MQLS: case-control association test of a binary trait in samples that contain related individuals
Release 1.5. March 14, 2011
Copyright(C) Timothy Thornton, Catherine Bourgain, Mary Sara McPeek
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 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.
The reference for the robust variance estimator (implemented in Version 1.5 and later) is Thornton T., McPeek M. S. (2010) ROADTRIPS: Case-control association
testing with partially or completely unknown population and pedigree
structure American Journal of Human
Genetics 86: 172-184, Equation (3).
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 of Catherine Bourgain and Qian Zhang.
The output file of the KinInbcoef program has the exact format required for the MQLS software.
(2) The IdCoefs software of Mark Abney.
The IdCoefs 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
Acknowledgments: We gratefully acknowledge Daniel E. Weeks and Mark Kvale for their
contributions to the programming.
Download the software