How DNA Paternity Testing Works

We take DNA samples by wiping cells off the inside of the cheeks of each patient using swabs. No blood. It is painless. (These are called "buccal cells" and "buccal swabs".) The DNA samples are then processed by the laboratory to compare the DNA of the patients.

No two people have exactly the same DNA (with the exception of identical twins).

We get half of our DNA from our father, and the other half from our mother. When we do a DNA paternity test, we compare the DNA of the child to the father. We can tell with accuracy of 99.99+ percent whether or not the child comes from the father.

The DNA between any two humans is about 99.9% the same (and humans are over 95% the same as some other primates such as monkeys, with bonobos the closest at around 98.7% the same as humans, and chimpanzees nearly the same amount). Therefore, between humans, we must know where on the other 0.1% to compare the DNA. Within this 0.1% are the variations from person to person such as hair color, eye color, skin color, and lots of other things.

Of this 0.1%, some of that has a little variation between people, and other parts have a lot of variation. We must be careful which parts of the DNA we compare. We compare a much smaller fraction where there is more variation in the human population.

Our laboratory is one of the oldest and biggest laboratories in the world, whereby our laboratory has privately built up its own database of human DNA variations over decades, and its statistics on the human population. This database is used to calculate the % probability of paternity.

Anybody can say 99.9999999%, but is it true? We show our calculation in detail.

For a given test, the result is normally 99.99+ percent, or 0%. It is very clear, father or not father.

On each person's DNA, we check at least 20 standard locations ("loci", plural for "locus"). We measure the length of the DNA "allele" at each locus (except one for gender, which just tells whether the person is a male or female).

(Our laboratory previously offered a minimum of 16 loci, many years ago, but that was increased to at least 20 at the same price, though some of the text and graphics on this website is from the time when 16 was offered.)

When we look at the laboratory report, we see two columns for each person, each with a number value equal to the size of DNA allele at that "locus" location, the two alleles of the child, the two alleles of the alleged father, and optionally the two alleles of the mother. The table lists 20 locus rows. At each locus we look at the child's two values (two alleles) first. One of the DNA allele values must come from the mother, and the other one must come from the father, in a paternity test. For example, if a child's alleles have the two values of 14 and 18, then the mother will have one of those two values in common (for example, she may have 5 and 14). If the mother has 14 in common then the father better have an 18 as one of his two values. If he does not, then he is excluded -- not the father. (See rare exceptions discussed later.) However, if he does have an 18, then that row (locus) has a match.

For a test of 20 loci (rows), comparing any two people (for example, comparing you with me, whereby we are not related) will probably have matches for several loci but for sure will have several mismatches for other loci. In a DNA test where the man is not the father, there will typically be 5 or more points of mismatch yet 5 or more matches, too. The matches are simply because all humans share over 99.9% of our DNA, and of the 0.1% remainder, different ancestors and families still share various alleles.

However, in a DNA test where the man is the father, there will normally be NO mismatches at all in these loci (see rare exceptions discussed later). When a calculation is done, the probability of paternity will usually be over 99%.

Just because one laboratory says 99.999999% and another says 99.998%, it doesn't mean that the first laboratory is better than the second laboratory. The first laboratory could be just making up that number for marketing reasons, or else their statistical data and calculation may be flawed. We have seen results from two different laboratories whereby the data is the exact same -- they compared the same loci and got precisely the same data results -- but they have two very different percent probability claims.

We can also show you different laboratory reports which compare different loci. The laboratory can choose which loci to compare.

Our laboratory focuses on loci which are highly variable between humans and well known statistically, in order to get a high probability of paternity or else to exclude the alleged father clearly. (An exception is one locus for gender, traditionally an extra error checking mechanism to help detect if an envelope of samples received at the laboratory had the wrong person's name written on it.) If you would like to discuss with us the particular loci listed on our laboratory's report, we would be happy to discuss that with you and show you why. On this page, we would like to keep things simple and get to the practical points.

There are two testing situations:

  1. Trio -- child, mother, and alleged father
  2. Duo -- only child and alleged father, no sample from the mother

For a Trio, for each locus (line), we first identify which one allele (column) they got from their mother, meaning that the other allele must come from the father, which we look for second. Of the father's two alleles, either of those two must match the child's one allele unclaimed by the mother's DNA.

For a Duo, we can compare only the father's alleles, so that one of the two alleles must come from the father, for each locus -- either of the father's two alleles should match either of the child's two alleles.

The results are extremely accurate, for either a trio or a duo. If the man is the father, then the probability of paternity will be greater than 99.99%. If the man is not the father, then the probability of paternity will be = 0%. The test is thorough enough to be sure it is either 0% or else a minimum of 99.99% accurate, whether a duo or a trio.

There are two main benefits of a trio: 1. You can see that the child is truly from the mother, because there will normally be a match on every line for the mother, whether or not there is a match for the father. (There have been cases where the child was not from the alleged mother, plus not from the alleged father, of course.) 2. The probability of paternity will be higher for a trio than a duo, if the man is the father, for example, 99.9999999% (and often even higher than that).

When the man is the father, the percent probability is not the same for every man. It varies from case to case depending upon one's particular alleles -- how common or unusual the matched alleles are within the human population. For example, if you have some rare DNA, and the child has this exact same rare DNA, then your percent probability will be higher than for a man who shares common DNA with his child. In any case, even for the most common DNA, the percent probability will still be more than 99.99%

In scientific language, the report will not say you "are the father", it will just state a probability of paternity which is usually 99.99...%, or else it will say 0% and that you are "excluded".

When a man is excluded, there are usually at least 5 points of difference, and often many more than that. It is very clear. There are usually at least 5 points that match simply because humans are similar in DNA. It is rare that there are less than 5 points of mismatch in a 20 loci test.

However, if there is only one mismatch, then we do not jump to the conclusion that the man cannot be the father. Occasionally there is a "mutation" whereby there can be one mismatch. For DNA paternity tests checking 20 loci, there may be a mutation in one locus per 100 cases, approximately, depending upon which loci are checked (different loci tend to mutate at different rates). Therefore, we need at least three mismatches to "exclude" a father. In these cases, we could continue to test additional loci, such as 25 loci, or even 35 loci, instead of the standard 20 loci, in order to make it abundantly clear whether or not the man is the father. By testing more loci, we either find an increase the probability of paternity over 99.99% or else the alleged father is excluded.

Notably, we have never yet had any case where it was not clear whether or not the man was the father. For the first 20 loci, we have not yet seen a result with just 2, 3, or 4 mismatches. It has been either 0, 1, or else 5+ mismatches. We have had many cases over the years with 1 mutation.

Based on the above explanation, a sample report for a trio looks like the one below. (For the blanks in the report, see the explanation below this graphic.)

The purple circles denote the first 4 matches to the mother.
The green circles denote the first 4 matches to the alleged father.
You can match the other 11 alleles as an exercise.

If no sample was submitted for the mother, i.e., if it was a duo, then there would be only 2 columns instead of 3, i.e., there would be no column for the mother.

The bottom loci, "Amelogenin", reveals the gender of each individual. X = Female. XY = Male.

In nearly all cases, there are some blanks on the sheet, whereby an individual has only one allele number reported on a particular row (loci), instead of two numbers. Here is why:

It is common for a person's two allele numbers to be identical, for example 12 and 12, instead of having two different numbers, for example 13 and 16. If the numbers are identical, for example 12 and 12, then in order to be compliant with the main American accrediting agency (AABB), the testing laboratory is permitted to report only one number. (When both alleles are the same for one loci, it is called a "homozygote".)

A more detailed explanation is that, in the laboratory, for each loci, the two alleles overlap in the readout, as shown on the right side below. For example, in the sample on the left side below, you can see two clear peaks, at 13 and 16. However, if the two allele sizes are identical, then they would overlap, which would show up as only one peak, as in the example on the right side. For a reading like the one of the right, it is considered a safe interpretation that it is a 12, 12 (homozygote).

However, in order to be compliant with AABB standards, testing laboratories are permitted to report only what is observed, not what is assumed or interpreted. The guidelines state "For any apparent homozygote, only the observed phenotype shall be listed. If a single band is visualized, its measured band size or repeat number is to be reported only once".

Reports from other laboratories which are not AABB compliant often list the results as  " 12   12 " which may be clearer to the ordinary person reading the report, but there is actually no observation of two 12's in the laboratory, only one 12.

How the probability of paternity is calculated

On the left side of the report, there is a column called "PI", which is "Paternity Index". Each loci has a different PI. The value of the PI will vary from report to report, depending upon a person's DNA.

For example, if a child and an alleged father match on an allele size of 22, but an allele size of 22 is very common in the human population, such as 40% of people in the world having an allele size of 22, then the PI will be low, meaning that this does not give a high probability of paternity for that one allele locus. However, if they match on an allele size of 8, and only about 5% of people have an allele size of 8, then the PI will be high for that one allele locus, meaning it gives a higher probability of paternity.

If you multiply together all the PI numbers, then you get the number at the bottom, the "Combined Paternity Index" CPI, for example, 323,769. What this means is that if we did a DNA test of every man, only about one man out of 323,769 men would "pass" a paternity test for this child, and the other 323,768 would fail it, generally speaking.

If only 1 out of 323,769 men would pass the test, then only
00.0004% would pass the test, so that the probability of paternity is
100.0000 - 00.0004 = 99.9996%, which is shown on the rightside.

(Actually, if you multiply all the PI numbers, you will probably get a very slightly different number for the CPI, because the actual PI may be 1.548 but the report shows only the rounded 1.55 for brevity, though the calculated number uses the slightly more accurate inputs.)

Most courts and other purposes require a CPI of at least 200 or a probability of paternity of 99.5% or better.

Calculating all the PI numbers and the CPI requires professional expertise. Some laboratories give you just a CPI and probability of paternity without showing you how they calculated it. Our reports show you each and every PI number.

We've had customers who tested with a second laboratory and compared their results to ours, and showed us the two reports side by side. Thus far, the other laboratories have always stated a much higher % probability of paternity with more 9's, e.g., 99.999999% instead of 99.996%. Obviously, one or the other is wrong. I believe that some other laboratories state a higher probability for bragging purposes.

It's also notable that our laboratory is so old and large, having processed so many DNA samples over the years, that it has an immense database of DNA allele frequencies in the human population on which to base its calculations.

If you are interested in knowing how the laboratory processes the DNA, then you may wish to read this last section, though it is not necessary for understanding the results.

When the DNA is received and processed by test tubes, the first step is to strip away everything else in the cell except the DNA.

After that, the tiny bit of DNA is then replicated by a process called "polymerase chain reaction" (PCR). In the natural world, cells replicate their DNA when you grow and during body maintenance, and this is basically the same way we do it artificially in the test tube. (When a cell divides in your body, enzymes called polymerases do the copying. We do the same thing in the test tube.)

This cycle of "DNA amplification" can be repeated as many times as necessary to provide enough DNA material from the specimen to get a strong enough readout in the laboratory.

We have tried to make this page as easy as possible to understand for the majority of our customers in Thailand. Please let us know if there is anything you don't understand, or anything further you would like to know.

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