[Expert Explanation] Why Does Paternity DNA Testing Require Two Separate Analyses?

Rewritten on: April 12, 2026

Because paternity DNA testing carries the risk of misjudgment due to human error such as sample mix-ups, a two-analysis (double-check) system as recommended by the international standard AABB is essential. This article explains the key points for choosing a trustworthy testing laboratory.

DNA testing, which scientifically confirms parent-child relationships, is an extremely important test that can have a major impact on one's life and family relationships.
In particular, a result of "the parent-child relationship is denied" places a heavy psychological and social burden, so test results must meet an extremely high standard of accuracy and reliability.
So why is "two-time analysis" necessary for paternity DNA testing? This article explains in detail the risks inherent in DNA testing and the importance of the double-check system adopted under international standards.
For anyone considering DNA testing, deciding "which laboratory to use" is an extremely important decision that determines the reliability of the results. Looking beyond just price and speed to the quality control system behind the analysis process is key to a choice you won't regret.

The risk of sample mix-ups in DNA testing

In DNA testing, testing laboratories handle a large number of samples simultaneously every day.
Because of this, even with a strict management system in place, the possibility of the following types of human error is never zero. (1)

• Mistakes in labeling samples
• Mix-ups during storage
• Mix-ups during the analysis process
• Sample contamination during the DNA extraction stage

If analysis is carried out on samples that have been mixed up, the results will be calculated based on the DNA of an unrelated third party, creating the danger that a result different from the true one will be reported.
This risk increases especially when samples from multiple clients are processed in the same batch. The more samples a laboratory accepts, the more the time and attention available for checking each individual case tends to be spread thin. In addition, when sample containers look similar (for example, when using oral swab kits from the same manufacturer), it can be hard to distinguish them by appearance alone, creating an environment prone to overlooked label checks. (2)

Why a denial result can occur even for a genuine parent-child relationship

The most serious problem in DNA testing is a result of "denial of the parent-child relationship."
Even when the biological parent-child relationship is genuinely true, a sample mix-up or a mistake in the process can cause an incorrect denial result to be produced. (3)

Such a misjudgment not only causes the client intense anxiety and doubt, but can also develop into family trouble or legal problems, and should never be taken lightly.
Specifically, the following kinds of serious impacts can occur.

• The trust between spouses collapses at its foundation, leading to divorce
• Legal disputes arise over child custody or inheritance rights
• The client falls into a depressive state from the psychological shock
• Family bonds are irreversibly damaged based on an incorrect result

Of particular note is the rare occurrence of mutation seen in STR (Short Tandem Repeat) analysis. Cases can occur where the alleles at an STR locus do not match between parent and child, and if the mismatch is limited to one or two loci, the possibility of mutation must be considered. However, this judgment tends to be ambiguous with only a single analysis, which is another reason a double-check is necessary. (3)

Two-time analysis to prevent human error

What is needed to minimize these risks is the "double-check," which involves performing analysis twice on the same sample.
In two-time analysis, the analysis process and the staff in charge are separated for the repeat test, to confirm whether the same result as the first analysis is obtained.
This "re-verification of the test result" makes it possible to check the following points.

• Whether a sample mix-up has occurred
• Whether there was any technical error in the first analysis
• Whether the result is reproducible
• Whether a mutation can be correctly distinguished from a genuine mismatch

Human errors that tend to be overlooked with a single analysis can be prevented with high probability through two-time analysis.
In the double-check process, it is recommended that the first and second analyses be conducted by different technicians in an independent environment. This eliminates bias arising from a particular technician's judgment or technical habits. Furthermore, by using a different DNA extract for the second analysis than for the first, it is also possible to simultaneously confirm whether contamination occurred during the extraction stage.

The difference between single-analysis and two-time analysis

Below is a comparison, from the client's perspective, of the difference between a single analysis and two-time analysis (double-check).

The double-verification system defined by the international standard AABB

Widely known as the international standard for DNA testing is the double-verification system defined by the American Association of Blood Banks (AABB: Association for the Advancement of Blood & Biotherapies).
AABB began with the oversight of blood banks and is now recognized as a global authority in establishing quality standards for DNA paternity testing as well.

Behind this concept lies the understanding that, while STR analysis is a scientifically established technique, confirming reproducibility is essential to guarantee analytical accuracy and the reliability of results.
Under AABB, results in which a parent-child relationship is denied require especially careful handling, and within the industry, confirming results through multiple analyses (double-check) is considered important. (4)

Specifically, testing laboratories accredited by AABB comply with quality control protocols such as the following.

1. Double ID verification at the time of sample receipt (cross-checked by two or more technicians)
2. Ensuring traceability at every stage from DNA extraction through analysis
3. Mandatory re-extraction and re-analysis when a result denying the parent-child relationship is obtained
4. Cross-checking of results by an independent technician
5. Participation in regular external proficiency testing programs

These standards are not simply about "measuring twice," but form a system that systematically guarantees the quality of the entire testing process. AABB-accredited testing laboratories exist worldwide, but within Japan, the number of institutions that have obtained this accreditation currently remains limited.

How STR analysis works and the scientific basis for double-checking

The STR (Short Tandem Repeat) analysis commonly used in DNA testing is a method that identifies individuals by using differences in the number of repeats of short repeating sequences scattered throughout the human genome. A typical paternity DNA test analyzes 15 to 20 or more STR loci simultaneously and confirms the inheritance pattern of alleles between parent and child. (3)

The accuracy of STR analysis is extremely high, and when properly conducted, the probability of confirming a parent-child relationship reaches 99.99% or higher. However, this high accuracy applies only when "the correct sample has been correctly processed." No matter how high the precision of the analysis equipment itself (the capillary electrophoresis device) may be, if a sample mix-up has occurred, the resulting data is not actually that of the person being tested in the first place, so the scientific precision becomes meaningless.

The reason the double-check is scientifically valid is that by independently obtaining data twice from the same sample and confirming that the two results match, it becomes possible to verify the basic precondition that "the sample being analyzed is indeed the client's DNA." If the two analysis results differ, a sample mix-up or contamination is suspected, and an investigation and retest are carried out immediately.

The current state of domestic DNA testing and points to check before applying

Unfortunately, in Japan, many testing laboratories currently report results based on only a single analysis.
As a result, when a denial result is obtained, the following kinds of doubts can remain.

• Is there truly no blood relationship?
• Could this be a misjudgment caused by a sample mix-up?
• Is the mismatch due to mutation, or is it a genuine non-parent-child relationship?

Before applying for DNA testing, it is important to always confirm whether a double-check system based on two-time analysis has been implemented — this is a key point for avoiding regret.
In addition, because Japan does not yet have sufficiently developed legal regulations or unified standards for DNA testing, there can be large differences in the level of quality control from one laboratory to another. Whether the laboratory has obtained ISO certification or the Privacy Mark, the number of loci analyzed, and the content included in the report are all important factors to check.

A checklist to review before applying for DNA testing

To receive a highly reliable DNA test, be sure to check the following points before applying.

1. Whether a double-check system is in place: Is two-time analysis included as a standard protocol?
2. Quality certifications obtained: Has the laboratory obtained ISO 9001 or the Privacy Mark?
3. Number of loci analyzed: How many STR loci are analyzed (more loci means higher accuracy)?
4. Content of the report: Are the allele data and calculation basis for each locus clearly stated?
5. Presence of specialized staff: Will a doctor or genetic counselor explain the results?
6. Personal information management: Are the rules for storing and disposing of samples and data clear?

Checking these items in advance allows you to undergo DNA testing with peace of mind.

The importance of choosing a trustworthy testing laboratory

Paternity DNA testing is a test in which every single result is deeply connected to a person's life.
seeDNA Genetic Medicine Research Institute conducts testing that prioritizes the accuracy and reliability of results above all else, under a strict quality control system based on international standards.
The institute has adopted double-checking (two-time analysis) as the standard protocol for all paternity DNA tests, establishing a system in which clients can accept a denial result with peace of mind even when one is obtained.

When choosing a testing laboratory, it is important to consider not only price and speed but also whether results are confirmed through two-time analysis.
Also important as a criterion for choosing a laboratory is whether specialized staff are available to consult with should any doubt arise about the results. Because the result of a DNA test affects not only the moment it is received but also the person's life afterward, choosing a trustworthy partner is more important than anything else.
For details on our testing system and approach to DNA testing, please visit the official website of seeDNA Genetic Medicine Research Institute.

Summary

In paternity DNA testing, confirming results through two-time analysis is essential to prevent misjudgment caused by human error such as sample mix-ups.
STR analysis itself is an extremely high-precision technology, but to make the most of that precision, the precondition that "the correct sample has been correctly processed" must be met. The double-check system is a mechanism for scientifically verifying this precondition.
Especially in the case of a denial result, it is important to choose a testing laboratory with a well-established double-check system. A testing laboratory that adopts two-time analysis as standard, in line with the international standard AABB's approach, ensures a high level of accuracy and reproducibility in its results. If you are considering DNA testing, please use the information in this article as a reference for choosing a trustworthy testing laboratory.

\Zero misjudgments through double-checking/

Frequently Asked Questions

Q1. What is "two-time analysis" in DNA testing?

A. Two-time analysis (double-check) is a quality control method in which two independent STR analyses are performed on the same sample to confirm that both results match. By having the analysis process and staff in charge separated for the repeat test, sample mix-ups and technical errors can be detected, increasing the reliability of the results.

Q2. Isn't a single analysis enough?

A. While the technical accuracy of STR analysis itself is extremely high, a single analysis alone may not be able to detect human errors such as sample mix-ups or contamination. In particular, when a result denies the parent-child relationship, there is no way to confirm whether that result is correct or a misjudgment, which is why two-time analysis is important.

Q3. What kind of organization is AABB?

A. AABB (Association for the Advancement of Blood & Biotherapies) is an international organization originally established as the American Association of Blood Banks. It now also plays a major role in establishing quality standards for DNA paternity testing, and testing laboratories accredited by AABB are considered to have a high level of international reliability.

Q4. Does performing two-time analysis significantly increase the cost of testing?

A. At laboratories that incorporate the double-check as a standard protocol, two-time analysis may be included at no additional charge. seeDNA Genetic Medicine Research Institute performs two-time analysis as standard, with no extra charge involved. On the other hand, if you request a retest afterward at a laboratory that only performs a single analysis, additional fees may apply.

Q5. What happens if a mutation is found during DNA testing?

A. If a mismatch is observed at one or two STR loci, the possibility of mutation is considered. In such cases, a comprehensive judgment is made by, for example, analyzing additional loci. At a testing laboratory with a proper double-check system, a protocol is built in to accurately distinguish between mutation and a genuine non-parent-child relationship.

Q6. What is the most important point when choosing a testing laboratory?

A. The most important point is "whether a two-time analysis (double-check) system is adopted as standard." In addition, whether ISO 9001 or the Privacy Mark and other quality certifications have been obtained, the number of STR loci used in the analysis, and whether specialized staff are available to explain the results are all important criteria. Choosing based on price and speed alone may leave doubts about the reliability of the results.

[References]

(1) SpringerLink, October 2017
(2) PR TIMES, April 2026
(3) seeDNA Genetic Testing & DNA Paternity Testing, February 2026
(4) Mainichi Shimbun, March 2026