sex linked disease and high thetas

Dean Flanders dean at birch.med.umn.edu
Tue Jan 16 13:37:14 EST 1996


I am working with a sex linked disease.  It is 100% penetrant in the males and 
one can observer carrier status in the females.  So in my linkage runs I am 
running it as a sex linked disease and I am calling the carrier females 
affected and affected males affected.  Is that the correct approach?  Or should 
I call the females unaffected?  Below is the preplink file, and I am running 
ilink:


 8 0 1 5  << NO. OF LOCI, RISK LOCUS, SEXLINKED (IF 1) PROGRAM
 0 0.0 0.0 0 << MUT LOCUS, MUT MALE, MUT FEM, HAP FREQ (IF 1)
  1  2  3  4  5  6  7  8
1   2  << AFFECTION, NO. OF ALLELES
 0.990000 0.010000  << GENE FREQUENCIES
 1 << NO. OF LIABILITY CLASSES
 0 1.0000 1.0000
 0 1.0000 << PENETRANCES
3   4  << ALLELE NUMBERS, NO. OF ALLELES
 0.076920 0.461540 0.230770 0.230770  << GENE FREQUENCIES
3   3  << ALLELE NUMBERS, NO. OF ALLELES
 0.153840 0.461540 0.384610  << GENE FREQUENCIES
3   6  << ALLELE NUMBERS, NO. OF ALLELES
 0.083330 0.250000 0.250000 0.166670 0.166670 0.083330  << GENE FREQUENCIES
3   5  << ALLELE NUMBERS, NO. OF ALLELES
 0.166670 0.333330 0.083330 0.250000 0.166670  << GENE FREQUENCIES
3   8  << ALLELE NUMBERS, NO. OF ALLELES
 0.230770 0.076920 0.153840 0.230770 0.076920 0.076920 0.076920 0.076920  << 
GENE FREQUENCIES
3   6  << ALLELE NUMBERS, NO. OF ALLELES
 0.076920 0.153840 0.230770 0.230770 0.230770 0.153840  << GENE FREQUENCIES
3   7  << ALLELE NUMBERS, NO. OF ALLELES
 0.071430 0.214290 0.071430 0.285710 0.214290 0.071430 0.071430  << GENE 
FREQUENCIES
 0 0  << SEX DIFFERENCE, INTERFERENCE (IF 1 OR 2)
  0.1000  0.1000  0.1000  0.1000  0.1000  0.1000  0.1000 << RECOMBINATION VALUES
 1 0.10000 0.45000 << REC VARIED, INCREMENT, FINISHING VALUE


The weird thing is that I am getting a lodscore that is reasonable, since I am 
told it is linked to this locus (Am I biased or what!).  However, I am getting 
thetas of 0.999 or so with my highest lodscores.  So I was thinking that possibly 
this is a result of the sex linked disease question.

Any help or insight is appreciated!

Thanks!



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