Linkage Newsletter
                       Vol. 12   No. 1   February 1998

Published by Jurg Ott                       Postal address:
  Email: ott@rockefeller.edu                Rockefeller University, Box 192
  URL: http://linkage.rockefeller.edu       1230 York Avenue, New York, NY 10021-6399

Edit. Assistant: Katherine Montague         Fax: 212-327-7996
  Email: montagk@rockvax.rockefeller.edu    Tel: 212-327-7979

(this and all previous newsletters are available at our web site,
http://linkage.rockefeller.edu/newsletter/)


EDITORIAL

 For various reasons, no newsletter was written last year. The last
published newsletter is dated December 1996 and was mailed just a little
over one year ago.  New issues of the newsletter will be published depending
on need and how much material we receive for inclusion.


LINKAGE COURSES

The next basic linkage courses will be held as indicated below. Interested
researchers are urged to apply early as our courses tend to fill up quickly.
To obtain information on these courses, please write to Katherine Montague,
course coordinator, by email (preferred) or fax.

March 16-20, 1998, at University of Zürich, Switzerland (maximum of 18
participants). Deadline for applications was January 15, 1998, but we still
have one or two open slots.

June 15-19, 1997, at Rockefeller University (maximum of 30 participants).
Deadline for applications is May 1, 1998.

We will use our book (Terwilliger and Ott, Handbook of Human Genetic
Linkage, Johns Hopkins University Press, 1994). Partici-pants are expected
to buy the book and bring it to the course; in case of problems please
contact Katherine Montague in advance of the course. For a list of
corrections see http://linkage.rockefeller.edu/ott/corr-ter.htm.

The date for this year’s advanced course (summer/fall of 1998) is not yet
known. Please watch our web page at
http://linkage.rockefeller.edu/course/here.html for dates. Advanced courses
are reserved for individuals with a very good background in linkage
analysis). Our advanced courses have been greatly modernized and now include
presentations by outside scientists who are experts in areas such as genomic
databases or particular computer programs. Therefore, we can no longer offer
advanced courses outside of New York. Depending on demand, we will offer
more than one advanced course per year. This will be particularly important
for foreign participants since for the advanced course supported by the
NIHGRR, the number of participants from outside the U.S. is very limited.


SOFTWARE

New program
(submitted by Dr. Alejandro Schaffer)

We announce the availability of CASPAR (Computerized Affected Sibling Pair
Analyzer and Reporter), a software package for studying the genetics
polygenic diseases. CASPAR's main novel feature is conditional linkage
analyses, in which the population can be subdivided according to criteria at
some loci and analyzed for linkage at other loci. CASPAR uses simulation to
overcome the problems inherent in such multiple testing.

To retrieve CASPAR:
ftp fastlink.nih.gov
cd pub/caspar
binary
get caspar.tar.Z

Then on your computer:
uncompress caspar.tar.Z
tar xvf caspar.tar

Please send comments, questions, complaints, and problem reports to:
Richa Agarwala (richa@helix.nih.gov) and
Alejandro Schaffer (schaffer@helix.nih.gov)

Other participants in CASPAR development are:
Jeremy Buhler, Kenneth Gabbay, Marek Kimmel, David Owerbach

FastLINK
(submitted by Dr. Alejandro Schaffer)

FASTLINK version 4.0P is now available. The principal improvement over
version 3.0P is a method to automatically select loop breakers that
addresses a problem posed in 1975 by Ken Lange and Robert Elston. The new
code was developed in collaboration with Ann Becker and Dan Geiger of
Technion. A description of what we did can be found in:

   A. Becker, D. Geiger, A. A. Schaffer (1998) Automatic Selection of
   Loop Breakers for Genetic Linkage Analysis. Hum Hered 48:49-60

This paper comes as paper6.ps with the code distribution.

To retrieve for other than DOS:
  ftp fastlink.nih.gov
  binary
  cd pub/fastlink
  get fastlink.tar.Z

For DOS replace the last two lines with:
  cd pub/fastlink/dos
  mget *

Thanks to Jim Tomlin (NIH) and John Powell (NIH) for vigorous beta testing.
Thanks to Marilyn Raymond (NIH) for a great challenge data set. Thanks to
Don Plugge for assistance with the port to VMS.

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