Sporadic imprinting defects in Prader-Willi syndrome and Angelman syndrome: implications for imprint-switch models, genetic counseling, and prenatal diagnosis

A critical appraisal of clinical epigenetics

Modern epigenetics emerged about 40 years ago. Since then, the field has rapidly grown. Unfortunately, this development has been accompanied by certain misconceptions and methodological shortcomings. A profound misconception is that chromatin modifications are a distinct layer of gene regulation that is directly responsive to the environment and potentially heritable between generations. This view ignores the fact that environmental factors affect gene expression mainly through signaling cascades and the activation or repression of transcription factors, which recruit chromatin regulators. The epigenome is mainly shaped by the DNA sequence and by transcription. Methodological shortcomings include the insufficient consideration of genetic variation and cell mixture distribution. Mis- and overinterpretation of epigenetic data foster genetic denialism ("We can control our genes") and epigenetic determinism ("You are what your parents ate"). These erroneous beliefs can be overcome by using precise definitions, by raising the awareness about methodological pitfalls and by returning to the basic facts in molecular and cellular biology.

The sperm epigenome does not display recurrent epimutations in patients with severely impaired spermatogenesis

BACKGROUND

In the past 15 years, numerous studies have described aberrant DNA methylation of imprinted genes (e.g. MEST and H19) in sperm of oligozoospermic men, but the prevalence and genomic extent of abnormal methylation patterns have remained unknown.

RESULTS

Using deep bisulfite sequencing (DBS), we screened swim-up sperm samples from 40 normozoospermic and 93 patients diagnosed as oligoasthenoteratozoospermic, oligoteratozoospermic or oligozoospermic, which are termed OATs throughout the manuscript, for H19 and MEST methylation. Based on this screening, we defined three patient groups: normal controls (NC), abnormally methylated oligozoospermic (AMO; n = 7) and normally methylated oligozoospermic (NMO; n = 86). Whole-genome bisulfite sequencing (WGBS) of five NC and five AMO samples revealed abnormal methylation levels of all 50 imprinting control regions in each AMO sample. To investigate whether this finding reflected epigenetic germline mosaicism or the presence of residual somatic DNA, we made a genome-wide inventory of soma-germ cell-specific DNA methylation. We found that > 2000 germ cell-specific genes are promoter-methylated in blood and that AMO samples had abnormal methylation levels at these genes, consistent with the presence of somatic cell DNA. The comparison between the five NC and six NMO samples revealed 19 differentially methylated regions (DMRs), none of which could be validated in an independent cohort of 40 men. Previous studies reported a higher incidence of epimutations at single CpG sites in the CTCF-binding region 6 of H19 in infertile patients. DBS analysis of this locus, however, revealed an association between DNA methylation levels and genotype (rs2071094), but not fertility phenotype.

CONCLUSIONS

Our results suggest that somatic DNA contamination and genetic variation confound methylation studies in sperm of infertile men. While we cannot exclude the existence of rare patients with slightly abnormal sperm methylation at non-recurrent CpG sites, the prevalence of aberrant methylation in swim-up purified sperm of infertile men has likely been overestimated, which is reassuring for patients undergoing assisted reproduction.

Update of the EMQN/ACGS best practice guidelines for molecular analysis of Prader-Willi and Angelman syndromes

This article is an update of the best practice guidelines for the molecular analysis of Prader-Willi and Angelman syndromes published in 2010 in BMC Medical Genetics [1]. The update takes into account developments in terms of techniques, differential diagnoses and (especially) reporting standards. It highlights the advantages and disadvantages of each method and moreover, is meant to facilitate the interpretation of the obtained results - leading to improved standardised reports.

Next-Generation-Sequencing in der Epigenetik

Molekulare Epigenetik bezieht sich auf die chemische und physikalische Modifikation von DNA und Chromatin. Transkriptionsfaktoren bestimmen die Chromatinzustände ihrer Zielgene, während Chromatinzustände andererseits die Bindung von Transkriptionsfaktoren an die DNA beeinflussen. Chromatinzustände sind gekennzeichnet durch spezifische Muster der DNA-Methylierung, Histonmodifikation, den Abstand der Nukleosomen und die 3‑D-Faltung von Chromatin. Seit dem Aufkommen des Next-Generation-Sequencing (NGS) ist es möglich, diese Muster im genomweiten Maßstab mit einer beispiellosen Auflösung zu analysieren. Solche epigenetischen Karten sind wertvoll, um regulatorische Elemente zu identifizieren, normale und gestörte Entwicklungsvorgänge zu verstehen und Epimutationen zu entdecken.

Clinical experience with multiplex ligation-dependent probe amplification for microdeletion syndromes in prenatal diagnosis: 7522 pregnant Korean women

Background

Conventional cytogenetic analysis using G-band karyotyping has been the method of choice for prenatal diagnosis, accurately detecting chromosomal abnormalities larger than 5 Mb. However, the method is inefficient for detecting the submicroscopic deletions and duplications that are associated with malformations and mental retardation. This study evaluated the results of the multiplex ligation-dependent probe amplification (MLPA) P245 assay used for prenatal diagnosis in cases with unusual ultrasonographic findings or specifically where parents wanted to be tested. The objective was to compare the results from MLPA with those from conventional cytogenetic testing in order to determine their concordance and the additional diagnostic yield of MLPA over G-band karyotyping.

Results

Of the 7522 prenatal cases analyzed, 124 were found to have genomic imbalances (1.6%). Of those 124 cases, 41 had gene loss (33.6%), and 83 had gene gain (66.4%). Most of the cases with genomic imbalances (64.5%) showed no abnormal karyotype. In particular, all cases with a 4p16.3 deletion (Wolf-Hirschhorn syndrome) showed an abnormal karyotype, whereas all of those with a 22q11–13 deletion showed a normal karyotype. In most of the cases with pathogenic deletions, the indication for invasive prenatal testing was an increase in the nuchal translucency (NT) alone (51.2%). Other indications observed in the remaining cases were abnormal serum screening markers (14.6%), other ultrasonographic findings (9.8%), pregnancy through in vitro fertilization and fertility assistance (9.8%), and advanced maternal age(2.4%).

Conclusions

These results show that for fetuses with an enlarged NT or abnormal ultrasonographic findings and normal conventional karyotype, additional genetic investigation like molecular testing would be for identifying the microscopic genomic aberrations (microdeletions, microduplications) responsible for syndromic associations including structural anomalies and mental retardation.

Newborn screening for Prader-Willi syndrome is feasible: Early diagnosis for better outcomes

Prader-Willi syndrome (PWS), is a complex genetic disease affecting 1/15,000 individuals, characterized by lack of expression of genes on the paternal chromosome 15q11-q13 region. Clinical features include central hypotonia, poor suck, learning and behavior problems, growth hormone deficiency with short stature, hyperphagia, and morbid obesity. Despite significant advances in genetic testing, the mean age for diagnosis in PWS continues to lag behind. Our goal was to perform a pilot feasibility study to confirm the diagnosis utilizing different genetic technologies in a cohort of 34 individuals with genetically confirmed PWS and 16 healthy controls from blood samples spotted and stored on newborn screening (NBS) filter paper cards. DNA was isolated from NBS cards, and PWS testing performed using DNA methylation-specific PCR (mPCR) and the methylation specific-multiplex ligation dependent probe amplification (MS-MLPA) chromosome 15 probe kit followed by DNA fragment analysis for methylation and copy number status. DNA extraction was successful in 30 of 34 PWS patients and 16 controls. PWS methylation testing was able to correctly identify all PWS patients and MS-MLPA was able to differentiate between 15q11-q13 deletion and non-deletion status and correctly identify deletion subtype (i.e., larger Type I or smaller Type II). mPCR can be used to diagnose PWS and MS-MLPA testing to determine both methylation status as well as the type of deletion or non-deletion status from DNA extracted from NBS filter paper. We propose that PWS testing in newborns is possible and could be included in the Recommended Uniform Screening Panel after establishing a validated cost-effective method.

Three siblings with Prader-Willi syndrome caused by imprinting center microdeletions and review

Prader-Willi syndrome (PWS) is a complex genetic imprinting disorder characterized by childhood obesity, short stature, hypogonadism/hypogenitalism, hypotonia, cognitive impairment, and behavioral problems. Usually PWS occurs sporadically due to the loss of paternally expressed genes on chromosome 15 with the majority of individuals having the 15q11-q13 region deleted. Examples of familial PWS have been reported but rarely. To date 13 families have been reported with more than one child with PWS and without a 15q11-q13 deletion secondary to a chromosome 15 translocation, inversion, or uniparental maternal disomy 15. Ten of those 13 families were shown to carry microdeletions in the PWS imprinting center. The microdeletions were found to be of paternal origin in nine of the ten cases in which family studies were carried out. Using a variety of techniques, the microdeletions were identified in regions within the complex SNRPN gene locus encompassing the PWS imprinting center. Here, we report the clinical and genetic findings in three adult siblings with PWS caused by a microdeletion in the chromosome 15 imprinting center inherited from an unaffected father that controls the activity of genes in the 15q11-q13 region and summarize the 13 reported cases in the literature.

CRISPR-Mediated Epigenome Editing

Mounting evidence has called into question our understanding of the role that the central dogma of molecular biology plays in human pathology. The conventional view that elucidating the mechanisms for translating genes into proteins can account for a panoply of diseases has proven incomplete. Landmark studies point to epigenetics as a missing piece of the puzzle. However, technological limitations have hindered the study of specific roles for histone post-translational modifications, DNA modifications, and non-coding RNAs in regulation of the epigenome and chromatin structure. This feature highlights CRISPR systems, including CRISPR-Cas9, as novel tools for targeted epigenome editing. It summarizes recent developments in the field, including integration of optogenetic and functional genomic approaches to explore new therapeutic opportunities, and underscores the importance of mitigating current limitations in the field. This comprehensive, analytical assessment identifies current research gaps, forecasts future research opportunities, and argues that as epigenome editing technologies mature, overcoming critical challenges in delivery, specificity, and fidelity should clear the path to bring these technologies into the clinic.

Benefits and limitations of prenatal screening for Prader-Willi syndrome

This review summarizes the status of genetic laboratory testing in Prader-Willi syndrome (PWS) with different genetic subtypes, most often a paternally derived 15q11-q13 deletion and discusses benefits and limitations related to prenatal screening. Medical literature was searched for prenatal screening and genetic laboratory testing methods in use or under development and discussed in relationship to PWS. Genetic testing includes six established laboratory diagnostic approaches for PWS with direct application to prenatal screening. Ultrasonographic, obstetric and cytogenetic reports were summarized in relationship to the cause of PWS and identification of specific genetic subtypes including maternal disomy 15. Advances in genetic technology were described for diagnosing PWS specifically DNA methylation and high-resolution chromosomal SNP microarrays as current tools for genetic screening and incorporating next generation DNA sequencing for noninvasive prenatal testing (NIPT) using cell-free fetal DNA. Positive experiences are reported with NIPT for detection of numerical chromosomal problems (aneuploidies) but not for structural problems (microdeletions). These reports will be discussed along with future directions for genetic screening of PWS. In summary, this review describes and discusses the status of established and ongoing genetic testing options for PWS applicable in prenatal screening including NIPT and future directions for early diagnosis in PWS. © 2016 John Wiley & Sons, Ltd.

Patients with mosaic methylation patterns of the Prader-Willi/Angelman Syndrome critical region exhibit AS-like phenotypes with some PWS features

Background

Loss of expression of imprinted genes in the 15q11.2-q13 region is known to cause either Prader-Willi syndrome (PWS) or Angelman syndrome (AS), depending on the parent of origin. In some patients (1 % in PWS and 2–4 % in AS), the disease is due to aberrant imprinting or gene silencing, or both.

Results

We report here a 4-year-old boy on whom a chromosomal microarray (CMA) was performed due to mild hand tremors, mild developmental delays, and clumsiness. CMA revealed absence of heterozygosity (AOH) spanning the entire chromosome 15, suggesting uniparental isodisomy 15. The patient had no definitive phenotypic features of PWS or AS. Methylation-sensitive multiplex ligation-dependent probe amplification (MS-MLPA) was performed to determine the parent of origin of the uniparental disomy (UPD) by examining methylation status at maternally imprinted sites. Interestingly, our patient had a mosaic methylation pattern. We identified nine additional previously tested patients with a similar mosaic methylation pattern. CMA was performed on these individuals retrospectively to test whether patients with mosaic methylation are more likely to have UPD of chromosome 15. Of the nine patients, only one had regions of AOH on chromosome 15; however, this patient had numerous regions of AOH on multiple chromosomes suggestive of consanguinity.

Conclusion

The patients with mosaic methylation had milder or atypical features of AS, and the majority also had some features characteristic of PWS. We suggest that quantitative methylation analysis be performed for cases of atypical PWS or AS. It is also important to follow up with methylation testing when whole-chromosome isodisomy is detected.

Angelman syndrome imprinting center encodes a transcriptional promoter

Clusters of imprinted genes are often controlled by an imprinting center that is necessary for allele-specific gene expression and to reprogram parent-of-origin information between generations. An imprinted domain at 15q11-q13 is responsible for both Angelman syndrome (AS) and Prader-Willi syndrome (PWS), two clinically distinct neurodevelopmental disorders. Angelman syndrome arises from the lack of maternal contribution from the locus, whereas Prader-Willi syndrome results from the absence of paternally expressed genes. In some rare cases of PWS and AS, small deletions may lead to incorrect parent-of-origin allele identity. DNA sequences common to these deletions define a bipartite imprinting center for the AS-PWS locus. The PWS-smallest region of deletion overlap (SRO) element of the imprinting center activates expression of genes from the paternal allele. The AS-SRO element generates maternal allele identity by epigenetically inactivating the PWS-SRO in oocytes so that paternal genes are silenced on the future maternal allele. Here we have investigated functional activities of the AS-SRO, the element necessary for maternal allele identity. We find that, in humans, the AS-SRO is an oocyte-specific promoter that generates transcripts that transit the PWS-SRO. Similar upstream promoters were detected in bovine oocytes. This result is consistent with a model in which imprinting centers become DNA methylated and acquire maternal allele identity in oocytes in response to transiting transcription.

Eating behavior, prenatal and postnatal growth in Angelman syndrome

The objectives of the present study were to investigate eating behavior and growth parameters in Angelman syndrome. We included 39 patients with Angelman syndrome. Twelve cases had a larger Class I deletion, eighteen had a smaller Class II deletion, whereas paternal uniparental disomy (pUPD) or a verified UBE3A mutation were present in five and four cases, respectively. Eating behavior was assessed by a questionnaire. Anthropometric measures were obtained from medical records and compared to Danish reference data. Children with pUPD had significantly larger birth weight and birth length than children carrying a deletion or a UBE3A mutation. We found no difference in birth weight or length in children with Class I or Class II deletions. When maternal birth weight and/or birth weight of siblings were taken into consideration, children with Class I deletion had a lower weight at birth than expected, and the weight continued to be reduced during the investigated initial five years of life. In contrast, children with pUPD showed hyperphagic behavior and their weight increased significantly after the age of two years. Accordingly, their body mass index was significantly increased as compared to children with a deletion. At birth, one child showed microcephaly. At five years of age, microcephaly was observed in half of the deletion cases, but in none of the cases with a UBE3A mutation or pUPD. The apparently normal cranial growth in the UBE3A and pUPD patients should however be regarded as the result of a generally increased growth. Eating behavior, pre- and postnatal growth in children with Angelman syndrome depends on genotype.

Epigenetics of discordant monozygotic twins: implications for disease

Monozygotic (MZ) twins share nearly all of their genetic variants and many similar environments before and after birth. However, they can also show phenotypic discordance for a wide range of traits. Differences at the epigenetic level may account for such discordances. It is well established that epigenetic states can contribute to phenotypic variation, including disease. Epigenetic states are dynamic and potentially reversible marks involved in gene regulation, which can be influenced by genetics, environment, and stochastic events. Here, we review advances in epigenetic studies of discordant MZ twins, focusing on disease. The study of epigenetics and disease using discordant MZ twins offers the opportunity to control for many potential confounders encountered in general population studies, such as differences in genetic background, early-life environmental exposure, age, gender, and cohort effects. Recently, analysis of disease-discordant MZ twins has been successfully used to study epigenetic mechanisms in aging, cancer, autoimmune disease, psychiatric, neurological, and multiple other traits. Epigenetic aberrations have been found in a range of phenotypes, and challenges have been identified, including sampling time, tissue specificity, validation, and replication. The results have relevance for personalized medicine approaches, including the identification of prognostic, diagnostic, and therapeutic targets. The findings also help to identify epigenetic markers of environmental risk and molecular mechanisms involved in disease and disease progression, which have implications both for understanding disease and for future medical research.

Change in prevalence of congenital defects in children with Prader-Willi syndrome

OBJECTIVE

The aim of this study was to assess the prevalence of congenital defects observed in patients with Prader-Willi syndrome (PWS) and to compare this prevalence with that described in the general population. In addition, these findings were correlated with the different etiologic subtypes.

METHODS

A total of 180 children with PWS followed for 13 years were included in this study. Diagnosis was confirmed by the methylation test, and genetic subtypes were established by using fluorescence in situ hybridization or multiplex ligation-dependent probe amplification and microsatellite analyses. The prevalence of congenital defects was compared with national and international registries of congenital defects in the general population (Estudio Colaborativo Latinoamericano de Malformaciones Congénitas, European Surveillance of Congenital Anomalies, and the New York Registry).

RESULTS

Twenty-two percent of the patients presented congenital defects with a risk of 5.4 to 18.7 times higher than that of the general population. The most frequent congenital defects were heart defects, renoureteral malformations, vertebral anomalies, hip dysplasia, clubfoot, and agenesis/hypoplasia of the corpus callosum. Each of these congenital defects was significantly more frequent in the children with PWS than in the general population. The congenital heart defects were more frequent in girls than in boys with PWS. No significant differences were found when the defects were correlated with the different etiologic subtypes.

CONCLUSIONS

An increased prevalence of congenital defects was found in our PWS patients. This finding suggests the need for further studies in PWS children that allow physicians to detect the congenital defects found in this series and, thus, to anticipate complications, with the ultimate aim of enhancing the management of PWS patients.

De novo interstitial duplication of 15q11.2-q13.1 with complex maternal uniparental trisomy for the 15q11-q13 region in a patient with Prader-Willi syndrome

Prader-Willi syndrome is caused by the lack of paternal contribution for the imprinted 15q11-q13 region that originates through a number of mechanisms such as paternal deletion of 15q11-q13, maternal uniparental disomy, or by an imprinting defect due to epimutations in the paternal imprinting center. In the present report, we describe a female patient with complex maternal uniparental trisomy for the 15q11-q13 Prader-Willi syndrome critical region due to a de novo interstitial duplication of 15q11-q13 region that is present in one of the maternal homologs. As a result, the patient has three maternally derived copies of the Prader-Willi syndrome critical region and absence of paternal 15 contribution and thus, presents with a Prader-Willi syndrome phenotype with risk for developing additional phenotypes (e.g., autism and psychiatric phenotypes) characteristic of maternally derived duplications of this region. We suggest that this is a rather unique mechanism leading to Prader-Willi syndrome that has not been previously reported.

Identification and proteomic analysis of distinct UBE3A/E6AP protein complexes

The E6AP ubiquitin ligase catalyzes the high-risk human papillomaviruses' E6-mediated ubiquitylation of p53, contributing to the neoplastic progression of cells infected by these viruses. Defects in the activity and the dosage of E6AP are linked to Angelman syndrome and to autism spectrum disorders, respectively, highlighting the need for precise control of the enzyme. With the exception of HERC2, which modulates the ubiquitin ligase activity of E6AP, little is known about the regulation or function of E6AP normally. Using a proteomic approach, we have identified and validated several new E6AP-interacting proteins, including HIF1AN, NEURL4, and mitogen-activated protein kinase 6 (MAPK6). E6AP exists as part of several different protein complexes, including the proteasome and an independent high-molecular-weight complex containing HERC2, NEURL4, and MAPK6. In examining the functional consequence of its interaction with the proteasome, we found that UBE3C (another proteasome-associated ubiquitin ligase), but not E6AP, contributes to proteasomal processivity in mammalian cells. We also found that E6 associates with the HERC2-containing high-molecular-weight complex through its binding to E6AP. These proteomic studies reveal a level of complexity for E6AP that has not been previously appreciated and identify a number of new cellular proteins through which E6AP may be regulated or functioning.

Molecular and Clinical Aspects of Angelman Syndrome

The Angelman syndrome is caused by disruption of the UBE3A gene and is clinically delineated by the combination of severe mental disability, seizures, absent speech, hypermotoric and ataxic movements, and certain remarkable behaviors. Those with the syndrome have a predisposition toward apparent happiness and paroxysms of laughter, and this finding helps distinguish Angelman syndrome from other conditions involving severe developmental handicap. Accurate diagnosis rests on a combination of clinical criteria and molecular and/or cytogenetic testing. Analysis of parent-specific DNA methylation imprints in the critical 15q11.2-q13 genomic region identifies 75-80% of all individuals with the syndrome, including those with cytogenetic deletions, imprinting center defects and paternal uniparental disomy. In the remaining group, UBE3A sequence analysis identifies an additional percentage of patients, but 5-10% will remain who appear to have the major clinical phenotypic features but do not have any identifiable genetic abnormalities. Genetic counseling for recurrence risk is complicated because multiple genetic mechanisms can disrupt the UBE3A gene, and there is also a unique inheritance pattern associated with UBE3A imprinting. Angelman syndrome is a prototypical developmental syndrome due to its remarkable behavioral phenotype and because UBE3A is so crucial to normal synaptic function and neural plasticity.

Genetic studies of Prader-Willi patients provide evidence for conservation of genomic architecture in proximal chromosome 15q

Prader-Willi syndrome (PWS) is a neurogenetic disorder associated with recurrent genomic recombination involving low copy repeats (LCRs) located in the human chromosome 15q11-q13. Previous studies of PWS patients from Asia suggested that there is a higher incidence of deletion and lower incidence of maternal uniparental disomy (mUPD) compared to that of Western populations. In this report, we present genetic etiology of 28 PWS patients from Taiwan. Consistent with the genetic etiology findings from Western populations, the type II deletion appears to be the most common deletion subtype. Furthermore, the ratio of the two most common deletion subtypes and the ratio of the maternal heterodisomy to isodisomy cases observed from this study are in agreement with previous findings from Western populations. In addition, we identified and further mapped the deletion breakpoints in two patients with atypical deletions using array CGH (comparative genomic hybridization). Despite the relatively small numbers of patients in each subgroup, our findings suggest that the genomic architecture responsible for the recurrent recombination in PWS is conserved in Taiwanese of the Han Chinese heritage and Western populations, thereby predisposing chromosome 15q11-q13 to a similar risk of rearrangements.

Diseases associated with genomic imprinting

Genomic imprinting is the phenomenon where the expression of a locus differs between the maternally and paternally inherited alleles. Typically, this manifests as transcriptional silencing of one of the alleles, although many genes are imprinted in a tissue- or isoform-specific manner. Diseases associated with imprinted genes include various cancers, disorders of growth and metabolism, and disorders in neurodevelopment, cognition, and behavior, including certain major psychiatric disorders. In many cases, the disease phenotypes associated with dysfunction at particular imprinted loci can be understood in terms of the evolutionary processes responsible for the origin of imprinting. Imprinted gene expression represents the outcome of an intragenomic evolutionary conflict, where natural selection favors different expression strategies for maternally and paternally inherited alleles. This conflict is reasonably well understood in the context of the early growth effects of imprinted genes, where paternally inherited alleles are selected to place a greater demand on maternal resources than are maternally inherited alleles. Less well understood are the origins of imprinted gene expression in the brain, and their effects on cognition and behavior. This chapter reviews the genetic diseases that are associated with imprinted genes, framed in terms of the evolutionary pressures acting on gene expression at those loci. We begin by reviewing the phenomenon and evolutionary origins of genomic imprinting. We then discuss diseases that are associated with genetic or epigenetic defects at particular imprinted loci, many of which are associated with abnormalities in growth and/or feeding behaviors that can be understood in terms of the asymmetric pressures of natural selection on maternally and paternally inherited alleles. We next described the evidence for imprinted gene effects on adult cognition and behavior, and the possible role of imprinted genes in the etiology of certain major psychiatric disorders. Finally, we conclude with a discussion of how imprinting, and the evolutionary-genetic conflicts that underlie it, may enhance both the frequency and morbidity of certain types of diseases.

Double-blind therapeutic trial in Angelman syndrome using betaine and folic acid

Angelman syndrome (AS) is caused by reduced or absent expression of the maternally inherited ubiquitin protein ligase 3A gene (UBE3A), which maps to chromosome 15q11-q13. UBE3A is subject to genomic imprinting in neurons in most regions of the brain. Expression of UBE3A from the maternal chromosome is essential to prevent AS, because the paternally inherited gene is not expressed, probably mediated by antisense UBE3A RNA. We hypothesized that increasing methylation might reduce expression of the antisense UBE3A RNA, thereby increasing UBE3A expression from the paternal gene and ameliorating the clinical phenotype. We conducted a trial using two dietary supplements, betaine and folic acid to promote global levels of methylation and attempt to activate the paternally inherited UBE3A gene. We performed a number of investigations at regular intervals including general clinical and developmental evaluations, biochemical determinations on blood and urine, and electroencephalographic studies. We report herein the data on 48 children with AS who were enrolled in a double-blind placebo-controlled protocol using betaine and folic acid for 1 year. There were no statistically significant changes between treated and untreated children; however, in a small subset of patients we observed some positive trends.

Clinical and genetic aspects of Angelman syndrome

Angelman syndrome is characterized by severe developmental delay, speech impairment, gait ataxia and/or tremulousness of the limbs, and a unique behavioral phenotype that includes happy demeanor and excessive laughter. Microcephaly and seizures are common. Developmental delays are first noted at 3 to 6 months age, but the unique clinical features of the syndrome do not become manifest until after age 1 year. Management includes treatment of gastrointestinal symptoms, use of antiepileptic drugs for seizures, and provision of physical, occupational, and speech therapy with an emphasis on nonverbal methods of communication. The diagnosis rests on a combination of clinical criteria and molecular and/or cytogenetic testing. Analysis of parent-specific DNA methylation imprints in the 15q11.2-q13 chromosome region detects approximately 78% of individuals with lack of maternal contribution. Less than 1% of individuals have a visible chromosome rearrangement. UBE3A sequence analysis detects mutations in an additional 11% of individuals. The remaining 10% of individuals with classic phenotypic features of Angelman syndrome have a presently unidentified genetic mechanism and thus are not amenable to diagnostic testing. The risk to sibs of a proband depends on the genetic mechanism of the loss of the maternally contributed Angelman syndrome/Prader-Willi syndrome region: typically <1% for probands with a deletion or uniparental disomy; as high as 50% for probands with an imprinting defect or a mutation of UBE3A. Members of the mother's extended family are also at increased risk when an imprinting defect or a UBE3A mutation is present. Chromosome rearrangements may be inherited or de novo. Prenatal testing is possible for certain genetic mechanisms.

Quantitative 1-Step DNA Methylation Analysis with Native Genomic DNA as Template

Background: DNA methylation analysis currently requires complex multistep procedures based on bisulfite conversion of unmethylated cytosines or on methylation-sensitive endonucleases. To facilitate DNA methylation analysis, we have developed a quantitative 1-step assay for DNA methylation analysis.

Methods: The assay is based on combining methylation-sensitive FastDigest® endonuclease digestion and quantitative real-time PCR (qPCR) in a single reaction. The first step consists of DNA digestion, followed by endonuclease inactivation and qPCR. The degree of DNA methylation is evaluated by comparing the quantification cycles of a reaction containing a methylation-sensitive endonuclease with the reaction of a sham mixture containing no endonuclease. Control reactions interrogating an unmethylated locus allow the detection and correction of artifacts caused by endonuclease inhibitors, while simultaneously permitting copy number assessment of the locus of interest.

Results: With our novel approach, we correctly diagnosed the imprinting disorders Prader–Willi syndrome and Angelman syndrome in 35 individuals by measuring methylation levels and copy numbers for the SNRPN (small nuclear ribonucleoprotein polypeptide N) promoter. We also demonstrated that the proposed correction model significantly (P &lt; 0.05) increases the assay’s accuracy with low-quality DNA, allowing analysis of DNA samples with decreased digestibility, as is often the case in retrospective studies.

Conclusions: Our novel DNA methylation assay reduces both the hands-on time and errors caused by handling and pipetting and allows methylation analyses to be completed within 90 min after DNA extraction. Combined with its precision and reliability, these features make the assay well suited for diagnostic procedures as well as high-throughput analyses.

Inheritance of epigenetic aberrations (constitutional epimutations) in cancer susceptibility

The pathogenic role for heritable mutations in the DNA sequence of tumor suppressor and DNA repair genes has been well established in familial cancer syndromes. These germ line mutations confer a high risk of developing particular types of cancer, according to the gene affected, at a young age of onset when compared to sporadically arising cancers of a similar type. The widespread role for epigenetic dysregulation in the development and progression of sporadic cancers is also well recognized. However, it has only become apparent in recent years that epigenetic aberrations can also occur constitutionally to confer a similar cancer phenotype as a genetic mutation within the same gene. These epigenetic errors are termed "constitutional epimutations" and are characterized by promoter methylation and transcriptional silencing of a single allele of the gene in normal somatic tissues in the absence of a sequence mutation within the affected locus. This is best exemplified in Lynch syndrome, which is an autosomal dominant cancer susceptibility syndrome characterized by the early development of colorectal, uterine, and additional cancers exhibiting microsatellite instability due to impaired mismatch repair. Lynch syndrome is usually caused by heterozygous loss-of-function germ line mutations of the mismatch repair genes, namely MLH1, MSH2, MSH6, and PMS2. Tumors develop following an acquired somatic loss of the remaining functional allele. However, a subset of Lynch syndrome cases without genetic mutations instead has a constitutional epimutation of MLH1 or MSH2. These epimutations are associated with distinct patterns of inheritance depending on the nature of the mechanisms underlying them.

The identification of microdeletion syndromes and other chromosome abnormalities: cytogenetic methods of the past, new technologies for the future

Chromosome analysis is an important diagnostic tool in the identification of causes of mental retardation, developmental delay, and other developmental disabilities. Cytogenetic approaches have revealed the chromosomal basis of a large number of genetic syndromes. The recent use of microarray-based comparative genomic hybridization (array CGH) has accelerated the identification of novel cytogenetic abnormalities. We present the results of array CGH in 8,789 clinical cases submitted for a variety of developmental problems. Of these cases, 6.9% showed clinically relevant abnormalities, 1.2% showed benign copy-number variants (polymorphisms), 2.5% showed recurrent alterations of unclear clinical significance-many of which are likely to be polymorphisms-and 1.4% showed novel alterations of unclear relevance. Although cytogenetic methods, including array CGH, have great potential for identifying novel chromosomal syndromes, this high-resolution analysis may also result in diagnostic challenges imposed on laboratories and clinicians regarding findings of unclear clinical significance. (c) 2007 Wiley-Liss, Inc.

Genomic imprinting and imprinting defects in humans

In placental mammals some 100-200 genes are expressed only from the paternal or the maternal allele. This peculiar expression pattern is the result of genomic imprinting, an epigenetic process by which the male and the female germ line confer a parent-of-origin specific mark (imprint) on certain chromosomal regions. The size of imprinted regions ranges from several kilobases to several megabases. The process of genomic imprinting is controlled by cis-acting imprinting centers (IC) and trans-acting factors. IC mutations affect the establishment or maintenance of genomic imprints and hence the expression of all imprinted genes controlled by this IC. Imprinting defects play a causal role in several recognizable syndromes.

Increased frequency of severe major anomalies in children conceived by intracytoplasmic sperm injection

The neurodevelopmental outcome of children born after intracytoplasmic sperm injection (ICSI) is controversial. We compared the medical and developmental outcome of 34 singletons born after ICSI (20 males, 14 females; mean ages of 18 mo and 40 mo [SD 9 mo]; range 2 y 10 mo-4 y 8 mo) with 39 case control studies (21 males, 18 females; mean ages of 18 mo and 40 mo [SD 4 mo]; range 3 y-4 y 1 mo). Each child was assessed physically and tested in three development domains (fine motor, gross motor, and language). Five children born after ICSI versus two control children (p=0.2) had major congenital anomalies (MaCAs). Four children born after ICSI versus no control children had severe MaCAs (p=0.04). These were defined as having a significant impact on development or causing chronic disease: Angelman syndrome (n=1), lissencephaly (n=1), Hanhart syndrome (n=1), and persistent hyperinsulinemic hypoglycaemia of infancy (n=1). Karyotyping in 23 children born after ICSI revealed no abnormalities. An imprinting defect was found in the child with Angelman syndrome. Results of developmental assessment were in all cases normal at the age of 18 months except for the three children with Angelman and Hanhart syndromes, and lissencephaly. At the second assessment, five more children born after ICSI and four control children showed abnormalities in one or more developmental domains. We conclude that there seems to be a higher frequency of severe major anomalies in children born after ICSI. An increased risk for imprinting defects cannot be excluded. If we exclude children with severe MaCAs, the incidence of an abnormal somatic or neurodevelopmental outcome in the fourth year of life in children born after ICSI is similar to that of spontaneously conceived children.

Clinical-etiologic correlation in children with Prader-Willi syndrome (PWS): An interdisciplinary study

Prader-Willi syndrome (PWS) is a multisystemic disorder caused by the loss of expression of paternally transcribed genes within chromosome 15q11-q13. Most cases are due to paternal deletion of this region; the remaining cases result from maternal uniparental disomy (UPD) and imprinting defects. To better understand the phenotypic variability of PWS, a genotype-phenotype correlation study was performed in 91 children with PWS. Patients were diagnosed by Southern Blot Methylation assay and genetic subtypes were established using FISH and microsatellite analyses. Fifty-nine subjects with deletion (31/28 males/females; mean age 3.86 years), 30 with UPD (14/16 males/females; mean age 3.89 years) and 2 girls with a presumed imprinting defect (mean age 0.43 yrs) were identified. For correlation purposes patients were grouped as "deleted" and "non-deleted." An increased maternal age was found in the UPD group. Four of Holm's criteria were more frequently present in the deleted group: need for special feeding techniques, sleep disturbance, hypopigmentation, and speech articulation defects. Concerning cognitive assessments, only 9.52% of subjects with deletion had Full-Scale IQ (FSIQ) > or =70, while 61.53% of subjects without deletion had FSIQ > or =70. Similar results were found in behavioral measures. Sleep disorders and carbohydrate metabolism were systematically assessed. Polysomnoghaphic studies revealed a higher frequency of central events with desaturations > or =10% in the deleted group (P = 0.020). In summary, the phenotype was significantly different between both groups in certain parameters related to the CNS. These results might be related to the differences in brain gene expression of the genetic subtypes.

Imprinting center analysis in Prader–Willi and Angelman syndrome patients with typical and atypical phenotypes

Prader-Willi syndrome (PWS) and Angelman syndrome (AS) are genetic disorders caused by a deficiency of imprinted gene expression from the paternal or maternal chromosome 15, respectively. This deficiency is due to the deletion of the 15q11-q13 region, parental uniparental disomy of the chromosome 15, or imprinting defect (ID). Mutation of the UBE3A gene causes approximately 10% of AS cases. In this present study, we describe the molecular analysis and phenotypes of two PWS patients and four AS patients with ID. One of the PWS patients has a non-familial imprinting center (IC) deletion and displayed a severe phenotype with an atypical PWS appearance, hyperactivity and psychiatric vulnerability. The other PWS and AS patients did not present genetic abnormalities in the IC, suggesting an epimutation as the genetic cause. The methylation pattern of two AS patients showed a faint maternal band corresponding to a mosaic ID. One of these mosaic patients displayed a mild AS phenotype while the other displayed a PWS-like phenotype.

Robust, Easy, and Dose-Sensitive Methylation Test for the Diagnosis of Prader–Willi and Angelman Syndromes

We present a new method for differential diagnosis of Prader-Willi (PWS) and Angelman syndromes (AS) that requires only a small amount of DNA including that obtained from amniocentesis specimens. This method not only proved to be robust and rapid, but, most importantly, it can be dosage sensitive, supplying additional information useful for genetic counselling. After methylation-dependent digestion of DNA with HpaII or McrBC, exon 1 of the SNRPN gene is amplified together with a sequence in the CpG island of the H19 gene. Given the similarities in sequence composition and methylation status between the amplified sequences, their co-amplification under semiquantitative conditions allows an easy discrimination between single dosage (present in deletions or chromosomal translocations) and a double-dosage state (uniparental disomy or imprinting error), when the appropriate controls are included. The method we have developed in combination with standard cytogenetic studies and segregation analysis of microsatellite markers offers a rapid and easy procedure to resolve most suspected cases of PWS and AS, and consequently to provide accurate genetic counselling.

Microarray based comparative genomic hybridization testing in deletion bearing patients with Angelman syndrome: genotype-phenotype correlations

BACKGROUND

Angelman syndrome (AS) is a neurodevelopmental disorder characterised by severe mental retardation, dysmorphic features, ataxia, seizures, and typical behavioural characteristics, including a happy sociable disposition. AS is caused by maternal deficiency of UBE3A (E6 associated protein ubiquitin protein ligase 3A gene), located in an imprinted region on chromosome 15q11-q13. Although there are four different molecular types of AS, deletions of the 15q11-q13 region account for approximately 70% of the AS patients. These deletions are usually detected by fluorescence in situ hybridisation studies. The deletions can also be subclassified based on their size into class I and class II, with the former being larger and encompassing the latter.

METHODS

We studied 22 patients with AS due to microdeletions using a microarray based comparative genomic hybridisation (array CGH) assay to define the deletions and analysed their phenotypic severity, especially expression of the autism phenotype, in order to establish clinical correlations.

RESULTS

Overall, children with larger, class I deletions were significantly more likely to meet criteria for autism, had lower cognitive scores, and lower expressive language scores compared with children with smaller, class II deletions. Children with class I deletions also required more medications to control their seizures than did those in the class II group.

CONCLUSIONS

There are four known genes (NIPA1, NIPA2, CYFIP1, & GCP5) that are affected by class I but not class II deletions, thus raising the possibility of a role for these genes in autism as well as the development of expressive language skills.

Imprinting defects on human chromosome 15

The Prader-Willi syndrome (PWS) and Angelman syndrome (AS) are two distinct neurogenetic diseases that are caused by the loss of function of imprinted genes on the proximal long arm of human chromosome 15. In a few percent of patients with PWS and AS, the disease is due to aberrant imprinting and gene silencing. In patients with PWS and an imprinting defect, the paternal chromosome carries a maternal imprint. In patients with AS and an imprinting defect, the maternal chromosome carries a paternal imprint. Imprinting defects offer a unique opportunity to identify some of the factors and mechanisms involved in imprint erasure, resetting and maintenance. In approximately 10% of cases the imprinting defects are caused by a microdeletion affecting the 5' end of the SNURF-SNRPN locus. These deletions define the 15q imprinting center (IC), which regulates imprinting in the whole domain. These findings have been confirmed and extended in knock-out and transgenic mice. In the majority of patients with an imprinting defect, the incorrect imprint has arisen without a DNA sequence change, possibly as the result of stochastic errors of the imprinting process or the effect of exogenous factors.

Identification of cis- and trans-acting factors possibly modifying the risk of epimutations on chromosome 15

In the majority of patients with a chromosome 15 imprinting defect (ID) causing Prader-Willi syndrome (PWS) or Angelman syndrome (AS), the defect is a primary epimutation that occurred spontaneously in the absence of a DNA mutation. We have investigated whether common DNA sequence variants in the bipartite imprinting centre (IC) are associated with an increased susceptibility to imprinting defects. We have determined the haplotype structure of the IC and found that the two IC elements called 'PWS-SRO' and 'AS-SRO' lie on separate haplotype blocks. To identify susceptible IC sequence variants, we have used the transmission disequilibrium test. While we did not observe preferential transmission of a paternal allele or haplotype in 41 PWS-ID trios, we found a trend for preferential maternal transmission of one AS-SRO haplotype (H-AS3) in 48 AS-ID trios (P=0.058) and could identify two sequence variants in H-AS3 that are responsible for this effect. We also obtained tentative evidence that homozygosity for the 677C>T variant of the 5,10-methylenetetrahydrofolate reductase (MTHFR) gene on chromosome 1 might increase the risk of a maternal imprinting defect: the frequency of the TT genotype was significantly higher in the mothers of the AS patients with an imprinting defect than in the patients' fathers or the general population (P=0.028). Our findings suggest that women with the IC haplotype H-AS3 or homozygosity for the MTHFR 677C>T variant may have an increased risk of conceiving a child with an imprinting defect, although the absolute risk is low.

Deletion of PREPL, a gene encoding a putative serine oligopeptidase, in patients with hypotonia-cystinuria syndrome

In 11 patients with a recessive congenital disorder, which we refer to as "the hypotonia-cystinuria syndrome," microdeletion of part of the SLC3A1 and PREPL genes on chromosome 2p21 was found. Patients present with generalized hypotonia at birth, nephrolithiasis, growth hormone deficiency, minor facial dysmorphism, and failure to thrive, followed by hyperphagia and rapid weight gain in late childhood. Since loss-of-function mutations in SLC3A1 are known to cause isolated cystinuria type I, and since the expression of the flanking genes, C2orf34 and PPM1B, was normal, the extended phenotype can be attributed to the deletion of PREPL. PREPL is localized in the cytosol and shows homology with prolyl endopeptidase and oligopeptidase B. Substitution of the predicted catalytic residues (Ser470, Asp556, and His601) by alanines resulted in loss of reactivity with a serine hydrolase-specific probe. In sharp contrast to prolyl oligopeptidase and oligopeptidase B, which require both aminoterminal and carboxyterminal sequences for activity, PREPL activity appears to depend only on the carboxyterminal domain. Taken together, these results suggest that PREPL is a novel oligopeptidase, with unique structural and functional characteristics, involved in hypotonia-cystinuria syndrome.

Genetics, epigenetics and gene silencing in differentiating mammalian embryos

A highly complex pattern of differentiation involving maternal and embryonic factors characterizes the early development of mammalian embryos. These complex genetic and proteonomic patterns of early growth also involve various forms of gene silencing and tissue reprogramming. Understanding the nature of fundamental developmental events is hence essential to appreciate the significance of natural and induced forms of remodelling, damaged forms of gene expression and gene silencing during the initial stages of growth. Natural forms of remodelling include subtle genetic events involved in, for example, the changing nature of imprinting from before fertilization or the inactivation of one X chromosome in female blastocysts. Induced forms include the consequences of nuclear transfer and embryo cloning or the immediate effects of placing embryos in culture media. Animal and human studies are described in this paper, relating reprogramming to detailed embryological and clinical knowledge gained through the use of IVF, preimplantation genetic diagnosis and the establishment in vitro of stem cells. Attention concentrates on the consequences of variations in all growth stages from the formation of oocytes, through fertilization, the differentiation of blastocysts and early haemopoietic stages in mammalian species. Unique features of gene expression or gene modification are described for each developmental stage.

Autism in Angelman syndrome: implications for autism research

Angelman syndrome (AS) is a neurodevelopmental disorder characterized by severe mental retardation, ataxia, and a happy/sociable disposition. Maternally, but not paternally, derived defects, such as duplications, within the AS critical region result in autistic symptomatology, suggesting that the UBE3A gene might be implicated in the causation of autism. This study examined the prevalence of autism in AS in 19 children representing three known molecular classes of AS. Children were studied over the course of 1 year. Forty-two percent of this population, eight of 19 children, met criteria for autism according to the Autism Diagnostic Observation Schedule (ADOS). Parents of children who were diagnosed with autism according to Diagnostic and Statistical Manual of Mental Disorders (DSM)-IV criteria as well as the ADOS - Generic, Module 1 (ADOS-G) were administered the Autism Diagnostic Interview - Revised (ADI-R). Data from the ADI-R were convergent with data from the ADOS-G in all cases. Children with comorbid autism and AS scored lower on measures of language, adaptive behavior, and cognition, and demonstrated a slower rate of improvement over the course of the study. Furthermore, they demonstrated deficits in communication and socialization that mirror those observed in children with idiopathic autism. The study highlights the phenotypic overlap between autism and AS and increases the probability that dysregulation of UBE3A may play a role in the causation of autism.

Unique maternal deletion of 15q in a patient with some symptoms of Prader-Willi syndrome

BACKGROUND

Human chromosome 15q11-q13 is a critical region for Prader-Willi syndrome (PWS) and Angelman syndrome (AS) and most of the genes are under the condition of imprinting mechanism. PWS results from the loss of expression of paternally expressed genes and AS of maternally expressed genes. In this study molecular studies about a patient with congenital anomalies and mental retardation are analyzed.

METHODS

Highly polymorphic microsatellite markers were analyzed by PCR. These markers exist within 15q11-q13 and distal to 15q13.

RESULTS

Only the maternal D15S986 locus within 15q11-q13 was deleted and other markers were biallelic.

CONCLUSIONS

The result of maternal small region deletion in this patient is different from the typical PWS with paternal chromosome deletion and it suggests that nearby the deleted region there exists a gene (genes) which is not imprinted but needs biallelic expression.

Uniparental disomy and imprinting defects in Japanese patients with Angelman syndrome

We examined 54 patients with deletion-negative Angelman syndrome (AS) using DNA methylation testing and microsatellite polymorphism analysis, and identified three patients with paternal uniparental disomy (UPD) and seven patients with imprinting defects (ID). The three patients with UPD were shown to have paternal isodisomy 15, which we hypothesized to have arisen from duplication of chromosome 15. Two of the patients with ID were siblings and carried microdeletions of the imprinting center (IC), while the remaining five patients had no evidence of deletions and represented sporadic cases. Two of the three patients with UPD and two of the seven patients with ID had not developed seizures. The only patients displaying microcephaly were those with ID who had microdeletions at the IC. These data support the previous findings that indicate that patients with UPD and ID may have a milder phenotype of AS.

Sudden cardiac death in a child affected by Prader-Willi syndrome

A case of sudden cardiac death in a 3-year-old young male affected by Prader-Willi syndrome, clinically diagnosed and confirmed by means of DNA methylation, is presented. The infant suddenly collapsed at home and was taken apparently unconsciousness by his mother to the emergency clinic where he was pronounced dead. A complete postmortem examination was performed and the histological findings led to the definition of cardiac death with a typical picture of contraction band necrosis. Pulmonary hypoxic alterations are frequently reported as the primary cause of death in PWS cases. In this fatal case according to the macroscopic and microscopic findings, the cause of death was most likely cardiac and possibly related to contraction band necrosis linked with ventricular fibrillation and sudden death.

Hydatidiform mole and triploidy: the role of genomic imprinting in placental development

Genomic imprinting, the differential expression of paternal and maternal alleles, is involved in the regulation of embryonic and fetal growth and development. In this review, we focus on the genetics of a disorder caused by a global defect in genomic imprinting, the hydatidiform mole. The ratio between the maternal and paternal genomes is critical in determining the development of both the embryonic and extraembryonic tissues, with an excess of paternally derived chromosomes leading to a complete (no maternal genome) or partial (lower amount of maternal chromosomes) mole. The recent identification and molecular studies in biparental complete moles may yield more insight into the regulation of imprinting during gametogenesis.

Deletion Analysis of the Imprinting Center Region in Patients with Angelman Syndrome and Prader-Willi Syndrome by Real-Time Quantitative PCR

The molecular basis of Angelman syndrome and Prader-Willi syndrome is well established, and genetic testing for these disorders is clinically available. Imprinting abnormalities account for up to 4% of patients with Angelman and Prader-Willi syndromes. Deletions of the imprinting center region are the molecular abnormality observed in a subset of Angelman and Prader-Willi syndrome cases with imprinting defects. Genetic testing of imprinting center deletions in patients with Angelman and Prader-Willi syndrome is not readily available. Such testing is important for the diagnostics of Angelman and Prader-Willi syndrome because it allows for more accurate diagnosis and recurrence risk prediction in families. Here we describe the development, validation, and implementation of a real time quantitative polymerase chain reaction (PCR)-based assay for imprinting center deletion detection in patients with Angelman and Prader-Willi syndrome, which we have incorporated into our genetic testing strategy for these disorders. To date we have tested, on a clinical basis, five patients with either Angelman or Prader-Willi syndrome in whom an imprinting center defect was implicated and found a deletion in one patient that was determined to be familial.

Disruption of the genomic imprint in trans with homologous recombination at Snrpn in ES cells

In gene targeting studies of the Prader-Willi syndrome (PWS)/Angelman syndrome (AS) domain in mouse ES cells, we recovered only recombinants with the paternal allele for constructs at exons 2 or 3 of the imprinted, maternally silenced Snurf-Snrpn gene. These sites lie close to the imprinting center (IC) for this domain. In contrast, recombinants for Ube3a within the same imprinted domain were recovered with equal frequency on the maternal and paternal alleles. In addition, gene targeting of the paternal allele for Snurf-Snrpn resulted in partial or complete demethylation in trans with activation of expression for the previously silenced maternal allele. The imprint switching of the maternal allele in trans is not readily explained by competition for trans-acting factors and adds to a growing body of evidence indicating homologous association of oppositely imprinted chromatin domains in somatic mammalian cells.

Characterization of quantitative trait loci for growth and meat quality in a cross between commercial breeds of swine

A three-generation resource family was created by crossing two Berkshire grandsires with nine Yorkshire granddams to identify QTL affecting growth, body composition, and meat quality. A total of 512 F2 offspring were evaluated for 11 traits related to growth and body composition and 28 traits related to meat quality. All animals were initially genotyped for 125 markers across the genome. The objectives of this advanced phase of the project were to further identify and characterize QTL after genotyping for another 33 markers in special regions of interest, and to develop and apply methods for detecting QTL with parent-of-origin effects. New marker linkage maps were derived and used in QTL analysis based on line-cross least squares regression-interval mapping. A decision tree for identifying QTL with parent-of-origin effects was developed based on tests against the Mendelian mode of expression. Empirical significance thresholds were derived at chromosomewise and genomewise levels using specialized permutation strategies to create data under the null hypothesis appropriate for each test. Significance thresholds derived by the permutation tests were validated based on simulation of a pedigree and data structure similar to the Berkshire-Yorkshire population. The addition of 33 markers resulted in the discovery of 29 new QTL at the 5% chromosomewise level using the Mendelian model of analysis. Thirteen of the original QTL were no longer significant at the 5% chromosomewise level. A total of 33 QTL with parent-of-origin effects were identified, including QTL with paternal expression for backfat and loin muscle area on chromosome 2, near IGF2, and QTL with maternal expression for drip loss and reflectance on chromosome 9. Tests for imprinting against Mendelian expression identified much fewer QTL with parent-of-origin effects than tests based on significance of paternal and maternal alleles, which have been used in other studies. The detected QTL and their identified mode of expression will allow further research in these QTL regions and their utilization in marker-assisted improvement of meat quality.

Epigenetics and assisted reproductive technology: a call for investigation

A surprising set of recent observations suggests a link between assisted reproductive technology (ART) and epigenetic errors--that is, errors involving information other than DNA sequence that is heritable during cell division. An apparent association with ART was found in registries of children with Beckwith-Wiedemann syndrome, Angelman syndrome, and retinoblastoma. Here, we review the epidemiology and molecular biology behind these studies and those of relevant model systems, and we highlight the need for investigation of two major questions: (1) large-scale case-control studies of ART outcomes, including long-term assessment of the incidence of birth defects and cancer, and (2) investigation of the relationship between epigenetic errors in both offspring and parents, the specific methods of ART used, and the underlying infertility diagnoses. In addition, the components of proprietary commercial media used in ART procedures must be fully and publicly disclosed, so that factors such as methionine content can be assessed, given the relationship in animal studies between methionine exposure and epigenetic changes.