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Old 06-02-2011
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Genetics Recombination frequency and LOD Score!

If recombination frequency for a disease is for example 40%, but then we calculate LOD SCORE AND IT IS not more than 3, then what should we say about this?
is there any linkage or not?

Somewhere in Kaplan notes it says if recombination frequency (teta?) is less than 50% there is no linkage, so I assume more than 50% means linkage.

but later it says we should calculate LOD score ,and if LOD is more than 3 then we say there is linkage?
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Old 06-03-2011
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if the LOD score is less than 3 (-2 - 3 ) you have to collect more data , if more than 3 it's linked but below -2 unlinked
and let me clarify something else too
if the recombination frequency is less than 50% ( which means the gene and the marker are closed to each other ) = LINKED
if the recombination frequency more than 50% = UNLINKED

if there is a table of LOD score and theta value , you have to ignore the entire table and take only the highest LOD score , let's say it's 4 or 3.5
and the theta value (recombination frequency) = 17 , then it's definitely linked
if LOD score is not more than 3 and Recombination frequency is 40% as you said = collect more data would be the answer

if lod score let's say -3 and recombination frequency 60% = not linked ( the gene and the marker are far away from each other by about 60 million base pairs ) . every 1% = 1 million base pairs

I hope it's clear for you now
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The above post was thanked by:
drnirajmavani (06-04-2011), pandaliu (07-08-2014)



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