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[Genetic-linkage] Re: Quick Genetics problem help

E. Wijsman wijsman at u.washington.edu
Tue May 2 00:28:14 EST 2006

The magnitude of the lod score and where it is high vs. low depends on a 
number of factors:
1) Heterogeneity. There can be genetic heterogeneity, and even slight 
nuances in how a sample was obtained can affect ones ability to detect 
linkage at one site vs. another.  Differences in the phenotype used to 
collect the sample would be one indicator of possible heterogeneity.
2) The "Suarez" effect.  When there is heterogeneity, replication of a 
result often requires a larger sample size than the initial finding, 
because the initial report is the best of several possiblities, while 
replication requires a strong score in the same location.  Are there any 
hints of positive lod scores at the second site across studies?
3) Bad luck or other "problems" with the analysis. One or both could be 
wrong. There are lots of ways one can end up with false positive results, 
some of which result from bad (naive) applications of the analysis 
methods, and some of which simply reflect badk luck.

Ellen M. Wijsman                        COURIER DELIVERY ADDRESS ONLY:
Research Professor                      Ellen M. Wijsman
Div. of Medical Genetics and            1914 N 34th St., suite 209
Dept. Biostatistics                     Seattle, WA   98103
BOX 357720, University of Washington    (Note:  Use this address
Seattle, WA   98195-7720                 EXACTLY as given above, and
phone:  (206) 543-8987                   use ONLY for courier delivery!!!)
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On Mon, 1 May 2006, Dembsky, Joshua Lyman (UMKC-Student) wrote:

> Hello all!
> I am a graduate student in Kansas City.  I have having some problems understanding a basic genetics concept that I am hoping one of you can help me with.
> If you have two chromosomes each with an area that has been identified as an area of linkage for a particular trait, what are some of the reasons you can have different lod scores?  For example, if two academic groups have identified an area of linkage of a trait, one study found an area on chromosome 7 with a lod score of 6.00 and another study found an area on chromosome 13 with a lod score of 5.20, how do you explain the different linkage results?
> Your assistance is greatly appreciated!
> jldxt9 at umkc.edu
> Josh Dembsky
> University of Missouri-Kansas City

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