Case-parent Triad Design Research Articles

Design efficiency in genetic association studies.

Selecting the best design for genetic association studies requires careful deliberation; different study designs can be used to scan for different genetic effects, and each design has its own set of strengths and limitations. A variety of family and unrelated control configurations are amenable to genetic association analyses, including the case-control design, case-parent triads, and case-parent triads in combination with unrelated controls or control-parent triads. Ultimately, the goal is to choose the design that achieves the highest statistical power using the lowest cost. For given parameter values and genotyped individuals, designs can be compared directly by computing the power. However, a more informative and general design comparison can be achieved by studying the relative efficiency, defined as the ratio of variances of two different parameter estimators, corresponding to two separate designs. Using log-linear modeling, we derive the relative efficiency from the asymptotic variance of the parameter estimators and relate it to the concept of Pitman efficiency. The relative efficiency takes into account the fact that different designs impose different costs relative to the number of genotyped individuals. We show that while optimal efficiency for analyses of regular autosomal effects is achieved using the standard case-control design, the case-parent triad design without unrelated controls is efficient when searching for parent-of-origin effects. Due to the potential loss of efficiency, maternal genes should generally not be adjusted for in an initial genome-wide association study scan of offspring genes but instead checked post hoc. The relative efficiency calculations are implemented in our R package Haplin.

MSX1 gene and nonsyndromic oral clefts in a Southern Brazilian population

Nonsyndromic oral clefts (NSOC) are the most common craniofacial birth defects in humans. The etiology of NSOC is complex, involving both genetic and environmental factors. Several genes that play a role in cellular proliferation, differentiation, and apoptosis have been associated with clefting. For example, variations in the homeobox gene family member MSX1, including a CA repeat located within its single intron, may play a role in clefting. The aim of this study was to investigate the association between MSX1 CA repeat polymorphism and NSOC in a Southern Brazilian population using a case-parent triad design. We studied 182 nuclear families with NSOC recruited from the Hospital de Clínicas de Porto Alegre in Southern Brazil. The polymorphic region was amplified by the polymerase chain reaction and analyzed by using an automated sequencer. Among the 182 families studied, four different alleles were observed, at frequencies of 0.057 (175 bp), 0.169 (173 bp), 0.096 (171 bp) and 0.67 (169 bp). A transmission disequilibrium test with a family-based association test (FBAT) software program was used for analysis. FBAT analysis showed overtransmission of the 169 bp allele in NSOC (P=0.0005). These results suggest that the CA repeat polymorphism of the MSX1 gene may play a role in risk of NSOC in populations from Southern Brazil.

Maternal Variation in EPHX1, a Xenobiotic Metabolism Gene, Is Associated with Childhood Medulloblastoma: An Exploratory Case-Parent Triad Study

Common epidemiologic study designs used for evaluating germline genetic determinants of childhood medulloblastoma are often subject to population stratification bias and do not account for maternal genetic effects, a proxy for the intrauterine environment, which may be important in determining etiologic factors for this outcome. The case-parent triad design overcomes these limitations. Therefore, we conducted an exploratory study among 27 childhood medulloblastoma case-parent triads recruited from the Childhood Cancer Epidemiology and Prevention Center at Texas Children's Hospital (Houston, USA) between 2003 and 2010. We assessed 13 single nucleotide polymorphisms (SNPs) in nine xenobiotic detoxification genes, as deficiencies in this pathway may induce brain tumorigenesis. Log-linear modeling was used to assess the association between medulloblastoma and both the offspring (i.e., case) and maternal genotypes of each SNP. In our population, there were no offspring genotypes that were significantly associated with disease risk. However, the maternal EPHX1 rs1051740 genotype (RR = 3.26, P = .01) was associated with medulloblastoma risk. This exploratory study highlights the utility of the case-parent triad design, but these results should be interpreted cautiously due to the limited sample size.

Commentary: Thoughts on assessing evidence for gene by environment interaction

Commentary: Thoughts on assessing evidence for gene by environment interaction

Candidate gene analysis of spontaneous preterm delivery: New insights from re-analysis of a case-control study using case-parent triads and control-mother dyads

BackgroundSpontaneous preterm delivery (PTD) has a multifactorial etiology with evidence of a genetic contribution to its pathogenesis. A number of candidate gene case-control studies have been performed on spontaneous PTD, but the results have been inconsistent, and do not fully assess the role of how two genotypes can impact outcome. To elucidate this latter point we re-analyzed data from a previously published case-control candidate gene study, using a case-parent triad design and a hybrid design combining case-parent triads and control-mother dyads. These methods offer a robust approach to genetic association studies for PTD compared to traditional case-control designs.MethodsThe study participants were obtained from the Norwegian Mother and Child Cohort Study (MoBa). A total of 196 case triads and 211 control dyads were selected for the analysis. A case-parent triad design as well as a hybrid design was used to analyze 1,326 SNPs from 159 candidate genes. We compared our results to those from a previous case-control study on the same samples. Haplotypes were analyzed using a sliding window of three SNPs and a pathway analysis was performed to gain biological insight into the pathophysiology of preterm delivery.ResultsThe most consistent significant fetal gene across all analyses was COL5A2. The functionally similar COL5A1 was significant when combining fetal and maternal genotypes. PON1 was significant with analytical approaches for single locus association of fetal genes alone, but was possibly confounded by maternal effects. Focal adhesion (hsa04510), Cell Communication (hsa01430) and ECM receptor interaction (hsa04512) were the most constant significant pathways.ConclusionThis study suggests a fetal association of COL5A2 and a combined fetal-maternal association of COL5A1 with spontaneous PTD. In addition, the pathway analysis implied interactions of genes affecting cell communication and extracellular matrix.

The Genetics of Preterm Birth: Using What We Know to Design Better Association Studies

Women delivering preterm are at greatly increased risk of another preterm birth in subsequent pregnancies, reflecting effects of the environment, genetics, or both. Recent literature tells an increasingly coherent story about genetic susceptibility. Women who change partners after delivering preterm retain their elevated risk, whereas fathers who change partners do not. Women who themselves were preterm are at increased risk, an association not seen in fathers. Women with a half-sister who delivered preterm are at increased risk only if the shared parent was the mother. Concordance for preterm delivery is elevated in monozygotic compared with dizygotic twin mothers but not in monozygotic twin fathers. Several mechanisms could be operating: mitochondrial genes, maternal genes, or fetal genes expressing only the maternally derived copy. The authors compare 3 study designs for their ability to detect variants and to distinguish among mechanisms underlying heritability of this common outcome. The case-parent triad design offers robustness against self-selection and genetic population stratification, providing for estimation of genetic effects that are fetal, maternal, or that depend on the parent of origin. A case-base approach compares case-mothers with randomly sampled baby-mother pairs and permits estimation of the same relative risk parameters. Both designs offer important advantages over the commonly applied case-mother/control-mother design.

A New Method to Account for Missing Data in Case-Parent Triad Studies

Background/Aims: The case-parent triad design is commonly used in genetic association studies. Generally, samples are drawn from an affected offspring, manifesting a phenotype of interest, as well as from the parents. The trio genotypes may be analyzed using a variety of available methods, but we focus on log-linear models because they test for genetic association and additionally estimate the relative risks of transmission. The models need to be modified to adjust for missing genotypes. Furthermore, instability in the parameter estimates can arise when certain kinds of genotype combinations do not appear in the dataset. Methods: In this paper, we kill two birds with one stone. We propose a new method to simultaneously account for missing genotype data and genotype combinations with zero counts. This method solves a zero-inflated Poisson (ZIP) regression likelihood. The maximum likelihood estimates yield relative risks and the information matrix gives appropriate variance estimates for inference. A likelihood ratio test determines the significance of genetic association. Results: We compared the ZIP regression to previously proposed methods in both simulation studies and in a dataset that investigates the risk of orofacial clefts. The ZIP likelihood estimates regression coefficients with less bias than other methods when the minor allele frequency is small.

Study of four genes belonging to the folate pathway: transcobalamin 2 is involved in the onset of non-syndromic cleft lip with or without cleft palate

Cleft lip with or without cleft palate (CL/P) is the most common inborn craniofacial anomaly. Affected individuals require extensive medical and psychosocial support. Although CL/P has a complex and poorly understood etiology, increasing evidence of folate pathway involvement has been collected. So far, only the MTHFR gene has been extensively investigated as a risk factor for CL/P, while little has been done to test genetic variations in the folate biosynthetic pathways that may influence the infant's susceptibility to these birth defects. To date, this paper presents the first attempt to verify the involvement of four genes belonging to the folate pathway in nonsyndromic cleft onset. We used a case-parent triad design to test for linkage disequilibrium in the case of seven SNPs mapping on four different genes: transcobalamin 1 and 2 (TCN1 and TCN2), methionine synthase (MTR), and MTR reductase (MTRR). Our finding suggests that TCN2 is involved in causing CL/P. Indeed, significant overtransmission of the C allele was observed at the polymorphism c.776C>G (p.Pro259Arg) to the affected offspring (P=0.01). Results obtained with additional TCN2 polymorphisms suggest that c.776C>G may be functionally related to CL/P. However, because conflicting data exist with regard to the effect of the polymorphism in transcobalamin 2 function or in perturbing plasma levels of key molecules in the folate pathway, further investigation is warranted to confirm our data.

Maternal and fetal variants of genetic thrombophilias and the risk of preeclampsia.

A woman's thrombophilic genes may increase her risk of preeclampsia in pregnancy. Vascular conditions of the placenta related to thrombophilic genes of the fetus could also be relevant for preeclampsia. The case-parent triad study design provides separate estimation of maternal and fetal genes. We recruited 92 mother-father-child triads of preeclamptic pregnancies from a birth clinic in Stavanger, Norway. All parents were of Norwegian origin. Maternal, paternal, and fetal DNA were genotyped for the methylenetetrahydrofolate reductase (MTHFR) C677T and Factor V Leiden (FVL) G1691A SNPs. Estimation of the relative risk (RR) associated with fetal and maternal genetic variants was performed by log-linear models. There was no indication of an effect of the child's FVL alleles on preeclampsia risk. For case babies with 2 copies of the variant allele, the association with the MTHFR variant was inconclusive (RR = 1.6; 95% confidence interval [CI] = 0.6-4.3). Case mothers who were homozygous for the MTHFR variant had a relative risk of 2.0 (CI = 1.0-4.1) assuming a recessive gene effect. A 2.5-fold risk (CI = 1.1-5.7) of preeclampsia was estimated when the mother carried one copy of the FVL. Among mothers homozygous for the MTHFR variant, the relative risk of the FVL variant was 4.6-fold (CI = 1.0-21). We found little evidence of an effect of the child's MTHFR or FVL alleles on the risk of preeclampsia. Our estimates of effects of maternal MTHFR and FVL alleles were consistent with estimates from case-control studies. The case-parent triad design may be a useful tool for studies of pregnancy complications such as preeclampsia.

Tests of Gene‐Environment Interaction for Case‐Parent Triads with General Environmental Exposures

As knowledge of the human genome continues to grow, more progress is being made towards not only identifying the genes involved in disease susceptibility but also in defining the synergistic role genes play with environmental exposures. The detection of gene-environment interactions is important as it can offer clinicians a potential means of intervention. The discovery of interactions relies heavily on powerful statistical methods. We present a test, FBAT-I, that can be used to investigate gene-environment interaction. The test uses the case-parent triad design and protects the statistical inference from potential spurious results due to population admixture.

Exploring the effects of methylenetetrahydrofolate reductase gene variants C677T and A1298C on the risk of orofacial clefts in 261 Norwegian case-parent triads.

Folic acid and the methylenetetrahydrofolate reductase (MTHFR) gene have both been implicated in the etiology of orofacial clefts. The authors selected 261 case-parent triads (173 cases with cleft lip with or without cleft palate (CL/P) and 88 cases with cleft palate only (CPO)) from a Norwegian population-based study of orofacial clefts (May 1996-1998). A case-parent triad design was used to examine whether MTHFR variants C677T and A1298C, and their haplotypes, are risk factors for orofacial clefts. Among CL/P cases, the child's genotype at C677T or A1298C did not influence the risk. However, children of mothers carrying the C677T variant allele had a lower risk of CL/P. For CPO, children carrying the C677T variant allele had about a twofold increased risk, whereas the mother's genotypes did not contribute to the risk. The haplotype-based transmission/disequilibrium test showed that except for 677T/1298A (p = 0.06), none of the other haplotypes showed evidence of excess transmission to the offspring. The authors also explored interaction of C677T with maternal use of folic acid among children with CPO. Surprisingly, the risk associated with the child's carrying either CT or TT was higher (fourfold) when the mother used folic acid. These findings suggest a possible role of MTHFR and folic acid in the causation of orofacial clefts, but the strength and direction of these effects remain to be clarified.

Relative risk for genetic associations: the case-parent triad as a variant of case-cohort design.

The contribution of this paper is to conceptualize the case-parent triad within an epidemiological framework. We propose that the case-parent triad design is a variant of the case-cohort design. The affected offspring of case-parent triads come from a source cohort of all offspring of parents in a population. We first demonstrate that if the source cohort is restricted to offspring of a certain parental mating type then the relative risk in relation to genetic exposure can be estimated simply from the ratio of the number of exposed to the number of unexposed affected offspring. We then extend the logic to studies including offspring of all parental mating types; provided that the allele frequencies and possible parental mating types are specified, a valid relative risk can still be estimated. Compared to prior descriptions of the case-parent triad design, the proposed approach is readily understandable, epidemiologically meaningful and provides a relatively simple perspective for estimating valid measure of effect. Also, by allowing the potential sources of selection bias to be revealed more easily the design is made more accessible both conceptually and practically to epidemiologists.