Comparison Between Karyotyping and Microarray

A karyotyping is a conventional cytogenetic technique that visualizes the chromosomes whilst the microarray is a molecular cytogenetic technique that analyses the chromosomes.

The cytogenetic techniques rely on the study of chromosomes either structure or numbers. Changes in any of the properties of chromosomes create phenotypic variation. 

For instance, we humans have 23 pairs of chromosomes, if any of the chromosomes are deleted or inserted into it, it can cause serious health-related problems. The classical example of it is trisomy 21, in which the whole new chromosome 21 is present in a genome with the pair. 

Chromosomal anomalies are as common as the gene! Traditional technique much like the karyotyping employed in order to study the structural and numerical differences in chromosomes. 

But unfortunately there are several limitations of it. And henceforth the molecular cytogenetic techniques are evolved. 

Much like the FISH- fluorescence in situ hybridization or chromosome microarray analyze each chromosome very precisely and overcome the limitations of the karyotyping. 

Still, the utility and the importance of karyotyping is unmatched. In the present article, we are going to compare two of the best cytogenetic techniques that are karyotyping and microarray. 

We are also given in sight of applications and limitations of both. 

Related article: Karyotyping vs Karyotype.

Karyotyping vs Chromosome microarray:

The karyotyping technique is a traditional cytogenetic analysis technique which visualizes chromosomes. While the microarray technique has recently evolved and analyses chromosomes at molecular level and hence known as molecular cytogenetic techniques. 

Technically the karyotyping method is based on the principle of cell culture and cell harvesting and on the other hand the microarray technique is based on DNA extraction and hybridization. 

To observe chromosomes under the microscope cells are arrested at metaphase stage, while on the microarray side, no need to culture cells or arresting chromosomes at metaphase. 

In karyotyping, cell culture is pivotal, therefore strict aseptic conditions are needed during the entire procedure. But it is not the case with the microarray procedure. 

In the microarray, although aseptic conditions should be maintained but not needed once DNA extraction is performed. The chance of contamination becomes negligible. 

During karyotyping we need to harvest the metaphase cells to separate it while the cell harvesting procedure is not needed in microarray. 

Also extensive hypotonic treatment is even not required in DNA microarray. 

To observe cells under microscope we need to stain cells in karyotyping while to make chromosomal DNA detectable, fluorescent molecules are attached to the probe. 

The slide of karyotyping is a collection of metaphase chromosomes which are visible under a microscope. While a slide or the array of CGH or microarray contains thousands of DNA probes which hybridize with the sample DNA. 

The fluorescent detector detects the hybridization signal during microarray. 

The karyotyping technique is labor extensive, time consuming and less accurate while the microarray technique is rapid, accurate and less time consuming. 

Only larger copy number variations above 10 to 20Kb and change in chromosome number are detectable using the karyotyping whistl using the microarray or chromosome microarray minor deletions, duplications and other copy number variations are detectable. 

Also, through karyotyping can detect several chromosomal abnormalities it is still not able to quantify the copy number variations. But contrary, using the microarray technique the copy number variations can be detected as well as quantified. 

These are the points that make the microarray technique stand above the karyotyping. Now let us see how karyotyping is superior over the microarray. 

Major structural chromosomal changes are detectable by karyotyping, but the microarray can’t detect larger copy number variations of 10 or 20Kb. 

DNA is not required in karyotyping but a high quality DNA sample is required in order to get good results during microarray analysis. 

Furthermore, additional amplification steps and DNA library preparation are needed in microarray but not in karyotyping. 

So we can say that though the karyotyping technique is tedious and time-consuming, it is simple. While the microarray procedure is complex and relies on hybridization. 

In terms of the cost, the karyotyping technique is cheaper in comparison with the DNA microarray. 

Fluorescent chemistry and fluorochromes are not required during karyotyping, however, the entire microarray technique is based on the fluoro-chemistry. 

High end instrumentation and state of the art laboratory facilities are not needed in setting up the karyotyping lab, although a good, decent and powerful microscopy system is needed.

On the other side, the microarray is a molecular cytogenetic technique which requires an extensive instrumentation system like PCR, automated DNA extractor, microarray detector, microarray software and DNA quantification machine.

One of the crucial limitations of the microarray technique is that prior sequence information must be required to design the microarray slide or probes whistl no sequence information of data is needed to perform the karyotyping. 

In addition to this, the control plays an important role in studying the expression of copy number variation hence control sample is also a key element of microarray while control slide or normal sample is not required in karyotyping. 

Karyotyping in nutshell: 

The karyotyping technique relies on cell culture and metaphase capture in order to visualize chromosomes. If you want to know why only the metaphase, read this article: which cell division phase is best for karyotyping?

Cell culture, metaphase preparation, cell harvesting and microscopy are steps by which a chromosome karyotype is prepared. 

Using Giemsa staining and banding different chromosomes are distinguished under the microscope. 

The advantages of karyotyping are that it is simple and powerful enough to detect numerical and major structural chromosomal anomalies. 

It is most widely accepted for the prenatal screening of samples to find out aneuploidies. 

The technique is more prone to contamination, time-consuming and needed an expert to evaluate results which are some of the limitations of it. 

Read more on karyotyping: What is karyotyping?- Definition, process, steps and Applications.

Microarray in nutshell: 

The microarray technique is based on the principle of fluorescent chemistry and hybridization in which the immobilized sequence-specific fluorescently labeled problem hybridizes with the complementary DNA sequence.

Thousands of probes are immobilized on the glass slide which hybridizes with the sample DNA and creates the hybridization picture of all chromosomes. 

Some of the advantages of the microarray technique are, 

It is so powerful that it can detect thousands of different copy number variations from all the chromosomes and even quantify it. 

Also it can detect minor variations which is not possible by conventional karyotyping. 

Requirement of prior sequence information, high end instrumentation and the cost of the entire assay are the major limitations of the present technique. 

Results of Karyotyping and Microarray: 

The results of karyotyping and microarrays also look so different. As we are doing microscopy in karyotyping a picture of all the chromosomes are given into the results.

Whilst, the microarray results are just a computer generated chromosomal picture showing the hybridization pattern of control as well as the sample DNA on chromosomes. 

The have given the image of karyotyping and microarray results here below, 

The results of Karyotyping and whole-chromosome microarray.


Karyotyping Microarray 
Technique Conventional cytogenetics Molecular cytogenetics 
Principle Analysis of metaphase chromosomesFluorochrome probe-DNA hybridization 
StepsCell culture, metaphase preparation, cell harvesting, slide preparation and microscopy DNA extraction, DNA fragmentation, DNA amplification, library preparation, DNA hybridization and results analysis. 
Must required Metaphase chromosome Whole genomic DNA 
Not needed DNA Metaphase chromosomes 
ProsCan identify numerical and major structural chromosome changes.  Can identify and quantify minor as well as major chromosome copy number variations. 
Plus point Not relies on fluoro-chemistry Not required cell culture and metaphase chromosomes. 
Limitations Can’t identify minor changes Prior sequence information must be required. 
New variations Can be detected, if vision Can’t be detected. 
Nature Time-consuming but cheaper Rapid and costlier 

Field of study: 

Although the technique karyotyping is slower, and prone to contamination, it is widely used in various fields. 

Various chromosomal anomalies like the monosomy, disomy, trisomy, chromosome deletion of duplication are screened by prenatal karyotyping.

It is also applicable to detect the role of chromosomal anomalies in recurrent miscarriate, infertility and product of conception studies. 

New copy number variations can also be studied 

On the other side, the microarray can locate various chromosomal anomalies on chromosomes. It can even locate and identify single nucleotide polymorphism as well. 

As it can give us vast data of the entire genome, it is commonly used genome-wide association studies and whole genome microarray studies. 

Related article: Karyotype of Down Syndrome (Trisomy 21)- Explained.


I had worked on both type of platforms but the karyotyping technique is my favourite one! though it is restricted, doing karyotyping is a challenging task, You don’t know every time what you will get.

On the other side, the microarray technique is highly versatile and accurate. It facilitate detection of thousands of copy number variations in single experiment.

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