Tuesday, June 30, 2015

Phasing the X chromosome for parents from yourself and siblings

I decided to look at the X chromosomes of my parents and for my brother of course as that is his only X chromosome and from our mother. My father has only one X chromosome and my brother's results do not show any information presumably for my father's X chromosome since only a Y is passed to a male child with my sister and I receiving an X chromosome from our father which he received from his mother and therein lies the mystery. Why do my sister and I not have the exact same results since the X does not recombine?  I had to think this one through. My brother's result is the X chromosome that results from the recombination of our mother's two X chromosomes hence he has no effect on how we look at our father's X chromosome.

As I work my way down there are occasional spots where the X chromosome which my brother received does not allow for the result that my sister and I have received so at that point it becomes either TT or CT / CC or AC / GG or AG etc. So what does this actually mean and does it then become useful to phase the X chromosome. When one looks at the chromosome browser one would think that the three of us matched exactly but a half/match gives the same result as a full/match. If there are two results for some snps on the helix then presumably one of them is switched off so that it is not expressed. I think I am beginning to understand x transmission and why males suffer more from x transmitted diseases because they do not have a second x chromosome to switch off particular snps that are recessive and perhaps unhealthy. I must admit to finding all of this very intriguing. I had a great deal of interest in DNA when I attended University in the 60s but it was still a new field and not yet down into undergraduate courses in a way that I would have found it more fascinating that Honours Chemistry which I did study. For the most part what we received, my sister, and I follows through quite logically although looking through as I now am I can see that in the first 50 snps there are seven either/or in my mother's results or 14% difference between the X chromosome which we inherited and the one that my brother inherited and we roughly share that difference 50/50.

The Xchromosome is also interesting because it lets us look at particular matches that we may have.

I have nine pages of X matches (90) at FT DNA my sister has 13 pages (130) and  my brother has only 3 matches which includes his two sisters and one individual that I can not place. The match has a fairly extensive tree and I can find a couple of lines that might be interesting but the X chromosome is our mother's lines and the Dorset that comes up is on our Father's side. My brother does not share this match with us and it actually includes two sets of surnames and two single surnames with just one that has a tree (but just because they match this singleton match does not mean that they match my brother necessarily). This is actually his first match outside the family so is rather interesting. The tree shows a family with deep Virginia/North Carolina roots and then moving west from there as far as Texas. He is said to be a 4th-distant cousin. To look at X matches for a male the restriction is always towards the female, so our mother and her paternal grandmother and her mother/maternal grandparents but excluding the male line further back each time so always following the female portion plus the husband of the female at each level. That means I am looking at Grace Gray whose family lines were from Bewcastle, Cumberland and Etton/Holme on the Wolds East Riding of Yorkshire; I am looking at Ellen Rosina Buller whose father was born in Birmingham and his mother born at Lichfield with the father from Rugeley Staffordshire and the mother from Ashby de la Zouch Leicestershire and Ellen's mother who is my mystery lady born at Birmingham of parents possibly Thomas Taylor and Ellen Roberts whose lineage both stretches back one more generation at Birmingham and then unknown for Taylor and Warwickshire/Shropshire for the Roberts lines moving back. So a fifth cousin I am looking at 4x great grandparents and comparing that with a chart of ancestry that dates back into early colonial Virginia without any known debarkation point for the emigrant ancestor is virtually impossible. But it is interesting none the less to see that there is only one individual who matches my brother other than his sisters on the X chromosome. That tells me that not very many have tested in these lines but the potential is now there for them to do so as Ancestry moves into the British Isles.

One of my strongest X matches (3rd to 5th cousin with 60.32 cM shared) other than my siblings is with someone whose father's paternal grandmother came directly from Ireland born circa 1850. Anna Foster born 1850 Ireland and the daughter of Robert Foster. She is rather interesting because Anna would have received from her father Robert his only X chromosome passed directly to him from his mother and unaltered in this exchange. Anna then would have passed to her daughter in this case this X chromosome from her father and the one she received from her mother and the two would recombine to form a new X chromosome along with the X chromosome which she received from her father who again received it as passed from his mother whose family tree goes back into Yorkshire and Ireland (an interesting combination). Her mother's side is principally from Ohio/Missouri and before that Virginia. American ancestry is quite fascinating with the variety of ancestral locations to be found in their lines. Comparing her to other known lines she shares almost the same on the X chromosome as another match said to be 2nd to 4th cousin. On Chromosome 11 I have three people with known Irish ancestry who share DNA at almost the same location. Makes you wonder if this is a special block inherited by a number of Irish families. But the largest parts that I share with each of these four individuals including the one I am discussing are on different chromosomes. I need to have more people test that are known to me but that is really difficult given that we have no first cousins, few second cousins and half second cousins but many many third cousins that I do not personally know.

I shall continue working on the phasing of the X chromosomes with somewhat more knowledge than before I think. Discussion even with oneself can be quite beneficial if properly channelled! My living memory has been most beneficial to me and on occasion from comments received has proven to be handy to others which was a side product that I never anticipated when I started my blog in 2008.

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