Sample Reproducibility of Genetic Association Using Different Multimarker TDTs in Genome-Wide Association Studies: Characterization and a New Approach

Multimarker Transmission/Disequilibrium Tests (TDTs) are very robust association tests to population admixture and structure which may be used to identify susceptibility loci in genome-wide association studies. Multimarker TDTs using several markers may increase power by capturing high-degree associations. However, there is also a risk of spurious associations and power reduction due to the increase in degrees of freedom. In this study we show that associations found by tests built on simple null hypotheses are highly reproducible in a second independent data set regardless the number of markers. As a test exhibiting this feature to its maximum, we introduce the multimarker -Groups TDT (), a test which under the hypothesis of no linkage, asymptotically follows a distribution with degree of freedom regardless the number of markers. The statistic requires the division of parental haplotypes into two groups: disease susceptibility and disease protective haplotype groups. We assessed the test behavior by performing an extensive simulation study as well as a real-data study using several data sets of two complex diseases. We show that test is highly efficient and it achieves the highest power among all the tests used, even when the null hypothesis is tested in a second independent data set. Therefore, turns out to be a very promising multimarker TDT to perform genome-wide searches for disease susceptibility loci that may be used as a preprocessing step in the construction of more accurate genetic models to predict individual susceptibility to complex diseases

Sliding window maps for the -affected data set.

<p>Window size is TDTs used were (red diamonds), (green squares), (purple circles) and (blue triangles).</p

The table used by .

<p>Only those parental genotypes with one haplotype in each group are used by The counts refer to the number of times haplotypes in one group are transmitted by heterozygous parents to their affected offspring.</p

Type I error rates in presence of population stratification and admixture for and .

<p>Results for different minor allele frequencies (MAFs) in the second subpopulation (q) and different proportion of trios from the first subpopulation (pp), obtained by (top half) and (bottom half) for nominal levels and and haplotypes of length , , , and (columns to respectively).</p

Sliding window maps for the -affected data set.

<p>Window size is TDTs used were (red diamonds), (green squares), (purple circles) and (blue triangles).</p

Sliding window maps for the -affected data set.

<p>Window size is TDTs used were (red diamonds), (green squares), (purple circles) and (blue triangles).</p

Genotype counts and their transmissions used by .

<p>Haplotypes in rows represent those transmitted haplotypes at each genotype. Haplotypes in columns represent those nontransmitted haplotypes at each genotype. Homozygous genotype counts (diagonal) are crossed off the tables as they are not used to compute Left grid: genotype counts from the training data set (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029613#pone-0029613-t002" target="_blank">Table 2</a>) used to make up groups and in Groups are: with those haplotypes with counts larger than counts (Ab: versus and aB: versus ) and with counts larger than counts ( versus ). Right grid: genotype counts from the test data set used to compute the statistic. As the length similarity measure is used to assign an haplotype to a group, and the two most similar haplotypes to haplotype belongs to group is assigned to All the haplotypes belonging to the same group are considered of having an equivalent effect and are collapsed. Therefore, parental genotypes in the test data set with haplotypes belonging to the same group are considered as homozygous and not used by (they are crossed off the table too).</p

An example of parental genotype counts showing transmitted and nontransmitted haplotypes in a training and test data sets of nuclear families and haplotypes of length ( different haplotypes: AB, AB, aB and ab).

<p>The total number of trios is ( parents) so that half of them ( trios, parents) were randomly assigned to the training data set and the others to the test data set. Each row shows counts for a possible configuration (there are possible configurations for haplotypes of length ) of the transmitted (second column) and nontransmitted (third column) haplotypes in a parental genotype.</p

Association rates of and using a second data set to test reproducibility.

<p>Results for 100 simulations of 250 family trios as a function of the recombination rate using the dominant and one-locus genetic model and haplotypes of lengths (left plot), (plot in the middle) and (right plot). A nominal level of and a relative risk of were used for all plots. Results for and are plotted in purple circles and blue triangles respectively. Dashed lines show results for the data subset (125 trios randomly chosen) used to build the model while solid lines show results for a second data subset (the remaining 125 trios) used to test reproducibility.</p

Association rates for different proportions of missing haplotypes.

<p>Results for 100 simulations of family trios as a function of the proportion of missing haplotypes using the additive and one-locus genetic model and haplotypes of lengths (left plot), (plot in the middle) and (right plot). A nominal level of and a relative risk of were used for all plots. Results for and i.e. all tests were applied under the holdout approach, are plotted in purple circles, blue triangles, green squares and red diamonds respectively.</p