Phenotypic delineation of Emanuel syndrome (supernumerary derivative 22 syndrome): Clinical features of 63 individuals

ZAP70: A Key Gene Identified by Differential Expression Analysis for Early Diagnosis of Fetuses with Emanuel Syndrome

Emanuel syndrome is a rare autosomal disorder characterized by microcephaly, heart defects, cleft palate and developmental delay. However, there is a lack of specific prenatal screening for Emanuel syndrome. To screen for early diagnostic marker genes in fetuses with karyotype+der[22]t(11;22)(q23;q11) of Emanuel syndrome. Transcriptome sequencing and clinical trait data of t(11;22)(q23;q11) translocation samples were screened from the GEO database. The differentially expressed genes (DEGs) were screened by principal component analysis of gene expression by R package, and intersections were taken with balanced and unbalanced DEGs. Then, the correlation with clinical traits was determined by WGCNA analysis, GO and KEGG enrichment analysis, and then univariate Cox analysis and Lasso analysis were performed to obtain the key genes. The core regulatory genes were obtained after protein-protein interaction (PPI) network analysis. A total of 50 DEGs were obtained after differential analysis. WGCNA analysis showed that DEG was associated with the chromosomal imbalance and age module. GO and KEGG enrichment analyses showed candidate genes were associated with exocytic vesicle membrane, synaptic vesicle membranes, glycoprotein complex, dystrophin-associated glycoprotein complex and malaria. COX and Lasso analyses yielded 5 hub genes, including ZBED9, RGS20, SGCB, ETV5, and ZAP70. The results of PPI identified the key regulatory gene associated with chromosomal imbalance as the ZAP70 gene. ZAP70 may be a key gene for early diagnosis of Emanuel syndrome in fetuses with+der[22]t(11;22)(q23;q11) karyotype.

Prenatal cfDNA Screening for Emanuel Syndrome and Other Unbalanced Products of Conception in Carriers of the Recurrent Balanced Translocation t(11;22): One Laboratory's Retrospective Experience

Prenatal cell-free DNA screening (cfDNA) can identify fetal chromosome abnormalities beyond common trisomies. Emanuel syndrome (ES), caused by an unbalanced translocation between chromosomes 11 and 22, has lacked a reliable prenatal screening option for families with a carrier parent. A cohort of cases (n = 46) sent for cfDNA screening with indications and/or results related to ES was queried; diagnostic testing and pregnancy outcomes were requested and analyzed. No discordant results were reported or suspected; there were ten true positives with diagnostic confirmation, six likely concordant positives based on known translocations and consistent cfDNA data, and twenty-six true negatives, by diagnostic testing or birth outcomes. For cases with parental testing, all affected ES cases had maternal translocation carriers. Expanded cfDNA may provide reassurance for t(11;22) carriers with screen negative results, and screen positive results appear to reflect a likely affected fetus, especially with a known maternal translocation. Current society guidelines support the use of expanded cfDNA screening in specific circumstances, such as for translocation carriers, with appropriate counseling. Diagnostic testing is recommended for prenatal diagnosis of ES and other chromosome abnormalities in pregnancy. To our knowledge, this cohort is the largest published group of cases with prenatal screening for carriers of t(11;22).

Auricular fistula: a review of its clinical manifestations, genetics, and treatments

Auricular fistula is a common congenital auricular malformation, characterized as a small opening in the skin and a subcutaneous cyst. It can be classified in different ways according to positions of pits and directions of fistula tracts. The term preauricular fistula and variant type of preauricular fistula (postauricular fistula) are used. Auricular fistula prevalence varies in countries and populations, and its actual prevalence is presently unknown. The most accepted and widely cited theory of auricular fistula etiopathogenesis is an incorrect or incomplete fusion of six auricular hillocks that are mesenchymal proliferations. Auricular fistula can occur either sporadically or genetically. The pattern in inherited cases is thought to be incomplete autosomal dominant, with variable expressions, reduced penetrance, and inapparent gender differences. Auricular fistula has several forms and is reported as being a component of many syndromes. In the field of genetics, currently, there is no related review to comprehensively summarize the genetic basis of auricular fistula and related disorders. This article provides a comprehensive review of auricular fistula, especially congenital preauricular fistula, which accounts for the majority of auricular fistula, by summarizing the clinical manifestations, histological and embryological development, genetics, examinations, and treatments, as well as syndromes with auricular fistula.

Orofacial Clefts: Genetics of Cleft Lip and Palate

Orofacial clefting is considered one of the commonest birth defects worldwide. It presents as cleft lip only, isolated cleft palate or cleft lip and palate. The condition has a diverse genetic background influenced by gene-gene and gene-environment interaction, resulting in two main types, syndromic and nonsyndromic orofacial clefts. Orofacial clefts lead to significant physiological difficulties that affect feeding, speech and language development and other developmental aspects, which results in an increased social and financial burden on the affected individuals and their families. The management of cleft lip and palate is solely based on following a multidisciplinary team approach. In this narrative review article, we briefly summarize the different genetic causes of orofacial clefts and discuss some of the common syndromes and the approach to the management of orofacial clefts.

Young Adult Case of Fontan-associated Liver Disease with Hepatocellular Carcinoma During the Transition from Pediatric to Internal Medicine Care and Follow-up

In recent years, the outcomes of the Fontan procedure have been good, but Fontan-associated liver disease (FALD), which causes congestive hepatopathy due to elevated central venous pressure (CVP), has become a serious problem when considering patients' long-term prognosis. A 28-year-old woman with Emanuel syndrome was admitted to our hospital for the treatment of hepatocellular carcinoma (HCC). She was diagnosed with pulmonary atresia and underwent a bidirectional pulmonary artery shunt at the age of 1 year and 10 months and the Fontan procedure at 4 years of age. Blood tests showed an increase in γ-glutamyltransferase in her early 20s and a marked increase in alfa-fetoprotein levels at age 27 years. She was diagnosed as having HCC in the S7 region by contrast-enhanced computed tomography and underwent hepatectomy. There were no serious adverse events, and the patient has survived 18 months after surgery without recurrence. In this report, the optimal time for the transition from the pediatrics department to adult healthcare units is also discussed, along with the management system for FALD in our hospital.

The 22q11.2 Low Copy Repeats

LCR22s are among the most complex loci in the human genome and are susceptible to nonallelic homologous recombination. This can lead to a variety of genomic disorders, including deletions, duplications, and translocations, of which the 22q11.2 deletion syndrome is the most common in humans. Interrogating these phenomena is difficult due to the high complexity of the LCR22s and the inaccurate representation of the LCRs across different reference genomes. Optical mapping techniques, which provide long-range chromosomal maps, could be used to unravel the complex duplicon structure. These techniques have already uncovered the hypervariability of the LCR22-A haplotype in the human population. Although optical LCR22 mapping is a major step forward, long-read sequencing approaches will be essential to reach nucleotide resolution of the LCR22s and map the crossover sites. Accurate maps and sequences are needed to pinpoint potential predisposing alleles and, most importantly, allow for genotype-phenotype studies exploring the role of the LCR22s in health and disease. In addition, this research might provide a paradigm for the study of other rare genomic disorders.

Approaches to long-read sequencing in a clinical setting to improve diagnostic rate

Over the past decade, advances in genetic testing, particularly the advent of next-generation sequencing, have led to a paradigm shift in the diagnosis of molecular diseases and disorders. Despite our present collective ability to interrogate more than 90% of the human genome, portions of the genome have eluded us, resulting in stagnation of diagnostic yield with existing methodologies. Here we show how application of a new technology, long-read sequencing, has the potential to improve molecular diagnostic rates. Whole genome sequencing by long reads was able to cover 98% of next-generation sequencing dead zones, which are areas of the genome that are not interpretable by conventional industry-standard short-read sequencing. Through the ability of long-read sequencing to unambiguously call variants in these regions, we discovered an immunodeficiency due to a variant in IKBKG in a subject who had previously received a negative genome sequencing result. Additionally, we demonstrate the ability of long-read sequencing to detect small variants on par with short-read sequencing, its superior performance in identifying structural variants, and thirdly, its capacity to determine genomic methylation defects in native DNA. Though the latter technical abilities have been demonstrated, we demonstrate the clinical application of this technology to successfully identify multiple types of variants using a single test.

Prenatal diagnosis of Emanuel syndrome - case series and review of the literature

We present three new cases and review of the literature on the prenatal diagnosis of Emanuel syndrome (ES). Twenty-one foetuses have been analysed. In all three cases diagnosed in our department, posterior fossa abnormalities were seen and in one hypoplastic right ventricle was diagnosed at the first trimester scan. Defects of the posterior fossa (62% of foetuses; 13/21) and left diaphragmatic hernia (29% of foetuses; 6/21) are the most frequently reported prenatal findings in ES syndrome. No pattern of specific prenatal ultrasound markers of ES exists. Abnormalities of the posterior fossa are frequent and may be diagnosed as early as in the first trimester of pregnancy. Specific diagnosis can be made only after invasive genetic testing.IMPACT STATEMENTWhat is already known on this subject? Emanuel syndrome (ES) is a rare genetic disorder. No pattern of specific prenatal ultrasound markers exists. The great majority of cases is diagnosed postnatally and only a few cases of prenatal diagnosis have been published to date.What do the results of this study add? The most frequent structural abnormalities in prenatally detected ES involved central nervous system (80.9%), namely posterior fossa defects (57.1%) and mild ventriculomegaly (23.8%). Other frequent abnormalities include left diaphragmatic hernia (28.6%), renal defects (23.8%) and foetal growth restriction (FGR) (23.8%).What are the implications of these findings for clinical practice and/or further research? Abnormalities of the posterior fossa are the most frequent defects in ES and may be diagnosed as early as in the first trimester of pregnancy. Specific diagnosis can be made only after invasive genetic testing.

A Novel Non-Allelic Homologous Recombination Event in a Parent with an 11;22 Reciprocal Translocation Leading to 22q11.2 Deletion Syndrome

The most prevalent microdeletion in the human population occurs at 22q11.2, a region rich in chromosome-specific low copy repeats (LCR22s). The structure of this region has eluded characterization due to a combination of size, regional complexity, and haplotype diversity. To further complicate matters, it is not well represented in the human reference genome. Most individuals with 22q11.2 deletion syndrome (22q11.2DS) carry a de novo, hemizygous deletion approximately 3 Mbp in size occurring by non-allelic homologous recombination (NAHR) mediated by the LCR22s. The ability to fully delineate an individual’s 22q11.2 regional structure will likely be important for studies designed to assess an unaffected individual’s risk for generating rearrangements in germ cells, potentially leading to offspring with 22q11.2DS. Towards understanding these risk factors, optical mapping has been previously employed to successfully elucidate the structure and variation of LCR22s across 30 families affected by 22q11.2DS. The father in one of these families carries a t(11;22)(q23;q11) translocation. Surprisingly, it was determined that he is the parent-of-deletion-origin. NAHR, which occurred between his der(22) and intact chromosome 22, led to a 22q11.2 deletion in his affected child. The unaffected sibling of the proband with 22q11.2DS inherited the father’s normal chromosome 22, which did not aberrantly recombine. This unexpected observation definitively shows that haplotypes that engage in NAHR can also be inherited intact. This study is the first to identify all structures involving a rearranged chromosome 22 that also participates in NAHR leading to a 22q11.2 deletion.

Emanuel syndrome and congenital diaphragmatic hernia: A systematic review

BACKGROUND

Emanuel Syndrome (ES), a rare chromosomal disorder caused by a supernumerary chromosome 22 derivative (der(22)t(11;22)), was identified in a fetus with congenital diaphragmatic hernia (CDH) at our fetal center. We aimed to identify a precedent for clinical care and patient outcomes to guide family decision-making.

METHODS

This non-funded and non-registered study queried the entire CDH Registry (CDHR) including >10,000 patients since 1995 and conducted a systematic literature review for patients with concomitant ES and CDH.

RESULTS

Literature review captured 12 citations and identified 9 patients with CDH+ES from over 400 known ES cases. Given the rarity of the disease and to reduce bias, there were no exclusion criteria aside from non-English language. Of these 9, two underwent surgical CDH repair with neither surviving. The CDHR identified 6 patients with ES, all reported after 2013 and prenatally diagnosed. Median estimated gestational age was 39 weeks (range 37-40) and median birth weight was 2.72 kg (range 2.4-3.4 kg). 3 patients died within the first few postnatal days; surgical repair was not offered due to "anomalies" and "pulmonary hypertension" in two and one family chose comfort measures. The other 3 patients underwent surgical repair, and 2 were supported with ECMO. Two patients survived to discharge, incurring surgical comorbidities associated with severe CDH including gastrostomy dependence, tracheostomy, and CDH recurrence.

CONCLUSIONS

ES patients with CDH have potential to tolerate repair and survive to discharge, however with significant additional morbidity combined with severe challenges inherent to ES. This represents the largest series of patients with CDH and ES to date.

LEVEL OF EVIDENCE

IV (Case series with no comparison group).

Patients with Chromosome 11q Deletions Are Characterized by Inborn Errors of Immunity Involving both B and T Lymphocytes

Disorders of the long arm of chromosome 11 (11q) are rare and involve various chromosomal regions. Patients with 11q disorders, including Jacobsen syndrome, often present with a susceptibility for bacterial and prolonged viral and fungal infections partially explained by hypogammaglobulinemia. Additional T lymphocyte or granular neutrophil dysfunction may also be present. In order to evaluate infectious burden and immunological function in patients with 11q disorders, we studied a cohort of 14 patients with 11q deletions and duplications. Clinically, 12 patients exhibited prolonged and repetitive respiratory tract infections, frequently requiring (prophylactic) antibiotic treatment (n = 7), ear-tube placement (n = 9), or use of inhalers (n = 5). Complicated varicella infections (n = 5), chronic eczema (n = 6), warts (n = 2), and chronic fungal infections (n = 4) were reported. Six patients were on immunoglobulin replacement therapy. We observed a high prevalence of low B lymphocyte counts (n = 8), decreased T lymphocyte counts (n = 5) and abnormal T lymphocyte function (n = 12). Granulocyte function was abnormal in 29% without a clinical phenotype. Immunodeficiency was found in patients with terminal and interstitial 11q deletions and in one patient with terminal 11q duplication. Genetically, FLI1 and ETS1 are seen as causative for the immunodeficiency, but these genes were deleted nor duplicated in 4 of our 14 patients. Alternative candidate genes on 11q may have a role in immune dysregulation. In conclusion, we present evidence that inborn errors of immunity are present in patients with 11q disorders leading to clinically relevant infections. Therefore, broad immunological screening and necessary treatment is of importance in this patient group.

Supernumerary derivative 22 chromosome resulting from novel constitutional non-Robertsonian translocation: t(20;22)-Case Report

Background

Maternal non-Robertsonian translocation-t(20;22)(q13;q11.2) between chromosomes 20 and 22resulting in an additional complex small supernumerary marker chromosome as derivative (22)inherited to the proband is not been reported yet.

Case presentation

A 4 years old boy with a history of developmental delay, low set ears, and facial dysmorphism was presented to the genetic clinic. Periauricular pit, downward slanting eyes, medially flared eyebrows, downturned mouth corners, and micrognathia were observed. He had congenital heart defect with atrial septal defect (ASD), ventricular septal defect (VSD), and central nervous system (CNS) anomalies with the gross cranium. Karyotype analysis, Fluorescent in-situ hybridization analysis (FISH), and Chromosomal microarray analysis (CMA) were used to determine the chromosomal origin and segmental composition of the derivative 22 chromosome. Karyotype and FISH analyses were performed to confirm the presence of a supernumerary chromosome, and Microarray analysis was performed to rule out copy number variations in the proband's 22q11.2q12 band point. The probands' karyotype revealed the inherited der(22)t(20;22)(q13;q11.2)dmat. Parental karyotype confirmed the mother as the carrier, with balanced non-Robertsonian translocation-46,XX,t(20;22)(q13;q11.2).

Conclusion

The mother had a non-Robertsonian translocation t(20;22)(q13;q11.2) between chromosomes 20 and 22, which resulted in Emanuel syndrome in the proband. The most plausible explanation is 3:1 meiotic malsegregation, which results in the child inheriting derivative chromosome. The parental karyotype study aided in identifying the carrier of the supernumerary der(22), allowing future pregnancies with abnormal offspring to be avoided.

Prenatal Diagnosis of Fetuses with Emanuel Syndrome: Results of Ultrasound Examination and Invasive Genetic Testing

OBJECTIVE

To investigate prenatal manifestations of Emanuel syndrome (ES) by retrospectively analyzing the results of prenatal diagnosis.

METHODS

Thirteen fetuses were collected from 5 hospitals, of which six were confirmed with 47,der(22)t(11;22) (ES) by karyotype and chromosomal microarray analysis (CMA). Seven were diagnosed with 46,t(11;22) balanced translocations by karyotype, including one de novo mosaic 46,XX,t(11;22). In 3/7, CMA was performed but did not identify chromosomal imbalances. The results of prenatal diagnoses were reviewed, including ultrasound examinations and genetic testing.

RESULTS

In ES fetuses, the derivative 22 was consistently inherited from the mother, while in the balanced translocation group, the t(11;22) chromosome was of paternal origin in 3/6 cases, All ES fetuses presented with multiple abnormalities by ultrasound examinations. Diaphragm hernia (3/6), Dandy-Walker complex (3/6), and kidney aplasia (3/6), were the most common ultrasound findings. Sonographic soft markers such as increased nuchal translucency, increased nuchal fold thickness appeared in 3 cases and all of these were associated with other anomalies. However, none of the ultrasound findings differentiated ES from other genetic syndromes during fetal period.

CONCLUSIONS

In this series, in fetuses with a der(22), the derivative chromosome was consistently of maternal origin. In contrast, 46,t(11;22) balanced translocations were of maternal or paternal origin. The results contribute to the literature regarding the fetal phenotype of ES. Due to the absence of specific features distinguishing ES from other genetic syndromes, confirming the diagnosis through invasive genetic testing is necessary. This article is protected by copyright. All rights reserved.

Opportunities and pitfalls of social media research in rare genetic diseases: a systematic review

PURPOSE

Social media may be particularly valuable in research in rare genetic diseases because of the low numbers of patients and the rare disease community's robust online presence. The goal of this systematic review was to understand how social media is currently used in rare disease research and the characteristics of the participants in these studies.

METHODS

We conducted a systematic review of six databases to identify studies published in English between January 2004 and November 2020, of which 120 met inclusion criteria.

RESULTS

Most studies were observational (n = 114, 95.0%) and cross-sectional (n = 107, 89.2%), and more than half (n = 69, 57.5%) utilized only surveys. Only 101 rare diseases were included across all studies. Participant demographics, when reported, were predominantly female (70.1% ± 22.5%) and white (85.0% ± 11.0%) adult patients and caregivers.

CONCLUSION

Despite its potential benefits in rare disease research, the use of social media is still methodologically limited and the participants reached may not be representative of the rare disease population by gender, race, age, or rare disease type. As scholars explore using social media for rare disease research, careful attention should be paid to representativeness when studying this diverse patient community.

Palindromes in DNA-A Risk for Genome Stability and Implications in Cancer

A palindrome in DNA consists of two closely spaced or adjacent inverted repeats. Certain palindromes have important biological functions as parts of various cis-acting elements and protein binding sites. However, many palindromes are known as fragile sites in the genome, sites prone to chromosome breakage which can lead to various genetic rearrangements or even cell death. The ability of certain palindromes to initiate genetic recombination lies in their ability to form secondary structures in DNA which can cause replication stalling and double-strand breaks. Given their recombinogenic nature, it is not surprising that palindromes in the human genome are involved in genetic rearrangements in cancer cells as well as other known recurrent translocations and deletions associated with certain syndromes in humans. Here, we bring an overview of current understanding and knowledge on molecular mechanisms of palindrome recombinogenicity and discuss possible implications of DNA palindromes in carcinogenesis. Furthermore, we overview the data on known palindromic sequences in the human genome and efforts to estimate their number and distribution, as well as underlying mechanisms of genetic rearrangements specific palindromic sequences cause.

Optical Genome Mapping as a Next-Generation Cytogenomic Tool for Detection of Structural and Copy Number Variations for Prenatal Genomic Analyses

Global medical associations (ACOG, ISUOG, ACMG) recommend diagnostic prenatal testing for the detection and prevention of genetic disorders. Historically, cytogenetic methods such as karyotype analysis, fluorescent in situ hybridization (FISH) and chromosomal microarray (CMA) are utilized worldwide to diagnose common syndromes. However, the limitations of each of these methods, either performed in tandem or simultaneously, demonstrates the need of a revolutionary technology that can alleviate the need for multiple technologies. Optical genome mapping (OGM) is a novel method that fills this void by being able to detect all classes of structural variations (SVs), including copy number variations (CNVs). OGM is being adopted by laboratories as a tool for both postnatal constitutional genetic disorders and hematological malignancies. This commentary highlights the potential for OGM to become a standard of care in prenatal genetic testing based on its capability to comprehensively identify large balanced and unbalanced SVs (currently the strength of karyotyping and metaphase FISH), CNVs (by CMA), repeat contraction disorders (by Southern blotting) and multiple repeat expansion disorders (by PCR-based methods or Southern blotting). Next-generation sequencing (NGS) methods are excellent at detecting sequence variants, but they are unable to accurately resolve repeat regions of the genome, which limits their ability to detect all classes of SVs. Notably, multiple molecular methods are used to identify repeat expansion and contraction disorders in routine clinical laboratories around the world. With non-invasive prenatal testing (NIPT) becoming the standard of care screening assay for all global pregnancies, we anticipate that OGM can provide a high-resolution, cytogenomic assay to be employed following a positive NIPT screen or for high-risk pregnancies with an abnormal ultrasound. Accurate detection of all types of genetic disorders by OGM, such as liveborn aneuploidies, sex chromosome anomalies, microdeletion/microduplication syndromes, repeat expansion/contraction disorders is key to reducing the global burden of genetic disorders.

Alternative DNA Structures In Vivo: Molecular Evidence and Remaining Questions

Duplex DNA naturally folds into a right-handed double helix in physiological conditions. Some sequences of unusual base composition may nevertheless form alternative structures, as was shown for many repeated sequences in vitro However, evidence for the formation of noncanonical structures in living cells is difficult to gather. It mainly relies on genetic assays demonstrating their function in vivo or through genetic instability reflecting particular properties of such structures. Efforts were made to reveal their existence directly in a living cell, mainly by generating antibodies specific to secondary structures or using chemical ligands selected for their affinity to these structures. Among secondary structure-forming DNAs are G-quadruplexes, human fragile sites containing minisatellites, AT-rich regions, inverted repeats able to form cruciform structures, hairpin-forming CAG/CTG triplet repeats, and triple helices formed by homopurine-homopyrimidine GAA/TTC trinucleotide repeats. Many of these alternative structures are involved in human pathologies, such as neurological or developmental disorders, as in the case of trinucleotide repeats, or cancers triggered by translocations linked to fragile sites. This review will discuss and highlight evidence supporting the formation of alternative DNA structures in vivo and will emphasize the role of the mismatch repair machinery in binding mispaired DNA duplexes, triggering genetic instability.

Double strand breaks (DSBs) as indicators of genomic instability in PATRR-mediated translocations

Genomic instability contributes to a variety of potentially damaging conditions, including DNA-based rearrangements. Breakage in the form of double strand breaks (DSBs) increases the likelihood of DNA damage, mutations and translocations. Certain human DNA regions are known to be involved in recurrent translocations, such as the palindrome-mediated rearrangements that have been identified at the breakpoints of several recurrent constitutional translocations: t(11;22)(q23;q11), t(17;22)(q11;q11) and t(8;22) (q24;q11). These breakpoints occur at the center of palindromic AT-rich repeats (PATRRs), which suggests that the structure of the DNA may play a contributory role, potentially through the formation of secondary cruciform structures. The current study analyzed the DSB propensity of these PATRR regions in both lymphoblastoid (mitotic) and spermatogenic cells (meiotic). Initial results found an increased association of sister chromatid exchanges (SCEs) at PATRR regions in experiments that used SCEs to assay DSBs, combining SCE staining with fluorescence in situ hybridization (FISH). Additional experiments used chromatin immunoprecipitation (ChIP) with antibodies for either markers of DSBs or proteins involved in DSB repair along with quantitative polymerase chain reaction to quantify the frequency of DSBs occurring at PATRR regions. The results indicate an increased rate of DSBs at PATRR regions. Additional ChIP experiments with the cruciform binding 2D3 antibody indicate an increased rate of cruciform structures at PATRR regions in both mitotic and meiotic samples. Overall, these experiments demonstrate an elevated rate of DSBs at PATRR regions, an indication that the structure of PATRR containing DNA may lead to increased breakage in multiple cellular environments.

Genetics and signaling mechanisms of orofacial clefts

Craniofacial development involves several complex tissue movements including several fusion processes to form the frontonasal and maxillary structures, including the upper lip and palate. Each of these movements are controlled by many different factors that are tightly regulated by several integral morphogenetic signaling pathways. Subject to both genetic and environmental influences, interruption at nearly any stage can disrupt lip, nasal, or palate fusion and result in a cleft. Here, we discuss many of the genetic risk factors that may contribute to the presentation of orofacial clefts in patients, and several of the key signaling pathways and underlying cellular mechanisms that control lip and palate formation, as identified primarily through investigating equivalent processes in animal models, are examined.

Integration and reanalysis of transcriptomics and methylomics data derived from blood and testis tissue of men with 47,XXY Klinefelter syndrome indicates the primary involvement of Sertoli cells in the testicular pathogenesis

Klinefelter syndrome (KS; 47,XXY) is the most common sex chromosomal anomaly and causes a multitude of symptoms. Often the most noticeable symptom is infertility caused by azoospermia with testicular histology showing hyalinization of tubules, germ cells loss, and Leydig cell hyperplasia. The germ cell loss begins early in life leading to partial hyalinization of the testis at puberty, but the mechanistic drivers behind this remain poorly understood. In this systematic review, we summarize the current knowledge on developmental changes in the cellularity of KS gonads supplemented by a comparative analysis of the fetal and adult gonadal transcriptome, and blood transcriptome and methylome of men with KS. We identified a high fraction of upregulated genes that escape X-chromosome inactivation, thus supporting previous hypotheses that these are the main drivers of the testicular phenotype in KS. Enrichment analysis showed overrepresentation of genes from the X- and Y-chromosome and testicular transcription factors. Furthermore, by re-evaluation of recent single cell RNA-sequencing data originating from adult KS testis, we found novel evidence that the Sertoli cell is the most affected cell type. Our results are consistent with disturbed cross-talk between somatic and germ cells in the KS testis, and with X-escapee genes acting as mediators.

Non-invasive prenatal screening for Emanuel syndrome

Objective

The aim of this study was to validate the results of two Emanuel syndromes detected by non-invasive prenatal screening (NIPS) screening using invasive methods, providing clinical performance of NIPS on chromosome microduplication detection.

Methods

NIPS was performed to diagnose the Emanuel syndrome. Amniocentesis or cordocentesis was performed to confirm the positive screening result of Emanuel syndrome cases. Fetal sample was detected by karyotyping, fluorescence in situ hybridization (FISH), and single nucleotide polymorphism array (SNP Array). Parental karyotyping and FISH were also carried out.

Results

Two cases with chromosomal abnormalities of 11q23.3q25 and 22q11.1q11.21 were found by NIPS. Chromosomal karyotyping showed that the two fetuses each have a small supernumerary marker chromosome (sSMC), SNP Array further demonstrated double duplications approximately 18 Mb in 11q23.3q25 and 3 Mb in 22q11.1q11.21. FISH confirmed that the small supernumerary marker chromosome (sSMC) was ish der(22)t(11;22) (TUPLE1+, ARSA-). Ultrasound scan and MRI showed some structure malformations in two fetuses. The two mothers were found to be a balanced carrier: 46,XX, t(11;22)(q23.3;q11.2).

Conclusion

NIPS could effectively identify Emanuel syndrome, which may indicate risks of a parent being a balanced rearrangement carrier. The followed confirmation test for positive sample is necessary and ensures the accuracy of the diagnosis.

Neuroimaging findings in Emanuel Syndrome

Emanuel syndrome is a rare inherited chromosomal abnormality caused by an unbalanced translocation of chromosomes 11 and 22. Clinically, Emanuel syndrome is characterized by a wide spectrum of congenital anomalies, dysmorphisms, and developmental disability often confused with other similar syndromes. Outside of genetic testing, diagnosis remains challenging and current literature on typical radiologic findings is limited. We present classic neuroimaging findings of Emanuel syndrome consistent with prior literature including microcephaly, microretrognathia, external auditory canal stenosis, and cleft palate; and also introduce the additional maxillofacial anomaly of dysplastic middle ear ossicles, to our knowledge not previously described in the literature. Recognition of findings leading to earlier diagnosis of Emanuel syndrome may improve outcomes and quality of life for patients and their families.

Oral and dental findings in emanuel syndrome

Emanuel Syndrome (ES; OMIM# 609029) is a rare disorder caused by an unbalanced chromosomal translocation [supernumerary der(22)t(11,22)] and characterized by multiple congenital abnormalities. With limited published cases and low prevalence (1:110 000), detailed ES-associated oro-dental findings have not previously been reported. This is a case report of a 14-year-old boy with ES who presented with congenital cardiac, renal, auditory, musculoskeletal problems, and global developmental delay. The patient was managed with risperidone, melatonin, omeprazole, guanfacine, and oxcarbazepine. Anxiety-associated self-injurious behaviour was seen along with stereotypic hand movements. Consistent with previous reports, microcephaly and micrognathia were noted. Oro-facial cleft or gross asymmetry, however, was not observed. Significant oro-dental findings included delayed eruption of primary and permanent teeth, oligodontia (two erupted and five unerupted permanent teeth), and short-root anomaly of central incisors. The patient demonstrated anxiety-triggered bruxism with generalized attrition. This case report provides a comprehensive list of systemic ES findings along with oro-dental manifestations, which have previously not been reported in detail.

The Recurrent t(11;22)(q23;q11.2) Can Occur as a Post-Zygotic Event

The AT-rich repeat on chromosome 22q11.2 is known to be involved in the recurrent constitutional t(11;22)(q23;q11.2). Segregation of this translocation has been reported in several hundred families, but a de novo translocation event has been identified in only 8 cases, and everytime the translocation originated in paternal germ-line chromosomes. Further, de novo t(11;22) rearrangements have been detected in the sperm of healthy males, leading to the hypothesis that it occurs somewhere along the meiosis-spermatogenesis pathway. This report describes a woman whose constitutional karyotype revealed mosaicism for the recurrent t(11;22) and the subsequent testing performed to determine the origin of the translocation event. Karyotype analysis, translocation-specific PCR, human identity testing, and a SNP genotyping array were performed to detect mosaicism and/or chimerism. As a result, the SNP genotyping array revealed no evidence for mosaicism in genomic DNA beyond mosaicism for the balanced t(11;22). Human identity testing and the SNP genotyping array ruled out chimerism. PCR of the translocation breakpoint followed by sequencing confirmed that the translocation had occurred at the typical t(11;22) breakpoints. In conclusion, these results indicate that the translocation occurred post-fertilization, providing the first evidence of a de novo t(11;22)(q23;q11.2) occurring in a maternal mitotic environment.

Chromosomal Abnormalities in Syndromic Orofacial Clefts: Report of Three Children

This case series of three children reports clinical features and chromosomal abnormalities seen in a craniofacial clinic. All presented with orofacial cleft, developmental or intellectual disability, and dysmorphism. Emanuel syndrome or supernumerary der (22)t(11; 22), the prototype of complex small supernumerary marker disorders, was seen in one child. Duplication 4q27q35.2 with concomitant deletion 21q22.2q22.3 and duplication 12p13.33p13.32 with concomitant deletion 18q22.3q23 seen in the remaining two children are not reported in literature. Maternal balanced translocation was established in both of these children.

Ocular manifestations of Emanuel syndrome

Emanuel syndrome is caused by a supernumerary der(22)t(11;22) and typically manifests with intellectual disability and craniofacial dysmorphism. Ocular abnormalities have infrequently been described. We report a 36-year-old man with severe intellectual disability, aphasia, and facial dysmorphism, with high myopia and juvenile open angle glaucoma (JOAG). Microarray analysis results included 47,XY,+der(22)t(11;22)(q23;q11.2), and a 269 kb deletion of 7q31.33(125,898,014-126,166,829). Two candidate genes were identified as possible etiologies for the ocular pathologies in our patient: a MFRP duplication on chromosome 11, which may play a role in high myopia and dysregulation of emmetropization, and a GRM8 deletion on chromosome 7, which may cause glutamate-induced excitotoxicity and therefore have a role in the development of JOAG, unrelated to the Emanuel syndrome genotype. We provide the first detailed description these ocular abnormalities in a patient with Emmanuel syndrome.

Phenotypic characterization of derivative 22 syndrome: case series and review

Emanuel syndrome is caused due to an additional derivative chromosome 22 and is characterized by severe intellectual disability, microcephaly, failure to thrive, preauricular tags or pits, ear anomalies, cleft or high-arched palate, micrognathia, kidney abnormalities, congenital heart defects and genital abnormalities in males. In 99% of the cases, one of the parents is a carrier of balanced translocation between chromosomes 11 and 22. It occurs due to malsegregation of the gametes with 3:1 segregation. In this case series, we describe four patients with diverse manifestations of this condition. The craniosynostosis observed in one case is a novel finding which has never been reported previously. This study aims to widen the phenotypic spectrum of Emanuel syndrome and provide cytogenetic microarray based breakpoints in two of the cases, thus supporting close clustering of the breakpoints of this common recurrent chromosomal rearrangement.

A clinical and molecular analysis of a patient with Emanuel syndrome

Emanuel syndrome (ES) is the most frequent type of recurrent non‑Robertsonian translocation that is characterized by numerous anomalies. Over 100 patients with ES have been described in the literature. The phenotype of this syndrome varies but often consists of facial dysmorphism, microcephaly, severe intellectual disability, developmental retardation, congenital heart disease and genital anomalies. The present study describes a 2‑year‑old boy with multiple malformations, including facial dysmorphism, severe intellectual disability, growth retardation, congenital heart disease, cleft lip and palate, genital malformation (micropenis), amblyopia, thymic dysplasia and hearing impairment. The karyotype of the patient was 47,XY,+del(22)(q13), and the maternal karyotype was 46,XX,t(11;22)(q25;q13),9qh‑,15p+. Single‑nucleotide polymorphism‑array analysis of the proband indicated a partial duplication of chromosomes 22 and 11 at 22q11.1‑q11.21 and 11q23.3‑q25, respectively, which confirmed the diagnosis of ES. To date, no cases of ES have been reported in mainland China. The present case further emphasizes the necessity and importance of high‑resolution techniques for genetic diagnosis and for subsequent genetic counseling. The present study contributed to the phenotypic delineation of ES and confirmed the first ES patient in mainland China.

Palindrome-Mediated Translocations in Humans: A New Mechanistic Model for Gross Chromosomal Rearrangements

Palindromic DNA sequences, which can form secondary structures, are widely distributed in the human genome. Although the nature of the secondary structure-single-stranded "hairpin" or double-stranded "cruciform"-has been extensively investigated in vitro, the existence of such unusual non-B DNA in vivo remains controversial. Here, we review palindrome-mediated gross chromosomal rearrangements possibly induced by non-B DNA in humans. Recent advances in next-generation sequencing have not yet overcome the difficulty of palindromic sequence analysis. However, a dozen palindromic AT-rich repeat (PATRR) sequences have been identified at the breakpoints of recurrent or non-recurrent chromosomal translocations in humans. The breakages always occur at the center of the palindrome. Analyses of polymorphisms within the palindromes indicate that the symmetry and length of the palindrome affect the frequency of the de novo occurrence of these palindrome-mediated translocations, suggesting the involvement of non-B DNA. Indeed, experiments using a plasmid-based model system showed that the formation of non-B DNA is likely the key to palindrome-mediated genomic rearrangements. Some evidence implies a new mechanism that cruciform DNAs may come close together first in nucleus and illegitimately joined. Analysis of PATRR-mediated translocations in humans will provide further understanding of gross chromosomal rearrangements in many organisms.

Increased Dosage of High-Affinity Kainate Receptor Gene grik4 Alters Synaptic Transmission and Reproduces Autism Spectrum Disorders Features

The understanding of brain diseases requires the identification of the molecular, synaptic, and cellular disruptions underpinning the behavioral features that define the disease. The importance of genes related to synaptic function in brain disease has been implied in studies describing de novo germline mutations and copy number variants. Indeed, de novo copy number variations (deletion or duplication of a chromosomal region) of synaptic genes have been recently implicated as risk factors for mental retardation or autism. Among these genes is GRIK4, a gene coding for a glutamate receptor subunit of the kainate type. Here we show that mice overexpressing grik4 in the forebrain displayed social impairment, enhanced anxiety, and depressive states, accompanied by altered synaptic transmission, showing more efficient information transfer through the hippocampal trisynaptic circuit. Together, these data indicate that a single gene variation in the glutamatergic system results in behavioral symptomatology consistent with autism spectrum disorders as well as in alterations in synaptic function in regions involved in social activity. Autistic features of these mice represent powerful tools for improving diagnosis and testing of specific treatments targeting abnormalities in glutamatergic signaling related to autism spectrum disorders.

SIGNIFICANCE STATEMENT

A genetic overlap exists between autism spectrum disorders (ASD), currently thought to represent a continuum of the same disorder with varying degrees of severity, and other neurodevelopmental and neuropsychiatric endophenotypes. We show that the duplication of a single gene coding for a high-affinity kainate receptor subunit (i.e., grik4) in a limited area of the brain recapitulates behavioral endophenotypes seen in humans diagnosed with autism (anhedonia, depression, anxiety, and altered social interaction), including some humans with GRIK4 duplications. Therefore, it should be possible to use mice overexpressing grik4 to directly address circuit dysfunctions associated with ASDs and test specific treatments of autism-related behaviors.

Anesthetic Management of a Patient With Emanuel Syndrome

Emanuel syndrome is associated with supernumerary chromosome, which consists of the extra genetic material from chromosome 11 and 22. The frequency of this syndrome has been reported as 1 in 110,000. It is a rare anomaly associated with multiple systemic malformations such as micrognathia and congenital heart disease. In addition, patients with Emanuel syndrome may have seizure disorders. We experienced anesthetic management of a patient with Emanuel syndrome who underwent palatoplasty. This patient had received tracheotomy due to micrognathia. In addition, he had atrial septal defect, mild pulmonary artery stenosis, and cleft palate. Palatoplasty was performed without any complication during anesthesia. Close attention was directed to cardiac function, seizure, and airway management.

A case with Emanuel syndrome: extra derivative 22 chromosome inherited from the mother

Emanuel syndrome (ES) is a rare chromosomal disorder that is characterized by multiple congenital anomalies and developmental disabilities. Affected children are usually identified in the newborn period as the offspring of balanced (11;22) translocation carriers. Carriers of this balanced translocation usually have no clinical symptoms and are often identified after the birth of offspring with an unbalanced form of the translocation, the supernumerary der(22) t(11;22) syndrome. We report a 3-year-old boy with the t(11;22)(q23;q11) chromosome, transmitted in an unbalanced fashion from his mother. He has several developmental delays; he is not independently ambulatory and language is significantly impaired. Using his peripheral blood, karyotyping was performed to define his multiple congenital anomalies, revealing the following chromosomal abnormality: 47, XY, +der(22)t(11;22)(q23.3;q11.2). To ascertain the origin and trait of this supernumerary marker chromosome [der(22)t(11;22)(q23.3;q11.2)], karyotyping of his parents was performed. The mother was found to be a balanced carrier: 46, XX, t(11;22) (q23.3; q11.2).

Small supernumerary marker chromosomes and their correlation with specific syndromes

A small supernumerary marker chromosome (sSMC) is a structurally abnormal chromosome. It is an additional chromosome smaller than one chromosome most often lacking a distinct banding pattern and is rarely identifiable by conventional banding cytogenetic analysis. The origin and composition of an sSMC is recognizable by molecular cytogenetic analysis. These sSMCs are seen in different shapes, including the ring, centric minute, and inverted duplication shapes. The effects of sSMCs on the phenotype depend on factors such as size, genetic content, and the level of the mosaicism. The presence of an sSMC causes partial tris- or tetrasomy, and 70% of the sSMC carriers are clinically normal, while 30% are abnormal in some way. In 70% of the cases the sSMC is de novo, in 20% it is inherited from the mother, and in 10% it is inherited from the father. An sSMC can be causative for specific syndromes such as Emanuel, Pallister-Killian, or cat eye syndromes. There may be more specific sSMC-related syndromes, which may be identified by further investigation. These 10 syndromes can be useful for genetic counseling after further study.

Partial trisomy of 11q23.3-q25 inherited from a maternal low-level mosaic unbalanced translocation

Partial trisomy of 11q is characterized by pre/postnatal growth retardation, microcephaly, dysmorphic craniofacial features, cognitive disability, abnormal muscle tone, inguinal hernia, and possible congenital heart defects. Here, we describe a 17-year-old male with a 17.77 Mb-sized [arr 11q23.3-q25 (116,667,559 -134,434,130) ×3] partial trisomy resulting from the unbalanced translocation between chromosomes 11 and 22. The terminal translocation was detected using oligonucleotide array comparative genomic hybridization (CGH) with fluorescence in situ hybridization (FISH) confirmation. The partial trisomy was inherited from his mother who had the low-level (22.7%) mosaic unbalanced translocation and a normal phenotype. The patient showed most of the common features of partial trisomy 11q syndrome, with additional findings, including mesenteric fibromatosis.

Anesthetic management of pediatric patients with Emanuel syndrome

Emanuel syndrome is a rare anomaly associated with multiple systemic malformations. We present two cases involving pediatric patients with Emanuel syndrome. The first patient presented with micrognathia and had patent ductus arteriosus and a single kidney. The patient was difficult to intubate with McGRATH(®) but was successfully intubated with an Airtraq(®) device. The second patient did not present with micrognathia and was not difficult to intubate. A thorough examination of the heart, kidney, and spinal cord is important when planning the anesthetic management of patients with Emanuel syndrome. Moreover, adequate preparation for a difficult airway is essential, and the Airtraq(®) device may be useful for intubating patients with Emanuel syndrome with micrognathia.

Breakpoint analysis of the recurrent constitutional t(8;22)(q24.13;q11.21) translocation

Backgrounds

The t(8;22)(q24.13;q11.2) has been identified as one of several recurrent constitutional translocations mediated by palindromic AT-rich repeats (PATRRs). Although the breakage on 22q11 utilizes the same PATRR as that of the more prevalent constitutional t(11;22)(q23;q11.2), the breakpoint region on 8q24 has not been elucidated in detail since the analysis of palindromic sequence is technically challenging.

Results

In this study, the entire 8q24 breakpoint region has been resolved by next generation sequencing. Eight polymorphic alleles were identified and compared with the junction sequences of previous and two recently identified t(8;22) cases . All of the breakpoints were found to be within the PATRRs on chromosomes 8 and 22 (PATRR8 and PATRR22), but the locations were different among cases at the level of nucleotide resolution. The translocations were always found to arise on symmetric PATRR8 alleles with breakpoints at the center of symmetry. The translocation junction is often accompanied by symmetric deletions at the center of both PATRRs. Rejoining occurs with minimal homology between the translocation partners. Remarkably, comparison of der (8) to der(22) sequences shows identical breakpoint junctions between them, which likely represent products of two independent events on the basis of a classical model.

Conclusions

Our data suggest the hypothesis that interactions between the two PATRRs prior to the translocation event might trigger illegitimate recombination resulting in the recurrent palindrome-mediated translocation.

Prevalence of Emanuel syndrome: theoretical frequency and surveillance result

Constitutional t(11;22)(q23;q11) is the most frequent recurrent non-Robertsonian translocation in humans. Balanced carriers of t(11;22) usually manifest no clinical symptoms, and are often identified after the birth of offspring with an unbalanced form of this translocation, known as Emanuel syndrome. To determine the prevalence of the disorder, we sent surveillance questionnaires to 735 core hospitals in Japan. The observed number of Emanuel syndrome cases was 36 and that of t(11;22) balanced translocation carriers, 40. On the basis of the de novo t(11;22) translocation frequency in sperm from healthy men, we calculated the frequency of the translocations in the general population. Accordingly, the prevalence of Emanuel syndrome was estimated at 1 in 110,000. Based on this calculation, the estimated number of Emanuel syndrome cases in Japan is 1063 and of t(11;22) balanced translocation carriers, 16,604, which are much higher than the numbers calculated from the questionnaire responses. It is possible that this discordance is partly attributable to a lack of disease identification. Further efforts should be made to increase the awareness of Emanuel syndrome to ensure a better quality of life for affected patients and their families.

Screening for intellectual disability using high-resolution CMA technology in a retrospective cohort from Central Brazil

Intellectual disability is a complex, variable, and heterogeneous disorder, representing a disabling condition diagnosed worldwide, and the etiologies are multiple and highly heterogeneous. Microscopic chromosomal abnormalities and well-characterized genetic conditions are the most common causes of intellectual disability. Chromosomal Microarray Analysis analyses have made it possible to identify putatively pathogenic copy number variation that could explain the molecular etiology of intellectual disability. The aim of the current study was to identify possible submicroscopic genomic alterations using a high-density chromosomal microarray in a retrospective cohort of patients with otherwise undiagnosable intellectual disabilities referred by doctors from the public health system in Central Brazil. The CytoScan HD technology was used to detect changes in the genome copy number variation of patients who had intellectual disability and a normal karyotype. The analysis detected 18 CNVs in 60% of patients. Pathogenic CNVs represented about 22%, so it was possible to propose the etiology of intellectual disability for these patients. Likely pathogenic and unknown clinical significance CNVs represented 28% and 50%, respectively. Inherited and de novo CNVs were equally distributed. We report the nature of CNVs in patients from Central Brazil, representing a population not yet screened by microarray technologies.

A de novo atypical ring sSMC(22) characterized by array CGH in a boy with cat-eye syndrome

BACKGROUND

Microduplications 22q11 have been characterized as a genomic duplication syndrome mediated by nonallelic homologous recombination between region-specific low-copy repeats. Here we report on a 19 years old boy with intellectual disability having an unexpected structurally complex ring small supernumerary marker chromosome (sSMC) originated from a larger trisomy and a smaller tetrasomy of proximal 22q11 harboring additional copies of cat eye syndrome critical regions genes.

RESULTS

PRINCIPAL CLINICAL FEATURES WERE: anorectal and urogenital malformations, total anomalous pulmonary venous return with secundum ASD, hearing defect, preauricular pits, seizure and eczema. The proband also presented some rare or so far not reported clinical findings such as hyperinsulinaemia, severe immunodeficiency and grave cognitive deficits. Chromosome analysis revealed a mosaic karyotype with the presence of a small ring-like marker in 60% of cells. Array CGH detected approximately an 1,2 Mb single and a 0,2 Mb double copy gain of the proximal long arm of chromosome 22. The 1,3 Mb intervening region of chromosome 22 from centromere to the breakpoints showed no copy alteration. The karyotype of the patient was defined as 47,XY,+mar[60]/46,XY[40].ish idic r(22)(q11.1.q11.21) × 4.arr 22q11(17,435, 645-18,656,678) × 3,(17,598,642-17,799,783) × 4 dn.

CONCLUSIONS

The present report is the first one with a detailed description of clinical presentation in a patient carrying an atypical size ring sSMC (22) analyzed by array CGH. The specialty of the finding is emphasized by the fact that although the patient had a mosaic sSMC and the amplified region was smaller than in typical cat eye syndrome cases, the clinical presentation was severe.

Analysis of the t(3;8) of hereditary renal cell carcinoma: a palindrome-mediated translocation

It has emerged that palindrome-mediated genomic instability generates DNA-based rearrangements. The presence of palindromic AT-rich repeats (PATRRs) at the translocation breakpoints suggested a palindrome-mediated mechanism in the generation of several recurrent constitutional rearrangements: the t(11;22), t(17;22), and t(8;22). To date, all reported PATRR-mediated translocations include the PATRR on chromosome 22 (PATRR22) as a translocation partner. Here, the constitutional rearrangement, t(3;8)(p14.2;q24.1), segregating with renal cell carcinoma in two families, is examined. The chromosome 8 breakpoint lies in PATRR8 in the first intron of the RNF139 (TRC8) gene, whereas the chromosome 3 breakpoint is located in an AT-rich palindromic sequence in intron 3 of the FHIT gene (PATRR3). Thus, the t(3;8) is the first PATRR-mediated, recurrent, constitutional translocation that does not involve PATRR22. Furthermore, we detect de novo translocations similar to the t(11;22) and t(8;22), involving PATRR3 in normal sperm. The breakpoint on chromosome 3 is in proximity to FRA3B, the most common fragile site in the human genome and a site of frequent deletions in tumor cells. However, the lack of involvement of PATRR3 sequence in numerous FRA3B-related deletions suggests that there are several different DNA sequence-based etiologies responsible for chromosome 3p14.2 genomic rearrangements.

Gene expression analysis of induced pluripotent stem cells from aneuploid chromosomal syndromes

Background

Human aneuploidy is the leading cause of early pregnancy loss, mental retardation, and multiple congenital anomalies. Due to the high mortality associated with aneuploidy, the pathophysiological mechanisms of aneuploidy syndrome remain largely unknown. Previous studies focused mostly on whether dosage compensation occurs, and the next generation transcriptomics sequencing technology RNA-seq is expected to eventually uncover the mechanisms of gene expression regulation and the related pathological phenotypes in human aneuploidy.

Results

Using next generation transcriptomics sequencing technology RNA-seq, we profiled the transcriptomes of four human aneuploid induced pluripotent stem cell (iPSC) lines generated from monosomy × (Turner syndrome), trisomy 8 (Warkany syndrome 2), trisomy 13 (Patau syndrome), and partial trisomy 11:22 (Emanuel syndrome) as well as two umbilical cord matrix iPSC lines as euploid controls to examine how phenotypic abnormalities develop with aberrant karyotype. A total of 466 M (50-bp) reads were obtained from the six iPSC lines, and over 13,000 mRNAs were identified by gene annotation. Global analysis of gene expression profiles and functional analysis of differentially expressed (DE) genes were implemented. Over 5000 DE genes are determined between aneuploidy and euploid iPSCs respectively while 9 KEGG pathways are overlapped enriched in four aneuploidy samples.

Conclusions

Our results demonstrate that the extra or missing chromosome has extensive effects on the whole transcriptome. Functional analysis of differentially expressed genes reveals that the genes most affected in aneuploid individuals are related to central nervous system development and tumorigenesis.

Derivative 11;22 (emanuel) syndrome: a case report and a review

Emanuel syndrome (ES) is a rare anomaly characterized by a distinctive phenotype, consisting of characteristic facial dysmorphism, microcephaly, severe mental retardation, developmental delay, renal anomalies, congenital cardiac defects, and genital anomalies in boys. Here, we report a male neonate, with the classical features of Emanuel syndrome.

Lipodermoid in a patient with Emanuel syndrome

We report an 8-month-old boy with Emanuel syndrome who also had the clinical features of Goldenhar syndrome. At birth, he was observed to have bilateral microtia with multiple auricular pits, retrognathia, and a unilateral lipodermoid. Further testing revealed cardiac defects. The finding of a lipodermoid in Emanuel syndrome demonstrates phenotypic overlap between Goldenhar and Emanuel syndromes and suggests a role for genetic analysis in all patients with clinical features that include ear anomalies and lipodermoids. Correct identification of patients with Emanuel syndrome is important for determining whether there is risk of long-term neurodevelopmental disability, and genetic testing can determine parental carrier status to aid in family planning.

Marker chromosomes

Marker chromosomes are a morphologically heterogeneous group of structurally abnormal chromosomes that pose a significant challenge in prenatal diagnosis. Phenotypes associated with marker chromosomes are highly variable and range from normal to severely abnormal. Clinical outcomes are very difficult to predict when marker chromosomes are detected prenatally. In this review, we outline the classification, etiology, cytogenetic characterization, and clinical consequences of marker chromosomes, as well as practical approaches to prenatal diagnosis and genetic counseling.

Wide clinical variability in cat eye syndrome patients: four non-related patients and three patients from the same family

A small supernumerary marker chromosome (sSMC) derived from chromosome 22 is a relatively common cytogenetic finding. This sSMC typically results in tetrasomy for a chromosomal region that spans the chromosome 22p arm and the proximal 2 Mb of 22q11.21. Using classical cytogenetics, fluorescence in situ hybridization, multiplex ligation-dependent probe amplification, and array techniques, 7 patients with sSMCs derived from chromosome 22 were studied: 4 non-related and 3 from the same family (mother, daughter, and son). The sSMCs in all patients were dicentric and bisatellited chromosomes with breakpoints in the chromosome 22 low-copy repeat A region, resulting in cat eye syndrome (CES) due to chromosome 22 partial tetrasomy 22pter→q11.2 including the cat eye chromosome region. Although all subjects presented the same chromosomal abnormality, they showed a wide range of phenotypic differences, even in the 3 patients from the same family. There are no previous reports of CES occurring within 3 patients in the same family. Thus, the clinical and follow-up data presented here contribute to a better delineation of the phenotypes and outcomes of CES patients and will be useful for genetic counseling.

Failure of homologous synapsis and sex-specific reproduction problems

The prophase of meiosis I ensures the correct segregation of chromosomes to each daughter cell. This includes the pairing, synapsis, and recombination of homologous chromosomes. A subset of chromosomal abnormalities, including translocation and inversion, disturbs these processes, resulting in the failure to complete synapsis. This activates the meiotic pachytene checkpoint, and the gametes are fated to undergo cell cycle arrest and subsequent apoptosis. Spermatogenic cells appear to be more vulnerable to the pachytene checkpoint, and male carriers of chromosomal abnormalities are more susceptible to infertility. In contrast, oocytes tend to bypass the checkpoint and instead generate other problems, such as chromosome imbalance that often leads to recurrent pregnancy loss in female carriers. Recent advances in genetic manipulation technologies have increased our knowledge about the pachytene checkpoint and surveillance systems that detect chromosomal synapsis. This review focuses on the consequences of synapsis failure in humans and provides an overview of the mechanisms involved. We also discuss the sexual dimorphism of the involved pathways that leads to the differences in reproductive outcomes between males and females.

Prenatal screening characteristics in Emanuel syndrome: a case series and review of the literature

PURPOSE

Emanuel syndrome is a rare chromosomal disorder characterized by severe mental retardation and multiple anomalies. The syndrome is caused by chromosomal imbalance due to a supernumerary derivative chromosome 22. Little is known regarding the characteristics of prenatal biochemical screening, or ultrasonographic markers in this syndrome. We aimed to identify a prenatal screening pattern characteristic of Emanuel Syndrome.

METHODS

We report the prenatal characteristics of five fetuses with Emanuel syndrome, four of which were diagnosed prenatally.

RESULTS

We found no consistent pattern of prenatal biochemical markers or other prenatal characteristics. Nevertheless, increased NT, low PAPP-A and ultrasound features such as intra uterine growth restriction, posterior fossa, cardiac and bowel abnormalities may be helpful in raising the suspicion for this rare genetic syndrome.

CONCLUSION

Review of the biochemical screening results, ultrasound findings, and demographic characteristics of this Emanuel syndrome case series, as well as of the relevant literature fail to suggest a characteristic prenatal pattern.

Modeling abnormal early development with induced pluripotent stem cells from aneuploid syndromes

Many human diseases share a developmental origin that manifests during childhood or maturity. Aneuploid syndromes are caused by supernumerary or reduced number of chromosomes and represent an extreme example of developmental disease, as they have devastating consequences before and after birth. Investigating how alterations in gene dosage drive these conditions is relevant because it might help treat some clinical aspects. It may also provide explanations as to how quantitative differences in gene expression determine phenotypic diversity and disease susceptibility among natural populations. Here, we aimed to produce induced pluripotent stem cell (iPSC) lines that can be used to improve our understanding of aneuploid syndromes. We have generated iPSCs from monosomy X [Turner syndrome (TS)], trisomy 8 (Warkany syndrome 2), trisomy 13 (Patau syndrome) and partial trisomy 11;22 (Emanuel syndrome), using either skin fibroblasts from affected individuals or amniocytes from antenatal diagnostic tests. These cell lines stably maintain the karyotype of the donors and behave like embryonic stem cells in all tested assays. TS iPSCs were used for further studies including global gene expression analysis and tissue-specific directed differentiation. Multiple clones displayed lower levels of the pseudoautosomal genes ASMTL and PPP2R3B than the controls. Moreover, they could be transformed into neural-like, hepatocyte-like and heart-like cells, but displayed insufficient up-regulation of the pseudoautosomal placental gene CSF2RA during embryoid body formation. These data support that abnormal organogenesis and early lethality in TS are not caused by a tissue-specific differentiation blockade, but rather involves other abnormalities including impaired placentation.