Chromosome 18p deletion syndrome (18p-) in children: the value of cytogenetic and molecular cytogenetic diagnosis

Chromosome 18p deletion syndrome (18p-) is associated with a loss of chromosomal material of the short arm (partial monosomy); however, the whole short arm is lost in the majority of cases. The frequency of 18p- syndrome is 1:60000. The syndrome is cytogenetically and clinically heterogeneous. The clinical manifestations vary extremely from mild forms with congenital anomalies and developmental delays to severe brain malformations. Rare cases demonstrate epilepsy and autism spectrum disorders. The deletion breakpoints are also variable. Accordingly, the syndrome needs the analysis of large groups of diseased children by current genomic technologies. Aim of the study: The evaluation of cytogenetic and molecular- cytogenetic technologies for defining critical breakpoints and possible phenotype- genotype correlations. Results: Here, we describe our observations of 15 patients (9 boys and 6 girls) with 18p deletion syndrome, revealed in a large cohort of patients (n=8536). The mean age was 5.1 years; the sex ratio was in favor of boys (1.5:1) in contrast to the literature data. Critical breakpoints associated with this syndrome within the short arm of chromosome 18 were not revealed. It is possible that the clinical features of the syndrome are associated with many breakpoints in chromosome 18 short arm (p11.1->pter). The frequency of 18p- syndrome in children with intellectual disability, developmental delays, and congenital anomalies was 0.2%. The diagnostic aspects of this pathology and the value of molecular cytogenetic methods in studying the syndrome are discussed. Conclusion: We highlight personalized approach to diagnosis of the syndrome for correct genetic counseling for the improvement the life quality and establishing phenotype-karyotype correlations.

Download Full-text

A 29 Mainland Chinese cohort of patients with Phelan–McDermid syndrome: genotype–phenotype correlations and the role of SHANK3 haploinsufficiency in the important phenotypes

Orphanet Journal of Rare Diseases ◽

10.1186/s13023-020-01592-5 ◽

2020 ◽

Vol 15 (1) ◽

Cited By ~ 1

Author(s):

Na Xu ◽

Hui Lv ◽

Tingting Yang ◽

Xiujuan Du ◽

Yu Sun ◽

...

Keyword(s):

Clinical Features ◽

Mainland China ◽

Clinical Manifestations ◽

Autism Spectrum ◽

Pain Tolerance ◽

Repetitive Behaviors ◽

Deletion Syndrome ◽

Loss Of Function ◽

Mainland Chinese ◽

Significant Difference

Abstract Background Phelan–McDermid syndrome (PMS) or 22q13 deletion syndrome is a rare developmental disorder characterized by hypotonia, developmental delay (DD), intellectual disability (ID), autism spectrum disorder (ASD) and dysmorphic features. Most cases are caused by 22q13 deletions encompassing many genes including SHANK3. Phenotype comparisons between patients with SHANK3 mutations (or deletions only disrupt SHANK3) and 22q13 deletions encompassing more than SHANK3 gene are lacking. Methods A total of 29 Mainland China patients were clinically and genetically evaluated. Data were obtained from medical record review and a standardized medical history questionnaire, and dysmorphology evaluation was conducted via photographic evaluation. We analyzed 22q13 deletions and SHANK3 small mutations and performed genotype–phenotype analysis to determine whether neurological features and other important clinical features are responsible for haploinsufficiency of SHANK3. Results Nineteen patients with 22q13.3 deletions ranging in size from 34 kb to 8.7 Mb, one patient with terminal deletions and duplications, and nine patients with SHANK3 mutations were included. All mutations would cause loss-of function effect and six novel heterozygous variants, c.3838_3839insGG, c.3088delC, c.3526G > T, c.3372dupC, c.3120delC and c.3942delC, were firstly reported. Besides, we demonstrated speech delay (100%), DD/ID (88%), ASD (80%), hypotonia (83%) and hyperactivity (83%) were prominent clinical features. Finally, 100% of cases with monogenic SHANK3 deletion had hypotonia and there was no significant difference between loss of SHANK3 alone and deletions encompassing more than SHANK3 gene in the prevalence of hypotonia, DD/ID, ASD, increased pain tolerance, gait abnormalities, impulsiveness, repetitive behaviors, regression and nonstop crying which were high in loss of SHANK3 alone group. Conclusions This is the first work describing a cohort of Mainland China patients broaden the clinical and molecular spectrum of PMS. Our findings support the effect of 22q13 deletions and SHANK3 point mutations on language impairment and several clinical manifestations, such as DD/ID. We also demonstrated SHANK3 haploinsufficiency was a major contributor to the neurological phenotypes of PMS and also responsible for other important phenotypes such as hypotonia, increased pain tolerance, impulsiveness, repetitive behaviors, regression and nonstop crying.

Download Full-text

A case of prenatal diagnosis of 18p deletion syndrome following noninvasive prenatal testing

Molecular Cytogenetics ◽

10.1186/s13039-019-0464-y ◽

2019 ◽

Vol 12 (1) ◽

Cited By ~ 2

Author(s):

Ganye Zhao ◽

Peng Dai ◽

Shanshan Gao ◽

Xuechao Zhao ◽

Conghui Wang ◽

...

Keyword(s):

Prenatal Diagnosis ◽

De Novo ◽

Prenatal Testing ◽

Nuchal Translucency ◽

Deletion Syndrome ◽

Chromosome 18 ◽

Partial Monosomy ◽

Noninvasive Prenatal Testing ◽

First Case ◽

Case Presentations

Abstract Background Chromosome 18p deletion syndrome is a disease caused by the complete or partial deletion of the short arm of chromosome 18, there were few cases reported about the prenatal diagnosis of 18p deletion syndrome. Noninvasive prenatal testing (NIPT) is widely used in the screening of common fetal chromosome aneuploidy. However, the segmental deletions and duplications should also be concerned. Except that some cases had increased nuchal translucency or holoprosencephaly, most of the fetal phenotype of 18p deletion syndrome may not be evident during the pregnancy, 18p deletion syndrome was always accidentally discovered during the prenatal examination. Case presentations In our case, we found a pure partial monosomy 18p deletion during the confirmation of the result of NIPT by copy number variation sequencing (CNV-Seq). The result of NIPT suggested that there was a partial or complete deletion of X chromosome. The amniotic fluid karyotype was normal, but result of CNV-Seq indicated a 7.56 Mb deletion on the short arm of chromosome 18 but not in the couple, which means the deletion was de novo deletion. Finally, the parents chose to terminate the pregnancy. Conclusions To our knowledge, this is the first case of prenatal diagnosis of 18p deletion syndrome following NIPT.NIPT combined with ultrasound may be a relatively efficient method to screen chromosome microdeletions especially for the 18p deletion syndrome.

Download Full-text

Clinical and molecular cytogenetic characterization of two cases of inverted duplication deletion 8p

Nauchno-prakticheskii zhurnal «Medicinskaia genetika» ◽

10.25557/2073-7998.2020.03.41-42 ◽

2020 ◽

pp. 41-42

Author(s):

Д.А. Юрченко ◽

М.Е. Миньженкова ◽

Е.Л. Дадали ◽

Н.В. Шилова

Keyword(s):

Mental Retardation ◽

Congenital Heart ◽

Heart Defects ◽

Clinical Manifestations ◽

Formation Mechanisms ◽

Agenesis Of Corpus Callosum ◽

Molecular Cytogenetic ◽

Inverted Duplication ◽

Cytogenetic Characterization

Синдром инвертированной дупликации короткого плеча хромосомы 8 со смежной терминальной делециенй (inv dup del(8p), ORPHA 96092) - редкая хромосомная аномалия (ХА) с частотой 1/10000-1/30000 живорожденных. В статье представлены клинические и молекулярно-цитогенетические характеристики двух неродственных пациентов с синдромом inv dup del(8p) и уточнены механизмы формирования хромосомного дисбаланса. Inverted duplication deletion 8p syndrome (inv dup del(8p), ORPHA 96092) is a rare chromosomal abnormality with a frequency of 1:10,000 - 30,000 newborns. Clinical manifestations of this syndrome include mental retardation, facial anomalies, hypoplasia/agenesis of corpus callosum, scoliosis and/or kyphosis, hypotonia, congenital heart defects. The article presents the clinical and molecular cytogenetic characteristics of two patients with inv dup del (8p) syndrome and clarifies the formation mechanisms.

Download Full-text

New Strategies for Clinical Trials in Autism Spectrum Disorder

Reviews on Recent Clinical Trials ◽

10.2174/1574887115666201120093634 ◽

2020 ◽

Vol 15 ◽

Author(s):

Rini Pauly ◽

Catherine A. Ziats ◽

Ludovico Abenavoli ◽

Charles E. Schwartz ◽

Luigi Boccuto

Keyword(s):

Autism Spectrum Disorder ◽

Clinical Trials ◽

Autism Spectrum ◽

Spectrum Disorder ◽

Genetic Profiling ◽

Omics Technologies ◽

Molecular Abnormalities ◽

Sequencing Technologies ◽

Linear Relationships ◽

Personalized Approach

Background: Autism spectrum disorder (ASD) is a complex neurodevelopmental condition that poses several challenges in terms of clinical diagnosis and investigation of molecular etiology. The lack of knowledge on the pathogenic mechanisms underlying ASD has hampered the clinical trials that so far have tried to target ASD behavioral symptoms. In order to improve our understanding of the molecular abnormalities associated with ASD, a deeper and more extensive genetic profiling of targeted individuals with ASD was needed. Methods: The recent availability of new and more powerful sequencing technologies (third-generation sequencing) has allowed to develop novel strategies for characterization of comprehensive genetic profiles of individuals with ASD. In particular, this review will describe integrated approaches based on the combination of various omics technologies that will lead to a better stratification of targeted cohorts for the design of clinical trials in ASD. Results: In order to analyze the big data collected by assays such as whole genome, epigenome, transcriptome, and proteome, it is critical to develop an efficient computational infrastructure. Machine learning models are instrumental to identify non-linear relationships between the omics technologies and therefore establish a functional informative network among the different data sources. Conclusion: The potential advantage provided by these new integrated omics-based strategies is to better characterize the genetic background of ASD cohorts, identify novel molecular targets for drug development, and ultimately offer a more personalized approach in the design of clinical trials for ASD.

Download Full-text

Neurodevelopmental Trajectories and Psychiatric Morbidity: Lessons Learned From the 22q11.2 Deletion Syndrome

Current Psychiatry Reports ◽

10.1007/s11920-021-01225-z ◽

2021 ◽

Vol 23 (3) ◽

Author(s):

Ania M. Fiksinski ◽

Maude Schneider ◽

Janneke Zinkstok ◽

Danielle Baribeau ◽

Samuel J. R. A. Chawner ◽

...

Keyword(s):

Genetic Variants ◽

Clinical Care ◽

Psychiatric Morbidity ◽

Phenotypic Expression ◽

22Q11.2 Deletion Syndrome ◽

Autism Spectrum ◽

Lessons Learned ◽

Deletion Syndrome ◽

22Q11.2 Deletion ◽

Variable Expression

AbstractPurpose of ReviewThe 22q11.2 deletion syndrome (22q11DS) is associated with a broad spectrum of neurodevelopmental phenotypes and is the strongest known single genetic risk factor for schizophrenia. Compared to other rare structural pathogenic genetic variants, 22q11DS is relatively common and one of the most extensively studied. This review provides a state-of-the-art overview of current insights regarding associated neurodevelopmental phenotypes and potential implications for 22q11DS and beyond.Recent FindingsWe will first discuss recent findings with respect to neurodevelopmental phenotypic expression associated with 22q11DS, including psychotic disorders, intellectual functioning, autism spectrum disorders, as well as their interactions. Second, we will address considerations that are important in interpreting these data and propose potential implications for both the clinical care for and the empirical study of individuals with 22q11DS. Third, we will highlight variable penetrance and pleiotropy with respect to neurodevelopmental phenotypes in 22q11DS. We will discuss how these phenomena are consistently observed in the context of virtually all rare pathogenic variants and that they pose substantial challenges from both a clinical and a research perspective.SummaryWe outline how 22q11DS could be viewed as a genetic model for studying neurodevelopmental phenotypes. In addition, we propose that 22q11DS research can help elucidate mechanisms underlying variable expression and pleiotropy of neurodevelopmental phenotypes, insights that are likely relevant for 22q11DS and beyond, including for individuals with other rare pathogenic genetic variants and for individuals with idiopathic neurodevelopmental conditions.

Download Full-text

Natural language processing (NLP) tools in extracting biomedical concepts from research articles: a case study on autism spectrum disorder

BMC Medical Informatics and Decision Making ◽

10.1186/s12911-020-01352-2 ◽

2020 ◽

Vol 20 (S11) ◽

Cited By ~ 1

Author(s):

Jacqueline Peng ◽

Mengge Zhao ◽

James Havrilla ◽

Cong Liu ◽

Chunhua Weng ◽

...

Keyword(s):

Autism Spectrum Disorder ◽

Natural Language Processing ◽

Natural Language ◽

Language Processing ◽

Clinical Manifestations ◽

Predictive Performance ◽

Autism Spectrum ◽

Spectrum Disorder ◽

Research Articles

Abstract Background Natural language processing (NLP) tools can facilitate the extraction of biomedical concepts from unstructured free texts, such as research articles or clinical notes. The NLP software tools CLAMP, cTAKES, and MetaMap are among the most widely used tools to extract biomedical concept entities. However, their performance in extracting disease-specific terminology from literature has not been compared extensively, especially for complex neuropsychiatric disorders with a diverse set of phenotypic and clinical manifestations. Methods We comparatively evaluated these NLP tools using autism spectrum disorder (ASD) as a case study. We collected 827 ASD-related terms based on previous literature as the benchmark list for performance evaluation. Then, we applied CLAMP, cTAKES, and MetaMap on 544 full-text articles and 20,408 abstracts from PubMed to extract ASD-related terms. We evaluated the predictive performance using precision, recall, and F1 score. Results We found that CLAMP has the best performance in terms of F1 score followed by cTAKES and then MetaMap. Our results show that CLAMP has much higher precision than cTAKES and MetaMap, while cTAKES and MetaMap have higher recall than CLAMP. Conclusion The analysis protocols used in this study can be applied to other neuropsychiatric or neurodevelopmental disorders that lack well-defined terminology sets to describe their phenotypic presentations.

Download Full-text