Linkage Analysis of Pedigrees with Loops

[Lucien Bachner]

Gregory M. Acland  wrote


 	I would appreciate advice from anyone with insight or experience into
	analysing pedigrees with multiple loops. I understand, from discussions at
	Dr Ott's introductory course on Linkage Analysis, that the Linkage package
	can be recompiled with the Maxloops constant set at a desired number other
	than the default.

	How severe are the trade offs?

	The pedigrees involved are canine, and do not have huge numbers of
	individuals. Probably somewhere in the order of 30 to 50 individuals per
	family. The loops are unavoidable, however, as they are prexisting rather
	than planned pedigrees. Something like 6 to 10 loops per pedigree is
	typical.

	Does changing Maxloops to something like 10 increase the compute time
	drastically for pedigrees of this sort of size?

	I am currently running the Linkage package on a DOS machine (100 Mhz 486,
	16 MB RAM), and don't have ready access to a Unix system.

	What source programs do I need to compile to yield a version of the Linkage
	package customized to deal with this many loops. What are the current
	versions that should be used? Is Borland Turbo/Pascal still the compiler of
	choice? Are there other compile options that should be considered at the
	same time?

	Alternatively, can Fastlink deal with loops at all, and if so, can it deal
	with this many loops.  If so, can I obtain a DOS-executable version with
	the capacity to handle this many loops?

	Gregory M. Acland        	       	       	       	       	  (607) 256-5684
	[phone]
	Center for Canine Genetics & Reproduction       	  (607) 256-5689 [fax]
	James A. Baker Institute for Animal Health      	   gma2 at cornell.edu
	College of Veterinary Medicine
	Cornell University
	Hungerford Hill Rd, Ithaca, New York 14853



My opinion, mainly heuristic but based on experience is that you have
no chance to run that kind of problems on a DOS machine even with fastlink
mainly because you will need a huge amount of RAM.
Moreover if you manage this first problem, anyway the run on DOS machines is likely to take
many months or years or maybe centuries.

As I'm beginning to manage a linkage server at INFOBIOGEN (France) I can try
to run your problem on powerful Unix machines.

If interested I just need the raw files, description of loops or pedigree drawings
and what kind of results you want.
(If I succeed I only ask you to quote INFOBIOGEN in Methods section of paper)

For any further infos about this topic please mail to

linkage at infobiogen.fr

Regards


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            Lucien Bachner                         
 Laboratoire de Biochimie Genetique,Hopital Cochin. 
   123 Bd. Port Royal, 75014 Paris, France.        
Tel: (33 1) 42-34-12-12 ext 3039 FAX: (33 1) 44-41-15-22 
e-mail : bachner at Cassini.genethon.fr 
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