About the amniotic fluid testing microarray method [supervised by a physician].

What is an amniotic fluid test?

An amniotic fluid test is one of the tests performed around 16 weeks’ gestation (16 weeks from the last menstrual period) to check for chromosomal abnormalities and congenital metabolic abnormalities in the unborn baby. The amniotic fluid is collected by inserting a needle into the abdomen while confirming the location of the fetus and placenta using ultrasound. The amniotic fluid is then analyzed for chromosomes, DNA, and metabolites to confirm whether there are any abnormalities. Because the test is performed by inserting a needle into the abdomen, it is somewhat more invasive than NIPT, which requires only blood from a needle inserted into the arm. However, NIPT cannot make a definitive diagnosis, and if a positive result is obtained, an amniotic fluid test is necessary to make a definitive diagnosis. The reason for this is to avoid a false positive result when the baby is born without any chromosomal abnormality. In the case of HIRO CLINIC NIPT, amniotic fluid can be tested by real-time PCR or exome analysis at Tokyo Daini Laboratory of Hygiene and Preventive Medicine. NIPT is performed by the Tokyo Daini Sanitary Laboratory, which allows us to quickly diagnose and communicate the results to the patient.

The following types of amniotic fluid tests are available

  • Real-time PCR
  • Exome Analysis
  • G-band method
  • FISH method
  • Microarray method

In other words, the microarray method is included in the amniotic fluid test and is a classification within the amniotic fluid test. The microarray method is the most up-to-date of the three tests and is capable of detecting minute changes in chromosomes.

What kind of test is the microarray method?

Microarray testing directly translated into Japanese means “fine array.
It is an analytical method that can observe changes in a large number of chromosomes in detail, and is said to be able to observe changes 100 times finer than the chromosome segregation method described above.
Prices vary from clinic to clinic.

Until now, chromosome aberrations could not be detected by the G staining method unless the change was 5~10 Mb in size. This means that until now, on the contrary, it has been difficult to detect duplications of DNA fragment deletions in the unit of Mb by sequence analysis.
The FISH method made it possible to confirm deletions and translocations of about 100 kb, but this was limited to specific regions.

However, innovations in microarray analysis have made it possible to detect chromosomal aberrations that are complicated by quantitative imbalances as small as several tens of kilobases in specific DNA regions.
In other words, it is now possible to detect even finer chromosomal aberrations and deletions that cannot be detected by conventional chromosome sequencing.

Then, if we ask whether unknown genes can be analyzed, the answer is no.
Currently, there are next-generation sequencers that can detect unknown genes in sequence analysis, but only known genes can be known by the microarray method. This is because there is a difference in the method of the microarray method.

The microarray method tests for gene mutations by placing mutated fragments of known genes and standard gene fragments on a chip to see how much they fluoresce, the intensity of the light, and the degree of color.
The amount of amniotic fluid required for the test is approximately 20 to 30 ml, and the test results are available approximately two weeks after the specimen arrives at the testing company.

In addition, the microarray method is basically incapable of detecting balanced reciprocal translocations and inversions because the method of analysis is different from chromosome analysis.

What is equilibrium mutual translocation and inversion?

So what does equilibrium reciprocal translocation or inversion mean?

Balanced reciprocal translocation

Equilibrium reciprocal translocation is a type of translocation that is found in about 1 in 400 people, or about 5 percent of infertile couples.

It is an abnormality that occurs when two different chromosomes undergo translocation and the broken fragments are exchanged with each other.
It is more likely to occur when two chromosomes cross.
In most cases, the position of the genetic information has only changed, so there is often no change in phenotypic characteristics or appearance.


Inversion occurs when a chromosome breaks are recombined within a chromosome and the direction of chromosome segmentation is inverted because the chromosome is sandwiched between two broken ends.
However, in rare cases, minor chromosomal duplications or deletions can be detected in conjunction with translocations and inversions.

Cautions for Microarray Methods

In addition, microarray methods unfortunately cannot find below-resolution deletions, duplications, or gene rearrangements. Therefore, it is not possible to detect 100 percent disease. Therefore, the absence of an abnormality by the microarray method does not mean that the disease is absolutely absent.

However, it is excellent at detecting entire genes and deletions and duplications. Because of its very good detection power, it can detect chromosomal changes that are very rare and can be found in normal individuals. In such cases, it may be recommended that both parents be tested to determine if the chromosomal abnormality found has pathological significance.

Because of this, this test is not performed on all people, and amniotic fluid testing is often performed using the microarray method on those for whom it is recommended. The microarray method is often used in the following cases: when the ultrasound examination indicates that the baby is likely to have an abnormality, when the chromosome analysis does not clarify whether the baby is abnormal or not, or when the baby’s family has a disease for which the microarray method is considered to be appropriate.

What should I do if the microarray method finds an abnormality?

First, please ask for an explanation from the hospital where you had that examination.

The microarray method is a sensitive test that detects minute chromosomal changes and is often difficult to interpret. If possible, it would be ideal to undergo testing at a clinic where there are specialists from the Japanese Society of Obstetrics and Gynecology.
If necessary, genetic counseling should be sought. Genetic counseling is to receive medical information and advice on genetic problems.

First, it is necessary to lay the groundwork for the family to be able to make their own decisions.
To this end, it is essential to understand the situation and the disease. If possible, it would be ideal to have a thorough discussion with the family in advance of the examination, including what to do if the test results are abnormal.

Ultimately, it is you who will decide the future of your baby.
Therefore, it is important to gather information on a daily basis so that you can eliminate any anxiety you may have before undergoing the test. It is also important to gather information on a regular basis so that you can eliminate any anxiety you may have before taking the test.

Please take advantage of this site of HIRO CLINIC NIPT as it has many other columns.

Article Editorial Supervisor

Private: Dr. Hiroshi Oka

Private: Dr. Hiroshi Oka

NIPT Specialist Clinic, Doctor of Medicine
Graduated from Keio University, School of Medicine


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