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Understanding Cytogenetic Tests vs. Molecular Genetics Tests: A Beginner’s Guide

Navigating the genetics world can be overwhelming, especially when distinguishing the different types of genetic tests. Two common categories of genetic analysis are cytogenetics and molecular genetics. In this blog, the fundamental differences between these two categories will be discussed. 


The area of cytogenetics focuses on studying the structure and number of chromosomes in cells. Chromosomes are thread-like structures found in the nucleus of cells and carry the genetic material (DNA) that determines our traits and instructs the body how to grow and develop. Cytogenetic evaluation can detect large-scale genetic abnormalities that involve whole chromosomes or large segments of chromosomes.

The examination of chromosomes (karyotyping) allows scientists to visualize and analyze them under a microscope. It involves taking a sample of cells and inducing them to grow and divide in culture. The chromosomes are then stained and examined under a microscope to identify any missing (deleted), extra (duplicates or copy number variants, or misplaced sections (translocation). Some chromosomal changes are too small to be seen under a microscope; scientists use another test called chromosomal microarray (CMA) to detect them. Examination by FISH (fluorescence in situ hybridization), utilizes fluorescent DNA probes that bind to specific targeted segments of chromosomes, which are then examined under a microscope. This technique can be used to count chromosomes and assess for certain duplications, deletions, and structural rearrangements.

Molecular genetics focuses on analyzing DNA sequences. These tests identify changes in specific genes (mutations or variants) or parts of genes (called nucleotides) which can provide valuable information in diagnosing genetic disorders or disease risk. Molecular genetic analysis is highly precise and can detect small-scale genetic changes, including single-nucleotide variations and small deletions or duplications. Two common methodologies for molecular analysis are PCR and DNA Sequencing

  • Polymerase chain reaction (PCR): PCR is a commonly used molecular technique where specific DNA sequences are amplified. This process is often employed as a first step to having enough copies of the target DNA to run other genetic tests  

  • DNA sequencing: DNA sequencing such as Sanger sequencing or next-generation sequencing is a powerful tool that allows scientists to determine the precise order of nucleotides in a DNA molecule. It can detect even a single change in the DNA code that might be linked to diseases like certain types of cancer, cystic fibrosis, or Tay Sachs disease.

Differences between cytogenetic and molecular genetic tests

  • Level of analysis: Cytogenetic tests study entire chromosomes or segments of chromosomes; molecular genetic tests analyze individual genes or specific DNA sequences.

  • Types of genetic changes detected:  Cytogenetic testing will detect large-scale chromosomal abnormalities, such as extra or missing chromosomes or segments of them, and structural changes. Molecular genetic testing will identify small-scale genetic changes, such as point mutations, insertions, deletions, and duplications within genes or specific DNA sequences.

  • Applications: Cytogenetic analysis is used to diagnose chromosomal disorders like Down syndrome, Turner syndrome, and DiGeorge syndrome, as well as other causes of developmental delay, intellectual disability, birth defects, and autism spectrum disorders. Cytogenetic testing is also used to diagnose certain forms of cancer. Molecular genetic tests are used to identify specific gene mutations associated with single-gene diseases, such as hereditary cancer syndromes, cystic fibrosis, Fragile X, and many other conditions

Is it cytogenetic or molecular genetics?

Identifying whether a genetic test falls under the category of cytogenetic or molecular genetics can often be recognized from the test's name or description. Here are some common naming conventions and key phrases that can help you determine whether a test belongs to the cytogenetic or molecular genetics category. 

  • Chromosome analysis: Tests with names containing "karyotype" or "chromosome analysis" often fall into the cytogenetic category. For example, "Chromosomal Karyotype Analysis" or "Prenatal Chromosome Testing"

  •  FISH: The term "FISH" in the test name is a clear indicator of a cytogenetic test. For example, "FISH, Prenatal Screen"

  • Chromosomal disorders: Tests specifically focused on diagnosing conditions like Down syndrome, Turner syndrome, or other large-scale chromosomal abnormalities usually belong to the cytogenetics category

  • Certain techniques: if the test name includes "PCR" or "amplification," it's a molecular genetics test. For instance, "PCR-Based Genetic Testing" or "Mutation Detection by Amplification". Tests with names including "sequencing" or "genetic sequencing" usually fall into the molecular genetics category. Examples include "DNA Sequencing for Genetic Mutations" or "Next-Generation Sequencing Analysis"

  • Specific gene names: tests targeting a specific gene or gene mutation, such as "BRCA Gene Mutation Test" or "CFTR Gene Analysis," are molecular genetic tests

  • Single-gene disorders: tests designed to identify mutations associated with single-gene disorders, like "Huntington's Disease Genetic Testing," typically belong to the molecular genetics category

In summary, cytogenetic tests analyze the structure and number of chromosomes, while molecular genetic tests focus on studying specific genes and DNA sequences. Both types of tests play critical roles in genetic research and medical diagnosis, enabling healthcare professionals and researchers to better understand the genetic basis of diseases and provide personalized care. 

It's important to consult with genetic counselors to ensure you correctly identfied the test and understand the nature of the test. Quest Diagnostics genetic counselors may be reached through the GENE INFO line at 1.866.GENE.INFO (1.866.436.3463)

  1. American Society of Human Genetics (ASHG). (2019). What is a cytogenetic test? Retrieved from:

  2. National Human Genome Research Institute (NHGRI). (2021). What are molecular genetic tests? Retrieved from:

  3. National Society of Genetic Counselors (NSGC). (2021). Genetic Testing: Frequently Asked Questions. Retrieved from:


Sheila Andre