Linkage Newsletter

Xiaoli XIE at nyspi.bitnet
Mon Jun 3 16:01:19 EST 1991


Linkage Newsletter
Vol. 5   No. 2   May 1991

Published by Jurg Ott, Columbia University, New York

Editorial Assistant:  Katherine Montague
      Tel. 212/960-2507   Fax: +1-212-568-2750   Bitnet: OTT at NYSPI

Postal address:  Columbia University, Box 58
      722 West 168th Street, New York, NY 10032


1. EDITORIAL

      On January 1 of this year, I succeeded Prof. Lars Beckman as the
editor of Human Heredity.  This journal was established in 1950 as Acta
Genetica et Statistica Medica and has a good tradition of publishing
articles on methods and applications in various areas of human genetics.  I
would like to extend an invitation to the readers of this newsletter to
submit manuscripts to Human Heredity, particularly in the areas of linkage
analysis and gene mapping.  A new category of articles will be created
shortly ("Methodological Issues") in which new, particularly difficult,
and/or important aspects of research methods may be discussed.  A contribu-
tion to this section need not represent an entirely new investigation but
it must be of general interest and of a high scientific standard.


2. LINKAGE COURSES

      An advanced linkage course will be held in New York from Monday
through Friday, October 14-18, 1991, in the week after the International
Congress of Human Genetics in Washington DC.  Tuition for the 5-day course
is $100 (supported by a grant from the National Center for Human Genome
Research).  The maximum number of participants is 25.  The course will take
place in the microcomputer classroom of the Health Sciences Library of
Columbia University.
      Topics to be covered include:  The LINKAGE and MENDEL computer
programs;  handling of inbreeding loops, age-dependent penetrance, and sex-
specific recombination fractions;  problems of interference in multipoint
mapping;  models of disease heterogeneity;  models for complex diseases;
genetic heterogeneity;  calculation of genetic risks, also under allelic
association and allelic heterogeneity (as in CF);  linkage analysis with
pseudoautosomal loci.
      Participants must be familiar with IBM PCs or compatible microcomput-
ers.  Extensive experience with a linkage program and/or an excellent
background in statistical genetics and linkage analysis are additional
criteria for admission.
      The course will be advertised in scientific journals.  To obtain
additional material and an application form, please write to the address
above.  Application deadline is August 15, 1991.

      An introductory course will be given from Wednesday through Saturday,
August 28-31, 1991, in Cardiff, Wales (in the week following the Human Gene
Mapping Workshop 11 in London).  The course will be taught by myself,
Lodewijk Sandkuijl, and Iain Fenton.  The topics to be covered include:
Introduction to population genetics, introduction to linkage analysis,
practical aspects of data collection, two-point linkage, multipoint link-
age, risk calculations, and linkage analysis for diseases with a complex
mode of inheritance.
      THE TOTAL COURSE FEE IS 650.- POUNDS INCLUDING FULL ROOM AND BOARD
ACCOMMODATION.  THE NUMBER OF PARTICIPANTS IS LIMITED TO 20.  THE COMPUTER
classroom will be equipped with 20 PC-compatible computers with 80386
microprocessors.  Requests for additional information and applications
should be directed to:

      Mrs. G. Gulliford, secretary to Prof. P.S. Harper
      Institute of Medical Genetics, Heath Hospital
      Cardiff, CF4 4XN, Wales
      Fax +44-222-747603
or to
      Dr. L.A. Sandkuijl, Voorstraat 27a
      2611 JK Delft, The Netherlands
      Fax +31-15-123638


3. SOFTWARE NOTES

      3.1 Another bug in the SLINK program

      The following contribution has been submitted by Dr. Weeks for
inclusion in the newsletter:

**********************************************************
                         Bug in SLINK

A bug in SLINK.PAS has recently been found.  This bug will cause problems
any time you try to simulate with only markers (i.e., no trait locus) and
the markers aren't in the order 1, 2, 3,....

The fix to this bug is simple:  Just change the line in SLINK.PAS contain-
ing
   j:=order[1];
to
   j:=1;
as indicated below:

Original code:

  FOR i:=1 TO 35 DO write(output, '-');
   writeln(output);
  {Setup unlinked trait locus}
  IF trait<>0 THEN
   j:=order[trait]
  ELSE
   j:=order[1];
  FOR i:=1 TO nlocus DO
   IF i<>trait THEN
    IF order[i]<j THEN
     order2[i]:=order[i]+1
    ELSE
     order2[i]:=order[i];

Corrected code:

  FOR i:=1 TO 35 DO write(output, '-');
   writeln(output);
  {Setup unlinked trait locus}
  IF trait<>0 THEN
   j:=order[trait]
  ELSE
   j:=1;
  FOR i:=1 TO nlocus DO
   IF i<>trait THEN
    IF order[i]<j THEN
     order2[i]:=order[i]+1
    ELSE
     order2[i]:=order[i];

If you have any questions about this fix, please contact:
      Daniel E. Weeks
      University of Pittsburgh
      Department of Human Genetics
      130 DeSoto Street, A300 Crabtree Hall
      Pittsburgh, PA 15261
      Tel. (412) 624-3066            FAX: (412) 624-3020
      WEEKS at PITTVMS.BITNET  or       WEEKS at VMS.CIS.PITT.EDU


      3.2 FTREE pedigree drawing program

      Dr. Rodney C.P. Go at the University of Alabama submitted a copy of
his FTREE-Family Tree Drawing Program.  It is written in Fortran and comes
in versions for Vax and IBM PC-compatible computers.  The manual is
supplied in a disk file, with one version in ASCII format and one in
WordPerfect format.

      The FTREE program may be obtained from:

      Rodney C.P. Go, Ph.D.
      UAB - University Station
      Birmingham, AL 35294-0008.   Tel. 205/934-6107


      3.3 Usage notes to LINKAGE version 5.10.

      In previously mailed versions of the PREPLINK program (Turbo Pascal
only), the M compiler switch (first program line, third number on that
line) was used to control the maximum amount of memory available to the
program.  Such a limitation was necessary for proper functioning of one of
the program features, that is, to see a directory listing of files.
However, the limitation imposed by the M switch may not leave enough memory
if you want to specify a large number of loci.  Therefore, the current
Turbo Pascal version of PREPLINK no longer contains the M switch and also
does not allow one to obtain a directory listing before specifying a file
name for input.

      When you try running MLINK with the dostream program constant set to
false, an error occurs.  The error may be fixed by adding and dostream to a
line towards the end of the iterpeds procedure, 11 lines before the start
of the initmlink procedure (in the file MLK3.PAS of the DOS version).  The
corrected line reads:

      if score and (not risk) and dostream
            then writeln(stream,tlike-scorevalue);


      The UNKNOWN program (DOS and other versions) does not properly read
the datafile when more than one quantitative factor is specified.  The
error occurs in the getquan procedure;  the corrected code reads as
follows:

      procedure getquan(VAR locus:locuspoint);
      VAR
       i:INTEGER;
      begin  {getquan}
       WITH locus^ DO
        begin
         READLN(datafile,ntrait);
         IF ntrait>maxtrait THEN inputerror(31,system,ntrait);
         IF ntrait<=0 THEN inputerror(32,system,nclass);
         FOR i:=1 TO ntrait+2 DO READLN(datafile);
        END;
      END; {getquan}


      3.4 Benchmark tests for LINKAGE programs

      The benchmark used previously to compare running times of linkage
programs on different machines (see Linkage Newsletter vol. 3, December
1989) is no longer suitable for todays microcomputers as it runs too
quickly and, thus, partially measures speed of video output.  Our new
benchmark consists of a 12-member family with an inbreeding loop in which a
recessive disease and three markers are segregating.  It was run on various
machines in the times shown below.  I would like to thank Drs. Catherine
Falk, New York, and John Rice, St. Louis, for running the benchmark on
their Sun machines.

      Generally, version 5.10 of the LINKAGE programs runs approximately 10%
faster than version 5.04.  The benchmark results listed below were obtained
with version 5.10 of the LINKAGE programs (Turbo Pascal for DOS machines).
All machines were equipped with numeric coprocessors as indicated.  For the
DOS machines the clock speed of the microprocessor is also given.  The run
time is the time in seconds taken by the MLINK program of the LINKAGE
package to calculate two likelihoods for the 12-member family described
above (elapsed time except where noted).  The UNKNOWN program was executed
and a speedfile produced prior to the test run.  Program constants were the
same in each of the runs listed below.  The benchmark data set is available
on disk 5c (see appendix).

      Machine                                        Run time
      -------------------------------------------------------
      Toshiba 3100-e (80286-12/80287)                    2099
      BUS Laptop 386SX (80386SX-16/80387)                 765
      IBM PS/2 model 70 (80386-16/80387)                  710
      Toshiba 5200 (80386-20/80387-20)                    449
      Dell System 310 (80386-20/80387-20)                 446
      BUS 386 (80386-25/80387-25)                         426
      Vaxstation 3100 model 30 (Vax Pascal, CPU time)     237
      Vaxstation 3100 model 38 (Vax Pascal, CPU time)     167
      Everex Step (80486-33)                               98
      BUS 486 (80486-33)                                   98
      Sun SLC (rated at 12.5 MIPS)                         70
      Sun 4/370 (rated at 16 MIPS)                         49
      Sun Sparcstation 1+ (rated at approx. 16 MIPS)       45
      -------------------------------------------------------

      In the comparisons given above, the purchase price of the machines
should also be taken into account.  The faster Sun machines listed run
approximately twice as fast as the fastest DOS machines but their cost
(with educational discount) is less than twice that of the DOS machines.


      3.5 LINKAGE programs for MS-OS/2

      The LINKAGE programs are now also available for running under OS/2
(IBM-compatible microcomputers;  see list of programs attached).  Details
of the OS/2 implementation will be given in the next issue of this newslet-
ter, and the benchmark problem will be run under this version when we
receive version 1.3 of OS/2.

      One important aspect of the OS/2 implementation is that the Prospero
compiler in principle allows for arrays larger than 64KB.  Records contain-
ing such arrays, however, cannot exceed 64KB.  Whereas this restriction is
not too serious, it also turns out that memory for large arrays cannot be
allocated by new(p), where p is a pointer pointing to an array larger than
64KB.  This limits the total number of loci that can be analyzed jointly,
but the OS/2 version of the LINKAGE programs can still accommodate problems
larger than can be run under MS-DOS.

      As mentioned in the previous issue of the newsletter, to run under
OS/2, the LINKAGE programs were adapted to Prospero Pascal.  Unfortunately,
the U.S. address and telephone number of the Prospero Software company are
no longer correct.  Readers interested in purchasing Prospero Pascal should
contact Prospero Software, 190 Castelnau, London SW13 9DH, England;  fax
+44-81-748-9344, tel. +44-81-741-8531.  I have no connection with that
company whatsoever and am providing this address in response to readers who
tried in vain to contact the company at their U.S. office.


4. APPENDIX: List of programs available

      These programs are designed for IBM type microcomputers, unless indi-
cated otherwise.  Program versions for the Macintosh SE/30 are being
developed by Dr. Daniel Weeks, who is now at Pittsburgh University.  Below,
sets of files are arranged as numbered disks.  Most of these 'disks' hold
up to 360 KB characters, but some (identified with 'DD') contain up to 720
KB.

** For ordering instructions, please write to us at the address above **

      Abbreviations:
TPS= Turbo Pascal (TP) source code (compiler needed).
TPC= Turbo Pascal, compiled for IBM PC
FSC= Fortran (Microsoft v.4.01), source and compiled.
EXE= executable code

Item  Contents
---------------------------------------------------------------------------
LINKAGE programs version 5.10, disks 4a-4c (Prospero Pascal, DOS or OS/2)
and disks 5a-5e (Turbo Pascal version 5, DOS).  The programs are in
archived form and will have to be uncrunched using a program supplied on
disks 4a and 5a.  Printed documentation (version 5.10, May 1991) will be
provided.  Our benchmark pedigree is on disk 5c.

LINKAGE programs in Prospero Pascal (general and CEPH pedigrees;  DOS or
OS/2, compiled for OS/2 only):  Users with a coprocessor installed in their
machines (eg. all 80486 machines) order disks 4a and 4b, those without a
coprocessor order disks 4a and 4c.
 4a   Source code, utility programs, and documentation
 4b   Executable code using coprocessor
 4c   Executable code not making use of coprocessor

LINKAGE programs in Turbo Pascal (general and CEPH pedigrees;  DOS only):
For general pedigrees order 5a-d, for 3-generation pedigrees order 5a-c + 5e.
 5a   LCP and other management programs
 5b   Various utility and batch programs, documentation files
 5c   Source code;  benchmark data (in unarchived form)
 5d   Executable code, general pedigrees
 5e   Executable code, 3-generation pedigrees

OTHER PROGRAMS (Turbo Pascal version 5 except where noted)
  6   Source code to disk 8 (TPS).
  7   NOCOM program for analysis of mixture of distributions. Includes the
      COMPMIX and HIST program.  FSC
  8   Linkage Utility programs (see list on last page).  TPC
  9   PC-LIPED (two-point linkage analysis, up to 5 alleles per locus),
      version Oct. 1988.  Includes SEXLODS program for approx. separation of
      male and female recombination fractions.  FSC
  9a  LIPED, same as disk 9 except that up to 6 alleles per locus are
      allowed and program requires more memory to run.
 10abc PC-WRITE version 3.02 text editor for data entry (Quicksoft) [3 disks]
 15   HOMOG programs and MTEST program to carry out homogeneity tests  TPS
 16   HOMOG programs and MTEST program to carry out homogeneity tests  TPC
 17   Kermit V2.30 program for electronic communication.
 18   LIPEDMAX program version Nov. 1987 for iterative estimation of age of
      onset parameters (lognormal distribution of age at onset).  FSC
 20a  SLINK simulation program, DOS and OS/2 version, Prospero Pascal source
      code and documentation file  [1 DD disk]
 20b  SLINK for DOS and OS/2, compiled for machines w/coprocessor  [1 DD disk]
 20c  SLINK for DOS and OS/2, compiled (ISIM not included), not requiring
      coprocessor  [1 DD disk]
 21   SLINK simulation program, VAX VMS version   [1 DD disk]
 22a  2-locus LINKAGE programs (TMLINK, TLINKM, TILINK) for DOS and OS/2
        [1 DD disk]
 22b  2-locus LINKAGE programs for VAX VMS   [1 DD disk]
---------------------------------------------------------------------------

We keep a list of people who ordered programs from us and/or who have taken
our linkage courses.  These individuals regularly receive the LINKAGE
NEWSLETTER which is so far being mailed free of charge a few times a year.

      PROGRAMS CONTAINED On DISKS 6/8 (version no. in parentheses)

2BY2 (1.0) carries out Fisher's exact test in 2x2 tables (n < 8000).
ASSOCIATE (2.3), for two loci with codominant alleles, partitions the chi-
      square for phenotypic association into two components, (1) due to
      allelic association, (2) other phenotypic association.
BINOM (1.63) calculates binomial probabilities (n<8000).
CELLIP (2.2) calculates points on a confidence ellipsis for two jointly
      estimated variables.
CHIPROB (2.2) computes the upper tail probability of the chi-square distri-
      bution.
CONTING (2.4) calculates chi-square for contingency table data.
EQUIV (2.6) calculates equivalent fully informative observations.
HIST (2.3) produces a histogram.
LSURF/LSMAX (3.3/1.3) calculate the lod score surface over the x1,x2-plane
      in 3-point linkage analysis (all 3 orders), where x1 and x2 are the
      map distances from locus 1 to 2 and from locus 2 to 3, respectively.
      Input is offspring counts from phase known data.
MAPFUN (2.31) converts recombination fractions into map distances (6
      mapping functions) and vice versa.
NORINV (1.31) accurately computes the normal deviate from a given tail
      probability.
NORPROB (3.2) accurately computes the tail probability associated with a
      normal deviate, x.
PERMUTE (2.3) produces a list of all n!/2 orders of n gene loci.
PIC (1.3) computes for given alleles at one locus the PIC value and hetero-
      zygosity.
RERI (2.2) calculates and combines relative risks from a set of 2x2 tables
      and carries out homogeneity tests among the tables.
VARCO3 (2.41) approximates mean and variance of an MLE of a variable x from
      three values of x and their log likelihoods or lod scores.  The
      likelihood is approximated by a normal density, i.e., the log likeli-
      hood is quadratic.
VARCO6 (2.21) approximates means, variances and correlation for two jointly
      estimated variables, x and y, from six points (x,y) and associated
      likelihood values.



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