The disequilibrium maximum-likelihood-binomial test does not replace the transmission/disequilibrium test

Review and evaluation of methods correcting for population stratification with a focus on underlying statistical principles

When two or more populations have been separated by geographic or cultural boundaries for many generations, drift, spontaneous mutations, differential selection pressures and other factors may lead to allele frequency differences among populations. If these 'parental' populations subsequently come together and begin inter-mating, disequilibrium among linked markers may span a greater genetic distance than it typically does among populations under panmixia [see glossary]. This extended disequilibrium can make association studies highly effective and more economical than disequilibrium mapping in panmictic populations since less marker loci are needed to detect regions of the genome that harbor phenotype-influencing loci. However, under some circumstances, this process of intermating (as well as other processes) can produce disequilibrium between pairs of unlinked loci and thus create the possibility of confounding or spurious associations due to this population stratification. Accordingly, researchers are advised to employ valid statistical tests for linkage disequilibrium mapping allowing conduct of genetic association studies that control for such confounding. Many recent papers have addressed this need. We provide a comprehensive review of advances made in recent years in correcting for population stratification and then evaluate and synthesize these methods based on statistical principles such as (1) randomization, (2) conditioning on sufficient statistics, and (3) identifying whether the method is based on testing the genotype-phenotype covariance (conditional upon familial information) and/or testing departures of the marginal distribution from the expected genotypic frequencies.

A marginal likelihood model for family-based data

This paper presents a marginal likelihood model for family-based data based upon the transmission of marker alleles from each heterozygous parent to his/her affected children. The proposed model, extending the maximum-likelihood-binomial (MLB) method and the disequilibrium maximum-likelihood-binomial (DMLB) method (Abel et al. 1998; Abel & Müller-Myhsok, 1998; Huang & Jiang, 1999), is adaptive to linkage disequilibrium (LD) and linkage heterogeneity. Compared with other procedures, the likelihood ratio test (LRT) derived from the proposed model enjoys superior qualities. First, simulations indicate that the power of the LRT is greater than that of the TDT or DMLB in all of our studied scenarios. Second, when we applied the LRT and other tests to a Tourette Syndrome data, the result was data favorable to the use of the LRT. Therefore, we recommend the use of the LRT as an additional linkage test wherever applicable, especially when the amount of LD is uncertain.