[Genetic-linkage] Query in linkage analysis-pls help!

devasena devasenaa at gmail.com
Fri Aug 19 01:09:55 EST 2005

I'm a PhD student working on genetic polymorphisms in drug metabolizing
and DNA repair genes, wherein we have analyzed the frequencies of DNA
repair gene XRCC1 at exon 6(Arg/Trp) and 10(Arg/Gln). In order to
understand the co segregation of these two polymorphisms in Indian
population, we carried out Linkage Analysis using EH program. The
results of our analysis are listed below.
Linkage Disequilibrium D = h-p1p2
			       = 0.586461 - 0.9*0.67
			       = -0.016

Linkage Coefficient r 	       = D/[p(1-p)q(1-q)]1/2
			       = -0.016/(0.9*0.1*0.33*0.97)1/2
			       = -0.046

                                   #param   Ln(L)     Chi-square
H0: No Association                      2  -1074.53      0.00
H1: Allelic Associations Allowed        3  -1072.23      4.59

1. How do we determine significant linkage values, is there a reference
or range available for interpretation?
2. What is the meaning of a negative LD and linkage coefficient?
3. What is the relationship between them?
4. What does the linkage coefficient tell us? how is the value

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