Linkage Newsletter

Vol. 9 No. 2 July 1995

Published by Jürg Ott

: Postal address: 722 West 168 Street, Unit 58, New York, NY 10032
Email: jurg.ott@columbia.edu
WWW: http://linkage.cpmc.columbia.edu

: Editorial Assistant: Katherine Montague
Email: km165@columbia.edu
Fax: 212-568-2750
Tel: 212-960-2507

World Wide Web server

Dr. Wentian Li has installed a WWW server for our group. It may be reached at http://linkage.cpmc.columbia.edu . Our anonymous ftp site ( linkage.cpmc.columbia.edu) is now fully functional and readers are encouraged to download programs and other files.

LINKAGE COURSES

The next two linkage courses are advanced courses and will take place as follows:

October 2-6, 1995: at the University of Zurich, Irchel Campus Computer Center, Switzerland
(maximum number of participants is 14).
January 8-12, 1996: at Columbia University, New York
(maximum of 20 participants).

To obtain information on these courses, please write to Katherine Montague, course coordinator, by email or fax. These courses are for researchers with experience in using the LINKAGE programs, or who have an otherwise excellent understanding of genetic linkage analysis. Also, course participants must be familiar with PCs. Topics: Working with age at disease onset; models for genetic heterogeneity; genetic linkage and allelic association; complex traits; etc. Course work will be divided between theoretical introductions to topics, practical exercises carried out on IBM PC's using the LINKAGE and other programs, and informal discussions. We will use our book (Terwilliger and Ott, Handbook of Human Genetic Linkage, Johns Hopkins University Press, 1994) and some handouts for topics not covered in the book. Participants are expected to buy the book and bring it to the course; in case of problems please contact Katherine Monta- gue in advance of the course. Participants are encouraged to bring their own data.

The next introductory courses will be held in the spring or early summer of 1996, one or two at Columbia University New York and one at the University of Zurich (dates not yet set).

SOFTWARE NEWS

PC versions of LINKAGE

In an earlier issue of this newsletter, we reported problems with version 5.2 of LINKAGE for DOS. This is to point out to users that similar problems may also occur on other platforms. For example, on our Sparcstation IPC, when version 5.2 is compiled without optimization, it yields the same results as version 5.1 and FastLINK. However, it tends to yield different results when compiled with optimization. Since a completely new version of LINKAGE (written in C) will be available soon, there would be no point in trying to fix these problems.

Haplotyping programs

The following announcement was contributed by Dr. Daniel Weeks:

We are pleased to announce that our haplotyping programs SIMCROSS
and SIMWALK are now available in the pub directory by anonymous
ftp to watson.hgen.pitt.edu (url:
 ftp://watson.hgen.pitt.edu/pub ).
These are programs for generating optimal haplotype configurations
on general pedigrees using a likelihood-based approach to correctly
take intermarker recombination fractions into account.

These two programs are described briefly in our Letter to the
Editor which just appeared in the June issue of the American
Journal of Human Genetics:

      Weeks DE, Sobel E, O'Connell JR, Lange K (1995) Computer
      programs for multilocus haplotyping of general pedigrees. 
      American Journal of Human Genetics 56:1506-1507.

and are described in depth in the forthcoming article:

      Sobel E, Lange K, O'Connell JR, Weeks DE (1995) Haplotyping
      algorithms. In: Speed TP, Waterman MS (eds) Genetic mapping
      and DNA sequencing.  Springer-Verlag, New York, in press.

If you have any questions or comments regarding these two pro-
grams, please feel free to contact me.

-- Dan Weeks --

________________________________________________________________


 Daniel E. Weeks, Ph.D.
 The Wellcome Trust Centre          Department of Human Genetics
 for Human Genetics                 University of Pittsburgh
 University of Oxford               Crabtree Hall, Room A310
 Windmill Road                      130 DeSoto Street
 Oxford OX3 7BN                     Pittsburgh, PA 15261
 United Kingdom                     USA

 (+44) 1865 740 043 (desk)          1 412 624-5388 (desk)
 (+44) 1865 742 441 (main)          1 412 624-3066 (secretary)
 FAX: (+44) 1865 742 196            FAX: 1 412 624-3020
 daniel.weeks@well.ox.ac.uk         dweeks@watson.hgen.pitt.edu

Support through grant HG00008 from the National Center for Human Genome Research is gratefully acknowledged.