present, it is desirable to increase the signal from an array. This signal- boosting can be accomplished either by increasing the amount of target (target amplification) or increasing the amount of signal per unit of target (signal amplification). Narrower terms:  branched DNA bDNA, Rolling Circle Amplification, Hybrid Capture® (HC) technology, Tyramide Signal Amplification TSA 

stringency: Reaction conditions - notably temperature, salt, and pH - that dictate the annealing of single- stranded DNA/ DNA, DNA/ RNA, and RNA/ RNA hybrids. At high stringency, duplexes form only between strands with perfect one- to- one complementarity; lower stringency allows annealing between strands with some degree of mismatch between bases. Susan A. Hagedorn [Life Sciences Dictionary]  Narrower term: hybridization stringency

Taq polymerase: a thermostable DNA polymerase named after the thermophilic bacterium Thermus aquaticus from which it was originally isolated by Chien et al. in 1976.[1] Its name is often abbreviated to Taq Pol or simply Taq. It is frequently used in the polymerase chain reaction (PCR), a method for greatly amplifying the quantity of short segments of DNA. Wikipedia accessed 2018 Feb 26

TaqMan probes are hydrolysis probes that are designed to increase the specificity of quantitative PCR. The method was first reported in 1991 by researchers at Cetus Corporation,[1] and the technology was subsequently developed by Roche Molecular Diagnostics for diagnostic assays and by Applied Biosystems (now part of Thermo Fisher Scientific) for research applications. Wikipedia accessed 2018 Feb 26

target (hybridization), target amplification: Drug targets 

template: The nucleic acid single strand that is copied during replication or transcription. IUPAC Biotech

whole genome amplification:  The concept of whole genome amplification is something that has arisen in the past few years as the polymerase chain reaction (PCR) has been adapted to replicate regions of genomes that are of biological interest. The applications are many - forensic science, embryonic disease diagnosis, bioterrorism genome detection, "immortalization" of clinical samples, microbial diversity, and genotyping. TL Hawkins et. al. "Whole genome amplification: applications and advances" Current Opinion in Biotechnology 13(1): 65- 67, Feb. 2002

PCR resources
PCR Glossary, Chang Bioscience 2002-2004
Real Time PCR Glossary, M Tevfik Dorak 2010 

How to look for other unfamiliar  terms

IUPAC definitions are reprinted with the permission of the International Union of Pure and Applied Chemistry.

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