Mapping loci influencing blood pressure in the Framingham pedigrees using model-free LOD score analysis of a quantitative trait

TDT-HET: a new transmission disequilibrium test that incorporates locus heterogeneity into the analysis of family-based association data

BACKGROUND

Locus heterogeneity is one of the most documented phenomena in genetics. To date, relatively little work had been done on the development of methods to address locus heterogeneity in genetic association analysis. Motivated by Zhou and Pan's work, we present a mixture model of linked and unlinked trios and develop a statistical method to estimate the probability that a heterozygous parent transmits the disease allele at a di-allelic locus, and the probability that any trio is in the linked group. The purpose here is the development of a test that extends the classic transmission disequilibrium test (TDT) to one that accounts for locus heterogeneity.

RESULTS

Our simulations suggest that, for sufficiently large sample size (1000 trios) our method has good power to detect association even the proportion of unlinked trios is high (75%). While the median difference (TDT-HET empirical power - TDT empirical power) is approximately 0 for all MOI, there are parameter settings for which the power difference can be substantial. Our multi-locus simulations suggest that our method has good power to detect association as long as the markers are reasonably well-correlated and the genotype relative risk are larger. Results of both single-locus and multi-locus simulations suggest our method maintains the correct type I error rate.Finally, the TDT-HET statistic shows highly significant p-values for most of the idiopathic scoliosis candidate loci, and for some loci, the estimated proportion of unlinked trios approaches or exceeds 50%, suggesting the presence of locus heterogeneity.

CONCLUSIONS

We have developed an extension of the TDT statistic (TDT-HET) that allows for locus heterogeneity among coded trios. Benefits of our method include: estimates of parameters in the presence of heterogeneity, and reasonable power even when the proportion of linked trios is small. Also, we have extended multi-locus methods to TDT-HET and have demonstrated that the empirical power may be high to detect linkage. Last, given that we obtain PPBs, we conjecture that the TDT-HET may be a useful method for correctly identifying linked trios. We anticipate that researchers will find this property increasingly useful as they apply next-generation sequencing data in family based studies.

Quantitative-trait-locus mapping in the presence of locus heterogeneity

Locus heterogeneity is a concern for quantitative trait locus mapping where phenotypes are likely to be influenced by more than one gene. We introduce a model which generalizes the locus heterogeneity model of Smith (1961) from dichotomous traits to quantitative traits and consider some test statistics for this model. The type I error rates and the power of these statistics are assessed through simulation studies. These statistics are applied to a linkage study of asthma genes.

Re-analysis of collaborative study on the genetics of alcoholism pedigrees suggests the presence of loci influencing novelty-seeking near D12S391 and D17S1299

A previous genome scan using variance components analysis of 758 sib pairs from families of alcoholics found evidence for linkage of harm avoidance (HA) to markers on 8p21-23, and this finding was supported in a subsequent linkage study of 384 sib pairs. Here the original dataset is analysed using a new method of linkage analysis for quantitative traits that deals with extended pedigrees. As well as supporting linkage of HA to D8S549, this method also produces an MALOD of 2.4 (P=0.002) near DBH and several positive lod scores for novelty-seeking, the largest being MALODs of 3.1 (P=0.0004) near D12S391 and 3.4 (P=0.0003) near D17S1299. There is no support for linkage of novelty-seeking or HA to the regions around DRD4 and 5HTT, respectively. Additional samples will need to be studied in order to discover which regions truly harbour genetic polymorphisms influencing personality traits.

Summary of Group 8: Development and extension of linkage methods

The diverse contributions to Group 8 focus on the development and extension of linkage methods, and share themes that are organized around approaches to analysis. The themes discussed include issues of the accuracy of estimates of marker identity-by-descent (IBD) information, the influence of such IBD information on linkage detection, and methods for dealing with genetic heterogeneity and multiple testing. In addition, challenges were identified and solutions were offered for coping with some of the common problems of complex trait analysis, including trait model selection and computational compromises. Analytic approaches based on Bayesian and Monte Carlo methods were prominent, and provided optimistic results.