The following files describe the usage, input and output of our software for case-control association testing for samples with related individuals. The main reference for this program is Thornton T., McPeek M. S. "Case-Control Association Testing with Related Individuals: A More Powerful Quasi-Likelihood Score Test" (2007) American Journal of Human Genetics, vol 81, pp. 321-337. The MQLS program can be considered as a significantly enhanced version of the CC-QLS program of Bourgain C., Hoffjan S., Nicolae R., Newman D., Steiner L., Walker K., Reynolds R., Ober C., McPeek M. S. Novel Case-Control Test in a Founder Population Identifies P-selectin as an Atopy Susceptibility Locus (2003) American Journal of Human Genetics vol 73, pp. 612-626. The MQLS program computes three different test statistics for association: the MQLS test statistic of Thornton and McPeek (2007), the WQLS test statistic of Bourgain et al. (2003), and the corrected chi-squared test statistic of Bourgain et al. (2003). These three tests are suitable for case control analysis in any sample with related individuals, including complex pedigrees, provided that their relationship is known. Kinship coefficients (and inbreeding coefficients for inbred pedigrees) are required to run the MQLS program. Two software programs that can be used to obtain kinship and inbreeding coefficients are

(1) The KinInbcoef software. The KinInbcoef program can be found at CC-QLS. The output file of the KinInbcoef program has the exact format required for the MQLS software.

and

(2) The idcoefs 2.0 software. The idcoefs 2.0 program can be found at idcoefs2.0. The idcoefs 2.0 software computes identity coefficients for pairs of individuals. Kinship and inbreeding coefficients can then easily be computed from the identity coefficients (the output from this software).

The current MQLS distribution includes modifcations by Daniel E. Weeks (weeks@pitt.edu) that (1) corrects the memory allocation so that MQLS does not as easily run out of memory when analyzing datasets with a large number of people and (2) prints an error message and exits when the number of markers to be analyzed is greater than the allowed maximum number of markers set by the user.