Saturday, November 18, 2006

The Non-recLOH Event Multi-copy Marker Distance Counting Protocol

Has a nice ring to it, doesn't it?

We have just considered recLOH events in which the multi-copy markers on a palindromic arm can all change significantly and only result in a genetic distance of one.   Pending authoritative directions otherwise I have determined how I will advise the members of this surname project to count genetic distances for differences in multi-copy markers that are not part of a recLOH event.   Multi-copy markers are those markers that have a small letter of the alphabet associated with them, i.e., DYS385a & b, DYS459a & b, DYS464a,b,c & d, CDYa & b, and YCAiia & b.

Consider that each of these markers is made up of two or more 'parts', each part represented by a value, e.g., DYS385a is 11 and DYS385b is 14, so we will designate DYS385 as 11-14, the two 'parts' being 11 and 14.   If either part changed to another value, no matter what value, it would be a mismatch of one 'part' and therefore a distance of one.   So 11-15 would be a distance of one from our example.  11-17 or 13-14 would likewise each be a change of one part from 11-14 and a distance of one.   12-13 or 13-15, however, would each be a mismatch of both (2) parts and a distance of two.   This illustration will apply to any of the two part markers.

The other case is DYS464 which is a four (or more) part marker.   The numbers for it are reported in lowest to highest format which is not necessarily their actual order.   So for DYS464 we have to determine how many markers the two people do not have in common.   Assume DYS464 is 14-14-16-18.   We want to know the genetic distance of 14-16-18-18.   Both have a 14, 16 and 18 in the series -- although not in the same positions -- position doesn't matter on this marker.   So 3 of the 4 numbers are the same, a 1 step mismatch, ergo a distance of one.   12-14-15-16, on the other hand, only has two markers in common, 14 and 16, so we have a two part mismatch or a distance of two.

Come to think of it, I have never seen the values of any multi-part markers reported in anything other than low to high format, no matter how many values.   That being the case I'll go out on a limb just a little and suggest that if we have a two part marker like CDY as 35-39 and we want to compare another marker of 39-40 with it, the distance should be one since we have a mismatch of only one value.

That's the way I see it.

Ann Turner, co-author of "Trace Your Roots with DNA:  Using Genetic Tests to Explore Your Family Tree" does not feel comfortable applying this method for my examples of DYS385 changes.   She says:
I think we need to wait for FTDNA to revise its algorithm, as used on YSearch as well as the adminstrator's page.   In the meantime, here's how I would count the changes in a situation where 11-14 is the ancestral haplotype:
11-15 one step
12-14 one step
11-11 one step due to recLOH (the 11 overwrites the 14)
14-14 one step due to recLOH (the 14 overwrites the 11)
11-16 two one-step changes, with a lower probability of one two-step change
11-17 a judgment call:  if the remainder of the markers are in line with the ancestral haplotype, then this could be a one-time sudden jump, a rare event (more like a SNP than an STR in terms of mutation rates).   However, it would also be unusual to have three one-step jumps (or a two and a one) all occuring on one marker in a single line of descent, and I don't know which scenario is more likely.   Father/son studies show that about 96% of mutations are one-step.
My conclusion:  Take your choice.


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