Population-based family study designs: an interdisciplinary research framework for genetic epidemiology

[Family history of affective disorders, the gender factor and clinical characteristics of depression]

OBJECTIVE

Analysis of clinical features of development and course of depression in patients with FH of mood disorders taking into account sex differences.

MATERIAL AND METHODS

This multicenter cross-sectional study included patients over 18 years of age with depressive episode/recurrent depressive disorder. Clinical characteristics of depression, presence of comorbid mental illness and family history (FH) information were obtained in a structured clinical interview.

RESULTS

One hundred and seventy-one patients (mean age (M (SD)) 40.87 (15.86) y.o.), including 64.5% of women, were enrolled in the study. FH was revealed in 30.2% of patients. The proportion of FH did not differ in men and women (p=0.375). Generalized anxiety disorder (GAD) was more frequent in FH positive patients (p=0.016). Logistic regression also revealed that FH is a risk factor for concomitant GAD (p=0.019, OR=2.4). The GLM demonstrated a significant joint effect of FH and sex on the maximum duration of a depressive episode (p=0.044), as well on the number of suicide attempts (p=0.055) and the number of depressive episodes as a trend (p=0.072).

CONCLUSION

We have demonstrated the specific interaction of FH of mood disorders with sex on clinical course of depression. Thus, the manifestation of a genetic influence on the clinical phenotype of depression can be significantly moderated by sex.

Pedigree analysis of lumbar developmental spinal stenosis: Determination of potential inheritance patterns

Lumbar developmental spinal stenosis (DSS) refers to multilevel pre-existing narrowed spinal canals, which predispose to neural compromise. The objective of this study is to identify any inheritance pattern of DSS by utilizing pedigree charts. This was a case series of 13 families with a total of 80 subjects having magnetic resonance imaging (MRI) from L1 to S1. Cases (subjects with DSS) or controls (subjects without DSS) were identified by measuring their anteroposterior (AP) vertebral canal diameters. Multilevel model analyses were also performed to evaluate whether there is substantial clustering of observations within the families, and the effect of multilevel DSS. The intraclass correlation coefficient (ICC) and Akaike information criteria (AIC) were compared between models. Correlations between subject demographics and AP vertebral canal diameter were statistically insignificant at all levels. Only vertebral canal cross-sectional area, and axial and sagittal vertebral canal diameter were found to be statistically different between cases and controls at all levels (all p < .05). Both males and females were affected by DSS and there was no skipping of generation, which highly suggested DSS followed an autosomal dominant inheritance pattern. After accounting for multilevel DSS, there was a drop of more than 10 in AIC and some variances were also explained within families. This is the first study that suggests multilevel lumbar DSS to have an autosomal dominant inheritance pattern. Within families with a background of DSS, subjects had a smaller canal size, contributed by shortened axial and sagittal AP vertebral canal diameter, and smaller canal cross-sectional area.

Genetic approaches toward understanding the individual variation in cardiac structure, function and responses to exercise training

Cardiovascular disease (CVD) accounts for approximately 30% of all deaths worldwide and its prevalence is constantly increasing despite advancements in medical treatments. Cardiac remodeling and dysfunction are independent risk factors for CVD. Recent studies have demonstrated that cardiac structure and function are genetically influenced, suggesting that understanding the genetic basis for cardiac structure and function could provide new insights into developing novel therapeutic targets for CVD. Regular exercise has long been considered a robust non-therapeutic method of treating or preventing CVD. However, recent studies also indicate that there is inter-individual variation in response to exercise. Nevertheless, the genetic basis for cardiac structure and function as well as their responses to exercise training have yet to be fully elucidated. Therefore, this review summarizes accumulated evidence supporting the genetic contribution to these traits, including findings from population-based studies and unbiased large genomic-scale studies in humans.

Familial aggregation of food allergy and sensitization to food allergens: a family-based study

BACKGROUND

The increasing prevalence of food allergy (FA) is a growing clinical and public health problem. The contribution of genetic factors to FA remains largely unknown.

OBJECTIVE

This study examined the pattern of familial aggregation and the degree to which genetic factors contribute to FA and sensitization to food allergens.

METHODS

This study included 581 nuclear families (2,004 subjects) as part of an ongoing FA study in Chicago, IL, USA. FA was defined by a set of criteria including timing, clinical symptoms obtained via standardized questionnaire interview and corroborative specific IgE cut-offs for > or =95% positive predictive value (PPV) for food allergens measured by Phadia ImmunoCAP. Familial aggregation of FA as well as sensitization to food allergens was examined using generalized estimating equation (GEE) models, with adjustment for important covariates including age, gender, ethnicity and birth order. Heritability was estimated for food-specific IgE measurements.

RESULTS

FA in the index child was a significant and independent predictor of FA in other siblings (OR=2.6, 95% CI: 1.2-5.6, P=0.01). There were significant and positive associations among family members (father-offspring, mother-offspring, index-other siblings) for total IgE and specific IgE to all the nine major food allergens tested in this sample (sesame, peanut, wheat, milk, egg white, soy, walnut, shrimp and cod fish). The estimated heritability of food-specific IgE ranged from 0.15 to 0.35 and was statistically significant for all the nine tested food allergens.

CONCLUSION

This family-based study demonstrates strong familial aggregation of FA and sensitization to food allergens, especially, among siblings. The heritability estimates indicate that food-specific IgE is likely influenced by both genetic and environmental factors. Together, this study provides strong evidence that both host genetic susceptibility and environmental factors determine the complex trait of IgE-mediated FA.

Colon Cancer Family Registry: an international resource for studies of the genetic epidemiology of colon cancer

BACKGROUND

Family studies have served as a cornerstone of genetic research on colorectal cancer.

MATERIALS AND METHODS

The Colorectal Cancer Family Registry (Colon CFR) is an international consortium of six centers in North America and Australia formed as a resource to support studies on the etiology, prevention, and clinical management of colorectal cancer. Differences in design and sampling schemes ensures a resource that covers the continuum of disease risk. Two separate recruitment strategies identified colorectal cancer cases: population-based (incident case probands identified by cancer registries; all six centers) and clinic-based (families with multiple cases of colorectal cancer presenting at cancer family clinics; three centers). At this time, the Colon CFR is in year 10 with the second phase of enrollment nearly complete. In phase I recruitment (1998-2002), population-based sampling ranged from all incident cases of colorectal cancer to a subsample based on age at diagnosis and/or family cancer history. During phase II (2002-2007), population-based recruitment targeted cases diagnosed before the age of 50 years are more likely attributable to genetic factors. Standardized protocols were used to collect information regarding family cancer history and colorectal cancer risk factors, and biospecimens were obtained to assess microsatellite instability (MSI) status, expression of mismatch repair proteins, and other molecular and genetic processes.

RESULTS

Of the 8,369 case probands enrolled to date, 2,602 reported having one or more colorectal cancer-affected relatives and 799 met the Amsterdam I criteria for Lynch syndrome. A large number of affected (1,324) and unaffected (19,816) relatives were enrolled, as were population-based (4,108) and spouse (983) controls. To date, 91% of case probands provided blood (or, for a few, buccal cell) samples and 75% provided tumor tissue. For a selected sample of high-risk subjects, lymphocytes have been immortalized. Nearly 600 case probands had more than two affected colorectal cancer relatives, and 800 meeting the Amsterdam I criteria and 128, the Amsterdam II criteria. MSI testing for 10 markers was attempted on all obtained tumors. Of the 4,011 tumors collected in phase I that were successfully tested, 16% were MSI-high, 12% were MSI-low, and 72% were microsatellite stable. Tumor tissues from clinic-based cases were twice as likely as population-based cases to be MSI-high (34% versus 17%). Seventeen percent of phase I proband tumors and 24% of phase II proband tumors had some loss of mismatch repair protein, with the prevalence depending on sampling. Active follow-up to update personal and family histories, new neoplasms, and deaths in probands and relatives is nearly complete.

CONCLUSIONS

The Colon CFR supports an evolving research program that is broad and interdisciplinary. The greater scientific community has access to this large and well-characterized resource for studies of colorectal cancer.

Aging syndrome genes and premature coronary artery disease

Background

Vascular disease is a feature of aging, and coronary vascular events are a major source of morbidity and mortality in rare premature aging syndromes. One such syndrome is caused by mutations in the lamin A/C (LMNA) gene, which also has been implicated in familial insulin resistance. A second gene related to premature aging in man and in murine models is the KLOTHO gene, a hypomorphic variant of which (KL-VS) is significantly more common in the first-degree relatives of patients with premature coronary artery disease (CAD). We evaluated whether common variants at the LMNA or KLOTHO genes are associated with rigorously defined premature CAD.

Methods

We identified 295 patients presenting with premature acute coronary syndromes confirmed by angiography. A control group of 145 patients with no evidence of CAD was recruited from outpatient referral clinics. Comprehensive haplotyping of the entire LMNA gene, including the promoter and untranslated regions, was performed using a combination of TaqMan^® probes and direct sequencing of 14 haplotype-tagging single nucleotide polymorphisms (SNPs). The KL-VS variant of the KLOTHO gene was typed using restriction digest of a PCR amplicon.

Results

Two SNPs that were not in Hardy Weinberg equilibrium were excluded from analysis. We observed no significant differences in allele, genotype or haplotype frequencies at the LMNA or KLOTHO loci between the two groups. In addition, there was no evidence of excess homozygosity at the LMNA locus.

Conclusion

Our data do not support the hypothesis that premature CAD is associated with common variants in the progeroid syndrome genes LMNA and KLOTHO.

A semiparametric method for analyzing matched case-control family studies with a continuous outcome and proband sampling

We consider matched case-control familial studies which match a group of patients, called "case probands," with a group of disease-free subjects, called "control probands," using a set of family-level matching variables. Family members of each proband are then recruited into the study. Of interest here is the familial aggregation of the response variable and the effects of subject-specific covariates on the response. We propose an estimating equation approach to jointly estimate the main effects and intrafamilial correlations for matched family studies with a continuous outcome. Only knowledge of the first two joint moments of the response variable is required. The induced estimators for the main effects and intrafamilial correlations are consistent and asymptotically normally distributed. We apply the proposed method to sleep apnea data. A simulation study demonstrates the usefulness of our approach.

Kin-cohort evaluation of relative risks of genetic variants

The kin-cohort study, an embedded retrospective cohort of first-degree relatives of probands, has been used frequently in conjunction with case-control studies to evaluate penetrance of high-risk genotypes. However, in principle, the kin-cohort approach can be used in conjunction with a case-control study in which family history data are carefully recorded to examine and validate the observed association of any candidate genotype with disease. Its utility for this purpose is governed by the relative efficiency of the kin-cohort analysis to test hypotheses about the relevant genotype-disease odds ratios, which in turn depends strongly on various factors, notably the magnitude of the disease incidence rate and the prevalence of the aberrant genotype. In this study, we compare the efficiencies of the two analytic approaches, case-control vs. kin-cohort, and illustrate the results in the context of cancer epidemiology. The kin-cohort analysis can provide substantial, important supplementary information for relatively common cancers such as breast, lung, colorectal, and prostate, and is also relatively efficient in general for the evaluation of the stronger and more rare genetic risk factors. Genet Epidemiol 24:220-229, 2003.

Statistical properties of Teng and Risch's sibship type tests for detecting an association between disease and a candidate allele

Risch and Teng [Genome Res 1998;8:1273-1288] and Teng and Risch [Genome Res 1999;9:234-241] proposed a class of transmission/disequilibrium test-like statistical tests based on the difference between the estimated allele frequencies in the affected and control populations. They evaluated the power of a variety of family-based and nonfamily-based designs for detecting an association between a candidate allele and disease. Because they were concerned with diseases with low penetrances, their power calculations assumed that unaffected individuals can be treated as a random sample from the population. They predicted that this assumption rendered their sample size calculations slightly conservative. We generalize their partial ascertainment conditioning by including the status of the unaffected sibs in the calculations of the distribution and power of the statistic used to compare the allele frequency in affected offspring to the estimated frequency in the parents, based on sibships with genotyped affected and unaffected sibs. Sample size formulas for our full ascertainment methods are presented. The sample sizes for our procedure are compared to those of Teng and Risch. The numerical results and simulations indicate that the simplifying assumption used in Teng and Risch can produce both conservative and anticonservative results. The magnitude of the difference between the sample sizes needed by their partial ascertainment approximation and the full ascertainment is small in the circumstances they focused on but can be appreciable in others, especially when the baseline penetrances are moderate. Two other statistics, using different estimators for the variance of the basic statistic comparing the allele frequencies in the affected and unaffected sibs are introduced. One of them incorporates an estimate of the null variance obtained from an auxiliary sample and appears to noticeably decrease the sample sizes required to achieve a prespecified power.

Some further results on incorporating risk factor information in assessing the dependence between paired failure times arising from case-control family studies: an application to prostate cancer

In a typical case-control family study, detailed risk factor information is often collected on cases and controls, but not on their relatives for reasons of cost and logistical difficulty in locating the relatives. The impact of missing risk factor information for relatives on estimation of the strength of dependence between the disease risk of pairs of relatives is largely unknown. In this paper, we extend our earlier work on estimating the dependence of ages at onset between paired relatives from case-control family data to include covariates on cases and controls, and possibly relatives. Using population-based case-control families as our basic data structure, we study the effect of missing covariates for relatives and/or cases and controls on the bias of certain dependence parameter estimators via a simulation study. Finally we illustrate various analyses using a case-control family study of early onset prostate cancer.

Design considerations for association studies of candidate genes in families

In genetic epidemiologic studies, investigators often use generalized linear models to evaluate the relationships between a disease trait and covariates, such as one or more candidate genes or an environmental exposure. Recently, attention has turned to study designs that mandate the inclusion of family members in addition to a proband. Standard models for analysis assume independent observations, which is unlikely to be true for family data, and the usual standard errors for the regression parameter estimates may be too large or too small, depending on the distribution of the covariates within and between families. The consequences of familial correlation on the study efficiency can be measured by a design effect that is equivalent to the relative information in a sample of unrelated individuals compared to a sample of families with the same number of individuals. We examine design effects for studies in association, and illustrate how the design effect is influenced by the intra-familial distribution of covariate values such as would be expected for a candidate gene. Typical design effects for a candidate gene range between 1.1 and 2.4, depending on the size of the family and the amount of unexplained familial correlation. These values correspond to a modest 10% increase in the required sample size up to more than doubling the requirements. Design effect values are useful in study design to compare the efficiency of studies that sample families versus independent individuals and to determine sample size requirements that account for familial correlation.

Genetic epidemiology with a capital "E"

Three characteristics of genetic epidemiology that distinguish it from its parent disciplines are a focus on population-based research, a focus on the joint effects of genes and the environment, and the incorporation of the underlying biology of the disease into its conceptual models. These principles are illustrated by a review of the genetic epidemiology of breast and ovarian cancer. Descriptive and mechanistic models for the joint effects of genes and "environmental" risk factors such as hormones and reproductive events are compared to illustrate the need to understand the biology. The contribution of population-based research to the development of the evidence for the involvement of major genes, the discovery of BRCA1 and BRCA2, and their characterization is reviewed. Interactions of major susceptibility genes, metabolic genes, and hormones are also discussed. I conclude with some suggestions for future directions for the field, the journal, and the Society, including recent bioethics initiatives. I believe that the Society should reach out more to the epidemiology community and that the journal should shift its emphasis from pure methodology to also include more substantive papers that illustrate these principles.

Family-based association studies

We review case-control designs for studying gene associations in which relatives of case patients are used as control subjects. These designs have the advantage that they avoid the problem of population stratification that can lead to spurious associations with noncausal genes. We focus on designs that use sibling, cousin, or pseudosibling controls, the latter formed as the set of genotypes not transmitted to the case from his or her parents. We describe a common conditional likelihood framework for use in analyzing data from any of these designs and review what is known about the validity of the various design and analysis combinations for estimating the genetic relative risk. We also present comparisons of efficiency for each of the family-based designs relative to the standard population-control design in which unrelated controls are selected from the source population of cases. Because of overmatching on genotype, the use of sibling controls leads to estimates of genetic relative risk that are approximately half as efficient as those obtained with the use of population controls, while relative efficiency for cousin controls is approximately 90%. However, we find that, for a rare gene, the sibling-control design can lead to improved efficiency for estimating a G x E interaction effect. We also review some restricted designs that can substantially improve efficiency, e.g., restriction of the sample to case-sibling pairs with an affected parent. We conclude that family-based case-control studies are an attractive alternative to population-based case-control designs using unrelated control subjects.

Integrated designs for gene discovery and characterization

Recent advances, including near completion of the human genome map, ever improving high-throughput technologies, and successes in discovering chronic disease-related genes, have stimulated the further development of genetic epidemiology. The primary mission of genetic epidemiology is to discover and characterize genes, whether independent of or interactive with environmental factors, that cause human diseases. To accomplish such a mission, genetic epidemiology needs to integrate both genetic and epidemiologic approaches. One of the challenges facing such an integrated approach is the identification of study designs that are efficient for both gene discovery and characterization. Because designs for gene discovery alone and designs for gene characterization alone have been elaborated in the other two panels, the focus of this paper is to describe those designs that may be useful for discovery and characterization jointly, including case-family and case-control-family designs. Examples of integrated designs are described, and studies of breast cancer conducted at the Fred Hutchinson Cancer Research Center are used for illustration. Finally, related analytic issues are also discussed.

Combined influence of genetic and dietary factors on colorectal cancer incidence in Japanese Americans

Colorectal cancer (CRC) rates for Japanese migrants to the United States increased rapidly to surpass the level of the host population. CRC rates for the Japanese in Hawaii and California are now the highest in the world. Rates for this disease have also increased in Japan, presumably as the result of the westernization of the diet. A series of population-based studies in Hawaii was undertaken to determine which dietary factors are responsible for this remarkable susceptibility of the Japanese to CRC and whether genetic factors are also involved. A first case-control study suggested that a high intake of red meat is a major risk factor for the disease in Hawaii Japanese men and that family history of CRC among first-degree relatives may strongly modify this association. A case-control family study is currently being completed to explore further the interaction between family history and the intake of red meat after adjustment for environmental covariates among family members. Also, a segregation analysis will guide gene discovery studies among high-risk Japanese families being recruited in the Cooperative Family Registry for Colorectal Cancer Studies. Retrospective and prospective studies are also ongoing to test associations of CRC with specific polymorphisms in genes controlling the metabolic activation or detoxification of the carcinogens associated with a diet high in red meat. Preliminary results suggest an association of the combined rapid NAT2 genotype and rapid CYP1A2 phenotype with CRC in individuals consuming well-done red meat. Populations in which dramatic changes in cancer incidence have occurred may offer opportunities to identify gene-environment interactions.

Design of gene characterization studies: an overview

This collection of papers from the Gene Characterization Panel addresses design issues in studies aimed at assessing the population characteristics of cloned genes, such as their allele frequencies, penetrance, variation in these parameters across subpopulations, and gene-environment and gene-gene interactions. This paper provides an overview of the various designs that have been suggested, including cohort and case-control designs using independent and related individuals as well as optimal multistage sampling and hybrid designs. Various statistical (bias and efficiency) and practical considerations are suggested for evaluation of the alternative designs, with the aim of posing the question, "What is the optimal design for a particular situation"? The answer to this question clearly depends on such contextual issues as nature of the outcome variable, the gene frequency and genetic relative risk, and the importance of gene-environment and gene-gene interactions. Further methodologic work might be usefully directed toward assessment of the seriousness of the population stratification problem in general as well as methods of dealing with it, the utility of registries of high-risk families, and the merits of various hybrid designs for gene discovery and gene characterization.