Can half siblings be "phased" for their common mother and different fathers?

+3 votes
599 views
I know about and have used the phasing feature of GEDmatch.

This is a tad different.  All of these kits are 23andMe so maybe someone knows of some "magic" at 23andMe Tech Support.

A person I am working with has the following 23andMe kits:

Daughter (D) (her), Father (F), Aunt (A), HerSon (HS), and HerDaughter (HD).  We also have a Phased kit for her mother (PM) who is deceased from GEDmatch based on D and F.

F and A are half siblings sharing a common mother so it would be helpful if the F DNA could be further "phased".  F and A inherited au DNA from the common mother but different fathers so....

Thanks,

 

Pete
in The Tree House by Pete Toemmes G2G4 (4.8k points)
edited by Pete Toemmes

4 Answers

+6 votes
 
Best answer
Hi, Pete. I read your question a couple of times, and I'm afraid I'm a bit unclear about whose genome you're looking to simulate, the father's mother (shared with the aunt) or the father's father. If the mother, you're best bet might be to look at the GEDmatch Lazarus tool. But to get good results, it takes some planning in advance. To save G2G space, I'd point you to a website if I knew somewhere this was fully discussed, but I don't.

If you haven't used it, it requires at least one direct descendant of the "pseudo-genome" to be created. Ideally this would be a child (which you have) but one or more grandchildren can also work (but don't use both; if you have a child's kit to enter, don't also include a grandchild). If the spouse of the target Lazarus run has a kit number at GEDmatch--and this can certainly be a kit created via phasing--you should enter it to help the tool differentiate between base pairs contributed to the child.

The trickier part comes under what's labeled as "Group 2"...and there's a reason they have entry fields for a whopping 100 different kit numbers. In this group you need to enter GEDmatch kit numbers for people directly related to the Lazarus target but who are not direct descendants. As examples, GEDmatch gives: "siblings, cousins, aunts/uncles, or parents." Brothers and sisters, full or half, are clear enough, as are parents, if in the rare event someone is trying to create a kit where the parents have DNA on file.

But aunts/uncles and cousins, in my personal experience, is where the advanced planning comes in. I'd point you to a website if I knew somewhere this was fully discussed, but I don't. So two caveats. First off, recognize that the resultant Lazarus output may not end up representing a parent, but would still be helpful in your search. As GEDmatch says: "If close relatives are not available, distant matches can be used in Group 2 but less Lazarus DNA data will be produced--you may still be able to create a virtual cousin instead of the hoped for virtual parent."

You'll need enough shared segment information input in order to build the new kit. I don't believe GEDmatch tells you that up front, but that minimum threshold is 1,500 cM in order for the new kit to "synthesize" and go through batch processing and make it usable for one-to-many or other comparisons.

Second, and a qualifier of that, you need to plan the kit input to make sure those cousins are coming from the Lazarus target's line of descendancy. In other words, if you're trying to re-create a grandfather (as strange as that sounds) on the father's side, you do not want to use cousins who are related to the child via the grandmother's family. The Lazarus tool really can't tell the difference between chromosome segments coming in from one line as opposed to another.

As an example, I recently I tried to help someone whose father was adopted. We had kits for the father, the mother, the child (the person I was helping), two grandchildren, plus a 1st cousin of the father, two 2nd cousins, and two 3rd cousins. Lotta material. The problem was that--unbeknownst to me up front--all the cousin's were from the father's mother's side of the family...who would have shared no DNA (ostensibly) with the Lazarus target, the father's father. Sure enough, the kit generated just fine. But in testing it afterward, the person I was helping said it was turning up matches that were suspicious, that were already known cousins from the grandmother's side of the family.

I had simply taken the kit numbers supplied and run them through the Lazarus tool. Save yourself some time and don't make my mistake. We had to start over at the place you should begin: clearly chart out--draw a little family tree sketch if you need to--who the Lazarus run is expected to re-create, and where all the known kit numbers fall with respect to the target's lineage. Kits for input need to be screened so that you absolutely know they're in that same line of descendancy, not from a spouse's.

Don't trust the family history only. Run one-to-one and triangulation comparisons in advance to make sure the Lazarus kit will see no unrelated input. In the example above, what I ended up doing was throwing out all those cousins, and based a second run only on kits from unknown cousins who had been triangulated to relate to the father only, not the mother, and at a minimum cM threshold of 15...false positives are just too likely below that. We got a kit generated, but it didn't represent the target grandfather's genome. It was still a level of refinement, though, on that particular line we were attempting to identify. Which leads me, finally, to...

Check your work. After the new kit completes batch processing, run it through a bunch of types of comparisons to make certain it does not match kits you know it shouldn't (in this case the cousins initially supplied), and does match kits you think it should. Make careful note of the shared cM among known relations so that you can evaluate at what level the new kit represents a biological relative. Our new kit came in showing about 650 cM in common with the father's child, placing it somewhere between a great aunt/uncle and a 1st cousin 1x removed; matching with the father's grandchildren was roughly consistent with that.

In the example, we didn't end up with a grandfather, but we ended up with something approximately like a half-great uncle. Not what we were after, but still useful for future research nonetheless.

Luck!
by Edison Williams G2G6 Pilot (250k points)
selected by Andreas West
Ellen beat me to it while I was typing. Or thinking. It's possible I may think more slowly than I type....  :-)
You have experience with the Lazarus utility, Edison. I don't. Your input was valuable!
Thank you Edison.  It will take more than one sitting to digest this along with the Lazarus documentation and examples.

But I will try to answer your question in light of the fact I might have asked differently had I known what Lazarus was and could do.

But first a bit more detail.

1) The people involved have anywhere from 78-30% Ashkenazi DNA - so this is a challenge in and of itself.

2) The father (F) for whom we have a real kit is circumstantially believed to have a 98%+ Ashkenazi father.

3) The father's (F)  mother's father - so the fathers maternal GF - is unidentified who, based on the DNA of the aunt (A) who is a half sibling of the father (shared mother) and is 30% Ashkenazi is also beleived to be 75%+ Ashkenazi.

Perhaps another way to describe this is that the father has gotten Ashkenazi DNA from:

1) His circumstantially identified biological father.  Note: we suspect this based on the extraordinary Ashkenazi kit matches between the father and my maternal maternal aunt by marriage kit.

2) His unidentified biological maternal GF.

So, with that in mind :-), being able to identify the Ashkenazi DNA inherited by the suspected biological father ,who is deceased ,is the idea.

But it does not sound like Lazarus does that - directly - unless we can come up with a scenario that approximates creating a Lazarus kit for the father (F) to go along with his real kit.

However, I think our goal may be to try to create a Lazarus kit for the circumstantially suspected biological father and use that for comparison.

Pete

PS

Along with all of this, we are trying to find and then convince descendants of siblings of this suspected Ashkenazi father to test so as to solidify the connection.  Either or both approaches will likleey not specifically ID this Ashkenazi father since there are 5 sibling brothers one of which is an absolute record ghost.  But then I think DNA generally corroborates theories and paper docs - not the other way around.

Pete: Now I need to sketch out the family tree to try to follow along.  :-)  You may be able to generate a useful Lazarus kit, especially if you can drum up some other cousins of the father (F). That said, however, anything derived will include both the missing grandfather's atDNA and his wife's; since her identity would also be unknown, I think it would be next to impossible to figure out what genetic contributions came from whom.

If a Lazarus run won't help, the phased kit for the father might be useful. Sounds a little counterintuitive, but since that phased kit specifically excludes anything in the daughter's DNA that doesn't match the mother, it removes some variables. Then the tedious process of manually comparing chromosomal segment matches and non-matches to all the other available kits might, by process of elimination, give you a better picture of what was actually contributed by the biological grandfather and his wife. But that still leaves her ancestors in the mix.

That all of these kits were done at 23andMe won't help with the next thought, but if the father (F) is living and willing to give another sample...

If identifying that paternal line is the specific goal, a yDNA test may be in order. Family Tree DNA began almost 20 years ago because the founders wanted more information about their own Ashkenazi heritage. There are more than a couple DNA projects there focused on Ashkenazi ancestry and diaspora, and at more than one FTDNA annual conferences case studies of Ashkenazi DNA research have been presented. If you want me to check to see if I have any of those presentations archived, drop me a private message so that I have your email address.

I'm not looking it up, going only by memory, but I believe there are some well-defined yDNA haplotypes associated with certain lines of the otherwise somewhat diverse Ashkenazi founders over 40 generations ago. Unlike autosomal DNA, yDNA is passed from father to son essentially unchanged from one generation to another. If that father's father is strongly believed to be paternal-line Ashkenazi, yDNA might give you very strong evidence, determine the actual Ashkenazi line involved, and maybe turn up immediate cousins who have the genealogy to fill-in some of the missing pieces.

Since two different DNA channels are open to you for this particular goal, chasing them both doubles your odds. And if matches from both directions come together--i.e., you find a cousin who is both a yDNA and atDNA match--I call that an "evidence force multiplier."  ;-)

Good hunting!

+2 votes
I need to read more about phasing.  I haven't don it since both my parents died before DNA testing got going.  But I do have a half aunt, a daughter of my paternal grandfather and his second wife.  she and her son have tested on AncestryDNA but I haven't gotten them to transfer the raw data to GEDmatch so far.  If I could explain to them the advantage of phasing. and since I share 880 cM with her and a bunch with him, It should be possible to, I think, get a lot of info on at least my grandfather.  As for you question, I don't know the answer, but I'll go read about phasing and see if I can figure it out.
by Dave Dardinger G2G6 Pilot (407k points)
+2 votes
Gedmatch has a Tier One utility called Lazarus to create a surrogate auDNA profile for a close ancestor, using data from other family members. I have no experience with it, and I have no idea how well it will work with your data, but it seems like it's worth trying.
by Ellen Smith G2G Astronaut (1.1m points)
Hmm... I guess you've already used that feature for the "PM" profile.
0 votes
Your terminology is not quite right (to my understanding) and your question is very hard for me to understand, but I'll try to answer.  It sounds like you are saying that you phased the daughter into her paternal and maternal phases.  You don't have the mother's DNA and one of the mother's parents, so you cannot phase the mom.  As best I can tell from your question you want to deduce DNA for the mother of daughter.

Assuming I understood you correctly, you would want to test the father for the half-sibling and then you would be able to phase the half-sibling.

At GEDmatch, under tier1 tools, you would then want to use the Lazarus tool to create a kit for the deceased mother for whom you do not have her DNA.  You would feed in the two phased kits, or if you can only get one phased because other father is not available, the one phase kit on maternal side and the full kit for half-sibling.  You would also feed in the Aunt if she is sister to the deceased mother.  The HerSon and HerDaughter, if these are children of Daughter are useless for this exercise as they add no information not already in their mother.
by William Foster G2G6 Mach 9 (92.1k points)

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