MQLS-XM is a C program that performs single-SNP, case-control association testing for the autosomal chromosomes and the X-chromsome in samples with known relatedness. The main references for this program are

(1) 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

and

(2) Thornton T, Zhang Q, Cai X, Ober C, and McPeek MS XM: Association Testing on the X-Chromosome in Case-Control Samples with Related Individuals" (2012) Genetic Epidemiology 36, vol 36:438-450

The MQLS-XM program can be considered a significantly enhanced version of the MQLS software of Thornton and McPeek.

Kinship coefficients (and inbreeding coefficients for inbred pedigrees) are required to run the MQLS-XM program. Two software programs that can be used to obtain autosomal and X-chromosome kinship and inbreeding coefficients are:

(1) The KinInbcoef software of Catherine Bourgain and Qian Zhang. The output file of the KinInbcoef program has the exact format required for the MQLS-XM software.

and

(2) The KinInbcoefX software of Qian Zhang, Catherine Bourgain, and Mary Sara McPeek. The output file of the KinInbcoefX program has the exact format required for the MQLS-XM software.



The Format_Ped_Pheno software of Timothy Thornton and Mary Sara McPeek can be used to to relabel all the families and the individuals in a pedigree/phenotype information file so that the family IDs and individual IDs conform to the requirements of the MQLS-XM, KinInbcoef and KinInbcoefX software. This program takes as input a pedigree/phenotype information file and outputs files that are in the required formats for the three software packages.

Acknowledgments: We gratefully acknowledge Jerry Halpern (funn@stanford.edu) for his contribution to the programming.