What is the difference between a karyotype and microarray analysis?

In this blog post, we will get a bit technical and discuss the difference between two diagnostic tests that are available: karyotype and microarray analysis. Someone may be offered either one of these analyses either for themselves or for their pregnancy. The post will start with a review of chromosomes as this is what both of these analyses will ultimately evaluate and then the differences between the two in the context of pregnancy. In order to perform the karyotype or microarray analysis in pregnancy, a procedure like the chorionic villi sampling (CVS) or amniocentesis would need to be performed. Check out the links to learn more about the procedures.

What are chromosomes?

Chromosomes are structures made up of our genes. We have about 20,000 genes that need to fit inside every one of our cells. Our genes package themselves into chromosomes in order to fit inside our cells. I like to think of a chromosome as a string with beads on it. The beads represent our genes. If you hold one end of the string and twist the other end, it will condense - this is similar to how genes become chromosomes. If we unravel a chromosome, we get an extremely long piece or string of our genes.

Typically, we have a total of 46 chromosomes. Our chromosomes come in pairs, so we have 23 pairs in total. We inherit one chromosome from our mom/egg donor and the other from our dad/sperm donor. We label the first 22 pairs based on their size. If you look at the pictures below, you can see that chromosome pair labeled one is the largest sized chromosome and chromosome pair 22 is the smallest. The last pair of chromosomes are our sex chromosomes. Two X chromosomes typically determine female reproductive organs and an X and Y chromosome determines male. Genes on the Y chromosome are what tell the developing human to create male genitalia; otherwise, the default is female reproductive organs (in general).

genetic male karyotype

genetic female karyotype

How are chromosomes assessed?

There are a few ways chromosomes can be assessed. Here we will discuss the two more common assessments.

Karyotype

A karyotype counts the number of chromosomes someone has as well as checks for any structural differences or rearrangements. The above pictures are karyotypes. It is a snapshot of what the chromosomes look like under a microscope after they have been lined up and organized.

Microarray

A microarray can also count the number of chromosomes but is better able to detect small pieces of the chromosome that may be extra or missing, called microduplications and microdeletions, respectively. Unlike the karyotype, it is not able to detect structural differences or rearrangements of the chromosomes.

Why chose one over the other?

To answer the question, the reason for pursing diagnostic testing is important. In the context of pregnancy, the karyotype analysis may be performed if a provider suspects the pregnancy has a common chromosomal condition like Down syndrome. The provider may suspect this because of blood test results, family history, or ultrasound findings.

Otherwise, a microarray may be chosen because it can detect the same conditions as the karyotype as well as conditions the karyotype cannot detect.

However, there is the possibility of “variants of uncertain significance” when having the microarray analysis performed. Variants of uncertain significance means there was a finding detected with the microarray, but, at this time in science, it is unclear if that finding has any impact to the pregnancy’s health. More testing or more time will be needed to figure out if the finding is impactful to the health of the pregnancy or if it’s normal.

Receiving a variant of uncertain significance result can make it challenging to figure out what to do with that information, particularly while pregnant.

Sometimes both assessments are ordered in order to look at the chromosomes in different ways. They may be ordered at the same time or one after each other. For example, if the microarray was ordered first and showed the pregnancy has Down syndrome, then the karyotype may be ordered to try to figure out how the extra chromosome came about. It can be helpful to figure where the extra chromosome came from to estimate the chance to have another pregnancy with Down syndrome in the future.

Ordering microarray and karyotype can be complex as shown below. There are difference approaches to ordering the tests. Each test has its benefits but limitations.

* This blog constitutes general information about genetic testing and medical screening. This blog does not offer or provide medical advice or diagnosis, and nothing in this blog should be construed as medical advice or diagnosis. Do not rely on the information in this blog/article to make medical management decisions. Please consult with a medical professional before making those decisions. Do not delay in seeking professional medical advice if you think you have a medical concern. Do not disregard professional medical advice based on any information received in this blog.