1. marker data file (e.g. 'markid') This file contains the marker data and status (case or control) information. It has the standard linkage format : 1 1 7 6 1 1 1 2 1 2 1 2 7 6 2 2 1 1 1 2 1 3 7 6 1 2 3 1 1 2 1 7 0 0 1 1 1 1 1 1 1 6 0 0 2 0 2 3 2 2 2 1 8 9 2 2 1 3 1 1 2 2 8 9 1 1 2 3 1 1 2 8 0 0 1 0 1 2 1 2 2 9 5 6 2 1 3 1 1 1 2 5 0 0 1 0 3 2 1 2 2 6 0 0 2 0 1 1 1 2 (1) (2) (3) (4) (5) (6) (7) (8) (9) (10) .... (1) family ID (2) individual ID (3) father's ID (0=unknown) (4) mother's ID (0=unknown) (5) sex (1=male, 2=female) (6) affection status (0=unknown, 1=control, 2=case) (7-8), (9-10)... marker genotype (0 for missing alleles) Families should be numbered from 1 to F, without gaps. There is no limit in the number of individuals (case and/or controls). But the number of families is set to be smaller than 500. To increase this limit, just change the value of MAXFAM in the CC-QLStest.c source file and recompile the program. Each individual (or monozygotic twins if any) should be entered only once. The number of columns should be the same for every individuals : Use 0 for missing information (status or missing genotypes) The number of markers to be analyzed is determined using the number of columns on the first line of this file. There is a limit in the number of markers (set to 100). To increase the limit, just change the value of MAXMARK in the CC-QLStest.c source file and recompile the program. Alleles at each marker locus should be numbered from 1 to M without gaps. There is no limit in the number of alleles at each marker locus. All the individuals with known affection status and marker typing information should also be listed in the kinship coefficient file (see below). 2. The kinship coefficient file (e.g. 'kinshipcoef') This file contains the kinship and inbreeding coefficients for all possible pairs of individuals phenotyped and genotyped for at least one marker in each family. If an individual has an inbreeding coefficient equal to 0 or if a pair has a kinship coefficient equal to 0, they must still be in the file or they will not be included in the analysis. All pairs should be considered (case/case, case/control and control/control) It has the following format : 1 1 1 0.0 1 1 2 0.25 1 1 3 0.25 1 1 7 0.25 1 1 6 0.25 1 2 2 0.0 1 2 3 0.25 1 2 7 0.25 1 2 6 0.25 1 3 3 0.0 1 3 7 0.25 1 3 6 0.25 1 7 7 0 1 7 6 0 1 6 6 0 1 3 3 1 2 1 1 0.01251 2 1 2 0.26124 . . . . . . . . (1) (2) (3) (4) (1) family ID (2) individual 1 ID (Id1) (3) individual 2 ID (Id2) (4) kinship coefficient between Id1 and Id2 if Id1 is different from Id2 inbreeding coefficient of Id1 is Id1 equals Id2 The family ID and individual ID should match exactly with the Id's in the marker data file. The program runs faster when the coefficients are ordered in the following way : In each family, the order of the pairs follow the order of the individuals given in the marker data file. Considering a family numbered 4 with 3 individuals 47, 48 and 49 listed in this order in the marker data file, the order in the kinship coefficient file would be : 4 47 47 H_47 4 47 48 phi_(47,48) 4 47 49 phi_(47,49) 4 48 48 phi_(48,48) 4 48 49 phi_(48,49) 4 49 49 phi_(49,49) We provide with a simple program to compute these kinship and inbreeding coefficients in general pedigrees : the KinInbcoef program. The output file of the KinInbcoef program have the exact format required here.