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This article waslast modified on 12 February 2019.

Laboratories use a variety of methodologies to test the countless analytes that are of interest to the medical community. Understanding the method used for a test provides a broader context for understanding your test results. Below are links to explanations of several common laboratory methods mentioned on this site.

Laboratory methods are based on established scientific principles involving biology, chemistry, and physics, and encompass all aspects of the clinical laboratory from testing the amount of cholesterol in your blood to analyzing your DNA to growing microscopic organisms that may be causing an infection. Such methods are much like the recipes in a cookbook, defining the procedures or processes that are used to test biological samples for particular analytes or substances. The laboratory scientist follows step-by-step procedures until the end product, a test result, is achieved.

Some methods, like some recipes, are much more complicated and labour-intensive than others and require varying degrees of expertise. Often, there may be more than one method that can be used to test for the same substance. Consequently, the same analyte may be tested differently in different laboratories, a fact that is crucial when comparing test results.

The descriptions of the methods listed below attempt to give some insight into the scientific principles used and the steps that are required to produce a result. Explanations of the methods and their differences are provided to give you a better understanding of some of the tests that you may undergo. These bulleted items are not intended to be a comprehensive list of available methodologies, but do represent some of those that are mentioned on this web site.

  • Immunoassay (IA)
  • Enzyme-linked immunoassay (ELISA)
  • Western blot
  • Fluorescence in situ hybridization (FISH)
  • Polymerase chain reaction (PCR)


Accordion Title
About Laboratory Methods
  • Immunoassay


    Immunoglobulins are proteins produced by the immune system to recognize, bind to, and neutralize foreign substances in the body. Immunoassays are tests based on the very specific binding that occurs between an immunoglobulin (called an antibody) and the substance that it specifically recognizes (the foreign molecule, called an antigen). Immunoassays can be used to test for the presence of a specific antibody or a specific antigen in blood or other fluids.

    When immunoassays are used to test for the presence of an antibody in a blood or fluid sample, the test contains the specific antigen as part of the detection system. If the antibody being tested for is present in the sample, it will react with or bind to the antigen in the test system and will be detected as positive. If there is no significant reaction, the sample tests negative. Examples of immunoassay tests for antibodies include Rheumatoid Factor (which tests for the presence of autoimmune antibodies seen in patients with rheumatoid arthritis), or antibodies made in response to a vaccination (such as tests for antibodies to Hepatitis B to assure that the vaccination was successful).

    When immunoassays are used to test for the presence of antigens in a blood or fluid sample, the test contains antibodies to the antigen of interest. The reaction of the antigen that is present in the person’s sample to the specific antibody is compared with reactions of known concentrations and the amount of antigen is reported. Examples of immunoassay tests for antigens include drug levels (like digoxin, vancomycin), hormone levels (like insulin, TSH, cortisol, and cancer markers (like PSA, CA 125, and AFP).


  • Enzyme-linked immunosorbent assay (ELISA)

    Enzyme-linked immunosorbent assay (ELISA)

    This testing method is a type of immunoassay. It is based on the principle that antibodies will bind to very specific antigens to form antigen-antibody complexes, and enzyme-linked antigens or antibodies can be used to detect and measure these complexes.

    To detect or measure an antibody in a person’s blood, a known antigen is attached to a solid surface. A solution containing the patient sample is added. If the patient’s sample contains antibody, it will bind to the antigen. A second antibody (against human antibodies) that is labelled with an enzyme is then added. If the enzyme-linked antibody binds to human antibodies, the enzyme will create a detectable change that indicates the presence and amount of the antibody in the patient sample.

  • Western blot 

    Western blot 

     This is an immunoassay test method that detects specific proteins in blood or tissue. It combines an electrophoresis step with a step that transfers (blots) the separated proteins onto a membrane. Western blot is often used as a follow-up test to confirm the presence of an antibody and to help diagnose a condition. Examples of its use include confirmatory HIV and Lyme disease testing.

    To perform a western blot test, a sample containing the protein is applied to a spot along one end of a layer of gel. Multiple samples and a control may be placed side by side along one end of the gel in separate “lanes.” An electrical current causes the proteins in the sample(s) to move across the gel, separating the proteins by size and shape and forming bands that resemble the steps of a ladder. These sample and control ladders are then “blotted” (transferred) onto a thin membrane that is put in contact with the gel. Labelled or tagged antibodies are then used in a one or two step process to detect the proteins bound to the membrane. For example, to confirm HIV or Lyme antibody tests, the proteins separated are those of the causative organism. A patient’s sample is then added to the blot and any antibodies to the organism are bound and later detected by labelled antibodies to human Immunoglobulins. The presence of the certain proteins is interpreted by comparison with known negative or positive control samples in the other lanes.


  • Fluorescence in situ hybridization (FISH)

    Fluorescence in situ hybridization (FISH)

    This testing method uses fluorescent probes to evaluate genes and/or DNA sequences on chromosomes

    Humans normally have 23 pairs of chromosomes: 22 pairs of non-sex-determining chromosomes (autosomes) and 1 pair of sex chromosomes (XX for females and XY for males). Chromosomes are made up of DNA, repeating sequences of four bases that form the thousands of genes that direct protein production in the body and determine our physical characteristics. DNA consists of two strands bound together in a double helix structure (like a spiral staircase). Each half of the helix is a complement of the other.

    For a FISH test, a sample of a person's cells containing DNA is fixed to a glass slide. Samples can include blood, bone marrow, amniotic fluid, or tumour cells, depending on the clinical indication. The slides with the "target" (person's) DNA are heated to separate the double strands of DNA into single strands. Fluorescent probes are then added to the sample. Fluorescent probes are sections of single-stranded DNA that are complementary to the specific portions of DNA of interest. The probe, which is labelled with a fluorescent dye, attaches to the specific piece of DNA. When the slides are examined using a special microscope, the genes that match the probe can be seen as areas of fluorescence, which will appear as bright spots on a dark background.

    This technique can be used to show the presence of extra gene copies (duplicated or amplified genes), and genetic sequences that are missing (deleted genes) or have been moved (translocated genes). Increased numbers of chromosomes, as seen in certain genetic disorders, can also be diagnosed using FISH technologies (trisomy 21 or Down’s syndrome, for example). The targeted area(s) or sequences of DNA are determined by the probes that are used. Multiple targeted areas in the DNA can be assessed at the same time using FISH probes labelled with a number of different fluorescent dyes.

    The following photographs show cells that have been evaluated using the FISH methodology. These are just a few examples of the use of FISH technique.

    Down’s syndrome
    In Figure 1, FISH testing is applied to cells in amniotic fluid, obtained from a pregnant woman carrying a baby suspected of having Down’s syndrome (trisomy 21). Three copies of chromosome 21 are observed (red signals). The green signals (two copies) are for chromosome 13; these are for control purposes and show that the test is working properly. FISH supports the clinical diagnosis of trisomy 21 in this baby. The doctors and genetic counsellors will work with the family to help them understand the results of the test.
    Breast cancer
    In Figure 2, FISH is used to assess breast tumour cells for the presence of an amplified gene, HER-2/neu (red signals). In approximately 25% of breast cancers, HER-2/neu is amplified. Women with amplified HER-2/neu tumours may be treated with a drug (Herceptin) that targets the protein that is the product of the abnormal gene. If a woman is NOT positive for HER-2/neu amplification, she is not likely to receive any therapeutic benefit from Herceptin therapy and other drugs will be considered.
    Figure 3 shows FISH used in a particular type of chronic leukaemia, chronic myelogenous leukaemia (CML). The specific probes used in this case detect BCR-ABL, an abnormal gene sequence formed by the exchange (translocation) of a portion of chromosome 22 (BCR, a green probe) with a portion of chromosome 9 (ABL1, a red probe). The areas of yellow fluorescence signify the abnormal, fusion gene (joining of red and green probes). Finding the BCR-ABL fusion confirms a diagnosis of CML. BCR-ABL positive patients may receive benefit from molecular-targeted drugs, such as imatinib.

  • Polymerase chain reaction (PCR)

    Polymerase chain reaction (PCR)

    The polymerase chain reaction (PCR) is a laboratory method used for making a very large number of copies of short sections of DNA from a very small sample of genetic material. This process is called "amplifying" the DNA and it enables specific genes of interest to be detected or measured.

    DNA is made up of repeating sequences of four bases – adenine, thymine, guanine, and cytosine. These sequences form two strands that are bound together in a double helix structure by hydrogen bonds (like a spiral staircase). Each half of the helix is a complement of the other. In humans, it is the difference in the sequence of these bases on each strand of DNA that leads to the uniqueness of each person's genetic makeup. The arrangement of the bases in each gene is used to produce RNA, which in turn is used to code the amino acid sequence of a protein. There are about 25,000 genes in a human genome, and expression of these genes leads to the production of a large number of proteins that make up our bodies. The DNA of other organisms such as bacteria and viruses is also composed of thousands of different genes that code for their proteins.

    How is the method performed?

     The PCR method uses cycles of repeated heating and cooling to enable separation and subsequent replication of the DNA strands. There are several components that are required for amplification of DNA by the polymerase chain reaction, each of which is described below:

    1. Template DNA. This is double stranded DNA that contains the DNA sequence of interest (i.e., the region which will be amplified in the PCR reaction).

    2. Primers: Primers are short sequences of bases made specifically to recognise and bind to the section of DNA to be amplified. Each PCR reaction mixture will contain two primers; one for each of the strands of the double stranded DNA template. The primers are called "forward" and "reverse" in reference to the direction that the bases within the section of DNA are copied.

    3. DNA Polymerase (frequently Taq polymerase): This is a DNA enzyme which copies DNA to make new strands. Taq polymerase is an enzyme found in a bacterium (Thermues aquaticus) that grows in very hot water, such as hot springs. The Taq polymerase is especially helpful for laboratory testing because (unlike many other enzymes) it does not break down at very high temperatures needed to do PCR.

    4. DNA bases: These are the individual DNA bases (adenine, thymine, guanine, and cytosine) that are incorporated by the DNA polymerase into the new DNA strands.

    5. A thermo cycler: PCR is carried out in several steps or "cycles" in an instrument called a thermo cycler. Within each of cycles, the instrument will increase and decrease the temperature of the specimen at defined intervals.

    Each cycle of PCR cycle involves 1) a denaturing step at 95 ºC, 2) an annealing stage at approximately 55 ºC and 3) an amplification step at 72 ºC. These steps are described further below:

    Step 1: The first step of PCR is to separate the strands of template DNA into two single strands by increasing the temperature of the sample to 95 ºC. This is called "denaturing" the DNA.

    Step 2: Once the strands separate, the sample is cooled slightly (to approximately 55 ºC). At this temperature the forward and reverse primers are allowed to anneal (bind) to the single DNA strands. This step is referred to as the annealing stage.

    Step 3: The temperature of the sample is then increased to 72 ºC. This is the optimum temperature for the DNA Taq polymerase . The polymerase works by incorporating DNA bases on to the end of the reverse and forward primers in a sequence that is complement to the template strand. The result is the formation of two double stranded sections of DNA each with one original strand and one new strand of DNA. This newly formed double stranded DNA can then act as a template for the next cycle. This step is referred to as the amplification stage.

    The above cycle of steps is then repeated many times within a single PCR reaction. In the second cycle, each of the two double strands separate to make four single strands and, when cooled, the primers and polymerase act to make four double strand sections. The four strands becomes eight in the third cycle, eight become sixteen, and so on. Within 30 to 40 cycles, as many as a billion copies of the original DNA section can be produced and are then available to be used in numerous molecular diagnostic tests. This process has been automated so that it can be completed within just a few hours.

    How is it used?

    This method can be used, for example, to detect certain genes in a person's DNA, such as those associated with cancer or genetic disorders, or it may be used to detect genetic material of bacteria or viruses that are causing an infection.

    These are just a few examples of laboratory tests that use PCR:

    Often PCR is used as a preparatory step to provide sufficient DNA for use in further diagnostic tests.

    Real-time PCR

    Real-time PCR (also known as quantitative PCR or qPCR) is similar to PCR except that data are obtained as the amplification process is taking place (i.e., "real time") rather than at a prescribed endpoint. This shortens the time for the test from overnight to just a few hours. The method requires incorporation of a fluorescent marker into the PCR products. The level of fluorescence is then measured by a detector, enabling quantification of the PCR products after each PCR cycle.

    RT – PCR (Reverse Transcriptase PCR)

    This method uses PCR to amplify RNA. RNA is a single stranded nucleic acid molecule and needs to be made into DNA before it can be amplified. The addition of a new strand that is the complement of RNA is achieved by the enzyme called Reverse Transcriptase (RT). A reverse primer binds to the single stranded RNA and the enzyme RT copies the RNA strand to make a single stranded DNA, which it then copies to make a double stranded DNA molecule. The double stranded molecule can then be amplified by PCR. Detection can also be by real-time methods.

    Here are two examples of laboratory tests that use RT-PCR: