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PubMed2001

Assessment of parent-of-origin effects in linkage analysis of quantitative traits.

Methods are presented for incorporation of parent-of-origin effects into linkage analysis of quantitative traits. The estimated proportion of marker alleles shared identical by descent is first partitioned into a component derived from the mother and a component derived from the father. These parent-specific estimates of allele sharing are used in variance-components or Haseman-Elston methods of linkage analysis so that the effect of the quantitative-trait locus carried on the maternally derived chromosome is potentially different from the effect of the locus on the paternally derived chromosome. Statistics for linkage between trait and marker loci derived from either or both parents are then calculated, as are statistics for testing whether the effect of the maternally derived locus is equal to that of the paternally derived locus. Analyses of data simulated for 956 siblings from 263 nuclear families who had participated in a linkage study revealed that type I error rates for these statistics were generally similar to nominal values. Power to detect an imprinted locus was substantially increased when analyzed with a model allowing for parent-of-origin effects, compared with analyses that assumed equal effects; for example, for an imprinted locus accounting for 30% of the phenotypic variance, the expected LOD score was 4.5 when parent-of-origin effects were incorporated into the analysis, compared with 3.1 when these effects were ignored. The ability to include parent-of-origin effects within linkage analysis of quantitative traits will facilitate genetic dissection of complex traits.

Alleles↗
PubMed1996

Parent-of-origin effect in transmission of bipolar disorder.

Recently, possible involvement of a parent-of-origin effect in the transmission of bipolar disorder has been suggested. We examined the possible contribution of parent-of-origin effect by using data from a large family and family history study of bipolar patients in the Collaborative Depression Study. In 276 probands with bipolar I disorder, family histories were examined using three diagnostic criteria: 1) bipolar I disorder, 2) bipolar I or bipolar II disorder, and 3) bipolar disorders or recurrent unipolar depression for parents and siblings. An excess of affected mothers was not observed when unipolar depression was excluded. Age-at-onset was significantly lower in probands having a father with bipolar disorders or recurrent unipolar depression than in probands with an affected mother. This difference was not observed when unipolar depression was excluded. There was no significant difference of prevalence rate in children of affected mothers and those with affected fathers. These data do not support the contribution of parent-of-origin effect in the transmission of bipolar disorder.

Adult↗
PubMed2002

Evidence for parent of origin effect in late-onset Alzheimer disease.

Evidence for a parent of origin effect in Alzheimer disease was obtained from a sample of 148 sibships on which affection status of the parents was sought using family history interviews. The parent study recruited families with two or more affected sibs for late onset AD utilizing rigorous diagnostic criteria. In 74 families, there was evidence of an affected parent, 49 maternal and 25 paternal. Genome scan data were analyzed for the sample as a whole and for the maternal and paternal families separately, using Genehunter-ASM. Seven regions with Z(lr) scores >or=2 were identified, four in maternal families (chr. 10,12,19,20) and three in paternal families (chr. 1,7,13). With the exception of the chromosome 10 finding, analysis by parent of origin greatly increased evidence of linkage in areas showing no linkage in the overall analyses. For example, a chr. 12 region reached a LOD = 2.29 among maternal families whereas the same region showed a LOD = 0.3 when all families were analyzed together. The strongest findings among maternal families (chr. 10 and 12) were followed up with fine mapping that resulted in an increase in maximum LOD scores from 2.7-3.2 on chr. 10, and 2.29-2.42 on chr. 12. These analyses highlight the importance of parent of origin effects in late-onset AD families and identify several genomic regions that may include genes linked to late-onset AD specific to disease transmission from the mother and require further investigation.

Age of Onset↗
PubMed1995

Evidence for linkage of bipolar disorder to chromosome 18 with a parent-of-origin effect.

A susceptibility gene on chromosome 18 and a parent-of-origin effect have been suggested for bipolar affective disorder (BPAD). We have studied 28 nuclear families selected for apparent unilineal transmission of the BPAD phenotype, by using 31 polymorphic markers spanning chromosome 18. Evidence for linkage was tested with affected-sib-pair and LOD score methods under two definitions of the affected phenotype. The affected-sibpair analyses indicated excess allele sharing for markers on 18p within the region reported previously. The greatest sharing was at D18S37: 64% in bipolar and recurrent unipolar (RUP) sib pairs (P = .0006). In addition, excess sharing of the paternally, but not maternally, transmitted alleles was observed at three markers on 18q: at D18S41, 51 bipolar and RUP sib pairs were concordant for paternally transmitted alleles, and 21 pairs were discordant (P = 0004). The evidence for linkage to loci on both 18p and 18q was strongest in the 11 paternal pedigrees, i.e., those in which the father or one of the father's sibs is affected. In these pedigrees, the greatest allele sharing (81%; P = .00002) and the highest LOD score (3.51; phi = 0.0) were observed at D18S41. Our results provide further support for linkage of BPAD to chromosome 18 and the first molecular evidence for a parent-of-origin effect operating in this disorder. The number of loci involved, and their precise location, require further study..

Adolescent↗
PubMed2001

Likelihood formulation of parent-of-origin effects on segregation analysis, including ascertainment.

We developed a likelihood-based method for testing for parent-of-origin effect in complex diseases. The likelihood formulations model parent-of-origin effect and allow for incorporation of ascertainment, as well as differential male and female ascertainment probabilities. The results based on simulated data indicated that the estimates of parental effect (either maternal or paternal) were biased when ascertainment was ignored or when the wrong ascertainment model was used. The exception was single ascertainment, in which we proved that ignoring ascertainment does not bias the estimation of parental effect, in a simple parent-of-origin model. These results underscore the importance of considering ascertainment models when testing for parent-of-origin effect in complex diseases.

Bias↗
PubMed1998

Failure to demonstrate parent-of-origin effect in transmission of bipolar II disorder.

BACKGROUND: Parent-of-origin effect (POE) is suggested in transmission of bipolar disorder. Bipolar II disorder (BPII) should be considered separately. METHODS: The gender difference of transmitting parents, prevalence rate in children, and age at onset of patients in relation to the sex of the transmitting parent, were examined in 220 BPII patients. RESULTS: No evidence suggesting involvement of POE was found. CONCLUSION: POE is not involved in transmission of BPII. LIMITATION: Number of subjects is not sufficient. Rate of interviewed subjects differs between mothers and fathers. CLINICAL RELEVANCE: Female BPII patients do not transmit the disease more often than male patients.

Adult↗
PubMed2000

Parent-of-origin effects on seed development in Arabidopsis thaliana require DNA methylation.

Some genes in mammals and flowering plants are subject to parental imprinting, a process by which differential epigenetic marks are imposed on male and female gametes so that one set of alleles is silenced on chromosomes contributed by the mother while another is silenced on paternal chromosomes. Therefore, each genome contributes a different set of active alleles to the offspring, which develop abnormally if the parental genome balance is disturbed. In Arabidopsis, seeds inheriting extra maternal genomes show distinctive phenotypes such as low weight and inhibition of mitosis in the endosperm, while extra paternal genomes result in reciprocal phenotypes such as high weight and endosperm overproliferation. DNA methylation is known to be an essential component of the parental imprinting mechanism in mammals, but there is less evidence for this in plants. For the present study, seed development was examined in crosses using a transgenic Arabidopsis line with reduced DNA methylation. Crosses between hypomethylated and wild-type diploid plants produced similar seed phenotypes to crosses between plants with normal methylation but different ploidies. This is consistent with a model in which hypomethylation of one parental genome prevents silencing of alleles that would normally be active only when inherited from the other parent - thus phenocopying the effects of extra genomes. These results suggest an important role for methylation in parent-of-origin effects, and by inference parental imprinting, in plants. The phenotype of biparentally hypomethylated seeds is less extreme than the reciprocal phenotypes of uniparentally hypomethylated seeds. The observation that development is less severely affected if gametes of both sexes (rather than just one) are 'neutralized' with respect to parent-of-origin effects supports the hypothesis that parental imprinting is not necessary to regulate development.

Arabidopsis↗
PubMed2006

Parent-of-origin effects on mRNA expression in Drosophila melanogaster not caused by genomic imprinting.

Parent-of-origin effects create differences in gene expression among genetically identical individuals. Using measurements of allele-specific expression, we demonstrate that previously reported parent-of-origin effects on standing mRNA levels in Drosophila melanogaster are not attributable to genomic imprinting. Offspring from reciprocal crosses exhibit differences in total expression without differences in allelic expression, indicating that other types of maternal and/or paternal effects alter expression.

Alleles↗
PubMed2001

Detection of parent-of-origin effects for atopy by model-free and model-based linkage analyses.

Parent-of-origin effects for atopy were investigated by a model-free affected sib-pair (ASP) method and two model-based approaches in the Busselton nuclear families. Among the regions showing potential linkages to atopy by the ASP method, a significant excess of paternal allele sharing as compared with maternal allele sharing was observed for a cluster of three markers on chromosome 13. The two model-based methods, which specify either sex-specific recombination rates or different penetrances for heterozygotes according to the parental origin of disease allele (imprinting), led to the same results, both suggesting a paternal effect. Thus, these two ways of modelling parent-of-origin effects appear equivalent in nuclear family data. Further simulations are needed to investigate whether the mechanisms underlying parent-of-origin effects can be distinguished in larger pedigree structures.

Adult↗
PubMed2005

Xlr3b is a new imprinted candidate for X-linked parent-of-origin effects on cognitive function in mice.

Imprinted genes show differential expression between maternal and paternal alleles as a consequence of epigenetic modification that can result in 'parent-of-origin' effects on phenotypic traits. There is increasing evidence from mouse and human studies that imprinted genes may influence behavior and cognitive functioning. Previous work in girls with Turner syndrome (45,XO) has suggested that there are X-linked parent-of-origin effects on brain development and cognitive functioning, although the interpretation of these data in terms of imprinted gene effects has been questioned. We used a 39,XO mouse model to examine the influence of the parental origin of the X chromosome on cognitive behaviors and expression of X-linked genes in brain. Our findings confirm the existence of X-linked imprinted effects on cognitive processes and identify a new maternally expressed imprinted gene candidate on the X chromosome, Xlr3b, which may be of importance in mediating the behavioral effects.

Animals↗
PubMed2006

Assessment of genetic linkage and parent-of-origin effects on obesity.

CONTEXT: Obesity is a growing health care problem worldwide and is a major underlying risk factor for common diseases such as diabetes. Parent-of-origin effect has been reported to be involved in the development of obesity. But the genes with imprinting effects related to obesity are largely unknown. OBJECTIVE: The objective of the study was to identify obesity-related genetic loci, both with and without imprinting effects. DESIGN AND SUBJECTS: We conducted genome-wide linkage analyses for obesity with and without consideration of imprinting effects in a large sample including more than 4000 individuals. In addition to body mass index (BMI), we also used a more stringent and accurate obesity definition, which simultaneously considers BMI and percentage of fat mass (PFM) in a gender-specific manner. Simulations were performed to identify the genome-wide significant and suggestive significant thresholds. RESULTS: In nonimprinted linkage analyses, we detected suggestive linkage at 2q31 (LOD = 2.23) and 16q22 (LOD = 1.87) for BMI and 2q37 (LOD = 2.23) for BMI and PFM. Interestingly, 2q37 also achieved a significant maternal linkage with BMI and PFM (LOD=3.34) in imprinted linkage analyses. Imprinted linkage analyses revealed suggestive linkage evidence for BMI at three additional genomic regions, including 3p14 (LOD = 2.20, paternal), 3q24 (LOD = 1.97, maternal), and 19q13 (LOD = 1.81, maternal). CONCLUSION: We reported linkage and imprinting effects for obesity on several chromosome regions and suggested the potential importance of parent-of-origin effects and phenotype definition of obesity in delineating the genetic basis of obesity.

Adipose Tissue↗
PubMed2000

Evaluating the parent-of-origin effect in bipolar affective disorder. Is a more penetrant subtype transmitted paternally?

BACKGROUND: Numerous genetic mechanisms and modes of transmission underlying bipolar affective disorder (BPAD) have been postulated. Recently, the discovery of genomic imprinting and mitochondrial transmission of illness in humans has stimulated study of parent-of-origin effects in the transmission of BPAD. METHODS: We examined a large sample of families from an associated linkage study to search for a possible parent-of-origin effect. Selecting for unilineal families with at least one offspring and/or parent diagnosed with BPAD after structured interview, we conducted three analyses: (1) the rates of illness among mothers and fathers of offspring affected with BPAD; (2) the observed frequency of transmission and rates of illness among maternal and paternal lineages; and (3) the rates of affective illness among offspring of parents affected with BPAD. RESULTS: Our results indicate no significant differences in the rates of illness among mothers and fathers of offspring affected with BPAD. Also, the frequency of transmission and rates of illness among maternal and paternal lineages did not differ significantly. However, the rate of BPAD among the offspring of fathers affected with BPAD was significantly higher than for mothers with the illness. LIMITATIONS: Substantially more women than men, and maternal than paternal relatives were studied - introducing possible gender biases. CONCLUSIONS: These results suggest a possible paternal parent-of-origin effect.

Bipolar Disorder↗
PubMed2003

Estimation and testing of parent-of-origin effects for quantitative traits.

Recent progress in developing family-based association methods has extended their use to the analysis of quantitative traits in the offspring and to the estimation, for dichotomous traits, of the relative contribution of genetic and environmental mechanisms for parent-of-origin effects. However, many traits of interest are not naturally measured on a binary scale yet are suspected or known to be influenced by imprinted genes, and there is consequent interest in seeking evidence for parent-of-origin effects at these loci. Here we show how simple linear models can be used to estimate these parent-of-origin effects for a broad class of phenotypes; in particular, normally distributed quantitative traits are easily dealt with.

Female↗
PubMed1999

Linkage analysis with adequate modeling of a parent-of-origin effect.

We present an extension to parametric linkage analysis that allows modeling diseases with a parent-of-origin effect (i.e., imprinting). Different penetrances are assumed for individuals being heterozygous at the disease locus, depending on their having inherited the disease allele from the father or mother. Motivated by the finding of a maternally expressed locus influencing alcohol consumption in mice (Alcp2), the analysis method has been included into the program GENEHUNTER for application to Problem 1, Collaborative Study on the Genetics of Alcoholism of Genetic Analysis Workshop 11. By this extension, a powerful tool is provided for adequately modeling an inherited disease in linkage analysis that supposedly has imprinting effects. The program has been used to analyze the data set on alcohol dependence in humans and can be applied to other genetically determined traits as well.

Alcoholism↗
PubMed2004

Parent-of-origin effect in multiple sclerosis: observations in half-siblings.

Multiple sclerosis is a complex trait in which occurrence rates in offspring are 20-50-fold greater than in the general population. Parent-of-origin effects have been difficult to screen for, since most cases are sporadic. We have compared recurrence risks in half-siblings with respect to their parent in common. Of the 1567 index cases with half-siblings in multiple sclerosis clinics across Canada, we recorded 3436 half-siblings and 2706 full-siblings. Age-adjusted full-sibling risk was 3.11%. By contrast, half-sibling risk in the same families was significantly lower at 1.89% (chi2 test, p=0.006), but higher than expected if familial risk was simply polygenic. For maternal half-siblings, the risk was 2.35% (34 affected siblings of 1859), and 1.31% for paternal half-siblings (15 of 1577), (p=0.048). The difference in risk suggests a maternal parent-of-origin effect in multiple sclerosis susceptibility.

Female↗
PubMed2000

No evidence for a parent-of-origin effect detected in the pattern of inheritance of schizophrenia.

BACKGROUND: Schizophrenia is a complex genetic disorder with no clear pattern of inheritance. Epigenetic modification of genes may thus play a role in its transmission. METHODS: In our study, 439 families with at least two ill siblings with schizophrenia (208 with unilineal transmission) were examined for evidence of a parent-of-origin effect (e.g., evidence of parental imprinting on the familial transmission of schizophrenia). RESULTS: No significant difference in the prevalence of maternal compared with paternal transmission was found. In addition, affected male subjects did not differ from affected female subjects in the proportion of their offspring diagnosed with schizophrenia. CONCLUSIONS: Although the transmission of schizophrenia may be influenced by epigenetic events, our study fails to find evidence that one epigenetic mechanism, a parent-of-origin imprinting effect, determines whether an individual expresses the illness.

Adult↗
PubMed2003

Natural selection and the evolution of genome imprinting.

Sexual reproduction results from the fusion of gametes in which the chromatin configuration of maternal and paternal chromosomes is distinct at fertilization. Although many of the differences are erased during successive cellular divisions and chromatin modifications, some are retained in both somatic and germline cells. These epigenetic modifications can confer different characteristics on maternal and paternal chromosomes and such differences can be selected during any process that has the ability to distinguish between homologues. The end result of these selective forces are parental origin effects, writ large. The range of effects observed, including transcriptional imprinting and effects on chromosome segregation and heterochromatization, reflects the diversity of selective forces in operation. However, a closer look at these effects suggests that parental origin-dependent differences in chromatin structure might be subject to some common forces and that these forces may explain many of the "nontranscriptional" parental origin effects observed in mammals.

Animals↗
PubMed1991

Survival of XO mouse fetuses: effect of parental origin of the X chromosome or uterine environment?

Using a recombinant product from the structurally abnormal Y chromosome, Y*, female mice with a single X of either maternal or paternal origin were generated. The two types of females were produced on the same genetic background and differ only in the origin of the X chromosome. Hence it has been possible to assess the effect of parental origin of the X on survival of females with a single X chromosome. A highly significant prenatal loss of females with a single X of paternal origin, but no comparable loss of females with a single X of maternal origin was observed. The reduced viability of females with a paternally derived X could be mediated by the parental origin of the X (i.e. X chromosome imprinting) or alternatively, since the mothers of females with a single paternally derived X have only a single X chromosome, the effect could be mediated by the genotype of the mother (i.e. maternal uterine effect).

Animals↗