My LOD score is too high!

Mike Morris mike at
Wed Feb 1 02:33:51 EST 1995

  Not a common complaint, I guess. But I cannot understand (or believe)
a result we recently had from LINKAGE 5.1.

  We have a consanguineous family, with a monogenic AR disease (locus
1). We have two perfectly linked markers (2 and 3), which complement 
each other in terms of informativity. The markers are at most 1% apart
(no rec. in this family).
  I ran MLINK, "Lod score table", with the following results:
  Locus order   Rec fractions   Rec varied   lod max (always theta=0)
      1 2             .0            1           3.1
      1 3             .0            1           1.3
  >>> 1 2 3         .0 .01          1          16.1  <<< 

  As I understand this, either I have screwed up somewhere, or the
program interprets the third line as "1 vs. superlocus 2+3", and I
get a genuine result. But 16 seems much too high!

  Can anyone clarify this for me?

	Mike Morris

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                  

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