Comparative analysis of isodisomic and heterodisomic segments in cases with maternal uniparental disomy 14 suggests more than one imprinted region

Further evidence for a parent-of-origin effect at the NOP9 locus on language-related phenotypes

BACKGROUND

Specific language impairment (SLI) is a common neurodevelopmental disorder, observed in 5-10 % of children. Family and twin studies suggest a strong genetic component, but relatively few candidate genes have been reported to date. A recent genome-wide association study (GWAS) described the first statistically significant association specifically for a SLI cohort between a missense variant (rs4280164) in the NOP9 gene and language-related phenotypes under a parent-of-origin model. Replications of these findings are particularly challenging because the availability of parental DNA is required.

METHODS

We used two independent family-based cohorts characterised with reading- and language-related traits: a longitudinal cohort (n = 106 informative families) including children with language and reading difficulties and a nuclear family cohort (n = 264 families) selected for dyslexia.

RESULTS

We observed association with language-related measures when modelling for parent-of-origin effects at the NOP9 locus in both cohorts: minimum P = 0.001 for phonological awareness with a paternal effect in the first cohort and minimum P = 0.0004 for irregular word reading with a maternal effect in the second cohort. Allelic and parental trends were not consistent when compared to the original study.

CONCLUSIONS

A parent-of-origin effect at this locus was detected in both cohorts, albeit with different trends. These findings contribute in interpreting the original GWAS report and support further investigations of the NOP9 locus and its role in language-related traits. A systematic evaluation of parent-of-origin effects in genetic association studies has the potential to reveal novel mechanisms underlying complex traits.

Increased Power for Detection of Parent-of-Origin Effects via the Use of Haplotype Estimation

Parent-of-origin (or imprinting) effects relate to the situation in which traits are influenced by the allele inherited from only one parent and the allele from the other parent has little or no effect. Given SNP genotype data from case-parent trios, the parent of origin of each allele in the offspring can often be deduced unambiguously; however, this is not true when all three individuals are heterozygous. Most existing methods for investigating parent-of-origin effects operate on a SNP-by-SNP basis and either perform some sort of averaging over the possible parental transmissions or else discard ambiguous trios. If the correct parent of origin at a SNP could be determined, this would provide extra information and increase the power for detecting the effects of imprinting. We propose making use of the surrounding SNP information, via haplotype estimation, to improve estimation of parent of origin at a test SNP for case-parent trios, case-mother duos, and case-father duos. This extra information is then used in a multinomial modeling approach for estimating parent-of-origin effects at the test SNP. We show through computer simulations that our approach has increased power over previous approaches, particularly when the data consist only of duos. We apply our method to two real datasets and find a decrease in significance of p values in genomic regions previously thought to possibly harbor imprinting effects, thus weakening the evidence that such effects actually exist in these regions, although some regions retain evidence of significant effects.

Position effect leading to haploinsufficiency in a mosaic ring chromosome 14 in a boy with autism

We describe an individual with autism and a coloboma of the eye carrying a mosaicism for a ring chromosome consisting of an inverted duplication of proximal chromosome 14. Of interest, the ring formation was associated with silencing of the amisyn gene present in two copies on the ring chromosome and located at 300 kb from the breakpoint. This observation lends further support for a locus for autism on proximal chromosome 14. Moreover, this case suggests that position effects need to be taken into account, when analyzing genotype-phenotype correlations based on chromosomal imbalances.

Parental effect of DNA (Cytosine-5) methyltransferase 1 on grandparental-origin-dependent transmission ratio distortion in mouse crosses and human families

Transmission ratio distortion (TRD) is a deviation from the expected Mendelian 1:1 ratio of alleles transmitted from parents to offspring and may arise by different mechanisms. Earlier we described a grandparental-origin-dependent sex-of-offspring-specific TRD of maternal chromosome 12 alleles closely linked to an imprinted region and hypothesized that it resulted from imprint resetting errors in the maternal germline. Here, we report that the genotype of the parents for loss-of-function mutations in the Dnmt1 gene influences the transmission of grandparental chromosome 12 alleles. More specifically, maternal Dnmt1 mutations restore Mendelian transmission ratios of chromosome 12 alleles. Transmission of maternal alleles depends upon the presence of the Dnmt1 mutation in the mother rather than upon the Dnmt1 genotype of the offspring. Paternal transmission mirrors the maternal one: live-born offspring of wild-type fathers display 1:1 transmission ratios, whereas offspring of heterozygous Dnmt1 mutant fathers tend to inherit grandpaternal alleles. Analysis of allelic transmission in the homologous region of human chromosome 14q32 detected preferential transmission of alleles from the paternal grandfather to grandsons. Thus, parental Dnmt1 is a modifier of transmission of alleles at an unlinked chromosomal region and perhaps has a role in the genesis of TRD.

Genome-wide prediction of imprinted murine genes

Imprinted genes are epigenetically modified genes whose expression is determined according to their parent of origin. They are involved in embryonic development, and imprinting dysregulation is linked to cancer, obesity, diabetes, and behavioral disorders such as autism and bipolar disease. Herein, we train a statistical model based on DNA sequence characteristics that not only identifies potentially imprinted genes, but also predicts the parental allele from which they are expressed. Of 23,788 annotated autosomal mouse genes, our model identifies 600 (2.5%) to be potentially imprinted, 64% of which are predicted to exhibit maternal expression. These predictions allowed for the identification of putative candidate genes for complex conditions where parent-of-origin effects are involved, including Alzheimer disease, autism, bipolar disorder, diabetes, male sexual orientation, obesity, and schizophrenia. We observe that the number, type, and relative orientation of repeated elements flanking a gene are particularly important in predicting whether a gene is imprinted.

Risk of mosaicism and uniparental disomy associated with the prenatal diagnosis of a non-homologous Robertsonian translocation carrier

OBJECTIVE

To estimate the fetal risk of uniparental disomy (UPD) associated with the presence of a Robertsonian translocation (RT) in a parent or in the fetus, to determine whether it is clinically indicated to test these pregnancies for UPD.

METHODS

Retrospective analysis of our Centre's experience in testing prenatal specimens for UPD in cases of known familial RTs or fortuitous RT finding. In addition, all reports dealing with prenatal UPD testing in similar populations obtained from PUBMED and the 1995-2001 American Society of Human Genetics Meeting's abstracts were assessed.

RESULTS

No case of UPD 14 or 15 was found among the 51 tests performed at our Centre. Meta-analysis identified one case of UPD13 out of 687 UPD studies, conducted in 400 prenatal diagnoses. The 95% confidence interval of the risk of UPD in the population studied (1 in 738) is 0.02-0.76%. In one report, trisomy mosaicism for one of the chromosomes involved in the translocation was found in 3 cases out of 169 (95% confidence interval: 0.1-3 %).

CONCLUSIONS

Fetuses carrying a Robertsonian translocation have a risk of UPD of 0.02-0.76% (95% CI). In this population, trisomy mosaicism is more frequent than UPD. This finding justifies the study of additional colonies in all cases of prenatally diagnosed RT.

Maternal UPD(14) in the patient with a normal karyotype: Clinical report and a systematic search for cases in samples sent for testing for Prader-Willi syndrome

Maternal uniparental disomy for chromosome 14 causes a recognizable phenotype that has a number of consistent features, irrespective of the underlying chromosome abnormality. To illustrate this, we describe a patient with a 46,XX karyotype whose short stature, hypotonia, feeding problems, truncal obesity, early puberty, learning difficulties, and craniofacial characteristics led to a diagnosis of maternal (mat) UPD(14). No evidence is available to indicate how common mat UPD(14) in patients with a normal karyotype might be. Because of the similarity between Prader-Willi syndrome (PWS) and the mat UPD(14) phenotype in childhood, we systematically tested samples from 35 patients with normal karyotypes and an unexplained PWS-like phenotype referred to the Wessex Genetics Service. We sought to address the practical question should laboratories carry out tests for mat UPD(14) on all samples received for PWS testing when PWS testing gives negative results? None of the samples tested showed evidence of mat UPD(14). Routine screening of DNA from patients with possible PWS cannot be recommended on this basis.

Mice lacking paternally expressed Pref-1/Dlk1 display growth retardation and accelerated adiposity

Preadipocyte factor 1 (Pref-1/Dlk1) inhibits in vitro adipocyte differentiation and has been recently reported to be a paternally expressed imprinted gene at human chromosome 14q32. Studies on human chromosome 14 deletions and maternal uniparental disomy (mUPD) 14 suggest that misexpression of a yet-to-be-identified imprinted gene or genes present on chromosome 14 causes congenital disorders. We generated Pref-1 knockout mice to assess the role of Pref-1 in growth and in vivo adipogenesis and to determine the contribution of Pref-1 in mUPD. Pref-1-null mice display growth retardation, obesity, blepharophimosis, skeletal malformation, and increased serum lipid metabolites. Furthermore, the phenotypes observed in Pref-1-null mice are present in heterozygotes that harbor a paternally inherited, but not in those with a maternally inherited pref-1-null allele. Our results demonstrate that Pref-1 is indeed paternally expressed and is important for normal development and for homeostasis of adipose tissue mass. We also suggest that Pref-1 is responsible for most of the symptoms observed in mouse mUPD12 and human mUPD14. Pref-1-null mice may be a model for obesity and other pathologies of human mUPD14.