Null values (reported as 0) occur when the lab gets no read for an STR marker value. This is not the same thing as a poor-quality result. A null value is obtained from a sample that produces good-quality results from other markers. Null values are given extra scrutiny and repeated testing if necessary to validate the results before they are reported. To read more about the testing process, see The Structure of DNA topic.
Causes of Null Values
There are two common reasons we might get a null value for a marker.
The first reason is if the entire marker is not present in the DNA sequence. In this case, a portion of the sequence has been deleted, and the marker and its surrounding sequence has been removed in part or in whole. Because the marker is not there, the test comes back with a null value.
The second reason is if there is a change in the sequence nearby that the test uses to find the marker. To find a marker, the test looks for a specific, unique sequence we know exists near the marker. Only once the marker is located by this unique sequence nearby can it be tested. If the nearby sequence has changed in a person's Y chromosome, then the test will not find what it is looking for and will get no read or a null result for that marker.
There are some markers that we know tend to experience one or the other of these two causes. Aside from those cases, it is not possible to tell from a null result whether the result is due to a change in the nearby sequence or the entire marker missing.
Multiple Null Values
Usually, only one marker is null. Sometimes, though, a person will come back with multiple null values. In this case, the most likely explanation is that a deletion took place that took out multiple markers.
If most markers are null, then it is possible the person does not have a full Y chromosome but instead has a portion of a Y attached to an X (an XX male with a small portion of a Y). It is also remotely possible for a woman to be XX with a small portion of Y attached to one of the X's and still be fertile, passing the X+ to some of her children. While we cannot come to conclusions like this based on the results of our test, the lesson here is: never say never.
If a test taker has multiple null values, it is possible that some SNPs have been deleted as well. If this is the case the lab will be unable to get results for those SNPs, which may limit the haplogroup assignment they receive to a more general haplogroup rather than a refined subgroup.
Multiple null values may adversely affect your match list. If you are missing some of the markers typically used in STR matching, you may not see as many matches as those without null values.
On a more encouraging note, when a null value occurs, it is unlikely the STR will mutate back to a pre-null state. This makes them very useful in identifying specific lineages, as the null is often unique to a specific lineage. In some cases, the lineage is defined primarily by a null value.
There are some STR markers that are more prone to null values for a variety of reasons. These are discussed in detail below.
The SNP L1 occurs in the sequence that neighbors DYS439. The original standard of testing this marker used the sequence containing L1 (this test design predates our knowledge of the SNP L1). The oldest results for DYS439 were tested with this standard. Once the SNP was discovered, some laboratories and producers adapted their tests to use a sequence that would not be affected by the L1 SNP. The GRC used this new standard, so L1 positive men tested at the GRC would get a value for DYS439 instead of a null. Even when tested with the original test setup, it was possible for an L1 positive male to get a non-null result for DYS439 if their sample quality was spectacularly good. Similarly, some men who do not have the L1 SNP might have a null value for DYS439 for some other reason. Therefore, testing DYS439 even under the original method of testing was not enough to confirm whether a person had the L1 SNP.
Background/History: L1 was discovered because every member of a cluster of families was coming back with a null value for DYS439. Leo Little, a FamilyTreeDNA customer, requested additional testing to determine why the families were seeing null values, and the "Little" SNP was discovered. At that time, there were no naming conventions for SNPs discovered by the public sector. After Leo Little passed away and when the SNP was added to the tree, we chose to name it with an L in honor of Leo Little: L1. Subsequent new SNPs discovered at the GRC were given names in the L series.
A null value for this marker has an odd effect on the results by nature of the way this marker is tested. There are two portions of DYS389 that we test in these two tests. DYS389-1 tests one portion (this portion happens to occur second in the sequence), and DYS389-2 tests both. The test for DYS389-1 captures only one portion of the DYS389 marker because it uses the sequence in between the two portions to single out the one it tests. In the case of a group of men with a DYS389 null value, a chunk of DNA is deleted out of the middle of this two-part marker. A portion of the first part, the sequence in between, and a portion of the second part are all deleted. Since the sequence in between is gone, DYS389-1 does not find that in-between sequence and cannot single out its portion of the test, so DYS389-1 is null. DYS389-2 obtains its result because the before and after sequences are intact, but the result it produces consists only of a small part of the pre-deletion whole.
Think of STR test results as being mapped on a number line. DYS389-1 and DYS389-2 are tested in the same number line, and the results appear right next to one another. That is, they normally do. DYS389-1 normally produces a result between 12 and 16. DYS389-2 normally produces a result between 27 and 33. When there is a deletion, the only result is for DYS389-2 and is in the range of 13-18. This is much closer to the value we normally see for DYS389-1, not DYS389-2. Because of this, the result may be recorded as the value for DYS389-1 and a null entered for DYS389-2. Truly, to reflect the mutation behind the scenes, the result is null for DYS389-1 and the 13-18 range value for DYS389-2.
Note: A family with a branch of men with this mutation is the Chamberlains.
There are two situations in which you might see null values across DYS459, DYS464, and CDY. The first is if half of the copies of these markers are deleted. These markers all occur in the same portion of the Y chromosome, and some types of mutations can affect all these markers at once. The Y chromosome can configure itself so that half the copies of DYS459, DYS464, and CDY are in a loop. This loop can be deleted, leaving half the copies of these markers behind.
All members of haplogroup N have this mutation. It also occurs in a branch of haplogroup E and in other families and individuals. At this time, the standard Y-STR results will indicate the full copy count, not the half. The results showing half the copy count will need to be looked up in the GRC or as results in advanced STR testing if the customer orders it. The mutation is inheritable. Bennett is an example. See the page on multi-copy markers for more about this mutation.
The second situation is when all copies of DYS459, DYS464, and CDY are null. This indicates a deletion that took out all copies of these three markers. See the notes on multiple null values above for this mutation.
DYS425 and DYF397 were discovered and named separately. Only later did researchers determine that DYS425 is in fact one copy of the multi-copy marker DYF397. Normally, copies of multi-copy markers cannot be distinguished; all the values for all copies are clustered together in the same readout regardless of which result belongs to which copy. Sometimes, however, there is a SNP mutation in the neighboring sequence that can distinguish one copy from the rest. If the test is designed to use the sequence containing this SNP, then the results can be separated between the copies that have the SNP and the copies that do not.
DYS425 specifically tests for a copy of DYF397 that has such a SNP in the neighboring sequence. The remaining copies of DYF397 do not typically have the SNP.
An important characteristic of multi-copy markers that can affect DYS425 is that one copy can duplicate itself and overwrite another. This is called a recLOH event (Recombinational Loss of Heterozygosity). When this duplication and replacement takes place, it is not only the marker itself that is affected; the surrounding sequence is duplicated and replaced as well. DYS425 could duplicate and replace another copy of DYF397, creating two copies of DYS425. Or, another copy of DYF397 could duplicate and replace DYS425. When this happens, the SNP that distinguishes DYS425 from the other copies of DYF397 is wiped out and DYS425 ceases to exist, even though technically there is still a marker in the sequence where DYS425 used to be. Testing for DYS425 after such an event will produce a null result.
This type of mutation in multi-copy markers can happen as frequently as markers shift up or down a digit, meaning mutations that cause a DYS425 null result are relatively common. Most people have a result for DYS425, but a substantial number of people have the null. The null value is still useful since men of the same family will typically share this value. For more about recLOH events and other multi-copy marker mutations, see the multi-copy marker page.