Sunday, November 19, 2006

Berry DNA Project website update

Well, I've added a new recLOH page to the Analysis section of the Project website on which I have gathered, compiled and hopefully clarified the three recent posts concerning the recognition of a recLOH event, its effect on genetic distances and, in addition, a methodology for counting genetic distances between non-recLOH multi-copy markers.

This suggested method is not universally accepted.   Ann Turner is not comfortable applying this method to DYS385 differences and John McEwan points out that the majority of "RecLOH" events in P1/P2 are NOT gene conversions as RecLOH is defined and as seems to have been suggested by the articles, but are instead deletions, i.e., RecNulls or RecDELs.

Nevertheless, and especially given the prevailing uncertainty as to the 'correct' or most accurate method, I believe that I will suggest that we use this model until we are shown why we should do otherwise.   Simply stated, it is that if it's a recLOH event we have a distance of one for the whole event (all multi-copy markers on a given palindromic arm) and if it's not a recLOH event we will count each multi-copy marker as a unit, not each part of the marker separately.

If this protocol has a bias, it's a bias toward 'relatedness'.


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