An extension of the transmission disequilibrium test incorporating imprinting

The recombination rates in meioses of females and males are often different. Some genes that affect development and behavior in mammals are known to be imprinted, and >1% of all mammalian genes are believed to be imprinted. When the gene is imprinted and the recombination fractions are sex specific, the conventional transmission disequilibrium test (TDT) is shown to be still valid for testing for linkage. The power function of the TDT is derived, and the effect of the degree of imprinting on the power of the TDT is investigated. It is learned that imprinting has little effect on the power when the female and male recombination rates are equal. On the basis of case-parents trios, the transmissions from the heterozygous fathers/mothers to their affected children are separated as paternal and maternal, and two TDT-like statistics, TDT(p) and TDT(m), are consequently constructed. It is found that the TDT(p) possesses a higher power than the TDT for maternal imprinting genes, and the TDT(m) is more powerful than the TDT for paternal imprinting genes. On the basis of the parent-of-origin effects test statistic (POET), a novel statistic, TDT incorporating imprinting (TDTI) is proposed to test for linkage in the presence of linkage disequilibrium, which is shown to be more powerful than the TDT when parent-of-origin effects are significant but slightly less powerful than the TDT when parent-of-origin effects are negligible. The validity of the TDT and TDTI is assessed by simulation. The power approximation formulas for the TDT and TDTI are derived and the simulation results show that they are accurate. The simulation study on power comparison shows that the TDTI outperforms the TDT for imprinted genes. The improvement can be substantial in the case of complete paternal/maternal imprinting.     

TLINKAGE-IMPRINT: a model-based approach to performing two-locus genetic imprinting analysis

OBJECTIVES: Imprinting refers to the expression of only one copy of a gene pair, which is determined by the parental origin of the copy. Imprinted genes play a role in the development of several complex diseases, including cancers and mental disorders. In certain situations, two-trait-loci models are shown to be more powerful than one-trait-locus models. However, no current methods use pedigree structure efficiently and perform two-locus imprinting analyses. In this paper, we apply the Elston-Stewart algorithm to the parametric two-trait-loci imprinting model used by Strauch et al. [2000] to obtain a method for qualitative trait linkage analyses that explicitly models imprinting and can be applied to large pedigrees. METHODS: We considered a parametric approach based on 4 x 4 penetrance matrix to account for imprinting and modified TLINKAGE software to implement this approach. We performed simulation studies using a small and a large pedigree under dominant and imprinted and dominant or imprinted scenarios. Furthermore, we developed a likelihood ratio-based test for imprinting that compares the logarithm of odds (LOD) score obtained using the two-locus imprinting model with that obtained using the standard two-locus model that does not allow for imprinting. RESULTS: In simulation studies of three scenarios where the true mode of inheritance included imprinting, accurate modeling through the proposed approach yielded higher LOD scores and better recombination fraction estimates than the traditional two-locus model that does not allow for imprinting. CONCLUSIONS: This imprinting model will be useful in identifying the genes responsible for several complex disorders that are potentially caused by a combination of imprinted and non-imprinted genes.     

Parametric approach to genomic imprinting analysis with applications to Angelman's syndrome

Genomic imprinting is a mechanism by which only one copy of a gene pair is expressed, and this expression is determined by the parental origin of the copy. The deregulation of imprinted genes has been implicated in a number of human diseases. The Imprinted Gene Catalogue now has more than 200 genes listed, and estimates based on mouse models suggest many more may exist in humans. Therefore, the development of methods to identify such genes is important. In this communication, we present a parametric model-based approach to analyzing arbitrary-sized pedigree data for genomic imprinting. We have modified widely used LINKAGE program to incorporate our proposed approach. In addition, our approach allows for the use of sex-specific recombinations in the analysis, which is of particular importance in a genome-wide analysis for imprinted genes. We compared our imprinting analysis approach to that implemented in the GENEHUNTER-IMPRINT program using simulation studies as well as by analyzing causal genes in Angelman's syndrome families, which are known to be imprinted. These analyses showed that the proposed approach is very powerful for detecting imprinted genes in large pedigrees.     

Testing for genetic linkage in families by a variance-components approach in the presence of genomic imprinting

Some genes that affect development and behavior in mammals are known to be imprinted; and > or = 1% of all mammalian genes are imprinted. Hence, incorporating an imprinting parameter into linkage analysis may increase the power to detect linkage for these traits. Here we propose theoretical justifications for a recently developed model for testing of linkage, in the presence of genetic imprinting, between a quantitative-trait locus and a polymorphic marker; this is achieved in the variance-components framework. We also incorporate sex-specific recombination fractions into this model. We discuss the effects that imprinting and nonimprinting have on the power of the usual variance-components method and on the variance-components method that incorporates an imprinting parameter. We provide noncentrality parameters that can be used to determine the sample size necessary to attain a specified power for a given significance level, which is useful in the planning of a linkage study. Optimal strategies for a genome scan of potentially imprinted traits are discussed.     

Methods for detecting interactions between imprinted genes and environmental exposures using birth cohort designs with mother-offspring pairs

Genomic imprinting is a form of epigenetic regulation in mammals in which the same allele of a gene is expressed differently depending on the parental origin of the allele. Traditionally, the detection of imprinted genes that affect complex diseases has been focused on linkage designs with pedigrees or case-parent designs with case-parent trios. In the past two decades, the birth cohort design with mother-offspring pairs has been applied to understand better the effect of environmental influences during pregnancy and beginning of life on the growth and development of children. No work has been done on the detection of imprinted genes using birth cohort designs. Moreover, although the importance of imprinting has been well recognized, no study has looked at how environmental exposures modify the effects of imprinted genes. In this study, we show that the proposed imprinting test using the birth cohort design with mother-offspring pairs is an efficient test for testing the interactions between imprinted genes and environmental exposures. Through extensive simulation studies and a real data application, the proposed imprinting test has demonstrated much improved power in detecting gene-environment interactions than that of a test assuming the Mendelian dominant model when the true underlying genetic model is imprinting.     

Comparative analysis of sequence characteristics of imprinted genes in human, mouse, and cattle

Genomic imprinting is an epigenetic mechanism that results in monoallelic expression of genes depending on parent-of-origin of the allele. Although the conservation of genomic imprinting among mammalian species has been widely reported for many genes, there is accumulating evidence that some genes escape this conservation. Most known imprinted genes have been identified in the mouse and human, with few imprinted genes reported in cattle. Comparative analysis of genomic imprinting across mammalian species would provide a powerful tool for elucidating the mechanisms regulating the unique expression of imprinted genes. In this study we analyzed the imprinting of 22 genes in human, mouse, and cattle and found that in only 11 was imprinting conserved across the three species. In addition, we analyzed the occurrence of the sequence elements CpG islands, C + G content, tandem repeats, and retrotransposable elements in imprinted and in nonimprinted (control) cattle genes. We found that imprinted genes have a higher G + C content and more CpG islands and tandem repeats. Short interspersed nuclear elements (SINEs) were notably fewer in number in imprinted cattle genes compared to control genes, which is in agreement with previous reports for human and mouse imprinted regions. Long interspersed nuclear elements (LINEs) and long terminal repeats (LTRs) were found to be significantly underrepresented in imprinted genes compared to control genes, contrary to reports on human and mouse. Of considerable significance was the finding of highly conserved tandem repeats in nine of the genes imprinted in all three species. Electronic supplementary material The online version of this article (doi: ) contains supplementary material, which is available to authorized users.     

Genome-wide linkage analysis assessing parent-of-origin effects in the inheritance of birth weight

Family studies suggest that genetic variation may influence birth weight. We have assessed linkage of birth weight in a genome-wide scan in 269 Pima Indian siblings (334 sibling pairs, 92 families). As imprinting (expression of only a single copy of a gene depending on parent-of-origin), is commonly found in genes that affect fetal growth, we used a recently described modification of standard multipoint variance-component methods of linkage analysis of quantitative traits. This technique allows for comparison of linkage models that incorporate imprinting effects (in which the strength of linkage is expressed as LOD(IMP)) and models where parent-of-origin effects are not included (LOD(EQ)). Where significant evidence of linkage was present, separate contributions of alleles derived from father (LOD(FA)) or mother (LOD(MO)) to the imprinting model were estimated. Significant evidence of linkage was found on chromosome 11 (at map position 88 cM, LOD(IMP)=3.4) with evidence for imprinting (imprinting model superior, P<0.001). In this region, birth weight was linked predominantly to paternally derived alleles (LOD(FA)=4.1, LOD(MO)=0.0). An imprinted gene on chromosome 11 may influence birth weight in the Pima population. This chromosome contains one of the two major known clusters of imprinted genes in the human genome, lending biological plausibility to our findings.     

Quantifying genomic imprinting in the presence of linkage

Genomic imprinting decreases the power of classical linkage analysis, in which paternal and maternal transmissions of marker alleles are equally weighted. Several methods have been proposed for taking genomic imprinting into account in the model-free linkage analysis of binary traits. However, none of these methods are suitable for the formal identification and quantification of genomic imprinting in the presence of linkage. In addition, the available methods are designed for use with pure sib-pairs, requiring artificial decomposition in cases of larger sibships, leading to a loss of power. We propose here the maximum likelihood binomial method adaptive for imprinting (MLB-I), which is a unified analytic framework giving rise to specific tests in sibships of any size for (i) linkage adaptive to imprinting, (ii) genomic imprinting in the presence of linkage, and (iii) partial versus complete genomic imprinting. In addition, we propose an original measure for quantifying genomic imprinting. We have derived and validated the distribution of the three tests under their respective null hypotheses for various genetic models, and have assessed the power of these tests in simulations. This method can readily be applied to genome-wide scanning, as illustrated here for leprosy sibships. Our approach provides a novel tool for dissecting genomic imprinting in model-free linkage analysis, and will be of considerable value for identifying and evaluating the contribution of imprinted genes to complex diseases.     

Genetic imprinting analysis for alcoholism genes using variance components approach

Genomic imprinting, which is also known as the parent-of-origin effect, is a mechanism that only expresses one copy of a gene pair depending upon the parental origin. Although many chromosomal regions in the human genome are likely to be imprinted, imprinting is not accounted for in the usual linkage analysis. In this study, using a variance-components approach with a quantitative phenotype ttth-FP1, we found significant evidence of imprinting at two loci, D7S1790 and D1S1631, on chromosome 1 and chromosome 7, respectively. Our results suggest that allowing for the possibility of imprinting can increase the power to detect linkage for localizing genes for alcoholism.     

Bayesian inference for genomic imprinting underlying developmental characteristics

The identification of imprinted genes is becoming a standard procedure in searching for quantitative trait loci (QTL) underlying complex traits. When a developmental characteristic such as growth or drug response is observed at multiple time points, understanding the dynamics of gene function governing the underlying feature should provide more biological information regarding the genetic control of an organism. Recognizing that differential imprinting can be development-specific, mapping imprinted genes considering the dynamic imprinting effect can provide additional biological insights into the epigenetic control of a complex trait. In this study, we proposed a Bayesian imprinted QTL (iQTL) mapping framework considering the dynamics of imprinting effects and model multiple iQTLs with an efficient Bayesian model selection procedure. The method overcomes the limitation of likelihood-based mapping procedure, and can simultaneously identify multiple iQTLs with different gene action modes across the whole genome with high computational efficiency. An inference procedure using Bayes factors to distinguish different imprinting patterns of iQTL was proposed. Monte Carlo simulations were conducted to evaluate the performance of the method. The utility of the approach was illustrated through an analysis of a body weight growth data set in an F(2) family derived from LG/J and SM/J mouse stains. The proposed Bayesian mapping method provides an efficient and computationally feasible framework for genome-wide multiple iQTL inference with complex developmental traits.     

Biallelic expression of<Emphasis Type="Italic"> HRAS</Emphasis> and<Emphasis Type="Italic"> MUCDHL</Emphasis> in human and mouse

At least eight genes clustered in 1 Mb of DNA on human chromosome (Chr) 11p15.5 are subject to parental imprinting, with monoallelic expression in one or more tissues. Orthologues of these genes show conserved linkage and imprinting on distal Chr 7 of mice. The extended imprinted region has a bipartite structure, with at least two differentially methylated DNA elements (DMRs) controlling the imprinting of two sub-domains. We previously described three biallelically expressed genes ( MRPL23, 2G7 and TNNT3) in 100 kb of DNA immediately downstream of the imprinted H19 gene, suggesting that H19 marks one border of the imprinted region. Here we extend this analysis to two additional downstream genes, HRAS and MUCDHL (mu-protocadherin). We find that these genes are biallelically expressed in multiple fetal and adult tissues, both in humans and in mice. The mouse orthologue of a third gene, DUSP8, located between H19 and MUCDHL, is also expressed biallelically. The DMR immediately upstream of H19 frequently shows a net gain of methylation in Wilms tumors, either via Chr 11p15.5 loss of heterozygosity (LOH) or loss of imprinting (LOI), but changes in methylation in CpG-rich sequences upstream and within the MUCDHL gene are rare in these tumors and do not correlate with LOH or LOI. These findings are further evidence for a border of the imprinted region immediately downstream of H19, and the data allow the construction of an imprinting map that includes more than 20 genes, distributed over 3 Mb of DNA on Chr 11p15.5.     

Imprinting evolution and the price of silence

In contrast to the biallelic expression of most genes, expression of genes subject to genomic imprinting is monoallelic and based on the sex of the transmitting parent. Possession of only a single active allele can lead to deleterious health consequences in humans. Aberrant expression of imprinted genes, through either genetic or epigenetic alterations, can result in developmental failures, neurodevelopmental and neurobehavioral disorders and cancer. The evolutionary emergence of imprinting occurred in a common ancestor to viviparous mammals after divergence from the egg-laying monotremes. Current evidence indicates that imprinting regulation in metatherian mammals differs from that in eutherian mammals. This suggests that imprinting mechanisms are evolving from those that were established 150 million years ago. Therefore, comparing genomic sequence of imprinted domains from marsupials and eutherians with those of orthologous regions in monotremes offers a potentially powerful bioinformatics approach for identifying novel imprinted genes and their regulatory elements. Such comparative studies will also further our understanding of the molecular evolution and phylogenetic distribution of imprinted genes.     

Comparative sequence analysis of imprinted genes between human and mouse to reveal imprinting signatures

We performed a comparative genomic sequence analysis between human and mouse for 24 imprinted genes on human chromosomes 1, 6, 7, 11, 13, 14, 15, 18, 19, and 20. The MEME program was used to search for motifs within conserved sequences among the imprinted genes and we then used the MAST program to analyze for the presence or absence of motifs in the imprinted genes and 128 nonimprinted genes. Our analysis identified 15 motifs that were significantly enriched in the imprinted genes. We generated a logistic regression model by combining multiple motifs as input variables and the 24 imprinted genes and the 128 nonimprinted genes as a training set. The accuracy, sensitivity, and specificity of our model were 98, 92, and 99%, respectively. The model was further validated by an open test on 12 additional imprinted genes. The motifs identified in this study are novel imprinting signatures, which should improve our understanding of genomic imprinting and the role of genomic imprinting in human diseases.     

Imprinting in neurons

Although most imprinted genes display parent-origin-specific gene expression in tissues where they are transcribed, some genes are imprinted in a tissue-specific manner. Genes that show brain-specific imprinting or brain-specific lack of imprinting present a unique opportunity to study the process of imprinting during tissue differentiation. In this review, I introduce the systematic study of brain-cell-lineage-specific imprinting using a primary brain cell culture system, where neurons or glial cells are cultured separately. Two reports using the primary brain cell culture revealed brain-cell-lineage-specific imprinting in Ube3a and Igf2r, which had previously been described to show brain-specific imprinting and brain-specific lack of imprinting, respectively. Such brain-cell-lineage-specific imprinting was associated with cell-specific epigenetic modifications, especially with their reciprocally imprinted antisense non-coding RNAs, Ube3a-ATS and Air. These results emphasize the necessity of imprinting analysis at the cell level rather than in whole brain tissue during brain differentiation. The brain cell culture system provides us with a new powerful tool to understand the molecular mechanism of brain-specific imprinting.     

A log-linear approach to case-parent-triad data: assessing effects of disease genes that act either directly or through maternal effects and that may be subject to parental imprinting.

We describe a log-linear method for analysis of case-parent-triad data, based on maximum likelihood with stratification on parental mating type. The method leads to estimates of association parameters, such as relative risks, for a single allele, and also to likelihood ratio chi2 tests (LRTs) of linkage disequilibrium. Hardy-Weinberg equilibrium need not be assumed. Our simulations suggest that the LRT has power similar to that of the chi2 "score" test proposed by Schaid and Sommer and that both can outperform the transmission/disequilibrium test (TDT), although the TDT can perform better under an additive model of inheritance. Because a restricted version of the LRT is asymptotically equivalent to the TDT, the proposed test can be regarded as a generalization of the TDT. The method that we describe generalizes easily to accommodate maternal effects on risk and, in fact, produces powerful and orthogonal tests of the contribution of fetal versus maternal genetic factors. We further generalize the model to allow for effects of parental imprinting. Imprinting effects can be fitted by a simple, iterative procedure that relies on the expectation-maximization algorithm and that uses standard statistical software for the maximization steps. Simulations reveal that LRT tests for detection of imprinting have very good operating characteristics. When a single allele is under study, the proposed method can yield powerful tests for detection of linkage disequilibrium and is applicable to a broader array of causal scenarios than is the TDT.