Large Scale Linkage

E. Wijsman wijsman at u.washington.edu
Thu May 22 13:47:10 EST 2003


Use a different analysis program.  If you are talking about "bits" you
must be using Genehunter or Allegro.  These programs are only suitable for
small pedigrees.  The algorithms employed allow for large numbers of
markers, but not so many individuals.  Depending on your pedigree
structure(s) you need to use Fastlink, or Vitesse, or some alternative
that isn't restricted by pedigree size.  The algorithms used by such
programs allow large pedigrees, but are restricted in the number of
markers that can be used simultaneously in a multipoint analysis.
However, given a choice between lots of markers but fragmenting the
pedigrees vs. using the full pedigree structures with only a subset of
markers, the latter is the more powerful approach.  A typical marker will
retrieve ~70-75% of the meiotic information that is available; a
multipoint cannot get you to more than 100% of this information, or
perhaps a maximum gain of ~30-40% in information.  Use of large pedigrees
can increase the amount of information by factors of 2 or 3 or even more.
For a really big pedigree you probably would get more information out of
an analysis based on the whole pedigree, with only 1 marker analyzed, than
you would out of fragmenting the pedigree into chunks that can be analyzed
with methods that can use all the markers, but only small pedigrees.

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On 21 May 2003, Sourav Bandyopadhyay wrote:

>
> I was wondering if there is anything that will automatically split and break
> loops if needed for large pedigrees around 100 bits in size. Is there
> anything that will split the pedigrees into something manageable and then
> put the output back together again for multipoint analysis?
> We are stumped because everything is max at ~30 bits or does not allow our
> complex pedigrees.
> any help would be great. thanks.
> -Sourav
>
>




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