MQLS-XM: autosomal and X-chromosome association testing of a
binary trait in case-control samples with related individuals
Release 1.0. July 30, 2012
Thornton and Mary Sara McPeek
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
(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.
(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.
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
(firstname.lastname@example.org) for his contribution to the programming.
Download the MQLS-XM software