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Linkage Software

I. Fenton ifenton at hgmp.mrc.ac.uk
Tue Feb 18 10:16:07 EST 1997

Gary Coulton <g.coulton at s1.cxwms.ac.uk> wrote:
>I would value your advice regarding a linkage study I am involved in. We
>have used automated genotyping (using microsatellite PCR) on an an ABI
>system to generate allele data for families segregating idiopathic
>scoliosis. The data is generated by the Genotyper program.
>The person who did the linkage analyses in the Dept. has recently left and
>I am at something of a loss to know how to analyse the data to assess
>linkage of the markers to the IS phenotype. I would be very grateful for
>any advice.

we are doing roughly the same for schizophrenia.  in what state
is the allele data ?  genotyper, or our version anyway, does not
produce "normal" linkage input files (as used by Lathrop/Lalouel/Ott
LINKAGE package) so some intermediate stage would be required.

if the data is in a form, or can easily be made in a form, that
LINKAGE can read then it is rather straightforward to analyse,
assuming that you know/can-guess the disease model.  i am sure
that many people in this group could perform the analysis if we
could get our grubby paws on your data !

if you have no experience of linkage analysis though, it will
be a problem for you - it is slightly more work than picking
up a book on linkage and downloading the programs.  i would
strongly suggest finding an "expert" (i.e. experienced person)
either locally or via this group.


Iain Fenton, Cardiff, UK.

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