Jurg Ott 2 Nov 1997 Rockefeller University Fax 212 327 7996 1230 York Avenue New York, NY 10021-6399 Email: ott@linkage.rockefeller.edu LINKAGE programs for 2-locus traits (TLINKAGE) INTRODUCTION The programs described here are an extension of the general LINKAGE programs for genetic linkage analysis. The extension consists of allowing for a disease phenotype to be under the control of two loci. The current version of this brief user's guide for TLINKAGE is available at URL http://linkage.rockefeller.edu/ott/tlinkage.htm. The two postulated disease loci are typically unlinked (on two different chromosomes), each with two alleles (one normal, one being the disease allele), although there is no such restric- tion in this implementation. Below, the two disease loci are implemented as "null loci". Each of the disease loci may be linked with a marker or map of markers. Typically, two recombi- nation fractions will be estimated, that between disease locus 1 and marker 1, and that between disease locus 2 and marker 2. If each of the two disease loci has two alleles and, thus, three genotypes, at both loci there is a total of 9 possible genotype constellations. Which of these confer susceptibility (are associated with positive penetrance) is often unknown but specific patterns of interaction between the two disease loci have been described (Risch 1990). Below, technicalities of implementation of the TLINKAGE programs are provided. The programs come in version for Turbo/Borland Pascal and NDP Pascal and Unix. See the document COMPILE.TXT for details. IMPLEMENTATION ----------------------------- Program name Corresponds to ----------------------------- TUNK UNKNOWN TMLINK MLINK TLINKM LINKMAP TILINK ILINK ----------------------------- The TLINKAGE programs implement a new locus type #4, called the null type because it may have no associated phenotype in the pedigree file. Each null locus is associated with the same phenotype. The number of null loci corresponds to the number of loci jointly responsible for a disease phenotype. That number is indicated as the last entry on the first line of the datafile (after the program number). In this version of TLINKAGE, you must have two null loci, or zero null loci. If two null loci are defined, there are thus two consecutive locus descriptions for these null loci in the datafile, but they correspond to only one phenotype in the pedfile. That phenotype must be an affection status phenotype, and it may be at any position among the phenotypes (ie, the null loci are not restricted to be the first two loci in the datafile). NOTE, however, the following restriction: if the two null loci are loci 1 and 2, their order must be 1 2 and not 2 1. For example, with loci 3 and 4 being markers, the orders 1 3 2 4 and 4 1 3 2 are all right but the orders 2 3 1 4 and 4 2 3 1 are not. An analogous restriction on order applies when the null loci are numbered other than 1 and 2. In the datafile, the description of a null locus contains only the number of alleles and gene frequencies, eg: 4 2 << null locus, number of alleles 0.9 0.1 << allele frequencies except that after the last null locus, a line specifying the number of liability classes must be present, followed by one or more tables of penetrances (as many tables as the number of liability classes). Each such table (see example below) has a single entry for each genotype combination at the two loci and is arranged as shown in the example below. The numbers to be entered in each table are only the penetrances, in this case the 3x3=9 numbers in the body of the table (do not enter any of the genotypes such as 1/2 or 2/2). Repeat this table with different entries for different liability classes. Remember that only the last null locus has an associated phenotype in the pedfile. An example may look as follows: ----------------------------- First Second null locus null ----------------- locus 1/1 1/2 2/2 ----------------------------- 1/1 0 0 0 1/2 0 0.8 0.8 2/2 0 0.8 1 ----------------------------- The current 2-locus version of LINKAGE allows analysis of autosomal loci only. Please make sure you do not use these programs for X chromosomal loci -- there is no check in the programs to ensure that you are adhering to this restriction. KNOWN BUGS In releases prior to 13 Feb 1991, two bugs were present in these programs: the programs did not work right when individuals with unknown disease status were present and when more than one liability class was used. Both bugs were fixed by Joseph Terwil- liger. SAMPLE INPUT FILES The files TESTML.DAT, TESTLM.DAT, and TESTIL.DAT are sample datafiles for TMLINK, TLINKM, and TILINK, respectively. A test pedigree file (before processing by MAKEPED) is included as TEST.PRE. The corresponding pedfile suitable for input to the programs is TEST.PED. To run the test example for TMLINK, copy the test files to your current directory in which you want to carry out the TLINKAGE runs. Then give the following commands: cp testml.dat datafile.dat cp test.ped pedfile.dat tunk tmlink In the regular LINKAGE programs, various utility programs such as LCP and PREPLINK may be used for the creation of the input files. Presently, these programs have not been adapted to the TLINKAGE programs. Therefore, you must create your input files with a text editor. LITERATURE Lathrop GM, Ott J (1990) Analysis of complex diseases under oligogenic models and intrafamilial heterogeneity by the LINKAGE programs. Am J Hum Genet 47, A188 (abstr) Risch N (1990) Linkage strategies for genetically complex traits. I. Multilocus models. Am J Hum Genet 46, 222-228 Schork NJ, Boehnke M, Terwilliger JD, Ott J (1993) Two trait locus linkage analysis: a powerful strategy for mapping complex genetic traits. Am J Hum Genet 53, 1127-1136