Overview and Prospects for Whole Chromosome Testing

Overview and Prospects for Whole Chromosome Testing

In contrast to conventional prenatal diagnosis, which tests only three autosomes, the all-chromosome test tests all autosomes as well as sex chromosomes.
In this article, we will introduce such all-chromosome testing with examples.


All-chromosome testing, which tests all autosomes, including sex chromosomes, rather than the conventional testing of only three autosomes in prenatal diagnosis.

In this article, I would like to explain the details regarding such all-chromosome testing.

We will provide basic information on all-chromosome testing and a deep dive into prenatal diagnosis that incorporates all-chromosome testing into the examination, which is being performed by several unlicensed facilities, as an example.

We will also mention other clinics in Japan where you can take a full chromosome test and the costs involved. We hope this will help those who are wondering whether or not to undergo prenatal diagnosis.

What is a whole chromosome test?

The all-chromosome test is a diagnostic method that has become increasingly popular in recent years, testing for abnormalities in all autosomes, including autosomes 1 through 22 and sex chromosomes, which are called autosomes.

Normally, only 13, 18, and 21 trisomies were tested for sex chromosomes in prenatal testing.

The reason for this is that these autosomes have relatively little negative impact on survival and some fertility even with complete trisomies, whereas other autosomes have lower hope for survival when abnormalities are present.

Furthermore, the guideline for prenatal testing around the world was that chromosomes other than chromosomes 13, 18, and 21 did not need to be tested in the first place, since the occurrence of an abnormality meant death.

On the other hand, conventional prenatal diagnosis can only provide information on three autosomal chromosomes, as described above, and there have been reports of cases in which a child who was relieved because there were no abnormalities in these chromosomes was found to have abnormalities in the sex chromosomes.

For these reasons, the need to test for all autosomes has become a necessity, and the number of clinics that offer all-chromosome testing has been increasing, driven by users who say that it is better to have many options to begin with.

Characteristics of prenatal diagnosis with all-chromosome testing

Currently, whole-chromosome testing is not permitted in licensed facilities.

In addition to the tests provided by Verinata, other tests such as Serenity24 by Cooper Genomics are available. In Japan, Human Investor has been conducting these tests on behalf of clinics since June 19, 2020.

In addition, sex chromosome abnormalities such as monosomy X (Turner's syndrome) can also be tested.

Therefore, it is one of the newest prenatal tests available in Japan.

In all chromosome tests, blood sampling can be performed in only one visit, and the average time until test results are available is around 10 days, which is a very short time, offering the advantage of a low time and physical burden.

If the fetus is a twin or larger, only the usual 13, 18, and 21 autosomal heterosomes and Y autosomes can be tested.

Unlicensed facilities are available to a wider range of people

New prenatal diagnosis, which tests only for 21-trisomy, 18-trisomy, and 13-trisomy at licensed facilities, was hampered by the high overall cost due to the separate fees for consultation and testing, and the requirement for genetic counseling.

Another problem is that the new prenatal diagnosis at licensed facilities has strict requirements, such as only pregnant women who are between 10 and 18 weeks post-pregnancy and over 35 years of age can undergo the test.

Currently, the age requirement is greatly relaxed at an increasing number of licensed facilities, and anyone who is at least 10 weeks pregnant can undergo the test.

The cost for a full chromosome test is around 200,000 yen in Japan, although it can go up or down depending on the plan.

Below is a list of clinics in Japan as of July 2020 that offer all-chromosome testing and an example of the cost.

As for locations, only representative locations are listed.

In addition to the stores listed in the table, all-chromosome testing is available at a wide range of clinics across the country.

<Example of facilities where whole chromosome testing is available>

Clinic Name Location Cost of a full chromosome test
NIPT japan Chiyoda Ward, Tokyo, etc. 160,000-180,000 yen
Hiraishi Clinic Roppongi, Minato-ku, Tokyo, etc. 210,000 yen
Hiro Clinic Yaesu, Tokyo, etc. 180,000 yen
Rajboo Clinic Ginza, Chuo-ku, Tokyo, etc. 17万円

Whether or not the practice of whole-chromosome testing should continue

Here we would like to discuss the significance and pros and cons of all-chromosome testing.

In fact, there are some controversial opinions about the whole-chromosome test in Europe, the U.S., and Japan.

As explained earlier, most autosomal abnormalities do not lead to birth, so the conventional rule is that it is sufficient to examine only trisomies 21, 18, 13, and sex chromosomes, which are the most common chromosomes that result in birth and the highest number of cases.

Nevertheless, since the mother has the right to know about her baby, it is only natural that she should make the final decision after knowing all the information through a full chromosome test (I dare not question the right or wrong of abortion here).

As for the ethical aspects of the abortion issue, please refer to the following article, which refers to the ethical aspects of the abortion issue.

In reality, in Europe and the United States, various testing companies offer whole-chromosome testing, so there is a definite need to know fetal information at an early stage.

Compared to the probability of finding abnormalities from chromosomes 21, 18, and 13, the percentage of positive results from the other chromosomes is low.

However, according to a statistical survey, the positive rate for all chromosomes in chorionic villus biopsies is 0.56%, or 1 in 2,000.

In light of this, it may be necessary to test all chromosomes in order to "know" the condition of the fetus as soon as possible.


Even if an autosomal abnormality other than chromosomes 21, 18, or 13 is present, it does not necessarily mean that the fetus will die, and there are still cases in which a fetus is born with the abnormality.

In light of this, it would be desirable for all mothers and their children if all-chromosome testing, which is more comprehensive and autosomal in nature, becomes more widespread.

As of July 2020, as mentioned above, in Japan, inspections previously performed by Verinata in the U.S. are now performed by the Tokyo Hygienic Laboratory in Japan.

This has succeeded in cutting down on transportation-related restrictions and risks, as well as time and financial costs that had previously been incurred during inspections.

Thus, the problems related to cost and age limits involved in all-chromosome testing are gradually being alleviated.

In turn, the author hopes that safer, more accurate, and less expensive prenatal diagnosis will become more widespread.