Cousin Mike Joins the Fray

I was presently surprised when looking over my AncestryDNA matches recently. I saw my second cousin Mike. Now due to the fact that I have many second cousins descending from James Hartley and Annie Snell, I don’t happen to know them all personally. Fortunately, I do know Mike and if I met him somewhere would surely say hi.

Mike at AncestryDNA

At AncestryDNA there is a button to push called Shared Matches. When I look for Shared Matches between me and Mike, I get a lot of people. I first get my 4 tested siblings. Then I get 11 second cousins. These are actually 2nd cousins by DNA. In other words, Ancestry looks at the amount of DNA shared and guesses that these should be in the 2nd cousin range. So Ancestry has the first four of my list of shared second cousins in the 1st to 2nd cousin range. The rest on the list are in the 2nd to 3rd cousin range. However, these are all actual second cousins that Mike and I share. These would be descendants of the 13 children that my great grandparents James Hartley and Annie Snell had. Actually, first on his list of 2nd cousins is Joyce. She is a first cousin once removed. I had her tested at the last family reunion. I wrote a Blog about her results here, and about Mike’s sister Holly here. Down in the Third Cousin Shared Matches there may be 2nd cousins once removed. There is also one non-Hartley Snell relative listed there.

Mike at Gedmatch

I asked Mike to upload his DNA results to Gedmatch. That is where you can find out more about your DNA. For example, here is how Mike matches his sister Holly on Chromosome 15:

I bring up this example, because full siblings match each other in a different way than any other relationship.

  • We all get a chromosome from our mom and one from our dad. They in turn got one from their mom and one from their dad. That means there are four ways that we can get DNA from our parents. Those four ways are from our four grandparents
  • The blue bar on the bottom shows where Mike and Holly match by DNA.
  • The yellow bar above the blue means that Mike and Holly share the DNA from one parent only. And they get their DNA from only one parent of that parent. However, we don’t know which one right now.
  • The green bar above the blue bar means that Mike and Holly share DNA from both their mother and father. Not only that, they share the DNA from one of the mother’s parents and one of the father’s parents. However, we don’t know which one yet.
  • The red area is where Holly and Mike share no DNA from either parent. That is the opposite of the green area. That means Mike may get his DNA from a maternal grandfather and Holly from a paternal grandmother in that area. I’ll give some examples below.

Here are Mike and Holly’s grandparents:

Here is how Mike and Holly match each other on Chromosome 7:

Below the first green bar (which is called a Fully Identical Region or FIR), I have split this out for Mike and Holly. This is split to identify Mike and Holly’s maternal and paternal sides (but we don’t know which yet). Mike and Holly have two of the same colors. That means that they got the DNA from the same two grandparents. One of those grandparents is paternal and one is maternal. We don’t know which is which yet, but we can easily figure out the paternal grandmother. We can do that because all of Mike and Holly’s second cousin DNA matches on the Hartley side that I mentioned above.

The first match is Mike’s 1st cousin once removed Joyce. Then there are my 4 siblings. #6 and 7 are two other Hartley-descended 2nd cousins. That means that all this DNA maps to Mike’s grandmother Grace May Hartley. Put together, these matches go from 15.6M to 95.6M for Mike.

Here I assigned blue as Mike and Holly’s paternal grandmother. In the green area, Holly had to have the same DNA from the same Hartley grandmother. In the red area, Holly had to have the DNA from her Gifford grandfather because neither grandparent matches in a red area. Now let’s look at Holly’s 2nd cousin matches.

Above, Holly matches Joyce from 6-42M.

Because Holly gets her DNA from her Hartley grandmother before about the 16M mark, that must mean Mike gets his paternal DNA in that area on his Gifford side. Otherwise, he would have matched at least one of his Hartley cousins there.  Then I moved some of the orange DNA to the left. This would be maternal DNA which is from either Jenney or Murray. This also meets the requirement of the first yellow area. That area is called an HIR or Half Identical Region. It is where Mike and Holly share the DNA from one grandparent but not the other. In order to know which grandparent that DNA is from, we would need to have a match to a Murray or Jenney. In order to do this right we would also need another color for the 2nd maternal grandparent.

This is also a lot easier when there are three siblings to compare because then we could find out where the crossovers are. An example of a crossover is on Mike’s DNA where the DNA he got on the paternal side goes from Gifford to Hartley.

Me and Mike and Our DNA

When I look at my DNA matches at Gedmatch, my match with Mike is the highest level shared between any of my second cousins – at least the cousins that have uploaded to Gedmatch. Mike’s sister Holly had the record before that. Here is what the specifics look like between Mike and myself:

At the bottom of the list is a number of 2.7 generations. That is how far back it looks like our common ancestors are. They are actually 3.0 generations away. That is just the way it is. Some of my second cousins will share more than average amounts and some will share less than average amounts of DNA. If I look at Mike’s match list, he shares more DNA with two of my sisters and another 2nd cousin than he does with me.

Mapping My DNA By Cousins

I showed one way to map DNA from your grandparents comparing siblings’ DNA. Another way is to directly map your cousins’ matches to a chart. Kitty Munson has developed some software to do this. Right now my map looks like this:

The darker blue maps to James Hartley and Annie Snell. That would be via my 1st cousins once removed and my 2nd cousins with the same ancestors. Mike’s DNA fills in a few blanks in my map:

I guess the changes are subtle. The Hartley side should only ever fill up about one half of my paternal chromosomes. The other half for me would be for Frazer and Frazer ancestors.

Mike’s X Chromosome Matches: No Hartleys There

Mike’s biggest X Chromosome match is with his sister Holly:

Mike, like me, won’t match any Hartley relatives on the X Chromosome. That is because a father never passes an X Chromosome down to a son – only a Y Chromosome. The big match between Mike and Holly is from their mom. She got her X Chromosome from some combination of Jenney and Murray.

Mike’s Lancashire DNA Match

These matches above represent Lee’s DNA matches on Chromosome 13 with 5 siblings in my family, our two 1st cousins once removed and Mike in the green.

I have mentioned in a previous Blog about Joyce, that Hartley descendants have a match with Lee at AncestryDNA and Gedmatch. Lee shows all his ancestors as being from England. The Snells came to this country in the 1600’s and the Hartleys in the 1800’s. That means that Lee’s matches would be on the Hartley side vs. the Snell side. Lee has two interesting people in his ancestry. One is Margaret Hartley b. 1836 and another is Mary Baldwin b. 1836.

  • Although these two women were born in 1836, they are in different generations from Lee
  • Margaret Hartley is on Lee’s paternal side and Mary Baldwin is on Lee’s maternal side. If Lee were to ever test his mom, we would know on which side the Hartleys match.
  • Lee doesn’t show any parents for Margaret Hartley or Mary Baldwin

I have our Trawden born ancestor Greenwood Hartley with a Baldwin grandmother:

This is really on the edge of my knowledge. I chose Betty Baldwin and James Hartley as the most likely parents for Robert Hartley out of many potential candidates.

Lee had a dead end for his Margaret Hartley ancestor. Here are some potential parents I found for Margaret:

This was the same issue I had for finding parents for Robert. Was Margaret the daughter of John and Susan Hartley, John and Hannah Hartley or John and Margaret Hartley? Or perhaps even someone else?

Greenwood is staring at me from the past and saying, “You can’t figure out who my are grandparents are? They are _______ and _______”

a look at Mary Baldwin b. 1836

Due to a problem finding Margaret Hartley’s parents, I’ll take a look at a less common surname in Mary Baldwin. Based on this scrawly writing, she was baptized a Wesleyan in Colne:

This baptism was outside the Church of England.  A Wesleyan, perhaps what we would consider Methodist was considered a non-conformist church. Here is some information on Mary’s dad Eli:

And here is a brother of Elis:

I still need to get back a ways to get to our potential ancestor, Betty Baldwin who was born perhaps around 1780. Any potential shared ancestor would likely be Betty’s parents. We’ll say that Jane Baldwin was actually Jenney Spencer:

Again, we get a multiple choice for the father of this James Baldwin. Here is a batch of them from around 1790:

Here I will choose the James from Barrowford for a few reasons. One is that his dad was Elias and two, he was from Barrowford. Here is the 1851 Census showing that this James Baldwin was born in Barrowford.

This also shows James son David b. in 1812. That gets us back to the old-timers: Elias and Peggy Baldwin. Unfortunately, it looks like Elias didn’t do too well:

He died of decline at age 35. Betty could have been his daughter, but it would have made for some tight time frames. She would have had to have been born perhaps late 1783. Then she would have been only about 17 at the time of her marriage. So the genealogy is the difficult part of the genetic genealogy.

 

Tracking Down DNA from Colne, Lancashire or Part One of the Hartley Brick Wall Series

So far, I have done pretty well at finding out from which grandparent I get my DNA. However, figuring out where the split is for my great grandparents is a bit more difficult. Due to a brick wall problem with the Hartley genealogy, I would like to know which of my DNA is Hartley and which is Snell. There are different ways to do this. One way is to find matches with UK, NZ or AU at the end of their emails. These matches would also match where I got DNA from my Hartley grandfather who was the son of a Hartley and a Snell. My Hartley ancestors came from England in the late 1800’s. My Snell ancestors were in England also, but going back to the 1600’s which should be too far back for the DNA to track in most cases.

One match I found was Linda. She has a UK address to her email. She is on Ancestry and Gedmatch and has trees at both places. Here is her match with my siblings, Heidi and Jonathan:

Linda also has a smaller match with my father’s cousin Joyce on Chromosome 10.

Linda and the Colne Connection

Linda has a large tree with over 16,000 people. I am interested in some of her ancestors in the Colne area. My ancestors lived in Colne, but the church where they were baptized and wed was in Colne.

This is the Ancestry map enlarged to the max. My dot is blue in Trawden. Linda had more than one ancestor in Colne and lists one in Winewall and one in Wycoller. Wycoller is now a park which explains the green area. It would be a short walk from Trawden to Winewall. All the places may be walked to with not too much difficulty. Linda’s ancestral surnames in the area are:

  • Jowett, b. 1878 Colne: too recent for what I am looking for
  • Three male Waddingtons, born in Colne: 1710; 1737; and 1805. The last male Waddington would be too recent my purposes.
  • Thomas Rycroft b. 1684; Matilda Rycroft b. 1772, both in Colne
  • Female Crook, b. 1711, Colne
  • Hannah Foulds, b. 1720, and a male Foulds, b. 1692 both in Colne. I recognize the Foulds name as a prominent local name from my previous research in the area.
  • Allison Blackburn, b. 1688, Winewall
  • Robert Waddington, b. 1770, Wycoller

Of course, there is a possibility that none of these names are associated with Hartley. However, as there is a DNA match and a place match, there is a possibility that there is a match on one of these lines.

Linda’s Colne area tree

I feel like I’m exploring in someone’s house when I look at their tree. Here is the part of the tree that I am interested in:

Coghill didn’t show up on the Colne area map as her birthplace is listed as Lancashire. There should be a sweet spot in the tree above assuming that we are related. I am looking for a connection to my tree, so connecting person cannot be too recent. If we go back too far, it becomes improbably that there is an autosomal DNA match. Here is my Trawden Tree:

Going down the middle row, I am not certain about James Hartley and Betty Baldwin. I am quite sure about Greenwood Pilling and Nancy Shackleton. That means that my first choice would be to connect Robert Hartley to Linda’s tree somehow. In Linda’s Waddington line, the William Waddington or Foulds Rycroft family could have had a daughter that married a Hartley that had Robert. That daughter would have come about following a Hartley/Waddington or Hartley/Rycroft wedding.

Hartley and Waddington

When I search the online Colne Parish records for Hartley/Waddington, I get these two records:

I was looking for a female Waddington that married a Hartley. We see that in the second listing above. Also of note in attendance was John Crook. Crook is a surname in Linda’s line. There is a Mary Waddington born in 1752, but she is the daughter of John possibly a generation earlier:

Here are some of the children of William and Mary Hartley in the time frame that I am interested in. There were very likely more than one William and Mary Hartley family. At least the family at Noyna-end and Aldershead seem to be different based on the closeness of baptisms. This is also assuming that the baptisms were close to the birth dates. In fact, three baptisms in 1773 could indicate three different families:

Baptism: 21 Mar 1773 St Bartholomew, Colne, Lancashire, England
William Hartley – son of Wm Hartley & Mary
Abode: Noyna-end
Register: Baptisms 1756 – 1774, Page 92, Entry 16
Source: LDS Film 1471023

Baptism: 12 Aug 1773 St Bartholomew, Colne, Lancashire, England
Jonathan Hartley – son of Wm Hartley & Mary
Abode: Aldershead
Register: Baptisms 1756 – 1774, Page 94, Entry 6
Source: LDS Film 1471023

Baptism: 17 Oct 1773 St Bartholomew, Colne, Lancashire, England
Robert Hartley – son of Wm Hartley & Mary
Abode: Greenfield
Register: Baptisms 1756 – 1774, Page 95, Entry 7
Source: LDS Film 1471023

Baptism: 25 Dec 1775 St Bartholomew, Colne, Lancashire, England
Robert Hartley – son of William Hartley & Mary
Abode: Wycoller
Register: Baptisms 1774 – 1789, Page 11, Entry 12
Source: LDS Film 1471023

Baptism: 22 Dec 1777 St Bartholomew, Colne, Lancashire, England
Ellin Hartley – daughter of William Hartley & Mary
Abode: Wycoller
Register: Baptisms 1774 – 1789, Page 25, Entry 24
Source: LDS Film 1471023

Baptism: 7 Oct 1781 St Bartholomew, Colne, Lancashire, England
Peter Hartley – son of William Hartley & Mary
Abode: Green-field
Register: Baptisms 1774 – 1789, Page 61, Entry 2
Source: LDS Film 1471023

Baptism: 2 Feb 1783 St Bartholomew, Colne, Lancashire, England
Richard Hartley – son of William Hartley & Mary
Abode: Two Laws
Register: Baptisms 1774 – 1789, Page 71, Entry 4
Source: LDS Film 1471023

I recognize the name of Aldershead where Jonathan was born. This was not far from Seghole where the Pillings lived. However, Jonathan appeared to have died young:

Burial: 16 Aug 1776 St Bartholomew, Colne, Lancashire, England
Jonathan Hartley –
Age: infant
Abode: Aldershead
Register: Burials 1774 – 1789, Page 7, Entry 12
Source: LDS Film 1471023

Robert would seem to be a good choice for the father of my Robert, but I see no Robert, son of Robert being born around 1803 when I believe my Robert was born based on his burial record:

Baptism: 8 Jan 1792 St Bartholomew, Colne, Lancashire, England
Robert Hartley – Son of Robert Hartley & Mary
Born: 8 Jul 1791
Abode: Edge
Occupation: Weaver
Register: Baptisms 1790 – 1812, Page 23, Entry 22
Source: LDS Film 1471024

Baptism: 22 Jan 1809 St Bartholomew, Colne, Lancashire, England
Robert Hartley – Son of Robert Hartley & Susan
Born: 26 Nov 1808
Abode: Lanshaw Bridge
Occupation: Innkeeper
Register: Baptisms 1790 – 1812, Page 254, Entry 13
Source: LDS Film 1471024

I have the same problem with Robert son of William:

Baptism: 7 Oct 1792 St Bartholomew, Colne, Lancashire, England
Robert Hartley – Son of William Hartley & Margaret
Born: 5 Jul 1790
Abode: Boughgap
Occupation: Weaver
Notes: [Robert & Henry bracketed together]
Register: Baptisms 1790 – 1812, Page 33, Entry 254
Source: LDS Film 1471024

Baptism: 20 May 1810 St Bartholomew, Colne, Lancashire, England
Robert Hartley – Son of Wm Hartley & Mary
Born: 6 Jan 1810
Abode: Spouthouses
Occupation: Weaver
Register: Baptisms 1790 – 1812, Page 279, Entry 158
Source: LDS Film 1471024

There was only one Robert born of a Peter Hartley in 1809. There was also only one Robert born of Richard in 1796. That seems to rule out those possibilities.

Let’s try Rycroft

I haven’t eliminated the Waddington line for the mother of Robert – only for the father of Robert. And I have only eliminated Waddington assuming that the baptisms took place at Colne. I am also not looking for the mother of Robert as that would be a more complicated search. For example, what if a Waddington married and her husband died. She then married a Hartley. Likely the wedding record would show the married and not the birth name.

There were not a lot of Hartley/Rycroft weddings that I could find. Here is a fairly early one.

I did find a Susanna:

Baptism: 16 Oct 1714 St Bartholomew, Colne, Lancashire, England
Susanna Rycroft – filia Johannis Rycroft
Abode: Winewall
Register: Baptisms 1697 – 1734, Page 155, Entry 16
Source: LDS Film 1471023

However, Linda doesn’t have a John Rycroft in her ancestry after 1640, so I’ll rule that out for now due to the fact that a DNA match may not make it that far back.

I found this entry interesting:

Here we have the names Hartley, Rycroft, Foulds and Waddington. This Hartley Rycroft was the daughter of Betty Rycroft:

Baptism: 2 Sep 1798 St Bartholomew, Colne, Lancashire, England
Hartley Rycroft – Son of Betty Rycroft, Spinster
Born: 25 Jun 1798
Abode: Lane Head
Register: Baptisms 1790 – 1812, Page 99, Entry 200
Source: LDS Film 1471024

Here we are getting complicated as the Hartley is only the first name. Was the mother trying to name the father? This Betty was likely the daughter of Foulds:

Baptism: 6 Nov 1774 St Bartholomew, Colne, Lancashire, England
Betty Rycroft – daugr of Foulds Rycroft & Mary
Abode: Trauden
Register: Baptisms 1774 – 1789, Page 4, Entry 3
Source: LDS Film 1471023

Any Hartley/Crook Connections?

In looking through my Blog, I see that I didn’t look at the Crook surname. I use the Lancashire online search when I look for my Colne records. Linda has a Thomasin Crook born in 1711, so that goes back quite a way. I see two Hartley/Crook weddings in the early 1600’s which would likely be too early for a DNA match. Here is a later Crook/Hartley wedding, but I am not sure how John Crook is related. Also Mary Hartley is from Otterburn in Yorkshire. Otterburn looks to be about 20 Km North of Colne.

So this is all very interesting, and I have learned more about Linda’s ancestors, but not so much about mine. However, I do feel that breaking down the brick wall could come from these kind of back door methods in conjunction with DNA matches.

Snell Autosomal DNA

I don’t think I’ve written specifically about Snell Autosomal DNA. This DNA has been difficult to separate out. I have lots of 2nd cousins that lead back to our common great grandparents: James Hartley and Annie Snell. But it is difficult to separate out the DNA from those two. The best way to do this is to find someone who goes back before Annie Snell. Here is one apparent match before Annie:

This is actually a match to my sister Sharon. I asked the administrator for M.M. to upload to Gedmatch. I’m pretty sure this is the match:

About One Eighth of My DNA is Snell DNA

I get exactly one half of my DNA from my dad and one half from my mom. I get on average 25% of my DNA from each of my grandparents. It is that point that the numbers start to vary. I get on average 12.5% of my DNA from each of my great grandparents. At this level the 12.5% number varies even more. Here is how I have mapped me and four of my siblings on Chromosome 5 where the match is to MM:

The above maps my four grandparents to my DNA. Stated another way it shows how much DNA I got from my 4 grandparents and where I got that DNA on each of my chromosome. About half of each grandparent color should be split up into two great grandparent colors. The bottom part was done by Martin MacNeill. I created the top part with visual phasing. I assumed that the bottom part was correct. There are some discrepancies of where the crossovers occur due to scale. My crossover from Hartley to Frazer is at 172.6. That explains why I don’t match M.M. If I take Gedmatch way down, I actually do match M.M. here:

If I was mapping this tiny segment, I could say that it came from either Anthony Snell or Betsey Luther. If I wanted to limit it to one person, I could say that this is my Otis Snell DNA [Anthony and Betsey’s son].

It is difficult to see, but there is now some new light blue at the end of my Chromosome 5 for Otis Snell. For my siblings, they would have longer patches of blue. Actually, this would be true for all my siblings except for Lori. She doesn’t match M.M. This means I made a mistake on my Chromosome Sibling Map. It should look like this:

Matches are a good way to check your work. Lori’s last crossover from Hartley to Frazer (Yellow) is at about position 167.5M.

What About Other Snell DNA?

One way to find other related Snells is through a Gedmatch utility. This utility finds people that are matched to both you and your match. Here are a few that match my brother Jonathan on Chromosome 5 :

Unfortunately, I either couldn’t find these people with overlapping DNA matches easily or they had a tree that didn’t go back far enough.

Snells at Ancestrydna

Here is a match that is perfect at AncestryDNA. Our common ancestors are the parents of Annie Snell [Isiah Hatch Snell and Hannah Thomas Bradford]:

I have gone to his mother on the chart above. However, he hasn’t uploaded to Gedmatch.com for comparison. And there is the problem for genetic genealogists. AncestryDNA has good information but no chromosome browser and tools. Gedmatch has good tools but not as many people and the trees aren’t as good.

So for now, I will be content with my little bit of DNA that I got from Otis Snell’s parents on my Chromosome 5.

Three New People in the Newfoundland Dicks DNA Project

I was happy to find out that Katherine and her two Aunts, Grace and Dorothy have tested their DNA. They are all descended from the Dicks Family of Newfoundland. Here is the Elisabeth Dicks Adams Line:

Here Dorothy, Grace and Katherine are shown on the lower left. If I compare the DNA of Dorothy, Grace and Katherine, it would show the DNA they have in common. That would be the DNA from Edna Slade and the husband of Edna Slade. If I then compare Katherine’s family to Cheryl, Sandra and Nelson, the matches eliminate the non-Dicks DNA of Edna’s husband. However, at that point, we would expect about half the DNA to be from the Elizabeth Dicks common ancestor and half from the Adams side. In order to eliminate the Adams DNA, I compare the Dicks/Adams DNA to the larger Dicks project. This comparison removes the Adams DNA.

Katherine’s family is still on the lower left. There are five Dicks siblings in the tree which make up the major lines. They are: Elisabeth; Frances; Christopher; Rachel; and Robert. The tree only represents Dicks descendants that have had their DNA tested and uploaded to gedmatch. One exception is Kenneth Albert who is only at FTDNA right now.

Comparing Dicks Descendants’ DNA

My next step is to compare the 18 Dicks above to see how their DNA matches with each other. If three people match each other on the same segment of the same chromosome, that indicates a common ancestor. That common ancestor should be Christopher Dicks or his wife Margaret. Here is how all the Dicks descendants match each other in general (without the specific segment information).

This compares Dicks descendants to Dicks descendants, however, as this is Newfoundland, there are other matches. The descendants of Elisabeth Dicks match each other in the top left box. The descendants of Frances Dicks match each other in the bottom right box. Normally, there would be higher matches within the boxes than outside. But note that for the Frances descendants, there are some higher matches outside the box. This means that are surname matches outside the Dicks family. One example of that is in the next Section.

Charles matches with Kathy, Deborah and grace

As I was looking at the triangulation between Dicks descendants, I noticed that Charles was triangulating with Kathy, Deborah, and Grace. Now Charles is from the Frances Line and K, D and G are from the Elisabeth Line. So finding Charles in a Triangulation Group with Kathy’s family was unexpected. Remember that triangulation means that those in the Triangulation Group (TG) have at least one most recent common ancestor. I was about to ask Kathy about this when I noticed this in one of her emails:

“I was also quite interested in Charles ______ as one of his biological grandmother’s a few generations back was a Ruth Slade.”

Notice above that Kathy has Slades in her ancestry. The good news was that I was able to tell something was going on out of the ordinary just by the DNA.

Here is a summary of Charles’ matches of the Dicks descendants:

The four notes in the TG column are areas where Charles could match Kathy and her family on the Slade line.

Triangulation Groups

I should say that all Triangulation Groups are not created equal. Based on the location of the Triangulation Group (TG) there are hints as to the results. For example, many of the TGs are within the Elisabeth Dicks/Thomas Adams Line. As a result, the TG could be pointing to Dicks or Adams. In addition, there is some consensus that siblings should not be used for TGs. I differ a little on that, however. I would say, why not? If we can use cousins, or Aunts, why can’t we use two Aunts as two parts of the triangle? However, again, the results of the triangle may be limited.

Adams TGs?

Here are the TGs that could point to an Adams ancestor:

I say this because there are only Dicks/Adams descendants in these TGs. I am running out of room in my TG Matrix, or I would add these possible Adams TG. I will add the one on Chromosome 12. This is because it looks like there is already a Dicks TG in this spot:

Note that it looks like there is a Dicks TG already on Chromosome 12 from position 114 to 127. As these are two separate TGs, that would indicate that this TG represents the DNA that came down from the Adams side. That was my same reasoning for having a James Joyce TG on the right side of the chart in this position.

a confusing Chromosome 4

There is a lot going on at Chromosome 4:

This is what is referred to as a rolling TG. Howie appears to be in the beginning of it, but drops out. Then later Pauline joins in. So this could be looked at as a rolling TG, or two TGs. To save room on my chart, I’ll call  it one TG located from (41-72).

Note that there is a non-triangulation between Joan and Nelson. This is important as it happens right in the middle of a triangulation between Pauline, Dorothy and Grace. This tells me that Joan and Nelson likely share a non-Dicks ancestor. The other possibility is that Dorothy, Grace and Pauline could share a non-Dicks ancestor. I don’t know all the genealogy to check. However, the two groups are showing different shared ancestors.

A head scratchin’ Chromosome 9

Here Esther shows up in a TG with Dorothy and Grace. However, she was already in a TG with Sandra, Nelson and Kenneth (whose DNA results no longer show up in Gedmatch). This means that Esther is related to these two groups of people in two different ways. Esther being related to two groups of people is not unusual given the intermarriage in Newfoundland. Also recall that many genetic genealogist wouldn’t consider this a TG as due to Dorothy and Grace being sisters.

Updated Dicks TG Matrix

Here is what I get for the updated Dicks TG Matrix based on the three newly DNA tested Dicks descendants:

Summary and Conclusions

  • Although the study is geared toward Dicks DNA, other DNA does show up. The Slade name was one example in this Blog.
  • Kathy, Dorothy and Grace have added to our knowledge of the Dicks family.
  • The dark green in the matrix above was for matches with a brother of Christopher Dicks who was born about 1784. However, I didn’t update that information for this Blog.
  • Where DNA overlaps and there are two groups of matches, that should point to two groups of ancestors. This gives a good pointer on where to search for additional common family ancestors.
  • The work I do here is similar to the Circles shown at AncestryDNA. My wife’s great Aunt Esther shows up in a Margaret Circle with 11 other people. Margaret was the wife of Christopher Dicks b. about 1789. However, Triangulation Groups are more detailed. What AncestryDNA does is a mechanized version. They just show people that match each other by DNA and match each other by family tree regardless of where they match on which Chromosome.
  • Here is AncestryDNA’s cookie cutter bio on Margaret: “Margaret was born in 1789. She married Christopher Dicks and they had four children together. She then married Christopher Dicks and they had 14 children together. She also had one son and one daughter from another relationship. She died on February 28, 1867, in Harbour Buffett, Newfoundland and Labrador, Canada, having lived a long life of 78 years, and was buried there.
  • One person in the AncestryDNA “Margaret” circle is not in this group and matches Esther at an ‘extremely high’ level of DNA. It would be worthwhile to get in touch with this person.

 

Part 7 – Raw DNA From 5 Siblings and a Mother – DNA From Mom

I’ve spent my last 6 Blogs on this topic finding out which alleles came from my dad. In this Blog, I would like to work on finding my siblings’ and my alleles that come from mom.

The Ironic Step of Phasing – Mom Alleles from Dad Alleles

I call this ironic step in that it was my mom that was tested for DNA. Based on her results we found out a lot of the alleles that her children got from our dad who passed away quite a while ago. Now, we use those alleles we got from dad to figure out which alleles we got from mom. From the Whit Athey Paper referenced at the ISOGG Web Page on Phasing:

If a child is heterozygous at a particular SNP, and if it is possible to determine which parent contributed one of the bases, then the other parent necessarily contributed the other (or alternate) base.

 

First I copy my FillinOne Table to a MomfromDadOne Table. Then I’ll do a query on that.

This says where I am heterozygous, and I have an allele from dad, I want to see where I’m missing one from mom.

I have over 50,000 of these which will be easy to update. I will want to put Joelallele2 in the blank where JoelfromDad = Joelallele1. Then I will want Joelallele1 in the JoelfromMom space when my allele from Dad is Joelallele2.

I ran this query twice for each sibling, so 10 times. This updated 50-60,000 alleles per sibling, so about a quarter of a million alleles altogether.

Finding Mom Patterns

Now that I have filled in more alleles from Mom, it should be easier to find Mom Patterns. Here is a Query to find Min and Max for the AAAAB Pattern:

Results in:

This saves a lot of time and gives me the start and stop positions of all the AAAAB Mom Patterns. In my previous look which I now see as premature, I only found 2 AAAAB Patterns. Now thanks to my MomfromDad update above, I have at least 17 AAAAB Patterns. The only drawback is that if there is more than one AAAAB Pattern within a Chromosome, it will not show that. However, if I run all the Mom Patterns, and find overlapping Patterns, that can be reconciled later. In fact, I see an overlap already:

The first AAAAB Pattern I found was 162-233M which I did see as large. I already had found an AAABA Pattern from 192-249M. This could mean that AAAAB goes from 162-192 and that the 233M AAAAB pattern was just an outlying singleton.

I also recall that I want ID’s, so I’ll add that to my query:

Because I have so much new information, I’ll put this into a new spreadsheet:

AAABA Mom Pattern

I just have to change the Query slightly to get the AAABA Mom Pattern:

The results of this Query go into the new spreadsheet. This spreadsheet will be sorted by Chromosome later.

I added a column for IDEnd minus IDStart:

Where this is zero, it would indicate a single Pattern.

I went through all the Mom Patterns and got a spreadsheet of 194 rows that need to be reconciled. Here are Chromosomes 1 and 2 sorted:

Reconciling Chromosome 1

I have added in a column for possible assignment of a crossover to a sibling. Note that up to about 20M everything looks OK. There are discrete Patterns. ABBBA to AABBA is a change in the second position which belongs to Sharon. The change from AABBA to AABBB goes to Lori. Then the AABBB is the same as BBAAA which goes to ABAAA. That would be my crossover [Joel].

I did a Query showing where all the alleles were filled in for the Mom Patterns:

This shows where my Crossover is at ID # 8984. I have added a few more columns to my Mom Pattern Spreadsheet to add the more refined cut points:

Next I’ll look at 77M.

As best I can tell, there are two single AABAB’s in the middle of an AABBB Pattern. Next I will want to find the start of that AABBB Pattern. To find that I do a query to look for the AABBB Pattern in Chromosome 1. That Query results in more AABBB Patterns.

A Problem

I have a problem in that it appears that the Mom Patterns of AABBB and AABAB appear to overlap each other on Chromosome 1. I assume that means that I did something wrong.

refilling the dad patterns

That means that I should go back and fill the Dad Pattern back in:

First I recreate a Fill-in Table using the old Three Principles Table. Then I do update queries on that. Hopefully these numbers will work:

Back to Mom Patterns From Dad Patterns

Just so I’m not going backwards, I’ll redo this step. I copied my revised fill-in Table to a revised Mom from Dad Table. This time I’ll keep track of the alleles for fun:

So in retrospect, I don’t know if I made a mistake with the Dad fill-in’s or in the Mom fill-in from the Dad Pattern. Hopefully, there were no mistakes this time.

 

Part 6 – Raw DNA From 5 Siblings and a Mother – Filling In Paternal Blanks

In my last Blog, I said that I would work on the Maternal Patterns and then fill in blanks. However, my Maternal Pattern Table is not very filled. After some thought and re-reading the Whit Athey Paper on Phasing, on which I base this work, I decided to:

  1. Fill in the Paternal Blanks
  2. Use the Paternal Data to fill in the Maternal alleles
  3. Fill out the Maternal Pattern Table
  4. Fill in the Maternal blanks based on the Maternal Pattern Table

Filling In Paternal Blanks

I might as well start filling in the AAAAA Patterns. On my Dad Pattern Excel Spreadsheet, I can filter for that pattern:

However, I now need a formula for Excel including all the ID positions above. This was the point of my starting this project over – to get those IDs. The formula will be in the form of “Between A And B OR Between C And D OR…” So first I need a formula in Excel to create the formula in Access. That formula is called Concatenate. According to a Google search, concatenate means to “link (things) together in a chain or series”. The symbol in Excel for concatenate is simply the ampersand (&).

Here is my formula and the outcome:

However, I have another idea. I can concatenate the concatenation. First, I add an extra space on the end of my “Or”. Then I drag down the formula to fill in the other chromosomes. Then I take off the last “Or”.

That gives me this helpful string of AAAAA Positions:

This will save me a lot of cutting and pasting in Access.

Back to Access

First I copied my old Table to a new one called tblFillInOne. I will create an Update Query for that Table.

I am only updating Dad alleles from other Dad alleles, so I import those 5 alleles plus the location ID. Then I use the expression builder, to paste in the location of the AAAAA Patterns in all 22 chromosomes. So now I have the Pattern and the location, but I need some more criteria. I would like the criteria to say if there is any allele in any of the five columns and any blanks in those columns, then replace the blank space with one of the existing alleles.

Here is a simple Update Query:

This says, that if my allele is null and Sharon’s isn’t, then replace mine with Sharon’s. The problem is that this would take four separate Update Queries. With 5 siblings, that would be 20 queries.

Another risky Update Query would use this form:

Here I am saying if any allele is not null (other than mine) replace that in my slot where I have a blank. The thing I don’t know if the Update To: field can have a variable criteria. I’ll try it. When I run this as a Select Query, it puts a bit of a strain on my computer. Eventually, it gives me 18,385 rows. When I run the View function on the Update Query, I get the same number of rows, so I’ll hit the Run button and hope for the best.

If I run this Select Query again, I should get no results if everything updated.  I did get no results, so I assume that it worked. I want to save this Update Query and use it for the other four siblings.

Filling in Sharon’s missing alleles from the AAAAA Paternal pattern

I used the same logic for Sharon:

Now she has all the Is Null values and I don’t. I moved the Update To: criteria over to Sharon. I took out Sharon’s allele and added mine in her place. Again, this gives my old computer a workout. I get 18,315 rows again which seems suspicious. I see the problem. I appears that Access updated my results with a (-1) rather than with an allele.

That means that I just have to do 20 Queries. However, they should go quickly.

Back to the Simple AAAAA Query

Due to all the Update Queries, I’ll make a Spreadsheet to keep track of each Update Query I do:

It turns out that it is easier to run this Update Query sorted by ‘From’:

That way, I can just move Sharon’s allele from Dad and the Is Null along the Update Query:

With these fast 20 Update Queries, I updated over 100,000 alleles:

AAAAB Fill-in

This could be a little easier. For this one, we don’t want to touch the last ‘B’. The last B represents Lori, so we will only be filling in to and with the other four siblings.

And then we need the fill-in locations.

AAABA and AAABB Fill-in

AAABA is about the same as AAAAB except the B in the AAABA corresponds to Jonathan. He is all alone as a B so he gives no alleles and takes no alleles. The other siblings share their AAAA’s in this Pattern.

In an AAABB Pattern, the three A’s will share with each other and the two B’s will share with each other. This happens to break down along V1 and V2 lines, so I expect there will not be as much sharing as between AncestryDNA versions.  The sharing of A’s and B’s looks like this in my Fill-in Tracker:

I have darkened out the areas where an A cannot share their A with a B and a B cannot share their B with an A. As I predicted, the AAABB filled-in alleles were less:

All the other patterns filled in

All the other patterns will be of the same type. There is one AAAAA which is all the same. The other combinations are four of one type and one of the other or three of one type and two of the other.

There are 20 fill-in’s for AAAAA. As a quality check, there are 12 fill-in’s for a 4-1 Pattern and there are eight fill-in’s for a 3-2 Pattern. I would recommend using a fill-in tracker to make sure all the combinations are being covered. The specific numbers of alleles being filled in for each combination of each Pattern are not all that important, but they are interesting.

Fixing an abbab mistake

When I was filling in the ABBAB Pattern, I noticed a mistake I made. I filled in 3754 rows of Joel alleles into Heidi blank spots. In an ABBAB Pattern, I am only supposed to be filling in my alleles into Jon’s blanks. Here is the mistake:

That means in those positions, I’ll have an ABAAB Pattern where I should have an ABBAB Pattern. Oh no. So how do I fix that? I need a fix query. Under Pos ID, I’ll put in all the locations that are supposed to be ABBAB. Then I’ll make sure the first position isn’t the same as the second:

That results in only 103 rows.

If I update those 103 rows to Null, that should be a start:

Next I set the first position to be different than the last in this ABBAB Pattern:

That fixes another 212 rows. That may be all the rows to fix. I looked for more JoelfromDad = Heidi from dad where JoelfromDad <> LorifromDad and where JonfromDad <> LorifromDad, but didn’t see anything. The other updates must have been in areas with AAAAA by chance areas. In the meantime, I copied the first two columns on the left to the right, so I don’t lose my place when I am scanning across the spreadsheet.

Dad Pattern Fill-in First Round

The dark blue areas are the ones where there should not be any filling in based on the Pattern.

Summary

  • The Fill-in Step is a major part of phasing. In this step I filled in over 1 million paternal alleles in my DNA and in my 4 siblings’ DNA.
  • I noticed a mistake I made along the way, but figured out a way to fix it.
  • I figured out a shortcut to describe the different patterns by way of ID’s. The shortcut involved using a concatenation of a concatenation.
  • I haven’t yet filled in the random AAAAA Patterns that are within the other patterns. I imagine that would be important to do at some point. I know that David Pike has a utility to find Runs of Homozygosity. I suppose that would be useful for filling in alleles.

 

 

 

Part 5 – Raw DNA From 5 Siblings and a Mother – A New and Improved Method

In my last Blog, Part 4, I found that I needed to go back to improve a method from an earlier step to make a later step work much easier. This did two things:

  1. Gave me a cleaner database
  2. Set me back a ways

Re-do Principle 1: Homozygous Siblings

I need now to create a new table. This will have the allele from Mom and Dad for each sibling. I copied my previous table to a new one called tblV1andV2HomozygousSibs. I opened my new table in design view and added the 10 new fields that I needed:

The first five of the new fields will be have the Mom Patterns and the last five will have the Dad Patterns. Right now they are just blank. I’ll use an update query to add in homozygous alleles:

This query says when my allele 1 is the same as allele 2 (homozygous), put allele 1 into the slot from my Mom and my Dad. The Dad slot goes off the page, but is there. When I run the update, it fills in over 485,000 lines. To do this by hand would have taken a while. This is the first step to filling in the Mom and Dad Patterns:

I do the same query for each of my four other siblings. Care needs to  be made the the right alleles are going in the right place. For example I wouldn’t want to put a Lori allele into a JonfromDad column. Then I check to see if the columns are filling in:

If I recall right, this step fills in (or phases) about 8 million alleles. We don’t see any patterns yet other than AAAAA, but patterns are emerging in other parts of the table.

Step 2 – Homozygous Mom

Here when mom has a GG for example, she would have to give a G to each child at that position, as that is all she has. I’ll use the Update Query again for this. Here is the Criteria:

Here is the Update part:

Step 3 – Heterozygous Siblings

Here is an example:

I have TC in my two alleles at this position as do my siblings. My mom must have had CC as she gave a C to each of her siblings. That leaves a T that we must have gotten from our dad. It looks like I may need 10 Update Queries for this one. Here is the criteria:

The query says that Joelallele1 is not the same as Joelallele2 (Heterozygous Sibling) and I received my allele1 from mom.

I update the table to say I got my other allele from my Dad. This is a little more complicated Update Query. I then reverse the Joelallele 1 and 2. When I get allele2 from mom, I get allele1 from Dad. Before I run the Update Query, I view it each time to see if there is a reasonable number of rows being updated. If no rows are updated, there is probably an error in my query. This update is in the 40-50,000 row range. Also, if I get values in the view panes, it often means I have put the results in the wrong field. Usually many empty rows in the view output is a good thing.

I forgot to copy and rename my Homozygous Sibs Table, so I just renamed it to tblV1andV2w3Principles.

Finding Patterns

This time, I want to add ID’s to my patterns, so I’ll add two columns to my old Pattern Spreadsheet in Excel:

Rather than do formulae for each pattern again, I’ll just scroll through my table to see if I can finesse the Pattern boundaries and add Position IDs.

Finessing Pattern Boundaries

Here is an example at Chromosome 1 in the 77M range. There I had a change from ABBBB to ABABB. In my previous query, I only looked at Dad patterns where all the alleles were filled in. However, in the original pattern, we can infer the pattern even when alleles are missing.

Previously, I had the change at the top row where there is a full pattern. However, in going from ABBBB to ABABB, we only need the first three positions to identify the pattern. And actually, we only need position 2 and 3 to identify ABABB. At ID 25839, there is an AGG??? Pattern. This has to be in the form of ABBBB. Then 4 lines later, is ?AG??. This has to be an ABABB Pattern. Here is how I noted the change in the 77M range on my Excel Dad Pattern Spreadsheet:

The DadStart and DadEnd columns have the refined Position numbers.

Refined Chromosome 1

  • I had noted previously a possible AAAAA Pattern between AAAAB and ABBBB. It turns out that that is required. This is because to go from AAAAB (same as BBBBA) to ABBBB would require two changes. Only one change is allowed at a time. I will need to fill in the Positions and IDs.
  • The three ABABA Pattern areas need to be combined into one. They occur in a Centromere and in an excess IBD area. The Genealogy Junkie has a good Blog on that topic. I downloaded a file she had with the exact areas.
  • I added the IDs for the start and stop of the Chromosome as tested as well as the start of the next Chromosome. These are highlighted in dark purple.
  • Only 22 chromosomes to go.
Chromosome 2 Refined

Here I added a new column. This is the number of IDs or SNP positions between patterns. Note that there is a negative 4 in one case. This was an odd case where the two patterns at the crossover were inverted. I didn’t know what to do there, so I left it as is. There is a Centromere from 92-95M, so I will combine the two AAAAB Patterns that I have when I create the clean version of this table.

Chromosome 4 refined

Here I had to add a green AAAAA Pattern to make this work. Note that I am getting fewer crossovers.

Chromosome 5

Here is another case where an AAAAA Pattern is needed:

The pattern is needed between AABAA and AAAAB for two reasons. For one, there is a large gap between the end of AABAA and the beginning of AAAAB. Also, to go from AABAA and AAAAB requires two changes and only one is allowed. That requires an intermediary step of AAAAA between these two patterns [AABAA > AAAAA > AAAAB].

Here is Chromosome 5 completed:

The addition of the AAAAA Pattern results in the addition of two crossovers. Another note is that I could have had the first pattern start at the beginning of the Chromosome and have the last pattern end at the end of the chromosome. That is because there is not much room there for other crossovers.

a chromosome 8 Decision

The issue here is the two AAAAB Patterns in a row. Should they be combined or should I add an AAAAA Pattern between the two AAAAB’s? I’m going with combining. The reason is that if I put an AAAAA between the two, that would give Lori two paternal crossovers in a fairly short span. This does not happen in nature – at least in the middle of a chromosome. This would be like inheriting a 2 cM segment from a grandparent.

Chromosome 9 decision

Lori has two crossovers in a row, which is not ideal. Then there are two ABAAA patterns in a row. I decided to combine these. This is because when I look at the table, there is a centromere in there and a lot of missing SNPs. If I did create an AAAAA pattern, that would result in two close crossover for Sharon.

Here is the cleaned up version with the rogue SNPs taken out:

Missing Pattern Chromosome 10

There is a missing pattern between Lori and Jonathan’s first crossovers. AABAA > ABAAA is two changes, so I need to insert an AAAAA Pattern between the two. This will result in two new crossovers: one for Heidi and one for Sharon.

Chromosome 11 – Halfway?

The good news is that I’m at about 2/3 of the way. I have over 900,000 locations and Chromosome 11 brings us past the 600,000 mark. Note again the need for an AAAAA Pattern between the last two patterns. That will add a Lori crossover and a Jonthathan crossover, so they won’t be left out.

Chromosome 12 patterns

Chromosome 12 looks like it is missing a lot betwee ABBBB and AABAA. However, it is just missing an AAAAA. That is because ABBBB is the same as BAAAA. The progress goes BAAAA > AAAAA > AABAA. As it turns out the crossovers that have to do with transposing relate to me (Joel). The extra crossovers go to me and Heidi.

Here are the numbers filled in for Chromosome 12:

Sketchy Chromosome 13

I note that Chromosome 13 is a bit sketchy, with no identified sibling crossovers. It appears that AAAAA Patterns are needed here also.  There is about a 4M space where there is room for an AAAAA Pattern between 24M and 28M. There is also room after the AAAAB Pattern which would give Lori another Paternal crossover. This last crossover is shown in Gedmatch:

These are matches of my father’s first cousin to myself and four other siblings. This shows Lori’s crossover on the bottom match. As all siblings match to the end of the Chromosome, that would be the AAAAA Pattern.

Here is the finished Chromosome 13:

Lori’s crossover as shown in Gedmatch shows on my table at about 90M. Keep in mind that Gedmatch uses Build 36 and my table is in Build 37.

Chromosome 21: Refinement Example

Here is an example of a refinement. In my initial query, I was looking for patterns that were filled. However, in going from AABBA to ABAAB (which defines my crossover), it is the same as going from BBAAB to ABAAB. The only change in pattern is in the first three letters: BBA to ABA. We can see that change here even though the last three letters are missing:

Chromosome 22: Extra AAAAA needed

On Chromosome 22, there is a lot of room at the beginning of the Chromosome to put in an AAAAA Pattern:

There are about 5M SNPs between the start of the Chromosome (16M) to where the AAABA Pattern starts at 21M. I have 4 of my siblings mapped out using visual phasing:

This shows on the paternal side (Frazer) that there is an AAAAA Pattern. That is represented above at the start of the Chromosome in blue. I am just missing Lori. Without looking at all her results, I see she has a full match with Heidi at the beginning of the Chromosome:

And here is the last Paternal Chromosome finished:

It was a lot of work, but now I have what should be the start and stop points for all the Paternal segments for me and my four siblings.

Summary

  • I needed sequential IDs for my Access Queries to fill in missing alleles
  • To do this I needed to go back to the beginning and re-import the raw data for six people
  • I created a table for five siblings showing where they got their paternal and maternal alleles based on three principals.
  • I went back to my Paternal Pattern Table and refined what I had already done
  • I also added IDs to my Paternal Pattern Table
  • Next up is to look at the Maternal Pattern Table and start filling in blanks using MS Access

 

 

 

Part 4 – Raw DNA From 5 Siblings and a Mother – A Problem with Filling in the Blanks

In my last Blog, I looked at Maternal and Paternal Patterns created by initial phasing of my raw DNA. The Paternal side patterns were pretty complete, but I didn’t have much on the Maternal side. I summarized the patterns I found in a spreadsheet. I added siblings’ crossovers where found and added start and end positions on each chromosome where found.

Filling in the Blanks

  • First I made copies of my Mom and Dad Spreadsheets
  • Then I cleaned them up, taking out the Patterns that were only at one location (one SNP)
  • Then I used a filter to get the patterns.

The AAAAB Pattern filter on the Paternal Patterns spreadsheet looks like this:

On the Maternal Table, it looks like this:

 

I’ll start with the maternal Patterns as it will be easier. First I copied that Table I was working on to create a new Fillin Table called tblFillinStep1.

Here is what I portion of the Chromosome 10 AAAAB Maternal Pattern looks like:

 

In my previous analyses before I had 5 siblings tested, I had sequential ID’s. This made things easier in choosing patterns. Now, however, I am having trouble getting the ID’s sequential. This is probably due to my adding the extra alleles. My options now are to update the missing alleles by hand or create queries to update them.

Just Like Starting Over – a New Access Database

I decided to try importing all the raw DNA files into a new Access Database. This time I won’t let Access assign the key data field. I’ll use the rsid as the key data field. Perhaps then I can assign a new ID that will apply to the merged V1/V2 AncestryDNA dataset.

One problem that I’ve noted with the AncestryDNA downloads is that they only give you a date on the filesname. There is no indication in the file or in the file name of who the data is for. That means that it is important to rename your files. I uploaded my sister Heidi’s results to Gedmatch on 26 April 2015, so that is a clue. I see an AncestryDNA zip file from 25 April 2015, so that is a clue. I guess I’ll add her name to the file now!

The Clean start

Here is the Access Database with just 5 tables:

Here’s my Query to create an AncestryDNA V1 Raw Data Table:

I see in my results, I got more lines than last time. I checked and I forgot to only include Chromosome 1-23. I corrected that and got the 700,153 lines as before. I did and analogous query for Jon and Lori and got 666,532 rows.

All V1 Results plus the v2 results where they are they match v1

Next, I’ll create a Query between the two tables I just made.

This will have a right hand join. As stated above, it will produce all the V1 data and only those records from V2 where they equal V1. That brings in Jonathan and Lori into the V1 results. I made this data into a new table.

Finding v2 data not in v1

Next I want to add only the V2 part that isn’t in V1. When I get this, I can add this to my query to get all the results. This is the query that I couldn’t remember how to do last time. I put V2 on the left, with a right hand query.

This gives everything from V2 plus the V2 that equals V1. However, the trick is that I set V1 to ‘Is Null’ which takes out the V1. That should give only the right section of the peach colored circle below.

For some reason, my new number for the right entire circle is 666,532. The new query results is the right hand circle minus the overlapping data which is 242,494. I’ll append this query to the table I made with my previous Query. I renamed this table as tblV1andV2 and it has 942, 647 rows.

Next, I want to sort the table and add an ID.  I copied the structure of the table to a new table. Then I added a Position ID (Pos ID) with an autonumber. Then I made a query to append the old data to the new table with the autonumbered Pos ID. This gave me what I wanted but not in the right order. So then I used the sort function to get the table in the shape I wanted:

I can tell the table is right by going to the last record:

Before the last record would include the V2 alleles that were added but they weren’t sorted. This long process gives me a sorted ID in the same relative position as the sorted Chromosome positions. The reason I need that is to describe my patterns  in a simpler way than by Chromosome start and stop.

Summary and Next Steps

  • Going down the road of filling in patterns, I found something that I needed to correct in an earlier step
  • This caused me to start afresh with cleaner tables.
  • I was able to add a unique ordered Position ID to the combined V1/V2 table
  • This position ID will be used to identify each Pattern for filling in missing alleles
  • However, I have to re-do the patterns. This time, I will include the Position ID in the start and end of each pattern in my summary of Mom and Dad Patterns.

 

 

Part 3 – Raw DNA From 5 Siblings and a Mother – Patterns

In my previous Blog, I looked at Whit Athey’s Principle 3 for my mom, my 4 siblings and myself. Based on that Priniciple and the previous 2, I phased our DNA up to a point. The next step in the phasing has to do with patterns.

Patterns

The patterns I am talking about are the patterns that the five siblings receive from either their mother or father.  For example, an AAAAB pattern means that the first 4 siblings received the same allele and the fifth sibling received a different one. I had mentioned previously that the patterns should be in this form:

  • AAAAA
  • AAAAB
  • AAABA
  • AAABB
  • AABAA
  • AABAB
  • AABBB
  • ABAAA
  • ABAAB
  • ABABB
  • ABBBB

The first situation is a special case as this situation can happen within the other patterns ‘by accident’ as Athey puts it.

AAAAB Dad pattern

First I’ll look at a query to find an AAAAB pattern.

That Query results in this:

Except there are actually over 8,000 lines. I summarized the rough starts and stops in an Excel Spreadsheet:

This part can get a bit tedious. In Chromosome 2, I noted a possible break between 89 and 96M, so I’ll need to keep an eye on that. Highlighted in yellow are single patterns which may or may not be significant.

quality check

I took my AAAAB Query results and put them into an Excel spreadsheet. Then I subtracted the previous position number from the current position number to see where there were gaps. Then I filtered the gap to 1,000,000 or more positions:

 

This is my gap analysis. I highlighted the 7 million position gap where I put in an extra segment on the AAAAB pattern. This points out some of the single AAAAB patterns also.

mapping the initial results

Let’s look at Chromosome 13 between 28 and 87M. With an AAAAB pattern, that means that Joel, Sharon, Heidi and Jon match the same paternal grandparent. Lori matches a different one. However, we don’t know which paternal grandparent without a reference cousin. Fortunately, I have one. He is my dad’s first cousin. He would match on my paternal grandfather’s side. That grandfather is James Hartley, b. 1891:

Paternal cousin Jim matches the 5 siblings here:

As you may guess, Lori is on the bottom (#5). She has a crossover at about 85.5M according to Gedmatch. That means that before 85.5M she is matching on my father’s mother’s side: Marion Frazer. So, if I wanted to, I could start to map Chromosome 13. From 28 to 87M, I could say that 4 siblings got their DNA from their paternal Hartley grandfather and one sibling, Lori got hers from her paternal Frazer grandmother.

Further, I would expect an AAAAA pattern starting at 87M based on the gedmatch browser results above. The bad thing about an AAAAA pattern is that there is some missing DNA for the other grandparent. In this case, the Frazer DNA is lost on the right side of the map below. Another point is that these patterns change one letter at a time. So it makes sense that an AAAAB would go to an AAAAA. For example, an AAAAA would never go directly to an ABABA.

Here is a paternal only map of Chromosome 13 based on our very initial results:

aaaab Mom pattern

I notice that the formula that I used to find the AAAAB Dad pattern, I can move over to the mom side. So I might as well do this while I’m thinking of AAAAB pattenrs and put the results in Excel.

I randomly used Heidi as the ‘A’. So Lori not matching Heidi becomes the ‘B’. The results for this maternal query was much smaller with only 189 lines.

 

This was a lot easier. The Mom and Dad Patterns don’t interrelate with each other, so I have them on separate worksheets. Note that there is the same AAAAB pattern in the same starting place on Chromosome 13 as there was on the paternal side. This is a coincidence and the starting spot is a coincidence. This is just a rough number now and may be refined later. I could make a map of this also.

Here is a cousin on my mom’s father’s side:

Here she matches Joel, Sharon, Heidi and Lori from about 74-99M. Here is a map drawn on the Gedmatch browser and raw data phasing:

 

This shows what a AAAAB pattern looks like that is both paternal and maternal between 28 and 45M. I also show two crossovers for Lori: (Frazer to Hartley) and (Rathfelder to Lentz). In addition, Jon has to have a crossover from Rathfelder to Lentz and Lori has to have another crossover from Lentz to Rathfelder somewhere in the white spaces. There is a reason that I could tell the maternal A’s of the AAAAB pattern were Rathfelder even though our cousin match did not overlap that area. It is because the patterns do not change that fast as I explained above.

Now that I know which sibling has one of the paternal crossovers I can mark it on the Dad Pattern Spreadsheet:

I name the crossover column in the spreadsheet for the end of the pattern position, so it will be clear where it is. This is the ultimate goal of the process: to find the crossover locations and assign them to the siblings. Once this is done a map may be drawn for all the siblings.

The Next Step

In the next step, I could fill in the missing alleles between the Start and End positions of the AAAAB patterns. Here is how that will be done:

The highlighted row is where the AAAAB Pattern starts. Basically, what will happen is if there is at least one Allele in the first four positions, I will be able to fill in any of the other alleles in those first four positions with the same allele. However, in the last row, for example, there is just one G in the last position. We don’t know if the other four alleles will be a G or another letter. The row that has TTT??. We know that we can fill in the fourth T to TTTT?. However, the last allele we don’t know if it will be a T again or a different alelle. So we also need to leave that space blank.

However, I want to make sure I have all my patterns right, so I will look at all the patterns first and reconcile them.

AAABA Pattern

If I drew my map correctly above, I will be expecting Lori to have a maternal AAABA pattern on Chromosome 13. This should change to an AAABB pattern at about position 95M. I’m already on a maternal query, so I’ll start there.

 

I used Heidi again as the A. Now Jon is the B that is different than Heidi. I was surprised with the results as I only had this maternal pattern in Chromosome 1 and 23:

 

My prediction of a Chromosome 13 AAABA Pattern did not come true. I wonder what went wrong?

Paternal AAABA Pattern

Here is a partial summary of the Paternal AAABA Pattern:

 

On Chromosome 11, we see the AAABA pattern twice with an AAAAB pattern in-between. To go from an AAAAB to AAABA there has to be a transition pattern: either AAAAA or AAABB. Hopefully this prediction will be correct! That leads me to the AAABB pattern.

AAABB

This pattern requires a slight modification of my previous query:

 

This pattern is adjacent to the AAABA Pattern, so I will be able to assign some crossovers:

 

These crossovers belong to Jon and Lori as Jon is in the next to the last position of the patterns and Lori is in the last position of the patterns. Note that in Chromosome 19, Lori goes from an AAABA to an AAABB at about 5M. However, there is a rogue AAABB in the AAABA pattern at around 3M. That could be due to a misread or a mutation. I’m not sure. Jon has a crossover on Chromosome 8. These are all Lori and Jon crossovers, due to the positions of the pattern changes we are looking at. The changes are all in the last two positions.

AAABB Maternal

I’m still getting very few crossovers here. I’m not sure why:

 

I’m not sure why the maternal side is not keeping up with the paternal. I have no crossovers here yet.

AABAA

Following my alphabetical reasoning, AABAA is my next pattern. I’ll start with the maternal:

 

I changed to having my [Joel’s] allele the ‘A’ in the Pattern. The results look right:

 

It seemed like there was a break in Chromosome 5 between 46 and 50M.

AABAA Paternal

 

On Chromosome 5, there was a gap similar to the one on the Maternal side.

Centromeres

According to ISOGG, these are the Build 37 Centromeres:

This is good information to have. I assume that the Centromere is not counted, so I will ignore the Chromosome 5 missing area and make a note that the centromere is there. This also makes a difference on all the results.

AABAB: Are We There Yet?

 

Here are Heidi’s first crossovers. I’ve also heard of crossovers referred to as cut points. I am noting where the centromere is – though not quite spelling it correctly above.

Here is the Maternal AABAB. I am still annoyed that there are so few patterns. They seem to be missing for some reason:

 

I suppose, if this trend continues, I could do the project over and add in my mother’s and my FTDNA raw DNA results.

AABBA

I didn’t find any AABBA Patterns on the maternal side. However, that was with a query using my results as A. However, from my previous Blog, I recall this chart:

 

This showed that on the Mom side, Jon and Lori had the most alleles. I’ll run the query again this way:

 

Still no patterns.

Here are some more Dad Patterns:

 

However, there are a few problems. Chromosome 17 is missing a pattern. I can solve this by looking at the original table.

 

Here the pattern is AABAA.

The next problem is that there are two patterns in one spot on Chromosome 22. I ran pattern AAABA again and see it should have ended earlier:

 

Here is the right answer below that also shows a Heidi crossover at that location:

 

AABBB

Paternal

 

Maternal side

Still nothing.

ABAAA

Maternal side

 

Paternal

This side had more patterns.

ABAAB

Had several of ABAAB Patterns on the dad side, but only one on the mom side. I think that there is a fill-in step that fills in the mom side from the dad side that may correct this later.

ABABA, ABABB, ABBAA

I did notice a Dad Pattern discrepancy on Chromosome 6:

 

There are three single patterns, I figured were discrepancies. However, there appeared to be a longer AAABB Pattern within the ABBAA Pattern. This is where it helps to look at the raw data.

 

The blue section is the start of the AAABB rogue pattern that I had. However, a closer examination reveals that this pattern is not continuous from position 30514810 to 30594827. Between those two there are a lot of ABBAA patterns. This is clear at position 30544401. However, this is also clear wherever the first 2 alleles are different. For example, on the last line, I see GT???. This will be filled in with GTTAA as this is within the ABBAA Pattern area. So what happened was that there were two single AAABB patterns. When I did the query for these, it looked like the pattern was continuous, but it was not. Based on the above, I’ve modified my Dad Pattern Spreadsheet to show two single discrepancies:

 

I won’t overwrite this information, but I will keep it in mind for later in case it is important. If this was a real crossover, it would be mine. However, crossovers in the middle of a chromosome don’t change that fast for one person on one copy of their chromosome.

Some of the Dad Pattern Crossovers are starting to fill in:

 

Starts and Ends of Chromosomes

At some point, it is important to know where the Chromosomes start and end. The testing companies don’t always start at the beginning positions of each chromosome. The ends are different also based on the lengths of the chromosomes.

I was able to find what I was looking for using a min/max Query in Access. I took my table with the 900,000 plus alleles and made a query that looks like this:

 

When I run the Query, I get this helpful table:

This tells me the start and end locations for each of the chromosomes that I am looking at.

I put this into Excel and highlighted the information in purple. Then I sorted it into my mom and dad pattern spreadsheets:

 

Now, I can tell that I am near the beginning and the end of Chromosome 20 with the pattern locations. However, on Chromosomes 21 and 22, there is still room for more at the beginning of those Chromosomes. As the Chromosome 20 patterns are complete, this also tells me that my sister Lori has no paternal crossover on Chromosome 20.

ABBAB, ABBBA, and ABBBB

These are the last three patterns, not counting AAAAA. I finally have one crossover on the maternal side. It is on the X Chromosome:

 

I have a mess to clean up on Paternal Chromosome 2 :

 

There appear to be two patterns occupying the same space between 123 and 128M, which is not good. I’ll take a look at my Table: It appears that the AAAAB at 127,841,390 is a one-time occurrence. Here is my correction:

 

Note that there is still a gap at AAAAB. There may be an AAAAA Pattern stuck in there.

Lessons Learned and Next Up

  • It is good to document the process in case something goes wrong
  • The start and end points are needed for each chromosome
  • The start and end for each centromere is needed also
  • Attention is needed for the location of each crossover and who it goes to as this is a main point of all the work.
  • Changes along each copy of the chromosome are gradual. They happen one at a time and those one at a time changes correspond to siblings.
  • Next up is filling in the blanks. That was discussed briefly in this Blog.

Raw DNA From 5 Siblings and a Mother: Part 2

In my previous Blog, I started to phase 5 siblings based on their raw data and the raw DNA data from their mom. I looked at homozygous results. That is, when each sibling had the same allele, it meant that they got one of each of those same alleles from each parent. Also when my Mom had homozygous results, say GG, she had to have given one of those G’s to each of her children in that location.

I am using an Athey paper on Phasing from 2010. I looked at his first 2 principles in my previous Blog. Here is Principle 3:

Principle 3 — A final phasing principle is almost trivial, but it is normally not useful because there is usually no way to satisfy its conditions: If a child is heter
ozygous at a particular SNP, and if it is possible to determine which parent contributed one of the bases, then the other parent necessarily contributed the other (or alternate) base.
Heterozygous is a fancy term meaning two different alleles. This principle also lends itself to MS Access, but it requires a few more steps. In my case, the known contributor is my Mom. So in the case where my Allele 1 is different from my Allele 2 and I have an allele from mom. My allele from dad will be my other allele. I just have to make a formula out of that. It sounds like a high school math word problem.
First, I copy my homozyous allele from mom table to a new table. This is in case I make a mistake and have to go back to my previous table. I’ll call my new table, ‘tbl5SiblsHeteroMomtoDad’. Again, I’ll use an Update Query, to update the table with the new ‘from Dad’ alleles. There shouldn’t be an allele from Dad in any of these situations, as we have only put those in where the children were homozygous.
I used the Access Expression Builder to get my heterozygous results:
Here is the second part of the criteria:
This part says that where I’m heterozygous, and my allele from mom was allele1, put allele2 in as from Dad. Before I run this, I presently have 485,834 alleles from Dad. When I go to run the Update Query, I get this message:
After I run the Update Query, I now have 533,517 results. This is the same as 485,834 plus 47,683, so I assume that I am on the right track. I next have to run this one more time for myself for the case when my allele from Mom is allele2 and my allele from Dad would then be allele1. Then I will run this eight times for my four siblings.
5 Phased Sibs Update: V1 and V2

I did all my Principle 3 phasing and here is the update:

What is a little surprising is that Jon and Lori who were tested as AncestryDNA V2 had more Mom-phased alleles. I did mention above that they were getting extra phasing on SNPs that they hadn’t tested from their mom, but I didn’t realize how much.

I mentioned in my previous blog that the combined number of SNPs tested between V1 and V2 is 942,269. That number represents the merging of V1 and V2.

Also some of the specifics are a bit off. For example, my numbers include phased results for myself from my dad (16,536) on the X Chromosome. Well, I didn’t get an X from my dad. This means that the JoelfromDad and JonfromDad numbers above are a bit high.

Next up: DNA patterns