What are DNA Pile Up Regions?


Learn how to do Visual phasing with 2 siblings' DNA

Are pile-up regions causing you problems in your genetic genealogy? Do you even know what a pile-up region is?


Pile Up Regions Are a Bane in Genetic Genealogy


Pile-up regions can be the bane of genetic genealogy research for a couple of reasons.


The major reason they're a pain is there's really no official definition. If you look on the ISOGG website, you can find a pseudo definition of,


"there are some regions of the genome that are prone to Excess IBD sharing. These regions are colloquially known as pile-up regions."


Colloquially. I've highlighted that word because it basically means that,


"Hey, that's what we call them. But we don't necessarily have a good definition of them."




Three Types of Pile-up Regions


Now Debbie Cruwys Kennet has a blog where she actually defines three different types of pile-up regions.


Lack of Phasing Pile-up Regions


During chromosome phasing, you separate segments along your chromosomes to your maternal and paternal lines.


If we can't classify the DNA segments, then it's entirely possible that a match doesn't actually match us all the way across.


For instance, you may have a seven-centimorgan match. After phasing, you may notice there's a three-centimorgan match on your mother's side and a four-centimorgan match on your father's side that happened to butt up next to each other in that area.


Or it might disappear completely because that match was actually zigzagging between the two chromosomes. If this happens, your DNA match doesn't have measurable segments once you phase those chromosomes.


You won't know if you have correctly phased your chromosomes without parental DNA to compare to yours.



SNP Poor Pile-up Regions


If you remember, SNPs are Single Nucleotide Polymorphism that basically is a point along your DNA sequence where the place could be one of two different letters. So it's the places where our DNA is different or potentially different from other people.


Now SNPs are not equally distributed across our chromosomes. However, using the Q-Matching One-to-One on GEDmatch Tier 1, you'll see the SNP density all along that.



Poor SNP Regions creating DNA Pile-ups
The circles regions are SNP poor


When you notice an area with a low density of SNPs, it's possible to match many people in those regions and have a pile-up.



Excess IBD Pile-up Regions


The third type of pile-up region that Debbie talks about is Excess IBD which goes back to what the ISOGG definition was. IBD means Identical By Descent.


In other words, we received the DNA from the same ancestors or that same ancestral population because it was pretty much ubiquitous.


Now there are several theories of why this could happen. Probably the most prevalent one is that these excess regions of IBD have an evolutionary advantage. In other words, there's a gene or something on there that gave the people that had that such an advantage that they had more offspring and hence passed on that section of DNA to more and more of the human population.


There are a couple of places on the human genome that scientists are pretty sure this is the case. One area of Excess IBD can actually be found on chromosome number 15. This is a known one that affects lots and lots of people.



Excess IBD on Chromosome 15 example
The red region is likely a pile-up region. The orange is normal matching.

What I've shown here is my chromosome 15, and this is just from the, I think, first thousand matches or 500 matches of all of my matches. So each line represents a different match to me.


We can see here that in this first part of chromosome number 15, basically the 20 to 30 million range, many people match me. But not only there are a lot of people that match me. If we look over here, it's all rather small. In many cases, less than 10 centimorgans.



Normal vs. Pile-Up Region DNA Matches


When we examine other portions of chromosome number 15, you'll notice the orange section (as shown above.)


We can see that I match several different people, but those matches are of varying sized segments. Notice the short orange ones and the longer ones.


This is what a normal matching segment looks like. You're probably not going to have everybody matching that same small segment as we saw with the red matches.


Almost 10 percent of the people that match me in this place. A pile-up represents a huge number of people sharing very small segments.



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Pile-Up Regions Are Not Consistent


While here are some known pile-up regions, the ones that you have might be different. You may not have these known pile-up regions. You may have some other regions in your DNA that are pile-up regions. Different populations have different known pile-up regions.


The Excess IBD may have something to do with an evolutionary advantage to that segment of DNA, and so it's been perpetuated through a population.


Lots of population over tens of thousands of years have had a chance to develop these. And so you're not always going to see the same pile-up regions as your neighbor. But, within your family, you probably have a lot of the same pile-up regions.


But just because you have those doesn't mean that everybody else will have them.


Pile-up regions can happen all along each one of our chromosomes. Unfortunately, there's no definitive known list of pile-ups for us to investigate. This is another reason why they are a pain to genealogists.


In short, pile-up regions provide DNA matches that, while we may be related, we're not going to be related in a genealogical time frame.


These segments have been passed down for hundreds and thousands of years in many cases because they're ubiquitous for that population.


More Tips on Using GEDmatch


Explore the following blog to continue your genetic genealogy education.

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