Recommenced phasing of the parent's DNA with one section X being worked on by one sibling and I am working on Chromosome 22. Wanted to try a particular pattern working on the shortest one and it does appear to be working well. I created a Mendelian Genetic Chart showing the different combinations. With five sets of data (four complete and one integrated in from FT DNA) I am getting better results than with the FT DNA data on three people. That is to be expected because five is always better than three! I continue to be amazed at how I am the one that is different. I guess when you feel different in a family then perhaps you actually are!
I am just starting now to write to cousins to see if they would be willing to test. That would let me work on my grandparent's DNA as well. Curiosity about DNA led me to genealogy back in the early 2000s and it continues to lead my research. I still delve into a lot of old records but the DNA helps me to focus on particular lines. A match in any of those lines helps to verify the research that I do further back in some lines - Lywood is a good example where I now have two separate DNA matches at AncestryDNA which are between seventh cousins. There do not appear to be any other lines on which we are related and these are 4th to 6th cousin matches. One would assume that I inherited more on my Grandmother's Blake side to have these matches show up so strongly. Once I have tested one of my brothers at Ancestry DNA I will see how his matches compare to mine. A project for this next month actually is getting that test kit mailed out.
Showing posts with label phasing. Show all posts
Showing posts with label phasing. Show all posts
Wednesday, September 30, 2015
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.
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.
Tuesday, June 9, 2015
Phasing DNA from siblings
I have now put into practise the methodology that David Pike used in the lecture that I attended. I am looking at 700,000 lines of data and I have placed the three sets of results side by side in an excel file. It can actually be quite speedy if you have the Chromosome Browser open as you can see where the long matching runs are. As it turns out one of my siblings is right at the limit of centimorgans between siblings (actually that is me) and quite a bit closer to my other sibling that has tested. I have completed 623 lines and have 123 sets (19.7%) that I can not definitively phase into the columns that I have set up for my parents. I can always see one of them but the second one is an either or. The first one is easy because one of us has a doublet i.e. GG at that point so both of them have a G as an example or that could be A or C or T. But one or both of us has AG and which means either parent could have AG or both of them could or one of them could have GG. My father was an only child and my mother had one brother who did not have any children thus limiting my ability to acquire information from others. I do have a second cousin in Canada though and I may ask if she would like to do FT DNA Family Finder. That would give me information on my Blake line. The lack of first cousins is certainly noticed when one is working on DNA! I also have second cousins in the States on my Buller line and I am thinking of trying to locate them and see if they would test. Persuading my other three siblings and the daughter of my deceased brother is another option and I will continue working away on that one. I think it could be very handy in the future to know the DNA of my parents.
I believe that we have now passed over a new watershed in genealogy. Prior to the last year or so genetics was just a new tool but now a year later I think it is a necessity in a project to really give it meaning.
I have one other set of data in the Chromosome Browser for a known 4th cousin who matches my siblings twice as much as I do and will watch for that as I am working away.
I believe that we have now passed over a new watershed in genealogy. Prior to the last year or so genetics was just a new tool but now a year later I think it is a necessity in a project to really give it meaning.
I have one other set of data in the Chromosome Browser for a known 4th cousin who matches my siblings twice as much as I do and will watch for that as I am working away.
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