New microdeletion and microduplication syndromes: A comprehensive review

Genetic Approaches to Understanding Psychiatric Disease

Human genetic studies have been the driving force in bringing to light the underlying biology of psychiatric conditions. As these studies fill in the gaps in our knowledge of the mechanisms at play, we will be better equipped to design therapies in rational and targeted ways, or repurpose existing therapies in previously unanticipated ways. This review is intended for those unfamiliar with psychiatric genetics as a field and provides a primer on different modes of genetic variation, the technologies currently used to probe them, and concepts that provide context for interpreting the gene-phenotype relationship. Like other subfields in human genetics, psychiatric genetics is moving from microarray technology to sequencing-based approaches as barriers of cost and expertise are removed, and the ramifications of this transition are discussed here. A summary is then given of recent genetic discoveries in a number of neuropsychiatric conditions, with particular emphasis on neurodevelopmental conditions. The general impact of genetics on drug development has been to underscore the extensive etiological heterogeneity in seemingly cohesive diagnostic categories. Consequently, the path forward is not in therapies hoping to reach large swaths of patients sharing a clinically defined diagnosis, but rather in targeting patients belonging to specific "biotypes" defined through a combination of objective, quantifiable data, including genotype.

A New Case of the Rare 10q22.3q23.2 Microdeletion Flanked by Low-Copy Repeats 3/4

Deletions in the 10q22.3q23.2 region are rare and mediated by 2 low-copy repeats (LCRs 3 and 4). These deletions have already been recognized as the 10q22q23 deletion syndrome. The phenotype associated with this condition is rather uncharacteristic, and most common features are craniofacial dysmorphisms and developmental delay. We describe a boy with craniofacial dysmorphic features, developmental delay, tetralogy of Fallot, hand/foot abnormalities, and recurrent respiratory tract infections. Chromosomal microarray analysis disclosed a 7.8-Mb microdeletion at 10q22.3q23.2, flanked by LCRs 3/4, and an additional 16q12.1 microdeletion of 189 kb. This article reviews the clinical signs of reported cases with similar deletions and compares them with our patient, contributing to a better understanding of genotype-phenotype correlation.

Congenital Generalized Hypertrichosis Terminalis with Gingival Hyperplasia and a Coarse Face: a Case Report

Congenital generalized hypertrichosis, in its most common form, is idiopathic. In the absence of underlying endocrine or metabolic disorders, congenital generalized hypertrichosis is rare in humans, affecting as few as one in a billion individuals and may be an isolated condition of the skin, or a component feature of other disorders or syndromes. Congenital generalized hypertrichosis terminalis is an extremely rare condition, a distinct subset of disorders with congenital hypertrichosis, presenting with excessive hair as the primary clinical feature. Congenital generalized hypertrichosis terminalis is characterized by universal excessive growth of pigmented terminal hair and often accompanied with gingival hyperplasia and/or a coarse face. Gingival hyperplasia may be delayed even until puberty. Its pathogenesis may be caused by one of the following mechanisms: conversion of vellus to terminal hairs and/or prolonged anagenetic stage, and/or increase in the number of hair follicles. Since the Middle Ages, less than 60 individuals with congenital hypertrichosis terminalis have been described, and, according to the most recent estimates, less than 40 cases were documented adequately and definitively in the literature. Recent articles identified congenital generalized hypertrichosis terminalis as a genomic disorder.

This report is a follow up of a six-year-old boy born from the first normal pregnancy of non-consanguineous parents, starting from delivery. Our investigation revealed a history of: excessive hair growth and a coarse face from birth; increased body weight with high blood pressure and gingival hyperplasia at the age of four months. The parents denied any medication or chemical intake during pregnancy, as well as a history of hypertrichosis in their families. The child had a congenital hydronephrosis of the right kidney. Ultrasound and magnetic resonance imaging revealed severe congenital hydronephrosis of the right kidney and suspicion of hypertrophy of the left adrenal gland suggestive of an adenoma. The follow up showed normal values of hormones which excluded adrenal tumor. At the age of 8 months the patient underwent right-sided nephrectomy after several urinary infections. The child was admitted again to our Clinic at the age of four years, with generalized hypertrichosis, gingival hyperplasia and a coarse face without any other pathological signs. He has had a normal intellectual development, but was extremely shy, unconfident and dependent on his mother. The relevant laboratory investigations showed normal full blood count, biochemical, hormonal test results and normal function of the single kidney. Molecular chromosome analysis revealed heterozygous deletion on chromosome 17q12 region. Prolonged follow-up with routine checkups every 6–12 months was advised, including regular outpatient appointments particularly with an endocrinologist, because of the risk of diabetes mellitus, and with a nephrologist, for control of renal function.

Laser hair removal was suggested and the patient underwent one procedure with long pulsed neodynium:yttrium-albumin-garnet laser with a wavelength of 1064 nm. The procedure was effective and well-tolerated and the treatment course is currently ongoing.

Although it is now believed that most people with congenital generalized hypertrichosis have an unknown genetic defect, up to date, a clear specific molecular abnormality has not been proved. It has been suggested that the distal portion of human chromosome 17q may contain dosage-sensitive genes that contribute to excessive hair growth.

We present a sporadic case of an extremely rare congenital generalized hypertrichosis terminalis in a six-year-old boy born to non-consanguineous parents, with gingival hyperplasia, a coarse face and congenital hydronephrosis, with heterozygous deletion on chromosomal region 17q12 consistent with his renal phenotype.

Cyclic mismatch binding ligand CMBL4 binds to the 5'-T-3'/5'-GG-3' site by inducing the flipping out of thymine base

A newly designed cyclic bis-naphthyridine carbamate dimer CMBL4: with a limited conformational flexibility was synthesized and characterized. Absorption spectra revealed that two naphthyridines in CMBL4: were stacked on each other in aqueous solutions. The most efficient binding of CMBL4: to DNA was observed for the sequence 5'-T-3'/5'-GG-3' (T/GG) with the formation of a 1:1 complex, which is one of possible structural elements involved in the higher order structures of (TGG)n repeat DNA triggering the genome microdeletion. Surface plasmon resonance assay also showed the binding of CMBL4: with TGG repeat DNA. Potassium permanganate oxidation studies of CMBL4: -bound duplex containing the T/GG site showed that the CMBL4: -binding accelerated the oxidation of thymine at that site, which suggests the flipping out of the thymine base from a π-stack. Preferential binding was observed for CMBL4: compared with its acyclic variants, which suggests the marked significance of the macrocyclic structure for the recognition of the T/GG site.

[Clinical phenotypes and copy number variations in children with microdeletion and microduplication syndromes: an analysis of 50 cases]

OBJECTIVE

To investigate the association between genotype and phenotype of microdeletion and microduplication syndromes (MMSs) and the pathogenesis of pathogenic copy number variations (CNVs).

METHODS

A total of 50 children with MMSs diagnosed by chromosomal microarray analysis (CMA) from June 2013 to September 2015 were enrolled, and the clinical manifestations and features of pathogenic CNVs were analyzed.

RESULTS

The main clinical manifestations of children with MMSs included mental retardation, developmental delay, short stature, and unusual facies, with the presence of abnormalities in multiple systems. There were 54 pathogenic CNVs in total, consisting of 36 microdeletion segments and 18 microduplication segments, with sizes ranging from 28 kb to 48.5 Mb (mean 13.86 Mb). Pathogenic CNVs often occurred in chromosomes X, 15, and 1.

CONCLUSIONS

The clinical manifestations of MMSs are not specific, and a genotype-first approach can be used for diagnosis. Mode of inheritance, type of recombination (deletion or duplication), size of segment, and functional genes included helps with the interpretation of CNVs of de novo mutations, and in-depth research on rare pathogenesis may become breakthrough points for the identification of new MMSs.

Performance Evaluation of NIPT in Detection of Chromosomal Copy Number Variants Using Low-Coverage Whole-Genome Sequencing of Plasma DNA

OBJECTIVES

The aim of this study was to assess the performance of noninvasively prenatal testing (NIPT) for fetal copy number variants (CNVs) in clinical samples, using a whole-genome sequencing method.

METHOD

A total of 919 archived maternal plasma samples with karyotyping/microarray results, including 33 CNVs samples and 886 normal samples from September 1, 2011 to May 31, 2013, were enrolled in this study. The samples were randomly rearranged and blindly sequenced by low-coverage (about 7M reads) whole-genome sequencing of plasma DNA. Fetal CNVs were detected by Fetal Copy-number Analysis through Maternal Plasma Sequencing (FCAPS) to compare to the karyotyping/microarray results. Sensitivity, specificity and were evaluated.

RESULTS

33 samples with deletions/duplications ranging from 1 to 129 Mb were detected with the consistent CNV size and location to karyotyping/microarray results in the study. Ten false positive results and two false negative results were obtained. The sensitivity and specificity of detection deletions/duplications were 84.21% and 98.42%, respectively.

CONCLUSION

Whole-genome sequencing-based NIPT has high performance in detecting genome-wide CNVs, in particular >10Mb CNVs using the current FCAPS algorithm. It is possible to implement the current method in NIPT to prenatally screening for fetal CNVs.

An atypical 12q24.31 microdeletion implicates six genes including a histone demethylase KDM2B and a histone methyltransferase SETD1B in syndromic intellectual disability

Microdeletion syndromes are frequent causes of neuropsychiatric disorders leading to intellectual disability as well as autistic features accompanied by epilepsy and craniofacial anomalies. From comparative deletion mapping of the smallest microdeletion to date at 12q24.31, found in a patient with overlapping clinical features of 12q24.31 microdeletion syndrome, we narrowed the putative critical region to 445 kb containing seven genes, one microRNA, and one non-coding RNA. Zebrafish in situ hybridization and comprehensive transcript analysis of annotated genes in the panels of human organ and brain suggest that these are all candidates for neurological phenotypes excluding the gene HPD. This is also corroborated by synteny analysis revealing the conservation of the order of these six candidate genes between humans and zebrafish. Among them, we propose histone demethylase KDM2B and histone methyltransferase SETD1B as the two most plausible candidate genes involved in intellectual disability, autism, epilepsy, and craniofacial anomalies. These two chromatin modifiers located approximately 224 kb apart were both commonly deleted in six patients, while two additional patients had either KDM2B or SETD1B deleted. The four additional candidate genes (ORAI1, MORN3, TMEM120B, RHOF), a microRNA MIR548AQ, and a non-coding RNA LINC01089 are localized between KDM2B and SETD1B. The 12q24.31 microdeletion syndrome with syndromic intellectual disability extends the growing list of microdeletion syndromes and underscores the causative roles of chromatin modifiers in cognitive and craniofacial development.

Genetic Evaluation and Use of Chromosome Microarray in Patients with Isolated Heart Defects: Benefits and Challenges of a New Model in Cardiovascular Care

Congenital heart defects (CHDs) are common birth defects and result in significant morbidity and global economic impact. Genetic factors play a role in most CHDs; however, identification of these factors has been historically slow due to technological limitations and incomplete understanding of the impact of human genomic variation on normal and abnormal cardiovascular development. The advent of chromosome microarray (CMA) brought tremendous gains in identifying chromosome abnormalities in a variety of human disorders and is now considered part of a standard evaluation for individuals with multiple congenital anomalies and/or neurodevelopmental disorders. Several studies investigating use of CMA found that this technology can identify pathogenic copy-number variations (CNVs) in up to 15-20% of patients with CHDs with other congenital anomalies. However, there have been fewer studies exploring the use of CMA for patients with isolated CHDs. Recent studies have shown that the diagnostic yield of CMA in individuals with seemingly isolated CHD is lower than in individuals with CHDs and additional anomalies. Nevertheless, positive CMA testing in this group supports chromosome variation as one mechanism underlying the development of isolated, non-syndromic CHD - either as a causative or risk-influencing genetic factor. CMA has also identified novel genomic variation in CHDs, shedding light on candidate genes and pathways involved in cardiac development and malformations. Additional studies are needed to further address this issue. Early genetic diagnosis can enhance the medical management of patients and potentially provide crucial information about recurrence. This information is critical for genetic counseling of patients and family members. In this review, we review CMA for the non-genetics cardiology provider, offer a summary of CNV in isolated CHDs, and advocate for the use of CMA as part of the cardiovascular genetics evaluation of patients with isolated CHDs. We also provide perspective regarding the benefits and challenges that lie ahead for this model in the clinical setting.

Overexpression of the 14-3-3gamma protein in embryonic mice results in neuronal migration delay in the developing cerebral cortex

The 14-3-3 protein family is a group of multifunctional proteins that are highly expressed in the brain; however, their functions in brain development are largely unknown. Williams Syndrome is a neurodevelopmental disorder caused by a deletion in the 7q11.23 chromosome locus, including the gene encoding 14-3-3gamma, resulting in developmental delay, intellectual disabilities and epilepsy. We have previously shown that knocking down the 14-3-3gamma protein in utero in mice results in delays in neuronal migration of pyramidal neurons in the cortex. Importantly, there is a reciprocal duplication syndrome to Williams Syndrome where the 7q11.23 locus is duplicated, resulting in epilepsy and intellectual disabilities. Thus, the deletion or the duplication of the 7q11.23 chromosome locus results in epilepsy. Taken together with the fact that defects in neuronal migration are one of main causes for epilepsy, we analyzed if the overexpression of 14-3-3gamma causes neuronal migration defects. In this work, we found that the overexpression of 14-3-3gamma in utero in the developing mouse cortex results in delays in pyramidal neuron migration, similar to what was previously observed when 14-3-3gamma was knocked down. These results, in conjunction with our previous research, indicate that a balance of 14-3-3gamma expression is required during cortical development to prevent delays in neuronal migration. This work provides clear evidence as to the involvement of 14-3-3gamma in neurodevelopmental disorders and how a disruption in 14-3-3gamma expression may contribute to the neurodevelopmental disorders that manifest when the 7q11.23 locus is altered.

Characteristics of 2p15-p16.1 microdeletion syndrome: Review and description of two additional patients

Many new microdeletion syndromes have been characterized in the past decade, including 2p15-p16.1 microdeletion syndrome. More than 10 patients with this syndrome have been described. Recently, we encountered two additional patients with 2p15-p16.1 microdeletion syndrome. All patients showed variable degrees of intellectual disability, with the autistic features characteristic of this syndrome. Seven out of 16 patients (44%) showed structural abnormalities in the brain, which is also an important feature of this syndrome. The shortest region of microdeletion overlap among the patients includes two genes, USP34 and XPO1. Although these genes have some functional relevance to cancer, they have not been associated with neurological functions. Diagnosis of additional patients with 2p15-p16.1 microdeletion syndrome and identification of pathogenic mutations in this region will help identify the genes responsible for the neurological features of the syndrome.