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soulblighter
09-19-2013, 11:24 PM
Someone asked me this question and I am stumped.
When browsing the raw data, Why does 23andme show only one X chromosome for women?

Also if a mom has Rr genotype for an SNP on the X chromosome as reported by 23andme, how can her biological son have RR? Is the son's reported genotype is on the X chromosome of the mom that is not reported for her? Or it could be mutation?

AJL
09-20-2013, 12:32 AM
For females it shows the X but as half or fully identical, same as autosomes. These are my aunt and 690 mother compared -- dark blue is double sharing, light is single.

soulblighter
09-20-2013, 01:02 AM
For females it shows the X but as half or fully identical, same as autosomes. These are my aunt and 690 mother compared -- dark blue is double sharing, light is single.

I understand the pictorial representation. But how about the raw data?
Let's say my mom is shown withgenotype GG for an SNP on the X chromosome...why am I AG for the same SNP as a male? Where did the A come from?

AJL
09-20-2013, 04:07 AM
Oh I see! I think you might be looking at the pseudoautosomal region (http://en.wikipedia.org/wiki/Pseudoautosomal_region).

geebee
09-20-2013, 09:28 AM
I understand the pictorial representation. But how about the raw data?
Let's say my mom is shown withgenotype GG for an SNP on the X chromosome...why am I AG for the same SNP as a male? Where did the A come from?

Soulblighter, as you probably know the data from 23andMe is unparsed -- with only the sex chromosomes as an exception, and only for males. That's because differences between the X and the Y usually make it possible to tell which chromosome a SNP is on. The reason is simple: some SNPs exist only on the Y, or only on the X.

However, as AJL was suggesting, there actually are two regions where both the X and the Y contain the same SNPs. These are at the two ends, and they are called "pseudoautosomal" because these regions behave just the way the autosomes do. That is, they can recombine.

Of course, for females the entire X can recombine. For males, only the ends of the X can recombine with only the ends of the Y. Now here's where it can get confusing. Just as with the autosomes or the X chromosomes of a female, 23andMe can't tell whether a SNP in the pseudoautosomal regions is actually on a man's X chromosome or on his Y chromosome.

So what do they do? Well, they have three choices in how they can report these SNPs. They can "guess", and just arbitararily report one on the X and one on the Y; they can report both on the X; or they can report both on the Y.

Since some people (women) expect two values on all the X, and no one expects two values on ANY of the Y, it seems to make the most sense to report these SNPs as if they were both on the X. Or, as if -- in the pseudo autosomal regions only -- a man had two X chromosomes. In a sense, we do. Or rather, we have one complete X chromosome plus our puny Y, which also has X-ish ends. Those ends get lumped in with our X.

Make sense?

EDIT: Here's something to think about. What I've said above means that if a man and his father have both tested, in these "doubled" portions of the X, a man should actually match his father on one of the two SNPs. In fact, that's exactly the situation of my father and me, or my father and my brother.

One of each pair of SNPs in the pseudoautosomal regions matches one of each pair in our father's pseudoautosomal regions. Our father passed these on to us as part of the Y chromosome we inherited from him. What we cannot know, however, is whether these SNPs were originally on his father's Y chromosome, or on his mother's X chromosome.

With enough grandfather-son-grandson trios, it ought to be possible to see this at work.

soulblighter
09-20-2013, 10:24 AM
AJL and Geebee, thanks a bunch! I get it now. I could not find 23andme's explanation on how the X was being reported in the raw data. Makes much more sense now!

vettor
11-21-2013, 05:35 AM
an X chromosome question

In 23andme , I am 99.7% european of which 33% is Southern european and 22% is northern european.

In my X chromosome , I am 100% northern european.............does this mean my maternal side is all french, german or above or is the 23andme x data in error?

ilmari
11-26-2013, 07:12 AM
an X chromosome question

In 23andme , I am 99.7% european of which 33% is Southern european and 22% is northern european.

In my X chromosome , I am 100% northern european.............does this mean my maternal side is all french, german or above or is the 23andme x data in error?

I think it is important to understand the unique inheritance pattern of the X Chromosome:

http://freepages.genealogy.rootsweb.ancestry.com/~hulseberg/DNA/xinheritance.html