Welcome to GENEHUNTER-TWOLOCUS * What is GENEHUNTER-TWOLOCUS GENEHUNTER-TWOLOCUS is a modification of the GENEHUNTER software package (version 1.3). The program performs complete parametric and nonparametric multi-marker linkage analysis with two autosomal, biallelic disease loci. It uses two unlinked marker maps with one disease locus linked to each map. Like the single-disease-locus version GENEHUNTER-IMPRINTING, GENEHUNTER-TWOLOCUS allows to perform parametric (LOD-score) analysis with imprinting disease models. It can take into account parent-of-origin effects at both loci. For clarification, let us look first at a single disease locus with imprinting. In this case, two penetrance parameters (instead of only one parameter) need to be specified for individuals who are heterozygous at the disease locus; one for paternal origin and one for maternal origin of the disease allele. Therefore, a single-disease-locus imprinting model has four penetrance parameters and looks as follows (with 'm' and '+' specifying the mutant and wild-type allele, respectively, and the paternally inherited allele named first): P(+/+) P(m/+) P(+/m) P(m/m) Accordingly, a two-disease-locus model that takes into account a parent-of-origin effect should have a four-by-four penetrance matrix. Here, the row specifies the genotype at the first disease locus, and the column specifies the genotype at the second disease locus: | (+/+) | (m/+) | (+/m) | (m/m) 2nd locus ----------------------------------------------- (+/+) | P_11 ..................... P_14 1st (m/+) | : : locus (+/m) | : : (m/m) | P_41 ..................... P_44 Of course, a model without imprinting (at one or both disease loci) can easily be specified by using equal penetrances for heterozygotes, i.e., for genotypes (m/+) and (+/m), at a locus. If no imprinting is assumed, the model is identical to the well-known two-locus model with a 3-by-3 penetrance matrix. Two-locus LOD scores are calculated as the decimal logarithm of the likelihood ratio for particular positions of the two disease loci within the first and second marker maps, respectively, vs. the null hypothesis that both disease loci are unlinked to their corresponding marker maps. With respect to NPL analysis, GENEHUNTER-TWOLOCUS uses extensions of the scoring functions S_pairs and S_all that evaluate sharing of alleles identical-by-descent for affected individuals, simultaneously at both disease loci. NPL scores are given with p-values, with the assumption of the null hypothesis that both disease loci are unlinked to their corresponding marker maps. In the current implementation, GENEHUNTER-TWOLOCUS calculates two-disease-locus NPL scores as the sum of the two single-disease-locus scores for each corresponding marker map. For calculation of two-locus LOD and NPL scores, the position of the first disease locus is held fixed at one site on the first marker map as specified by a parameter given with the 'scan pedigrees' command. The position of the second disease locus is being varied on the second marker map in the same way as in a single-disease-locus GENEHUNTER or GENEHUNTER-IMPRINTING analysis, taking into account parameters given with the 'increment' and 'off end dist' commands. Complete inheritance information is extracted by using all markers selected for analysis on both maps. The analysis with GENEHUNTER-TWOLOCUS needs more computation time than a single-trait-locus analysis. Therefore, the number of effective meioses in a pedigree, 2*nonfounders - founders, should not exceed 11 or 12. The use of the GENEHUNTER-TWOLOCUS commands is identical to GENEHUNTER or GENEHUNTER-IMPRINTING, except for 'load markers', 'scan pedigrees', and 'use'. In the current version of GENEHUNTER-TWOLOCUS, the 'load markers' command expects three filenames as parameters; one marker-locus data file for each of the two marker maps, and a third file specifying a two-disease-locus model needed for LOD-score analysis. Accordingly, two names of pedigree files need to be given with the 'scan pedigrees' command (again, one file with the marker data for each map), along with a third parameter specifying the position of the first disease locus which is held fixed on the first marker map. The original 'use' command, which allows to select markers used for the analysis (and recombination fractions between them), has been replaced by 'use1' and 'use2'. These commands affect the first and second marker map, respectively. See help texts for 'load markers', 'scan pedigrees', 'use1', and 'use2' for details. On-line help can be obtained at the GENEHUNTER-TWOLOCUS prompt by typing 'help' (or '?') followed by the command name. Further modifications include the following: - Family and individual IDs do not need to be integers, but may contain other characters as well. - A new NPL scoring function, 'hom', has been implemented. It is similar to the 'all' scoring function, but uses both alleles (at a locus) of each affected individual at the same time, instead of choosing one out of two alleles. Type 'help score' at the prompt for details. - If NPL analysis is turned off ('analysis lod'), calculation is truly omitted, not just the score report. This accelerates calculation of LOD scores. * What is GENEHUNTER GENEHUNTER is a software package that allows the very rapid extraction of complete multipoint inheritance information from pedigrees of moderate size. This information is then used in exact computation of multipoint LOD scores and in a powerful new method of non-parametric linkage analysis. Quick calculations involving dozens of markers, even in pedigrees with inbreeding and marriage loops, is possible with GENEHUNTER. In addition, the multipoint inheritance information allows the reconstruction of maximum-likelihood haplotypes for all individuals in the pedigree and information content mapping which measures the fraction of the total inheritance information extracted from the marker data. All of these calculations are performed in a user-friendly environment familiar to MAPMAKER, SIBS, or HOMOZ users. * How to Obtain GENEHUNTER-TWOLOCUS The zipped GENEHUNTER-TWOLOCUS tar file, ght.tar.gz, can be obtained by sending an e-mail to Konstantin Strauch: strauch@imsdd.meb.uni-bonn.de * How to Install GENEHUNTER-TWOLOCUS To extract the GENEHUNTER-TWOLOCUS files from this file, create a subdirectory for the program, move the ght.tar.gz file into it, and enter the commands: gunzip ght.tar.gz tar xvpf ght.tar The directory will now be filled with the following files: Makefile - Unix Makefile for compilation of GENEHUNTER-TWOLOCUS Makefile.aix - special Makefile for IBM/AIX machines ght.help - on-line help file - do not edit! ght.ps - PostScript version of on-line help for printing linkloci.dat - sample marker data file linkped.pre - sample pedigree data file INSTALL.ght - this installation document COPYRIGHT.ght - copyright and licensing agreement for GENEHUNTER-TWOLOCUS and GENEHUNTER along with the subdirectories src and ansilib which contain the source code for the program. If the extraction is successful, you can now delete the ght.tar archive. * Compiling GENEHUNTER-TWOLOCUS You need to compile the code to create an appropriate executable version for your particular system. One or two simple changes must be made to the Makefile: 1) line 5 (SYS= -D_SYS_OSF) must be replaced with one of the following: SYS= -D_SYS_SUNOS - for compilation on SUN machines SYS= -D_SYS_OSF - for compilation on DEC/Alpha machines, as well as on i386 machines running LINUX SYS= -D_SYS_ULTRIX - for compilation on Ultrix systems SYS= -D_SYS_HPUX - for compilation on HP workstations SYS= -D_SYS_AIX - for compilation on IBM/AIX RISC systems SYS= -D_SYS_SOLARIS - for compilation on Solaris machines If your system is not listed among those above, you can probably use one of the above definitions anyway - for example -D_SYS_OSF adheres to the ANSI standard and can be used with almost any ANSI compiler. For IBM/AIX RISC systems, a special Makefile is provided. It can be activated by entering the following commands: mv Makefile Makefile.sav mv Makefile.aix Makefile 2) line 12 in Makefile (CC = gcc) determines the C-compiler to be called and should be replaced if another C-compiler is used on your system (for example, CC = cc) After the Makefile is edited for your system, the Unix command "make" should automatically create the GENEHUNTER-TWOLOCUS executable "ght" appropriate for your system. If compilation is unsuccessful, contact your system administrator for assistance first as he or she will be familiar with bringing code to your particular system. If further assistance is required, feel free to contact us for help. * Getting Ready to Run It will often be useful to store your data in a separate subdirectory from the GENEHUNTER-TWOLOCUS program (for various reasons such as diskspace or to make the program available to multiple users). In such cases, it can be helpful to include the directory containing the GENEHUNTER-TWOLOCUS program in your Unix path. In addition, to use the on-line help facility, you will need to inform the program where to find the help and related documents. For instance, if the subdirectory you created for the programs is named /home/GHT, you will want to change your .cshrc file as follows: 1. change the line which reads something like: set path=(. /bin /usr/local /usr/bin /etc) to include /home/GHT set path=(. /bin /usr/local /usr/bin /etc /home/GHT) 2. add the following line to the end of the file setenv GHT_DIR /home/GHT Now GENEHUNTER-TWOLOCUS can be called from anywhere on your system by simply typing the executable name (ght). (If you wish to hardwire the GHT_DIR into the code, replace the body of get_code_directory in ansilib/syscode.c with the line: nstrcpy(buf,"",PATH_LENGTH); return(TRUE); and recompile.) * Using GENEHUNTER-TWOLOCUS To run the program just type the name of the executable and the shell will start up. To get a quick start in running the commands enter 'help' at the prompt. * How to cite or get more information on GENEHUNTER-TWOLOCUS K. Strauch, R. Fimmers, T. Kurz, K.A. Deichmann, T.F. Wienker, and M.P. Baur. "Parametric and Nonparametric Multipoint Linkage Analysis with Imprinting and Two-Locus-Trait Models: Application to Mite Sensitization". American Journal of Human Genetics 66:1945-1957 (June 2000). * How to cite or get more information on GENEHUNTER L. Kruglyak, M.J. Daly, M.P. Reeve-Daly, and E.S. Lander. "Parametric and Nonparametric Linkage Analysis: A Unified Multipoint Approach". American Journal of Human Genetics 58:1347-1363 (June 1996). L. Kruglyak and E.S. Lander. "Faster Multipoint Linkage Analysis Using Fourier Transforms". Journal of Computational Biology 5:1-7 (1998).