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Quick Genetics problem help
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Dembsky, Joshua Lyman (UMKC-Student)
May 1, 2006, 7:40:45 AM5/1/06
to gen-...@magpie.bio.indiana.edu
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!
jld...@umkc.edu
Josh Dembsky
University of Missouri-Kansas City
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!
jld...@umkc.edu
Josh Dembsky
University of Missouri-Kansas City
E. Wijsman
May 2, 2006, 1:28:14 AM5/2/06
to Dembsky, Joshua Lyman (UMKC-Student), gen-...@magpie.bio.indiana.edu
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.
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.
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Dept. Biostatistics Seattle, WA 98103
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