Sunday, August 20, 2017

An Issue With Lazarus

I've written about Lazarus before, a tool available via GedMatch which allows for you to reconstruct a partial genome of a deceased ancestor using living relatives' DNA.  Lazarus requires you to put direct descendants of this ancestor into Group 1 and other relatives of that person in Group 2.  The idea is that if a segment is shared between a descendant of that individual as well as by one of his or her cousins, that segment can be attributed to the deceased ancestor (weeding out segments that come from other ancestors of those in Group 1).  Particularly when dealing with endogamy, there could be extra segments introduced, but that's not the point of this post.

Enough of my relatives have tested that I've been able to create Lazarus kits for multiple ancestors.  But I've been noticing some odd results for many of them.  Here's one example, in trying to recreate my grandfather's genome.
My Uncle's Shared Segments with Don

Don is a half second cousin to my father--they share a great grandfather (Yechiel Suttleman) but have different great grandmothers.  Don and my uncle share two nice-sized segments--a 22.5cM segment on chromosome 9 and a 46.2cM segment on chromosome 21.  So if I try to recreate my grandfather's genome, I can use my father, uncle and aunt in Group 1; I also have 14 relatives (including Don) who can go in Group 2.  I would have thought that my grandfather's Lazarus kit would share all of the above segments with Don, as well as some others (from segments Don shares with my father and aunt).
Segments shared with Don and my Grandfather's Lazarus Kit
That 46.2cM segment that Don shared with my uncle doesn't appear in my grandfather's Lazarus kit at all!  I re-ran the kit multiple times, but that large segment never appeared in the "Resulting Segments" section--in fact Don had no shared segments with my grandfather's Lazarus kit on chromsome 21.  How could that be?

When my grandfather's Lazarus kit is simplified to have Group 1 as my father, aunt and uncle and Group 2 as only Don and Dave (Dave is not related to Don--they share 0cM of DNA according to GedMatch's default threshold), Don shares the following with the resulting Lazarus kit:
DNA shared between Don and a Lazarus Kit for my Grandfather with Only Dave and Don in Group 2
While we do get some of Don's Chromosome 21 segment that he shares with my uncle, we're still missing 12.2cM of that segment.

Dave and Don share no DNA with one another.  Neither my aunt nor my father share any DNA with Don on Chromosome 21.  My uncle shares no DNA with Dave on chromosome 21, but my father and aunt do:
My father and Dave share a 15.5cM segment on Chromosome 21; my aunt shares the exact same segment
Even if I only have my father and uncle in Group 1, plus Don and Dave in Group 2, Don only shares that same 34.0cM segment with my grandfather's Lazarus kit on chromosome 21 rather than the expected 46.2cM.

My grandfather had two copies of chromosome 21--one from each parent.  Don is related on his mother's side; Dave is related through my grandfather's father.  But it seems like the algorithm isn't accounting for that.  One copy of chromosome 21 should contain the entire 46.2cM segment that Don shares with my uncle.  The other copy should contain the entire 15.5cM segment that Dave shares with my father and aunt.

But he doesn't.  So Lazarus is missing segments that should be part of this kit.  So any Lazarus kit you are creating may be more incomplete than it should be!

Note:  I'm on Twitter.  Follow me (@larasgenealogy).

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1 comment:

  1. I have stopped creating Lazarus kits. At least until they begin addressing the outstanding issues. I am not sure that piling on more of them is going to get their attention.