What can your raw DNA file tell you about coeliac disease?
Coeliac disease is one of the few areas where a consumer DNA file carries genuinely useful information, and it is useful in an unusual direction: the reassuring result is the informative one.
That is the reverse of how most people read a DNA report, which is why it is worth setting out carefully.
Which genetic markers are linked to coeliac disease?
Two immune-system variants, HLA-DQ2 and HLA-DQ8. Almost everyone who develops coeliac disease carries at least one of them, which makes them close to necessary for the condition. Consumer arrays typically include tag markers such as rs2187668 and rs7454108 that indicate their presence.
The HLA region is one of the most variable parts of the human genome, which is why arrays use tag markers rather than reading it directly. A tag is a nearby position that usually travels with the variant of interest.
That word “usually” is doing real work. Tag markers are good but not perfect proxies, and how well they perform varies by ancestry.
What does a negative HLA-DQ result mean?
More than a positive one does. Because these variants are close to necessary for coeliac disease, someone carrying neither is very unlikely to develop it. That makes a clear result genuinely informative — it is one of the few places where a consumer file can meaningfully lower a concern rather than raise one.
Clinically, this property is used the same way: HLA typing is valued for its ability to make coeliac disease unlikely, not to establish it.
The caveat is coverage. A negative reading only means something if the markers were actually present in your file. Absent markers and a negative result look the same in a badly written report, and they are not the same at all.
What does a positive HLA-DQ result mean?
Much less than people expect. Roughly a third of people of European ancestry carry DQ2 or DQ8, and the large majority of them will never develop coeliac disease. Carrying the variant is common; developing the condition is not. A positive reading is a long way from a conclusion.
This is the asymmetry that consumer reports handle badly. A section headed with an alarming label, showing a result that a third of the population shares, generates worry with no corresponding information.
If you have symptoms, the path is a doctor, not a genotype — and importantly, coeliac testing requires you to still be eating gluten, so cutting it out before being investigated makes the investigation harder. A line in a raw DNA file is not a diagnosis.
Does this marker work equally well for everyone?
No. The tag markers on consumer arrays were selected largely against European reference data, and how reliably they indicate the underlying HLA type varies across populations. Coeliac disease also occurs at different frequencies in different parts of the world, and it is under-recognised in several of them.
This is the same limitation that runs through consumer genetics generally, and the HLA region is a particularly acute case because it is so variable. A tag that works well in one population can perform noticeably worse in another.
Where a marker is well established for one ancestry and unstudied in others, that belongs in the report rather than in a footnote.
Is coeliac in your raw DNA file?
Usually. The common tag markers appear on most consumer arrays, so you can search for rs2187668 and read the genotype directly. Whether your particular file carries them is worth checking rather than assuming, because coverage of the HLA region varies more between arrays than most other positions.
We include coeliac-related markers in our nutrition section and report coverage alongside the reading. Where the marker is not in your file, we say that rather than presenting the absence as a negative result.
What we look at for nutrition → · How to find a marker in your own file →