sex linked disease and high thetas

Lucien Bachner bachner at lovelace.infobiogen.fr
Thu Jan 18 05:35:05 EST 1996


Dean Flanders (dean at birch.med.umn.edu) wrote:
: 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!

Dear Dean,

The result you got is due to the starting theta values
of your ilink run.
You should first of all run 2 point mlink
with all couples disease-marker and marker-marker.
Then set the starting thetas values to or close to
the thetas corresponding to Z (2 point) max.
You may call carrier females affected, it is surely
not the cause of your problem.

Hope it helps.

Regards

Lucien Bachner

P.S : The real cause of your result is that ilink has converged
to a local maximum because of your starting values.
--
Lucien Bachner

Infobiogen

bachner at infobiogen.fr  linkage at infobiogen.fr



More information about the Gen-link mailing list