Technologies Hub

PCR technologies for workflow planning, compatibility, and QC

PCR technology choices shape workflow complexity, validation burden, staffing needs, contamination risk, and procurement readiness. This hub organizes automation, multiplexing, extraction, QC, performance, compatibility, throughput, and reagent stability into one decision structure.

Start with workflow model, not product list.
Compare technologies by use case, validation effort, and installed base fit.
Use tools to estimate throughput and compatibility before evaluation.
Link technical choices to procurement packs and deployment evidence.

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Technologies

Core technology topics

Compare workflow, compatibility, QC and deployment requirements.

Guidediagnostic-methods

Acid Fast Bacillae Staining Method

The use of acid-fast stain to examine a specimen for the presence of acid-fast microorganisms, specifically mycobacteria.

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Affinity Chromatography

A chromatographic separation technique based on the ability of proteins to bind specific ligands reversibly.

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Agarose Gel Electrophoresis

A type of electrophoresis that uses a matrix of highly purified agar to separate large molecules.

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Allele Specific Primer Polymerase Chain Reaction

A modified polymerase chain reaction (PCR) technique in which a specific primer can amplify its corresponding allele only; this allows for the determination of the presence or absence of a single, specific allele during genotype testing.

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Anchored Multiplex Polymerase Chain Reaction

A technique designed to rapidly enrich and amplify targets derived from samples that yield low levels of nucleic acids, such as formalin-fixed paraffin-embedded (FFPE) tissues, for use in next-generation sequencing. Briefly, total nucleic acid or genomic DNA (gDNA) is isolated from fresh or FFPE tissues. Total nucleic acid is converted to double-stranded cDNA (dscDNA) and cleaned by solid-phase reversible immobilization (SPRI). Then the dscDNA or gDNA is subjected to end repair, adenylation and ligation with a universal half-functional adapter. The modified DNA sample is then subjected to two rounds of nested low-cycle PCR, where the first round uses target gene-specific primers and the second round uses nested target gene-specific primers that are 5' tagged with a common sequencing adapter. The resulting target amplicon library is cleaned using SPRI and is suitable for use in next generation genomic assays.

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Array-based Comparative Genomic Hybridization

A molecular cytogenetic method combining chromosomal comparative genomic hybridization technique and microarray to detect chromosomal aberrations and changes in DNA copy numbers in the genome, using oligonucleotides immobilized on a solid support as targets for hybridization.

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ATAC-Seq

A molecular genetic technique that isolates and sequences chromosomal regions that are rich in open chromatin. First, nuclei are harvested from a cellular sample. Then a hyperactive Tn5 transposase is added to the nuclei where it excises non-nucleosomal DNA strands and ligates co-administered high-throughput sequencing adapters (tagmentation). The tagged DNA fragments are isolated, amplified by PCR and sequenced. The number of reads for specific region of DNA correlate with increased chromatin accessibility and this method can identify regions of transcription factor and nucleosome binding.

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Atomic Absorption Spectroscopy

A spectrometric method that determines the type and concentration of metal elements in a sample, based upon the principle that each elemental metal absorbs a particular wavelength of ultraviolet light when exposed to heat.

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Atomic Force Microscopy

A technique utilizing a scanning probe to image and analyze the surface of a material with atomic-level resolution.

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Atomic Resolution Microscopy

Several related technologies for imaging and measuring surfaces on a fine scale, down to the level of molecules and groups of atoms. These technologies share the concept of scanning an extremely sharp tip (3-50 nm radius of curvature) across the object surface. The tip is mounted on a flexible cantilever, allowing the tip to follow the surface profile. When the tip moves in proximity to the investigated object, forces of interaction between the tip and the surface influence the movement of the cantilever. Various interactions can be studied depending on the specific mechanics of the probe. Specialized sensors detect and record the movements of the cantilever, providing an image with resolution at the atomic level.

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Bioluminescence

The production of light by certain living organisms, including fireflies and phytoplankton, by the conversion of chemical to radiant energy.

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Bisulfite Sequencing

A DNA sequencing technique that can differentiate cytosine from 5-methylcytosine in a DNA sample. First, a denatured DNA sample is treated with bisulfite which converts non-methylated cytosine to uracil. Next, the sample is amplified using a PCR method that does not discriminate between non-methylated and methylated sequences. The amplified DNA is subjected to nucleotide sequencing. The resulting sequence is compared to an identical control sample of DNA that was not treated with bisulfite. Unmethylated cytosines will be displayed as cytosines in the control sample and as thymines in the bisulfite-treated sample.

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Capillary Electrophoresis

An electrophoresis procedure, in which a sample is introduced into a capillary tube and the components are separated by the application of high voltage. Due to the large surface to volume ratio, cooling is more efficient, allowing use of higher voltages. As a result, separation occurs more quickly and sensitivity is increased. The technique allows for separation of proteins, nucleic acids, and carbohydrates.

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Cell Culture

General term referring to the maintenance of cell strains or lines in the laboratory.

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Cell Sorting

Any of various processes to isolate one or more specific cell populations from a heterogeneous mixture of cells.

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Centrifugation

A process where a rotating machine exposes a specimen to centrifugal force. This process can be used to remove moisture from a specimen, to subject an organism to increased gravitational forces, or to separate the components of heterogeneous mixtures based on density differences.

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Chemiluminescence

The emission of light as the result of a chemical reaction.

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ChIP-Seq

A molecular genetic technique that combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to map the binding sites of DNA-associated proteins in a sample of cells. First, crosslinked protein-DNA complexes are isolated using ChIP. Next, the crosslinks are broken, the proteins are removed and the purified DNA is modified with adaptor oligonucleotides to facilitate massively parallel DNA sequencing. Following sequencing, the DNA sequences that are obtained can be mapped to their genomic locations.

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Chromatin Immunoprecipitation

A technique that utilizes immunoprecipitation to find protein-DNA interactions in a biological sample. First, the sample is treated causing the formation of protein-chromatin crosslinks. Then, the sample is sheared to separate individual protein-DNA complexes. Finally, an antibody directed against a protein of interest is applied and the protein-DNA complexes are immunoprecipitated.

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Chromogenic In Situ Hybridization

A laboratory procedure that combines the sequence-specific detection aspects of FISH with the simple detection methods of immunohistochemistry. Briefly, sequence-specific probes are hybridized to cells fixed on slides and the sequestered probe is visualized by a peroxidase reaction. It has the advantage of being a less costly assay that does not require fluorescence microscopy with results that are stable over time.

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Chromosome Banding

The treatment of chromosomes to reveal characteristic patterns of horizontal bands. The banding patterns lend each chromosome a distinctive appearance so the 22 pairs of human non-sex chromosomes and the X and Y chromosomes can be identified and distinguished without ambiguity. Banding also permits the recognition of chromosome deletions (lost segments), chromosome duplications (surplus segments) and other types of structural rearrangements of chromosomes.

Technologycold-chain-stability

Cold Chain and Reagent Stability Guide for PCR Supply and Cross-border Delivery

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Colorimetry

An assessment used to quantify and describe the colors within the visible spectrum of light.

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Comparative Genomic Hybridization

Comparative genomic hybridization (CGH) is a technique that allows the detection of losses and gains in DNA copy number across the entire genome without prior knowledge of specific chromosomal abnormalities. Comparative genomic hybridization utilizes the hybridization of differentially labeled tumor and reference DNA to generate a map of DNA copy number changes in tumor genomes. Comparative genomic hybridization is an ideal tool for analyzing chromosomal imbalances in archived tumor material and for examining possible correlations between these findings and tumor phenotypes. (from Ried et al. J Mol Med 1997 75:801-14)

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Competitive Enzyme-linked Immunosorbent Assay

A type of ELISA assay that uses a reference antigen to competitively bind labeled antibody against an antigen of interest. The strength of the signal interference caused by antibody bound to the reference antigen is used to determine the concentration of the antigen of interest.

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Confocal Microscopy

A system of (usually) epifluorescence light microscopy in which a fine laser beam of light is scanned over the object through the objective lens. The technique is particularly good at rejecting light from outside the plane of focus and so produces higher effective resolution than is normally achieved.

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Cryo-Electron Microscopy

Electron microscopy involving an aqueous suspension of a sample which is applied in an extremely thin film to a grid, frozen in liquid nitrogen and maintained in this state by means of a special mount. The imaging of frozen-hydrated molecules and organelles permits the best possible resolution closest to the living state, free of chemical fixatives or stains.

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Cytochemistry

Branch of histochemistry associated with the localization of cellular components by specific staining methods, as for example the localization of acid phosphatases by the Gomori method.

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Cytogenetic Analysis

Techniques for analysis of chromosomal and subchromosomal properties and structures, such as those to diagnose, classify, screen for, or manage genetic diseases and abnormalities.

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Cytology

The light microscopic study of normal and abnormal cells in fine needle aspirates (FNAs), body cavity fluids, and smears.

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Dark Field Microscopy

A light microscopic technique in which the light that does not come into contact with the structures or details of interest is subtracted from the ocular image. This yields an image in which the structures or details are alight while the areas where the structures or details are absent are dark.

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Density Gradient Centrifugation

A method of separating macromolecules by either their differential rate of sedimentation in a centrifugal gradient or their differential buoyancy in a density gradient. (from biology-text.com)

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Dideoxy Chain Termination DNA Sequencing

A DNA sequencing technique in which a mixture of deoxynucleosidetriphosphates (dNTPs) and chain-terminating dNTPs, which are radioactively or fluorescently labeled, are combined within the reaction mixture. Once the reaction is complete, the DNA strands are separated by size, and the labeled chain terminating dNTPs can be read in sequence by the investigator or by a machine.

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Digital Polymerase Chain Reaction

A type of polymerase chain reaction technique in which the sample is fractionated, within which individual PCR reactions occur in each fraction.

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Direct Antiglobulin Test

A measurement of the antibody or complement-coated erythrocytes in a blood specimen in vivo.

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DNA Fingerprinting

Identification of an individual's genetic information from their DNA.

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DNA Isolation

Any method that extracts and purifies DNA from biological samples, which can include the proper handling of biological samples prior to nucleic acid isolation, the separation of DNA from the rest of the components in the samples, and the storage of the DNA isolates.

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DNA Sequencing

The determination of the sequence of purines and pyrimidines in deoxyribonucleic acid (DNA).

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Electrochemiluminescence Immunoassay

A method in which electromagnetic radiation, in the form of light emission, is generated from an electrochemical reaction in a solution due to the formation of antigen-antibody complexes.

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Electron Microscopy

Any form of microscopy in which the interactions of electrons with the specimens are used to provide information about the final structure of that specimen.

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Electrophoretic Mobility Shift Assay

A molecular biology technique used to detect the interaction of a DNA binding protein with its cognate binding sequence. Labeled DNAs were reacted with crude cell extracts and the complexes are run through a non-denaturing polyacrylamide gel. The migration of the labeled DNA through the gel will be slower by being bound. This shift in electrophoretic mobility indicates functional binding between the protein and the DNA.

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Electrospray Ionization

A procedure used in mass spectrometry analysis. Means of delivering nonvolatile analytes into the gas phase for mass analysis. Best used on molecules which are charged in solution or readily accept a charge. Particularly well suited to the analysis of biomolecules. Can be used to probe tertiary structure and non-covalent interactions (from NCSU Mass Spectrometry Facility web site)

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ELISA

A highly sensitive technique for detecting and measuring antigens or antibodies in a solution; the solution is run over a surface to which immobilized antibodies specific to the substance have been attached, and if the substance is present, it will bind to the antibody layer, and its presence is verified and visualized with an application of antibodies that have been tagged in some way. (BioTech Life Science Dictionary)

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Enzyme Immunoassay

Any of several immunoassay methods that use an enzyme covalently linked to an antigen or antibody as a label; the most common types are enzyme-linked immunosorbent assay (ELISA) and enzyme-multiplied immunoassay technique (EMIT).

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Enzyme Multiplied Immunoassay Technique

A type of homogenous immunoassay in which sample is applied to a reagent mixture of enzyme-labeled ligand, antibody, and substrate. Substrate binding to enzyme leads to inactivation and unlabeled-ligand in the sample can be quantified by colorimetric analysis.

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Epsilometry

A method to determine microbial susceptibility to antibiotics in which a plastic strip impregnated with the antibiotic of interest is placed on an agar plate that has been inoculated with bacteria. The antibiotic diffuses from the strip producing a concentration gradient of drug on the agar. The point at which the elliptical shaped area of growth inhibition meets the strip is the minimum inhibitory concentration of the drug of interest.

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Filtration

The process of passing a liquid or gas through a filter.

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Flow Cytometry

A technique for counting, examining and sorting microscopic particles suspended in a stream of fluid.

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Fluorescence Activated Cell Sorting

Selection and deposition of individual cells of a particular phenotype from a mixed population into a separate tube or tissue culture plate by the use of a fluorescence-activated cell sorter (FACS) and fluorescently-labeled antibodies specific for surface molecules on the cells to be sorted.

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Fluorescence In Situ Hybridization

A physical mapping approach that uses fluorescent tags to detect hybridization of probes within metaphase chromosomes or less condensed somatic interphase chromatin. This technique can be used for identification of chromosomal abnormalities and for gene mapping.

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Fluorescence Microscopy

A technique in which samples that either contain fluorescent compounds or are stained with fluorescent dyes are exposed to a wavelength of light that excites the fluorophore, allowing for an image to be captured by a microscope.

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Fluorescence Polarization Immunoassay

An immunoassay in which a fluorescent tracer is used to detect an analyte of interest by triggering the emission of photons when subjected to polarized light.

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Fluorescence Resonance Energy Transfer

A process to measure the proximity of two fluorochromes whereby the excitation energy of one fluorochrome is released and absorbed by the second fluorochrome. It is used to study interactions and structure of macromolecules. (NCI)

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Fluorescence Spectroscopy

Fluorescent spectroscopy or fluorometry is a type of electromagnetic spectroscopy used for analyzing fluorescent spectra. It involves using a beam of light, usually ultraviolet light, that excites the electrons in molecules of certain compounds and causes them to emit light of a lower energy, typically, but not necessarily, visible light.

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Fluorescent Antibody Procedure

An immunological procedure in which the antibodies are coupled with molecules which fluoresce under ultra violet (UV) light. This makes them particularly suitable for detection of specific antigens in tissues or on cells.

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G-Banding

Use of Giemsa stain to produce a characteristic staining pattern on chromosomes

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Gas Chromatography

A chromatographic technique in which the stationary phase is solid while the mobile phase is gaseous samples. The gaseous samples are separated based on their different adsorption ability to the solid phase.

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Gas Chromatography Mass Spectrometry

An analytical technique wherein gas chromatography is coupled to mass spectrometry in order to separate, identify, and quantify substances in a sample.

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Gel Electrophoresis

Gel electrophoresis is a method of separating large molecules (such as DNA fragments or proteins) from a mixture of similar molecules by electrophoretic filtration through a gelatinous matrix. Subject to an electric field, each molecule in the sample mixture migrates through the matrix at a different rate, depending mainly on electrical charge and size, resulting in spatial separation within the matrix of each molecular species in the sample mixture. Agarose and acrylamide in a cylindrical tube or slab gel are commonly used media for electrophoresis of proteins and nucleic acids.

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Gel Filtration Chromatography

Gel permeation or sieve chromatography that is performed on porous gels that separate solutes on the basis of size. Smaller solutes are included within the particles of the gel matrix more frequently than larger solutes, thus affecting elution rates.

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Genetic Linkage Analysis

The process of measuring the extent of crossovers between chromosomes as a gauge of the distance between genes.

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Gram Staining Method

This is a method (named after the Danish bacteriologist, Hans Christian Gram) for staining and identifying bacteria. It is based on the differential retention of a crystal violet-iodine complex within the cell membrane. Gram-positive organisms will appear blue-black or purple while Gram-negative organisms will appear red.

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Hemagglutination Inhibition Assay

An in vitro assay that is used to determine whether antibodies present in serum samples will prevent hemagglutination in a cell culture plate containing red blood cells and influenza virus.

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Hematoxylin and Eosin Staining Method

Hematoxylin-and-eosin, or H&E, is a routine staining procedure of tissue sections. This staining method uses two separate dyes, one staining the nucleus and the other staining the cytoplasm and connective tissue. Hematoxylin is a dark purplish dye that stains the chromatin (nuclear material) within the nucleus. Eosin is an orangish-pink to red dye that stains the cytoplasmic material including connective tissue and collagen.

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High Performance Liquid Chromatography

Frequently referred to simply as HPLC, this form of column chromatography is used frequently in biochemistry. The analyte is forced through a column by liquid at high pressure, which decreases the time the separated components remain on the stationary phase. Less time on the column then translates to narrower peaks in the resulting chromatogram and thence to better selectivity and sensitivity.

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Histochemistry

The study of cells and tissues using chemical staining techniques.

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Histopathologic Examination

The microscopic study of characteristic tissue abnormalities by employing various cytochemical and immunocytochemical stains.

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Immunoaffinity Chromatography

Affinity chromatography using monoclonal or polyclonal antibodies, or (less commonly) antigens, as the immobilized binding phase.

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Immunochromatography

A type of chromatography assay in which an antibody-conjugate is passed over an immobilized antigen, giving a visual indication of positive or negative result.

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Immunocytochemistry

A method for the detection of proteins or antigens on samples of cells that are grown in monolayers or in suspension and deposited on slides using antibodies or other biomolecules that bind the target and can be visualized through a chemical process.

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Immunodiffusion

A quantitative technique used to detect and estimate the concentration of an antigen by measuring the precipitation which is formed as a result of the interaction of the antigen and an antibody at optimal concentration.

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Immunoelectrophoresis

A laboratory testing method to determine the concentrations of immunoglobulins in the blood.

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Immunofixation

An enhancement of immunoelectrophoresis in which a series of post-electrophoretic gel slabs are layered with cellulose-acetate gels saturated with specific antibodies. The resulting antigen-antibody complexes fixed on the second gel may then be stained, allowing sensitive and specific qualitative visual identification of paraproteins by electrophoretic position. It can be used to identify specific proteins in the blood or urine. It has greatest application in the identification and monitoring of monoclonal proteins that are produced in conditions like Waldenstom's macroglobulinaemia and multiple myeloma.

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Immunohistochemistry Staining Method

Immunohistochemical staining techniques allow for the visualization of antigens via the sequential application of a specific antibody to the antigen (primary antibody), a secondary antibody to the primary antibody and an enzyme complex with a chromogenic substrate. The enzymatic activation of the chromogen results in a visible reaction product at the antigen site. The specimen may then be counterstained and coverslipped. Results are interpreted using a light microscope and aid in the differential diagnosis of pathophysiological processes, which may or may not be associated with a particular antigen.

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Immunology Test

Laboratory test involving interaction of antigens with specific antibodies.

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Immunoperoxidase Procedure

An immunological procedure in which antibodies are coupled with a peroxidase molecule. Following localization via the antibody, the peroxidase is reacted with a corresponding substrate to produce a product which can be seen with a light microscope.

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Immunoprecipitation

Antigen aggregation with antibody, in the right ratios, to cause precipitation.

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In Situ Hybridization

Use of a DNA or RNA probe to detect the presence of complementary sequences in chromosomes, cells, or tissues.

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Indirect Antiglobulin Test

A test that uses Coombs' reagent to detect the presence of anti-erythrocyte antibodies in serum.

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Inductively-Coupled Plasma Mass Spectrometry

A mass spectrometry technique that uses inductively-coupled plasma generated from argon gas to atomize and ionize a sample. The resulting ions are separated and analyzed using a mass spectrometer.

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Technologyinternal-control-qc

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Isoelectric Focusing

A type of gel electrophoresis in which charged molecules travel through a pH gradient. The molecules will come to stop at the point where the net charge on the molecule is equal to that of the surrounding gel.

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Karyotyping

The preparation, analysis, and interpretation of a karyotype, the representation of the chromosome set of a cell.

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Laser Capture Microdissection

A high-resolution method used to isolate cells from their surrounding tissues, with the aid of a laser beam, under direct microscopic visualization. Specific cells can be isolated directly by cutting target cells away from unwanted cells, to obtain enriched cell populations.

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Light Microscopy

Light Microscopy is a technique for producing visible images of structures or details which are too small to be otherwise seen by the human eye. It involves passing light transmitted through or reflected from the subject through a series of lenses to be detected directly by the eye, imaged on a photographic plate, or captured digitally.

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Liquid Chromatography

A type of chromatography in which separation of a mixture is achieved by passing a sample in a stream of liquid solvent through some form of material that will provide resistance by virtue of chemical interactions between the components of the sample and the material.

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Liquid Chromatography Mass Spectrometry

LC/MS is a hyphenated technique, combining the separation power of liquid chromatography (LC), an analytical chromatographic technique for separating ions or molecules dissolved in a solvent, with the detection power of mass spectrometry(MS), a technique to separate gas phase ions according their m/z (mass to charge ratio) value. Used for drug screening, pharmacology studies, environmental analyses and forensics.

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Liquid Chromatography/Tandem Mass Spectrometry

An analytical technique wherein liquid chromatography is coupled to tandem mass spectrometry in order to separate, identify, and quantify substances in a sample.

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Loop-mediated Isothermal Amplification

A type of nucleic acid amplification test in which sample DNA is exposed to a single temperature in the presence of multiple sets of primers and a polymerase with replication and high strand displacement activity. This test negates the need for thermal cyclers and may be a low cost alternative to PCR.

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Loss of Heterozygosity Analysis

An analysis done to detect monoallelic loss of genes or DNA regions in a diploid cell.

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Magnetic Bead Separation

A cell-separation technique where magnetizable microspheres or beads are first coated with monoclonal antibody, allowed to search and bind to target cells, and are then selectively removed when passed through a magnetic field. Among other applications, the technique is commonly used to remove tumor cells from the marrow of patients who are to undergo autologous bone marrow transplantation.

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Mass Cytometry

A flow cytometry technique that utilizes mass spectrometry to detect antibodies labeled with heavy metal ion tags that are bound to antigens of interest on single cells.

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Mass Spectrometry

An analytical technique wherein ions are separated according to their ratio of charge to mass. From the mass spectrum produced, the atomic weight of the particle can be deduced.

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Methylation Analysis

An analysis of DNA or protein to detect the presence and/or location of methyl groups.

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Microarray Analysis

Analysis using microarray technology (e.g., cDNA arrays to see gene expression or protein microarrays to profile the pattern of proteins).

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Microdissection

A laboratory method in which the tissue from a histology slide is dissected under a microscope to procure specific cells or cell populations.

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Microparticle Enzyme Immunoassay

A type of enzyme immunoassay that uses antigen-coated microparticles as a substrate for antibody binding.

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Microsatellite Instability Analysis

A laboratory procedure to detect microsatellite instability.

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Minimum Inhibitory Concentration Test

A laboratory test to determine the lowest concentration of a substance that will inhibit a biological or biochemical function, such as microorganism growth or enzymatic activity.

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Molecular Cytogenetics

Studies of chromosome biology and behavior at the molecular level.

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Multiphoton Microscopy

An imaging technique that uses multiple photons to absorb infrared light, thereby minimizing phototoxicty and photobleaching, making it an ideal method for imaging living specimens, especially those involving deep tissue.

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Multiplex Ligation-dependent Probe Amplification

A type of high-throughput, multiplex PCR method used to determine abnormal DNA copy number changes of up to 50 genomic DNA or RNA sequences with a single pair of PCR primers. It is frequently used in the detection of genetic aberrations in tumors, and can distinguish sequences differing in only a single nucleotide.

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Nanopore Sequencing

A proprietary next-generation DNA sequencing technology from Oxford Nanopore Technologies that can directly identify and sequence a DNA molecule as it passes through a nanopore, driven by electrophoresis.

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Nephelometry

A method to quantify the concentration of particulate matter suspended in a liquid or gas using a nephelometer.

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Nested PCR

Polymerase chain reaction that uses two sets of primers, in two sequential runs of amplification, with the second set intended to amplify a target within the first run product.

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Next Generation Sequencing

Technologies that facilitate the rapid determination of the nucleotide sequence of large numbers of strands or segments of DNA or RNA.

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Next Generation Targeted Sequencing

A technique that determines the nucleotide sequence of a pre-specified region of DNA or RNA by using primers that are specific for that region.

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Northern Blotting

A common molecular biology procedure for detection of RNA molecules. RNA extracted from a sample was denatured and separated by slab gel electrophoresis, then blotted on to a nitrocellulose or nylon sheet and hybridized with labeled DNA or RNA that is complementary to the desired RNA, whose presence is subsequently indicated by autoradiography or other visualization techniques.

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Nuclear Magnetic Resonance Spectroscopy

Detection and measurement of the resonant spectra of molecular species in a tissue or sample.

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Optical Densitometry

Measuring the optical density of a substance by shining light on it and measuring its transmission.

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Paired-End Sequencing

A DNA sequencing strategy where a single read is initiated from each end of a DNA fragment.

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Parallel Reaction Monitoring

A method for collecting tandem mass spectrometry data where an ion of a particular mass is selected in the first stage and a fragmented ion product is selected in the second mass spectrometer stage for detection. Parallel reaction monitoring (PRM)-based experiments are generally performed in a high-resolution hybrid quadrupole-Orbitrap (Q-OT) or time-of-flight mass spectrometer.

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Periodic Acid Schiff Staining Method

This is an all-round useful stain for many things, including glycogen, mucin, mucoprotein, glycoprotein, as well as fungi. The reaction is based on the oxidation of glycol group to aldehydes by periodate. The schiff's reagent selectively stains the aldehydes to a rose pink color. PAS is useful for outlining tissue structures--basement membranes, capsules, blood vessels, etc.

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Phase-Contrast Microscopy

A simple non-quantitative form of interference microscopy of great utility in visualising live cells. Small differences in optical path length due to differences in refractive index and thickness of structures are visualised as differences in light intensity.

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Photon Correlation Spectroscopy

A type of spectroscopy that utilizes a laser beam to irradiate a sample containing particles in suspension, resulting in light scattering. Rapid fluctuations in scattering intensity, around a mean value at a certain angle, occur because of particle diffusion and are dependent upon on particle size. The calculated correlation function yields a diffusion coefficient, for a given temperature and viscosity, which can be used to calculate particle size.

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Plaque Reduction Neutralization Assay

A serological test that measures the ability of antibodies in specific concentrations of serum to prevent the formation of plaques in a cell monolayer when combined with a viral suspension.

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Platelet Aggregation Assay

An assay performed to assess platelet clumping, often with the addition of agonists.

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Polyacrylamide Gel Electrophoresis

Analytical and separative procedures in which molecules, particularly proteins or nucleic acids, are separated by their different electrophoretic mobilities in a hydrated gel. The gel suppresses convective mixing of the fluid phase through which the electrophoresis takes place and contributes molecular sieving. For proteins, commonly carried out in the presence of the anionic detergent sodium dodecylsulphate (SDS). SDS denatures proteins so that noncovalently associating sub unit polypeptides migrate independently and by binding to the proteins confers a net negative charge roughly proportional to the chain weight.

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Polymerase Chain Reaction

A method for amplifying a DNA base sequence using multiple rounds of heat denaturation of the DNA and annealing of oligonucleotide primers complementary to flanking regions in the presence of a heat-stable polymerase. This results in duplication of the targeted DNA region. Newly synthesized DNA strands can subsequently serve as additional templates for the same primer sequences, so that successive rounds of primer annealing, strand elongation, and dissociation produce rapid and highly specific amplification of the desired sequence. PCR also can be used to detect the existence of the defined sequence in a DNA sample.

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Polymorphic Microsatellite Marker Analysis

Analysis that looks for differences in the lengths of microsatellite repeats between alleles. Polymorphic microsatellites are present in the genome every few thousand base pairs and can function as molecular markers.

Guidediagnostic-methods

Potentiometry

An electroanalytical technique in which the electrical potential of a solution is measured to determine the composition of the sample, by comparing the constant potential of the reference electrode with the actual potential of the indicator electrode.

Guidediagnostic-methods

Protein Purification

Separation of protein fractions by precipitation, chromatography, or other methods.

Guidediagnostic-methods

Protein Sequencing

The process of determining the sequence of amino acids within a protein molecule.

Guidediagnostic-methods

Pulsed-Field Gel Electrophoresis

Pulsed-field gel electrophoresis (PFGE) is a method used to separate proteins or high molecular weight linear DNA fragments that are greater than 50 kilobases (kb) in size. Fragments are separated by pulsing an electrical field across an agarose gel rather than applying the constant field used in conventional electrophoresis.

Guidediagnostic-methods

Pyrosequencing

A DNA sequencing method that uses a "sequencing by synthesis" strategy. The strand complementary to a template is synthesized a single base at a time through the sequential addition of individual solutions of each base. Incorporation of a base into the growing strand generates free pyrophosphate that is detected as light, as generated by a luciferase-catalyzed reaction.

Guidediagnostic-methods

Quantitative Reverse Transcriptase PCR

Quantitative PCR: a method to measure very small amounts of RNA transcripts as cDNA targets. There are two strategies currently used, one is called Competitive RTPCR and the other is called Real-Time PCR.

Guidediagnostic-methods

Radial Immunodiffusion

A quantitative technique used to detect and estimate the concentration of an antigen by measuring the diameter of the ring of precipitation (precipitin ring), which is formed as a result of the interaction of the antigen and an antibody at optimal concentration.

Guidediagnostic-methods

Radioimmunoassay

Radioimmunoassay (RIA) is an immunological technique, which quantitatively determines antigen and antibody concentrations, using a radioactively labeled substance (radioligand), either directly or indirectly.

Guidediagnostic-methods

Raman Spectroscopy

Emission of electromagnetic energy with a shorter frequency (longer wavelength) than that of the incident monochromatic light. Arises from the low probability absorption of quanta with a higher energy than that required for a transition: the difference in energy is emitted as a lower frequency (energy) photon. Allows analysis of vibrational and rotational energy levels using visible incident light.

Guidediagnostic-methods

Rapid Amplification of cDNA Ends

A procedure for amplification of nucleic acid sequences from a messenger RNA template between a defined internal site and unknown sequences at either the 3'- or 5'-end of the mRNA.

Guidediagnostic-methods

Real Time PCR

An application of PCR that measures the products generated during each cycle of the polymerase chain reaction process in order to determine the starting amount of template in the reaction.

Guidediagnostic-methods

Refractometry

A method to measure the refractive index (propensity for light to bend) of a sample.

Guidediagnostic-methods

Restriction Fragment Length Polymorphism

Variation occurring within a species in the length of DNA fragments generated by a specific endonuclease. Such variations are generated by mutations that create or abolish recognition sites for these enzymes.

Guidediagnostic-methods

Reverse Transcriptase-Polymerase Chain Reaction

A laboratory procedure in which an RNA strand is first transcribed into a DNA complement and then subjected to PCR amplification. Transcribing an RNA strand into a DNA complement is termed reverse transcription and is done by the enzyme reverse transcriptase.

Guidediagnostic-methods

Scanning Electron Microscopy

Technique of electron microscopy in which the specimen is coated with heavy metal and then scanned by an electron beam. The resolution is not as great as with transmission electron microscopy, but preparation is easier (often by fixation followed by critical point drying), the depth of focus is relatively enormous, the surface of a specimen can be seen (though not the interior unless the specimen is cracked open) and the image is aesthetically pleasing.

Guidediagnostic-methods

Selected Reaction Monitoring

A method for collecting tandem mass spectrometry data where an ion of a particular mass is selected in the first stage and a fragmented ion product is selected in the second mass spectrometer stage for detection. Selected reaction monitoring (SRM)-based experiments are generally performed in a triple quadrupole (QqQ) mass spectrometer.

Guidediagnostic-methods

Sequence Alignment

The process of arranging protein, DNA or RNA sequences to identify regions with similar sequences that may elucidate functional, structural, or evolutionary relationships between the sequences.

Guidediagnostic-methods

Shotgun Sequencing

Unordered sequencing. Unmapped clones spanning a region of interest are sequenced and then assembled into a continuous sequence.

Guidediagnostic-methods

Silver Staining Method

Silver Staining or GMS staining is a technique for demonstrating fungi in tissue sections. It is primarily based on staining the polysaccharides in fungal cell wall (From BioGenex).

Guidediagnostic-methods

Single Cell Gel Electrophoresis

A rapid, simple, visual and sensitive technique for measuring DNA breakage in individual mammalian cells in response to a test agent. A cell is immobilized in agarose and made permeable and the broken DNA migrates out under the influence of the electric field. A damaged cell has the appearance of a comet with a brightly fluorescent cell body and a tail whose length and fluorescence intensity are related to the number of DNA-strand breaks induced by the test agent.

Guidediagnostic-methods

Single Cell RNA Sequencing

A procedure that can determine the nucleotide sequence for all of the RNA transcripts in an amplified nucleotide sample that was derived from a single cell.

Guidediagnostic-methods

Sodium Dodecylsulfate-Polyacrylamide Gel Electrophoresis

Sodium dodecyl sulfate (SDS) polyacrylamide gel electrophoresis is a procedure for estimating molecular weights of polypeptides, and uses SDS, a detergent that dissociates and unfolds oligomeric proteins into its subunits. The SDS binds to the polypeptides to form complexes with fairly constant charge to mass ratios. The electrophoretic migration rate through a gel is therefore determined only by the size of the complexes.

Guidediagnostic-methods

Southern Blotting

A technique for the detection of specific DNA fragments that have been separated by polyacrylamide-gel electrophoresis, transferred to a nitrocellulose or other type of paper or nylon membrane, and detected by hybridization and visualization with a labeled probe.

Guidediagnostic-methods

Spectral Karyotyping

A novel karyotyping procedure which is based on the simultaneous hybridization of 24 chromosome-specific painting probes labeled with different fluorochromes or fluorochrome combinations. The measurement of defined emission spectra by means of interferometer-based spectral imaging allows for the definitive discernment of all human chromosomes in different colors. (from Schrock et al., Hum Genet 1997:101:255-62)

Guidediagnostic-methods

Spectrophotometry

A laboratory test that produces a quantitative measurement of the reflection or transmission properties of a material as a function of wavelength.

Guidediagnostic-methods

SSCP Analysis

A procedure used to demonstrate nucleotide sequence variations that occur in the same region of DNA between individuals within a species, or between alleles in an individual to detect mutations in various genes, such as oncogenes, tumor suppressor genes, or genes responsible for genetic diseases. The method detects different conformations adopted by partially denatured DNA fragments resulting from their specific nucleotide sequences under denaturing conditions. Denatured single-stranded DNA fragments are allowed to partially renature without formation of double-stranded DNA. The particular conformations adopted by each of the renatured fragments depend on each of their specific nucleotide sequences. The fragments are run on polyacrylamide gels to detect subtle changes in migration due to their particular secondary structures. Resulting fragment band in the gel will misalign if any point mutations are present to alter the conformation.

Guidediagnostic-methods

Strand Displacement Amplification

An isothermal, in vitro nucleic acid amplification method that allows primer-directed amplification of a target sequence. It utilizes a primer that can be nicked to create a polymerase start site and a DNA polymerase that will displace a downstream strand as it tracks along the template.

Guidediagnostic-methods

Surface Plasmon Resonance

A quantum optical-electrical phenomena consisting of an alteration in light reflectance as a result of binding of molecules to a surface from which total internal reflection is occurring. Used to detect macromolecular interactions, SPR can be used as the basis for a sensor which is capable of sensitive and quantitative measurement of a broad spectrum of chemical and biological entities.

Guidediagnostic-methods

Tandem Mass Spectrometry

Mass spectrometers coupled in series. The targeted compound is selectively ionized, and its characteristic ions are separated from others in the mixture in the first mass spectrometer. The selected primary ions are then decomposed by collision, and from the resulting products the final mass analyzer selects secondary ions characteristic of the targeted compound. Tandem mass spectrometry can achieve specificities and sensitivities equivalent of those of methods such as radioimmunoassay and gas chromatography/mass spectrometry, while performing analyses in much shorter times.

Technologythroughput-planning

Throughput Planning for PCR Labs: 48, 96 and 384 Sample Workflow Choices

Translate daily volume, turnaround targets, staffing, and automation fit into a practical PCR workflow model instead of overbuilding capacity.

Guidediagnostic-methods

Time-of-Flight Mass Spectrometry

A method for determining the mass-to-charge ratio (m/z) of gas-phase ions based on measuring how quickly they travel a known distance in an electric field of known strength.

Guidediagnostic-methods

Tissue Culture Infectious Dose 50%

A potency unit defined as a minimal dose of infectious material at which preparation causes cytopathic effects (changes in the morphology and metabolism of tissue culture cells, indicating cell death, due to suspected infection) in the 50% of the tissue culture-containing flasks inoculated with that dilution of infectious material in the product potency assay or pathogen activity assay.

Guidediagnostic-methods

Transcription-mediated Amplification

A technique used to selectively replicate nucleic acid sequences from RNA templates using reverse transcriptase and RNA polymerase. Reverse transcriptase generates cDNA from the region of interest using primers and then RNA polymerase generates copies of the original RNA template.

Guidediagnostic-methods

Transmission Electron Microscopy

An electron microscopy imaging technique that is utilized to examine structural components of a sample by passing electrons through the specimen.

Guidediagnostic-methods

Turbidimetry

A method to quantify the opaqueness of a liquid using a turbidimeter, by measuring the decrease in light intensity due to the scattering effect of suspended particles in the liquid sample.

Guidediagnostic-methods

Two Dimensional Gel Electrophoresis

A laboratory procedure in which proteins are first separated across a gel, usually polyacrylamide, according to their isoelectric point, and then separated in a perpendicular direction on the basis of their molecular weight.

Guidediagnostic-methods

Variant Calling

Technology that detects differences between an individual's DNA sequence and a reference DNA sequence.

Guidediagnostic-methods

Viral Identification

A diagnostic procedure to identify and characterize a viral organism.

Guidediagnostic-methods

Western Blotting

A laboratory procedure for the detection or identification of proteins or peptides that have been separated by gel electrophoresis and transferred onto nitrocellulose or other type of paper or nylon membrane. The proteins are then detected by reaction with enzymatically labeled or radiolabeled antibody probes.

Guidediagnostic-methods

Whole Exome Sequencing

A procedure that can determine the DNA sequence for all of the exons in an individual.

Guidediagnostic-methods

Whole Genome Amplification

Any technique designed to amplify a limited genomic DNA sample so as to generate a new sample that is indistinguishable from the original but with a higher DNA concentration.

Guidediagnostic-methods

Whole Genome Sequencing

A procedure that can determine the DNA sequence for nearly the entire genome of an individual.

Guidediagnostic-methods

Whole Transcriptome Sequencing

A procedure that can determine the nucleotide sequence for all of the RNA transcripts in an individual.

Tools

Decision support tools

Instrument Compatibility Matrix

Planning guide for assay-to-instrument matching across channels, formats, and validation scope.

Open tool brief

Sample Type Selector

Planning guide for translating sample type into extraction, workflow, QC, and buyer-guide next steps.

Open tool brief

Throughput Planner

Planning guide for converting throughput assumptions into workflow, staffing, and automation planning decisions.

Open tool brief