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What Is Cytogenetic Testing and How Does It Work?

Posted on May 07, 2021
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Medically reviewed by
Anna C. Edens Hurst, M.D., M.S.
Article written by
Maureen McNulty

Cytogenetic testing provides information about a cell’s chromosomes (pieces of DNA). These tests can be used to diagnose different genetic diseases or different types of cancer. Cytogenetics can also be used during prenatal (before birth) tests. If a couple is struggling with infertility or has a chance of passing down a chromosome change that causes disease, doctors may find answers by performing a chromosome analysis of the amniotic fluid (liquid that surrounds a fetus).

Cytogenetic tests are often an important part of a leukemia diagnosis. Leukemia is usually first diagnosed using other tests, including:

  • A physical exam, in which the doctor checks for leukemia signs and symptoms
  • A complete blood count (CBC), a test that measures the levels of each type of blood cell
  • A peripheral blood smear, in which a doctor closely examines blood cells under a microscope to look for abnormalities
  • Bone marrow tests, in which a small sample of cells is taken from the bone marrow (tissue inside of certain bones) to look for cancer cells there

If these tests confirm that you have leukemia, your doctor will usually want to use cytogenetic tests to learn more about a cell’s chromosomes. This information helps your doctor diagnose what subtype of leukemia you have, evaluate your prognosis, and determine which treatments may be most helpful.

What Are Chromosomes?

Every cell contains many genes. A gene is a set of instructions that tells the cell how to make a particular protein, each of which has a different job within the cell. Genes and their proteins determine what we look like, shape how our bodies work, and influence our health.

Genes are made up of DNA. Each cell has several long pieces of DNA that are packed into a tiny shape using proteins. Each long piece of DNA is a chromosome.

Each human cell generally has 23 pairs of chromosomes or 46 chromosomes in total. Within each chromosome pair, one chromosome was passed down from your mother and the other from your father. Each chromosome is assigned a number from 1 to 22. An additional chromosome pair is the sex chromosomes, which are called X or Y.

Chromosome Changes in Cancer

Cells often develop changes in their genes or chromosomes. Usually, these changes are harmless. In some cases, however, multiple mutations collect within a cell. The gene or chromosome changes may make the cell grow too quickly, stop the cells from dying when they should, or prevent the cells from repairing damage. The cell becomes cancerous, growing out of control and making too many copies of itself. Some cancer-causing changes affect entire chromosomes, and others only affect one tiny part of one gene.

Chromosome Changes

Some cancer cells have changes in their number of chromosomes. Rather than having 46 chromosomes, they have too few or too many. There are different types of chromosomal abnormalities in this category:

  • Monosomy — A cell has only one of a particular chromosome, rather than a pair.
  • Trisomy — A cell has three instead of two of a particular chromosome.
  • Hypodiploidy — A cell has fewer than 46 chromosomes in total.
  • Hyperdiploidy — A cell has more than 46 chromosomes in total.

Cancer cells may also have changes that affect the structure of a chromosome. These may include:

  • Deletion — A piece of a chromosome is missing.
  • Duplication — Part of a chromosome has been copied.
  • Translocation — Part of one chromosome abnormally attaches to the end of a different chromosome.
  • Inversion — A piece of chromosome breaks, flips around, and reattaches itself to the chromosome, so that the piece is now backward.
  • Insertion — Part of one chromosome inserts itself into a different chromosome.

Gene Changes in Cancer

When a gene has a small change in its DNA, it is known as a gene mutation. Often, gene mutations do not affect the way a gene works. Other times, a single change can have big impacts on the protein that is made from the gene. The cell may make too little or too much of the protein. Or, the protein may work differently than it used to or completely stop working. The abnormal proteins can then change the way the cell behaves. Gene mutations can be found using other types of genetic testing.

What Happens During Cytogenetic Testing?

To measure chromosome changes, doctors use cytogenetic tests. These tests are sometimes run using a small sample of blood, which can be taken during a normal blood draw. Your doctor may also use a bone marrow sample for cytogenetic testing. Two procedures are often used to get a bone marrow sample:

  • A bone marrow aspiration is the removal of fluid from the bone marrow.
  • A bone marrow biopsy is the removal of cells from the bone marrow.

These tests may then be sent to a laboratory, where a doctor called a pathologist will closely study the cells and help provide a diagnosis. When you undergo cytogenetic tests, the laboratory is only looking for specific changes that are associated with cancer. These tests don’t uncover your unique genetic information. Neither the laboratory nor your doctor’s office will have information about your normal genes if you undergo these tests.

Types of Cytogenetic Tests

Different tests can identify different types of chromosome changes. There are three major types of cytogenetic tests that your doctor may use:

  • Karyotyping
  • Fluorescence in situ hybridization
  • Chromosomal microarray analysis


A karyotype test forms a picture of all of a cell’s chromosomes. During karyotyping, cells are taken from a blood or bone marrow sample and stained with special dyes. Then pictures are taken of the cells under a microscope. This process is performed by a pathologist, a geneticist, or a cytogenetics technician. They line up all of the chromosomes into pairs of 23 and count them. Each chromosome has a unique banding pattern — a series of light and dark areas that help the pathologist tell which chromosome is which. A karyotype can be used to see all of the major chromosome changes in a cell, such as translocations or changes in the number of a cell’s chromosomes.

Fluorescence in Situ Hybridization

Fluorescence in situ hybridization (FISH) is another test that finds chromosome changes. If you have a type of leukemia that is often linked to a specific chromosome change, your doctor may use FISH to find out whether that particular change is present in your cells.

To perform FISH, the pathologist will use a probe. This probe is a small piece of DNA that matches the DNA of part of a chromosome. The probe is attached to a fluorescent dye. When the pathologist mixes the probe with a cell’s DNA, the probe will attach to the specific area of the chromosome that it matches. The pathologist can look at the chromosomes under a microscope and see where the probe is located.

FISH can find chromosome deletions or translocations. For example, a pathologist may use one probe that matches part of chromosome 9 and another probe that attaches to chromosome 22. In normal cells, the two fluorescent probes are located on different chromosomes and will appear far away from each other within the cell. In cells that have a translocation between chromosomes 9 and 22, which is commonly seen in people with chronic myeloid leukemia (CML), the two probes will be right next to each other.

FISH can’t detect all chromosome changes. Each probe used in FISH only detects one specific change. Before running a FISH test, the pathologist needs to choose which chromosome change to look for and then select the appropriate probe. FISH will then show whether or not the cells have that particular chromosome abnormality.

Chromosomal Microarray Analysis

Doctors can use chromosomal microarray analysis (CMA) to look for chromosome duplications or deletions. CMA tests use a tool called a microarray, in which many small pieces of DNA are attached to a glass slide. All of these pieces of DNA match different sections of each chromosome. During a CMA, a pathologist takes a sample of cells, breaks apart the chromosomes, and stains the chromosomes with a fluorescent dye. Next, the chromosome pieces are added to the glass slide. When a piece of chromosome finds its matching piece of DNA on the slide, it attaches. If an area of the slide has no attached chromosome pieces, the pathologist knows there is a chromosome deletion in that area. If there are double the number of chromosome pieces attached in another area, the pathologist can tell that section of the chromosome was duplicated.

There are two main types of CMA: microarray-based comparative genomic hybridization (aCGH) and single nucleotide polymorphism (SNP) arrays. Both of these array types can show different small chromosome changes found throughout a cell.

CMA is not commonly used while diagnosing leukemia. However, in some cases, CMA may help a doctor learn more about a person’s prognosis or best treatment options.

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Posted on May 07, 2021
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All updates must be accompanied by text or a picture.
Anna C. Edens Hurst, M.D., M.S. specializes in general pediatrics as well as medical genetics. Review provided by VeriMed Healthcare Network. Learn more about her here.
Maureen McNulty studied molecular genetics and English at Ohio State University. Learn more about her here.

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