GEDmatch Lazarus and Phase Kit Numbers

+18 votes
1.7k views

I'm discovering just how powerful Wikitree can be on discover potential genetic matches and possibly isolating parts of chromosome segments to certain ancestors (assuming the two people being compared aren't unknowningly connected elsewhere).

My question.  
Has anyone worked on incorporating their phased kits or Lazarus kits into their wikitree profiles? If so, who have they went about doing so?

For those unfamiliar with the two.  Phasing on GEDmatch allows one to split themselves into the half they received from their father, and the half from their mother into two new kits.  This requires one parent to be tested.

Lazarus allows for an experimental recreation of a untested ancestor to be generated based on a carefully design testing strategy.  For example, my grandfather passed a month before I could test him.  He has 4 children (tested one for now), a sister (I've tested her), etc.  By using Lazarus when I test more of my aunts and uncles (his children) I can build a decent facsimile of himself almost comparable to testing him.  If done in a careful manner, these facsimile's are almost as good as the real thing.

It maybe interesting for Wikitree to incorporate Paternal / Maternal fields for phased gedmatch kits in the future.

in Policy and Style by Zack Daugherty G2G2 (2.6k points)
For now how I'm handling Lazarus kits is to add "Other auDNA" test to the profile of the person with the rebuilt Lazarus kit and then add the Lazarus number.  I also comment on the kit what individuals kits were used to construct the Lazarus.  In the future this comment will include the Wikitree hyperlinks to the profiles of the individuals used in the reconstruction.

Regarding the phased kits, I simply added each paternal/maternal kit to the comments as Peter Roberts suggested.

Loving this platform more and more!
Great question, Zack. Thanks for asking.
Can this Lazarus thing be used if several cousins from grand-siblings have been tested to determine the DNA for a common great grandfather?

It is possible.  You also need someone that is above or horizontal of the person you are building the Lazarus of.  So a cousin that is not a direct descendant of the individual. Here are some links describing Lazarus and highlighting some uses.  

Here is the Lazarus Description on GEDmatch Wiki:

Lazarus

Create surrogate DNA kits of close ancestors.

Designed to re-create a target kit# DNA profile by combining the matching segments between a deceased person's descendants and their other relatives (ancestors, siblings, aunts, uncles, etc.).

While not specifically designed to work with half-siblings, they can be used as descendants too since the same concept applies. It will produce a kit containing the DNA data common to both half-siblings, corresponding to their common parent.

Lazarus kits typically contain much less DNA data than normal kits (though, not always), but may be useful nonetheless.

The more close relatives' kit#s you have - the better your results will be. You can also use more distant cousin matches, but it will likely take many more. In extreme cases, it's not unheard of to use over 100 kit#s to produce a single Lazarus kit.


What can I do with a Lazarus produced kit?

You can use a Lazarus produced kit# in the comparison tools like any other kit#. You can reconstruct a recent ancestor and use matches to their Lazarus kit# to identify distant cousins related through them. For the one to many tools there is a minimum data threshold - your Lazarus kit# must have over 1500cM of DNA data to be eligible for batch-processing needed for the one to many tools.


Data Entry and Choice of Thresholds

You must have at least one kit in Group 1 (Descendants) and one kit in Group 2 (Other Relatives).

It is not necessary to add data for every blank on the entry form, but more data usually produces better results.

If you have a Kit# for the Target Kit#'s partner this can also be used to increase accuracy (must be the other parent of all descendants used in Group 1)

Group 1 is close descendants (son, daughter, or perhaps grandchild) and Group 2 is siblings, cousins, aunts/uncles, or parents of the target person for whom you want to recreate the DNA. Each kit can provide a piece of the DNA for the resulting target kit.

One example using 2 siblings in Group1, and 3 aunts/uncles in Group 2, was able to achieve almost 100% restoration of a full SNP count of a parent.

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.

There is no additional benefit from putting both children and grandchildren in Group 1. Use the person closest to the Target Kit# (the child of the target) if they are available.

The default included segment size thresholds, 6cM, 700SNPs, are a good starting point. You can triangulate small segments in the One-to-one tool between the relatives to check the validity of smaller segments to see if smaller thresholds could be used to yield more Lazarus DNA. As always, using smaller segments increases the chance of including random deep ancestry segments and IBS (Identical by State), false positives.

 

Example: Using Lazarus to reconstruct Paternal Kit# from Distant Cousins, Maternal Spouse Kit# and 2 Daughter Kit#s

Use the People who match one or both of two KIT#s tool. Use one daughter Kit# (for the descendant), and the mother (as the target Kit#'s partner). The application gives 3 lists. Use the results that match the daughter, but not the mother. The resulting list will be the ones that are related to the target father. Also, keep a copy of the list of the top few matches to the mother and daughter. Click the check marks for the top 98 matches (or fewer if you get tired of clicking) to daughter only (and not mother). Click the "Submit" button at the top of that section. It will bring up a menu with several "Visualization options". The last option is Lazarus. Select Lazarus. It will have all of Group 2 filled in, with daughter and mother as the first 2. Move daughter kit number from group2 to group 1. Add the other sister to group 1. Move your mother to spouse. Generate your Lazarus kit.

Do some trial one-to-one comparisons to make sure the resulting Lazarus kit does not match the ones (from above) that match your mother and you. If you find any kits that should not match, look at the results page from Lazarus, and find the kit(s) that contribute to the matching segments. Remove the offending kit(s), and run Lazarus again. Repeat until it gives the expected results. Delete any of the kits that didn't work out.

Evaluate and Revise your results:

After you generate a Lazarus kit, you should test the results to ensure that they are consistent with your expectations.

1. Use the one-to-one utility to compare the resulting kit with your own kit, to ensure that it is a perfect match.

2. Compare the results with a kit on the other side of the family, that should not match. If you find any matching segments, look at the "Contributions" list on the results page to see what kit(s) the matching segment(s) came from. Remove that kit from your entry form, and generate new results.

 

Notes:

It is generally a good idea to print (or otherwise save) the input form before starting processing. Usually, this is an iterative process where you need to go back and change 1 or 2 entries and run the program again. Select the 'Trial Run' option for the first few attempts, until you feel like the results are good enough to generate a test kit and start evaluating it.

When the new surrogate parent kit has been created, it should be verified by comparing it with yourself, and with cousins known to be on the branch of your other parent. A parent should be a perfect match with their child. It should not match any segments with the other parent or cousins related to the other parent, unless you have reason to believe there has been a recent intermarriage.

Created kits must contain at least 1500 cM total segment length before they will be eligible for batch processing. Smaller kits may be used only for one-to-one matches.

If you create a replacement or revised kit, please delete the old one to reduce the clutter (and the load on the servers). Thanks.


Lazarus Kit#s not showing on One-to-many results.

There are 2 kinds of Lazarus kits.  The ones with Kit numbers starting "LL" have at least 1500 cM of segments, and the ones with kit numbers starting "LX" have less than 1500 cM.  The LX kits do not have enough information to provide valid one-to-many matches, so they do not show up in the one-to-many report. Another thing that would have caused that would be if "no batch processing" was selected for "Processing" on the entry form when you entered your data.

Caveats:

The resulting surrogate kit does not contain any SNPs for segments where there was no reference data. You must keep this in mind when evaluating any results from the use of this kit.


A blog describing Lazarus: https://dna-explained.com/2015/01/14/lazarus-putting-humpty-dumpty-back-together-again/

There is also a closed Facebook group for GEDmatch Lazarus. Here is the link: https://www.facebook.com/groups/818555341528048/

2 Answers

+13 votes
 
Best answer
Having a fields for Lazarus and phased kits numbers are great ideas which I would like to see happen.  Thank you.

Right now the best you can do is add them to the note field for your autosomal test.
by Peter Roberts G2G6 Pilot (711k points)
selected by Debbie Parsons
+10 votes
I created a Lazarus kit for my Dad and posted it as Other DNA on his profile: [[Foster-118 | Bill Foster]].
by William Foster G2G6 Pilot (122k points)
I tried to add a Lazarus kit and I got an error, it will only except a kit with one letter and six numbers
@T. Stewart, I think your comment should be a new question, but all the GEDmatch kit numbers I've ever seen are one letter and six numbers except the Lazarus kits begin LL.  Were you trying to create a Lazarus kit using another Lazarus kit?  Or were you using the FTDNA or other 3rd party site number?
Thank you for responding,

How were you able to post the kit for your dad in Other DNA?

I created a Lazarus kit for my maternal grandfather [[Johnson-55097 | Sam Johnson]] (LL845199) using my maternal grandmother and aunt. When I tried to post the DNA to Wikitree using 'Other auDNA', I got the error that Wikitree would not accept the Gedmatch ID.

Related questions

+4 votes
1 answer
+9 votes
4 answers
+3 votes
2 answers
272 views asked Nov 7, 2018 in The Tree House by Living Hampson G2G6 Pilot (114k points)
+3 votes
4 answers
377 views asked Oct 20, 2022 in WikiTree Tech by BB Sahm G2G6 Mach 3 (31.9k points)
+3 votes
0 answers
+10 votes
3 answers
428 views asked Sep 2, 2017 in Policy and Style by Kelly Rishor G2G6 Mach 1 (14.4k points)
+6 votes
2 answers
1.2k views asked Oct 1, 2016 in WikiTree Tech by Rosemary Potter G2G Crew (600 points)

WikiTree  ~  About  ~  Help Help  ~  Search Person Search  ~  Surname:

disclaimer - terms - copyright

...