Combining the sibling disequilibrium test and transmission/disequilibrium test for multiallelic markers

Within-sibship genome-wide association analyses decrease bias in estimates of direct genetic effects

Estimates from genome-wide association studies (GWAS) of unrelated individuals capture effects of inherited variation (direct effects), demography (population stratification, assortative mating) and relatives (indirect genetic effects). Family-based GWAS designs can control for demographic and indirect genetic effects, but large-scale family datasets have been lacking. We combined data from 178,086 siblings from 19 cohorts to generate population (between-family) and within-sibship (within-family) GWAS estimates for 25 phenotypes. Within-sibship GWAS estimates were smaller than population estimates for height, educational attainment, age at first birth, number of children, cognitive ability, depressive symptoms and smoking. Some differences were observed in downstream SNP heritability, genetic correlations and Mendelian randomization analyses. For example, the within-sibship genetic correlation between educational attainment and body mass index attenuated towards zero. In contrast, analyses of most molecular phenotypes (for example, low-density lipoprotein-cholesterol) were generally consistent. We also found within-sibship evidence of polygenic adaptation on taller height. Here, we illustrate the importance of family-based GWAS data for phenotypes influenced by demographic and indirect genetic effects.

Assortative mating and within-spouse pair comparisons

Spousal comparisons have been proposed as a design that can both reduce confounding and estimate effects of the shared adulthood environment. However, assortative mating, the process by which individuals select phenotypically (dis)similar mates, could distort associations when comparing spouses. We evaluated the use of spousal comparisons, as in the within-spouse pair (WSP) model, for aetiological research such as genetic association studies. We demonstrated that the WSP model can reduce confounding but may be susceptible to collider bias arising from conditioning on assorted spouse pairs. Analyses using UK Biobank spouse pairs found that WSP genetic association estimates were smaller than estimates from random pairs for height, educational attainment, and BMI variants. Within-sibling pair estimates, robust to demographic and parental effects, were also smaller than random pair estimates for height and educational attainment, but not for BMI. WSP models, like other within-family models, may reduce confounding from demographic factors in genetic association estimates, and so could be useful for triangulating evidence across study designs to assess the robustness of findings. However, WSP estimates should be interpreted with caution due to potential collider bias.

Family-based designs in the age of large-scale gene-association studies

Both population-based and family-based designs are commonly used in genetic association studies to locate genes that underlie complex diseases. The simplest version of the family-based design--the transmission disequilibrium test--is well known, but the numerous extensions that broaden its scope and power are less widely appreciated. Family-based designs have unique advantages over population-based designs, as they are robust against population admixture and stratification, allow both linkage and association to be tested for and offer a solution to the problem of model building. Furthermore, the fact that family-based designs contain both within- and between-family information has substantial benefits in terms of multiple-hypothesis testing, especially in the context of whole-genome association studies.

Tumor necrosis factor haplotype analysis amongst schizophrenia probands from four distinct populations in the Asia-Pacific region

A single nucleotide polymorphism (TNF(-308A)) within the promoter region of the gene encoding tumor necrosis factor (TNF), has been significantly associated with schizophrenia in a study of Italian patients and control subjects Boin et al. [2001: Mol Psychiatry 6:79-82]. We have applied case-control analyses to examine TNF promoter haplotypes (containing TNF(-308) and two additional promoter variants: TNF(-376) and TNF(-238)) in four schizophrenia cohorts drawn from Australian, Indian Fijian, Indigenous Fijian, and Brahmin populations. In addition, we have applied the sibling transmission disequilibrium (STD) test to promoter haplotypes within 81 trios drawn from Australian Caucasian pedigrees with multiple schizophrenia cases, and 86 trios drawn from the Brahmin population of Tamil Nadu province in Southern India. Within each of these cohorts, we found no evidence of recombination between these tightly linked promoter variants, supporting previous studies which demonstrated that only a subset of the eight possible haplotypes exist. Of the four observed haplotypes, we and others have observed only one carries the TNF(-308A) variant allele. We report no significant differences in TNF promoter haplotype frequencies between the patient and control groups within each population, although the Indian Fijian cohort showed a trend towards reduced TNF(-308A) alleles amongst schizophrenia cases (P = 0.07). We found no evidence of bias in TNF promoter haplotype transmission to schizophrenia probands. Very similar results were obtained when only the TNF(-308) polymorphism was considered. Taken together, these data provide no support for the involvement of TNF promoter variants TNF(-308), TNF(-376), and TNF(-238) in schizophrenia susceptibility within four ethnically distinct cohorts.

Human population structure and genetic association studies

Population substructure and recent admixture may confound the results of genetic association studies in unrelated individuals, leading to a potential excess of both false positive and false negative results. The possibility of false associations depends on the population sampled, the trait being studied and the marker being tested. Although family based tests of association avoid the possibility of confounding due to population substructure and admixture, association studies in unrelated individuals may be preferred in many situations due to their feasibility. Unlinked genetic markers may be used to detect confounding in association studies. In addition, the information from unlinked markers may be used to adjust genetic associations.

Joint tests of linkage and association for quantitative traits

In this paper we describe various study designs and analytic techniques for testing the joint hypothesis that a genetic marker is both linked to and associated with a quantitative phenotype. Issues of power and sampling are addressed. The distinction between methods that explicitly examine association and those that infer association by examining the distribution of allelic transmissions from a heterozygous parent is examined. Extensions to multivariate, multiallelic, and multilocus situations are addressed. Recent approaches that combine variance-components-based linkage analyses with joint tests of linkage in the presence of association for disentanglement of the linkage and association and the application of such methods to fine mapping are discussed. Finally, new classes of joint tests of linkage and association that do not require samples of related individuals are described.

Multimarkerhaplotypes within the serotonin transporter gene suggest evidence of an association with bipolar disorder

Previously we obtained modest linkage evidence implicating 17q11. 1-12 in bipolar disorder. A modified genome screen, based on gene-rich regions, on a collection of Irish sib-pair nuclear families revealed excess allele sharing at markers flanking the gene encoding the serotonin transporter (5-HTT; hSERT). Here we describe a study designed to combine the advantages of family-based association studies with the consideration of multiple polymorphic markers within a candidate gene. Ninety-two Irish families, with a total of 106 proband-parent trios, have been genotyped for 3 previously known polymorphisms within hSERT (5-HTTLPR, intron 2 VNTR, and 3' UTR G/T). Data from two and three polymorphic marker haplotypes revealed a number of marker combinations that showed evidence supportive of association; the most significant being for polymorphisms 5-HTTLPR and 3' UTR G/T (global chi(2), 12.91, df 3, P = 0.005). In addition, modest evidence of association also was observed for 5-HTTLPR alone. Am. J. Med. Genet. (Neuropsychiatr. Genet.) 96:845-849, 2000.

Family-based association studies

Over the past decade, attention has turned from positional cloning of Mendelian disease genes to the dissection of complex diseases. Both theoretical and empirical studies have shown that traditional linkage studies may be inferior in power compared to studies that directly utilize allele status. Case-control association studies, as an alternative, are subject to bias due to population stratification. As a compromise between linkage studies and case-control studies, family-based association designs have received great attention recently due to their potentially higher power to identify complex disease genes and their robustness in the presence of population substructure. In this review, we first describe the basic family-based association design involving one affected offspring with its two parents, all genotyped for a biallelic genetic marker. Extensions of the original transmission disequilibrium tests to multiallelic markers, families with multiple siblings, families with incomplete parental genotypes, and general pedigree structures are discussed. Further developments of statistical methods to study quantitative traits, to analyse genes on the X chromosome, to incorporate multiple tightly linked markers, to identify imprinting genes, and to detect gene-environment interactions are also reviewed. Finally, we discuss the implications of the completion of the Human Genome Project and the identification of hundreds of thousands of genetic polymorphisms on employing family-based association designs to search for complex disease genes.