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Generalized LOD score??

Mike Morris mike at divsun.unige.ch
Thu Sep 29 02:30:20 EST 1994

  I have the following simple linkage problem:
  We are a studying a disease which is perfectly linked to two markers,
which are approximately 1 cM apart. We have a small consanguineous family,
which gives us a lod (theta=0) of 3.09 for one marker and 2.2 for the
  The problem: when I run ilink and then lrp, I get a "generalized lod
score" of 5.06, for the three possible locus orders. 
  What is a generalized lod score? How is it calculated? Why is it higher 
than my better marker?
thanks in advance,  
Michael Morris PhD            
Division of Medical Genetics       tel (Switzerland) (22) 702.56.94
CMU, University of Geneva          fax (Switzerland) (22) 702.57.06
Geneva, Switzerland                email mike at medsun.unige.ch                  

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