用高分辨率微阵列比较基因组杂交分析一个孤独症家系的新生拷贝数变异

目的 对1个孤独症家系进行新发拷贝数变异(copy number variations,CNV)分析.方法 应用高分辨率全基因组芯片(Affymetrix Cytogenetics Whole-Genome 2.7M Array)检测该家系4名成员的基因组拷贝数,用Affymetrix Chromosome Analysis Suite软件分析结果.以基因组变异数据库亚洲正常人群及先证者父母、同胞为对照,分析先证者的新发CNV.结果 先证者存在89个新发拷贝数变异,其中5号、11号和14号染色体新发CNV总长占染色体全长超过1‰.3p26.1、4q22.2、5p15.2等区域也存在新发CNV,涉及GRM7、GRID2、CTNND2等10个与神经系统发育相关基因.结论 先证者多个与神经系统发育相关的基因存在新发拷贝数变异,这为探索孤独症的发病机理提供了新的线索.高分辨率基因组CNV芯片能够快速、准确地检测基因组的微小失衡,在遗传病诊断方面具有广阔的应用前景.     

拷贝数变异的分型检测技术

拷贝数变异（copynumbervariants,CNVs）是生物基因组中一种重要的遗传变异形式。研究发现CNVs与许多人类复杂疾病相关,在研究个体表型差异和基因组进化上具有重要意义。现就各CNVs检测技术的原理、发展现状、优缺点及意义作一综述。     

Prospective diagnostic analysis of copy number variants using SNP microarrays in individuals with autism spectrum disorders

Copy number variants (CNVs) have repeatedly been found to cause or predispose to autism spectrum disorders (ASDs). For diagnostic purposes, we screened 194 individuals with ASDs for CNVs using Illumina SNP arrays. In several probands, we also analyzed candidate genes located in inherited deletions to unmask autosomal recessive variants. Three CNVs, a de novo triplication of chromosome 15q11–q12 of paternal origin, a deletion on chromosome 9p24 and a de novo 3q29 deletion, were identified as the cause of the disorder in one individual each. An autosomal recessive cause was considered possible in two patients: a homozygous 1p31.1 deletion encompassing PTGER3 and a deletion of the entire DOCK10 gene associated with a rare hemizygous missense variant. We also identified multiple private or recurrent CNVs, the majority of which were inherited from asymptomatic parents. Although highly penetrant CNVs or variants inherited in an autosomal recessive manner were detected in rare cases, our results mainly support the hypothesis that most CNVs contribute to ASDs in association with other CNVs or point variants located elsewhere in the genome. Identification of these genetic interactions in individuals with ASDs constitutes a formidable challenge.     

基因拷贝数变异与智力障碍病因学研究进展

基因拷贝数变异(copy number variations,CNVs)是指DNA片段大小从1 kb至Mb的亚微观结构变异,已成为探讨与疾病相关遗传变异的研究热点,特别是神经认知系统的遗传病,如精神分裂症、智力障碍等综合征、本文综述了基因拷贝数变异与智力障碍的关联关系和基因拷贝数变异检测技术进展在智力障碍诊断中的应用,这对揭示智力障碍发病机制有着重要意义.     

Copy number variations associated with autism spectrum disorders contribute to a spectrum of neurodevelopmental disorders

PurposeAutism spectrum disorders represent a range of neurodevelopmental disorders that have been shown to have a strong genetic etiological component. Microarray-based comparative genomic hybridization and other molecular cytogenetic techniques are discovering an increasing number of copy number variations in individuals with autism spectrum disorder.MethodsWe examined the yield of abnormal microarray-based comparative genomic hybridization findings in our laboratory for individuals referred for testing for autism spectrum disorder. We also examined the presence of autistic features among 151 additional individuals who were referred for microarray-based comparative genomic hybridization testing for indications other than autism spectrum disorder but had genomic alterations overlapping those found in cases referred for autism spectrum disorder.ResultsWe identified 1461 individuals referred for testing for autism spectrum disorder, with likely significant abnormalities reported in approximately 11.6% of individuals analyzed with whole-genome arrays. These abnormalities include alterations that encompass novel candidate genes such as SNTG2, SOX5, HFE, and TRIP38. A minority of individuals with overlapping abnormalities (19%) had autistic features, and many of the copy number variations identified in our study are inherited (69% among those found in individuals with autism spectrum disorder).ConclusionsOur results suggest these copy number variations are one of multiple factors contributing to the development of an autism spectrum disorder phenotype. Additionally, the broad phenotypic spectrum of the patients with these copy number variations suggests that these copy number variations are not autism spectrum disorder-specific but likely more generally impair neurodevelopment.     

Copy number variation characteristics in subpopulations of patients with autism spectrum disorders

Autism spectrum disorders (ASDs) are a heterogeneous group of disorders with a complex genetic etiology. We used high‐resolution whole genome array‐based comparative genomic hybridization (array‐CGH) to screen 223 ASD patients for gene dose alterations associated with susceptibility for autism. Clinically significant copy number variations (CNVs) were identified in 18 individuals (8%), of which 9 cases (4%) had de novo aberrations. In addition, 20 individuals (9%) were shown to have CNVs of unclear clinical relevance. Among these, 13 cases carried rare but inherited CNVs that may increase the risk for developing ASDs, while parental samples were unavailable in the remaining seven cases. Classification of all patients into different phenotypic and inheritance pattern groups indicated the presence of different CNV patterns in different patient groups. Clinically relevant CNVs were more common in syndromic cases compared to non‐syndromic cases. Rare inherited CNVs were present in a higher proportion of ASD cases having first‐ or second‐degree relatives with an ASD‐related neuropsychiatric phenotype in comparison with cases without reported heredity (P = 0.0096). We conclude that rare CNVs, encompassing potential candidate regions for ASDs, increase the susceptibility for the development of ASDs and related neuropsychiatric disorders giving us further insight into the complex genetics underlying ASDs. © 2010 Wiley‐Liss, Inc.     

基因拷贝数变异与智力障碍病因学研究进展

基因拷贝数变异(copy number variations,CNVs)是指DNA片段大小从1 kb至Mb的亚微观结构变异,已成为探讨与疾病相关遗传变异的研究热点,特别是神经认知系统的遗传病,如精神分裂症、智力障碍等综合征、本文综述了基因拷贝数变异与智力障碍的关联关系和基因拷贝数变异检测技术进展在智力障碍诊断中的应用,这对揭示智力障碍发病机制有着重要意义.     

Copy number changes of the microcephalin 1 gene (MCPH1) in patients with autism spectrum disorders

Autism spectrum disorder (ASD) represents a set of neurodevelopmental disorders with a strong genetic aetiology. Chromosomal rearrangements have been detected in 5–10% of the patients with ASD, and recent applications of array comparative genomic hybridisation (aCGH) are identifying further candidate regions and genes. In this study, we present four patients who implicate microcephalin 1 ( MCPH1) in band 8p23.1 as an ASD susceptibility gene. Patient 1 was a girl with a syndromic form of autistic disorder satisfying the Autism Diagnostic Interview-Revised (ADI-R), Autism Diagnostic Observation Schedule (ADOS) and Diagnostic and Statistical Manual of Mental Disorders (DSM-IV) criteria. Oligonucleotide aCGH (oaCGH) showed that she had a classic inv dup del(8)(qter-> p23.1::p23.1-> p21.2) containing at least three candidate genes; MCPH1 and DLGAP2 within the 6.9-Mb terminal deletion and NEF3 within the concomitant 14.1-Mb duplication. Three further patients with MCPH1 copy number changes were found using single-nucleotide polymorphism (SNP) array analysis in a cohort of 54 families with ASD patients. Our results show that ASD can be a component of the classical inv dup del(8) phenotype and identify changes in copy number of MCPH1 as a susceptibility factor for ASD in the distal short arm of chromosome 8.     

一个汉族自闭症谱系障碍家系的拷贝数变异分析

目的 对一个中国汉族自闭症谱系障碍(autistic spectrum disorder,ASD)家系进行拷贝数变异(copy number variation,CNV)的分析.方法 该家系共3例患者.建立家系成员EB病毒转染永生化的B淋巴细胞系,并提取基因组进行核型分析与Affymatrix 500k SNP芯片检测,所获结果由Genotyping Console与GeneChip(R)Chromosome Copy Number Analysis Tool软件分析,采用家系中3名正常儿童作为对照,对患者中的拷贝数变异进行分析.结果 核型分析未发现染色体变异情况,而15q11位点在患者中都存在拷贝数变异,其中物理位置为19827281-19998230的片段出现了拷贝数减少,含有OR11K1P、OR4Q1P、OR4H6P、OR4M2、OR4N3P等基因,而另外3条分别为37 kb、1316 kb、37 kb的片段则出现了拷贝数增加,含有LOC388079、LOC441709等基因.结论 位于这一拷贝数变异位点上有OR11K1P、OR4Q1P、OR4H6P、OR4M2等嗅觉受体基因,也有功能未明的LOC388079基因,为自闭症的遗传机理研究提供了新的提示.     

基因拷贝数变异与智力障碍病因学研究进展

基因拷贝数变异(copy number variations,CNVs)是指DNA片段大小从1 kb至Mb的亚微观结构变异,已成为探讨与疾病相关遗传变异的研究热点,特别是神经认知系统的遗传病,如精神分裂症、智力障碍等综合征、本文综述了基因拷贝数变异与智力障碍的关联关系和基因拷贝数变异检测技术进展在智力障碍诊断中的应用,这对揭示智力障碍发病机制有着重要意义.     

Anxiety in children and adolescents with autism spectrum disorders

Anxiety and poor stress management are common concerns in clinical samples of children with autism spectrum disorders (ASD). Anxiety may worsen during adolescence, as young people face an increasingly complex social milieu and often become more aware of their differences and interpersonal difficulties. This review summarizes the state of research on the prevalence, phenomenology, and treatment of anxiety in youth with autism and related conditions such as Asperger's Disorder. Using search words autism, asperger(s), or pervasive developmental disorder and anxiety or anxious to find reports published between 1990 and 2008, this review identified 40 papers. The results of the review suggest that anxiety, whether measured categorically or dimensionally, is indeed common in children and adolescents with autism spectrum disorders and may be a source of additional morbidity. The assessment of anxiety disorders in ASD should be conducted using multiple informants and modalities, as children with ASD often do not display age-typical symptoms of anxiety. To date, relatively few controlled intervention studies using well-characterized samples have been conducted despite preliminary evidence for efficacy of select pharmacological and psychosocial approaches. Recommendations for future applied research are presented and clinical implications are explored.     

Copy number variants in patients with short stature

Height is a highly heritable and classic polygenic trait. Recent genome-wide association studies (GWAS) have revealed that at least 180 genetic variants influence adult height. However, these variants explain only about 10% of the phenotypic variation in height. Genetic analysis of short individuals can lead to the discovery of novel rare gene defects with a large effect on growth. In an effort to identify novel genes associated with short stature, genome-wide analysis for copy number variants (CNVs), using single-nucleotide polymorphism arrays, in 162 patients (149 families) with short stature was performed. Segregation analysis was performed if possible, and genes in CNVs were compared with information from GWAS, gene expression in rodents'' growth plates and published information. CNVs were detected in 40 families. In six families, a known cause of short stature was found (SHOX deletion or duplication, IGF1R deletion), in two combined with a de novo potentially pathogenic CNV. Thirty-three families had one or more potentially pathogenic CNVs (n=40). In 24 of these families, segregation analysis could be performed, identifying three de novo CNVs and nine CNVs segregating with short stature. Four were located near loci associated with height in GWAS (ADAMTS17, TULP4, PRKG2/BMP3 and PAPPA). Besides six CNVs known to be causative for short stature, 40 CNVs with possible pathogenicity were identified. Segregation studies and bioinformatics analysis suggested various potential candidate genes.     

Interpretation of clinical relevance of X-chromosome copy number variations identified in a large cohort of individuals with cognitive disorders and/or congenital anomalies

Genome-wide array studies are now routinely being used in the evaluation of patients with cognitive disorders (CD) and/or congenital anomalies (CA). Therefore, inevitably each clinician is confronted with the challenging task of the interpretation of copy number variations detected by genome-wide array platforms in a diagnostic setting. Clinical interpretation of autosomal copy number variations is already challenging, but assessment of the clinical relevance of copy number variations of the X-chromosome is even more complex. This study provides an overview of the X-Chromosome copy number variations that we have identified by genome-wide array analysis in a large cohort of 4407 male and female patients. We have made an interpretation of the clinical relevance of each of these copy number variations based on well-defined criteria and previous reports in literature and databases. The prevalence of X-chromosome copy number variations in this cohort was 57/4407 (∼1.3%), of which 15 (0.3%) were interpreted as (likely) pathogenic.     

散发孤独症谱系障碍核心家系神经-突触发育相关共有变异基因分析

目的探讨散发孤独症谱系障碍(autism spectrum disorders,ASD)核心家系患儿的疾病易感基因。方法对60例散发ASD核心家系患儿及父母进行全外显子测序。选取总体样本10%以上患者共存的变异基因,应用Phenolyzer数据库进行基因-表型关联评分,进一步利用metascape数据库进行基因功能通路富集分析,重点关注与神经-突触发育相关的通路或过程基因,结合基因-表型得分筛选ASD易感基因。结果共发现170个共有基因与ASD表型相关,其中高置信基因(high-confidence gene)1个:SHANK2(0.8146分);中置信基因(medium-confidence gene)4个:ERBB2(0.1322分)、LAMC3(0.1117分)、PPFIA4(0.1059分)、DISC1(0.1002分)。通过基因功能通路富集分析发现20条通路及生物学过程达到统计学意义,其中投射神经元形态发生(GO:0048812)、神经母细胞增殖的调控(GO:1902692)、兴奋性突触后电位的调节(GO:0098815)、树突形态发生(GO:0048813)等4个生物学过程,共计21个基因与神经-突触发育相关,其中SHANK2、ERBB2、DISC1基因为中度以上置信基因。结论投射神经元形态发生(GO:0048812)过程异常可能与ASD的发生密切相关,SHANK2、ERBB2、DISC1基因可能是ASD的遗传易感基因。     

Copy number variations in a Brazilian cohort with autism spectrum disorders highlight the contribution of cell adhesion genes

Prediction of pathogenicity of rare copy number variations (CNVs), a genomic alteration known to contribute to the etiology of autism spectrum disorder (ASD), represents a serious limitation to interpreting genetic tests, particularly for genetic counseling purposes. Chromosomal microarray analysis (CMA) was conducted in a unique collection of 144 Brazilian individuals with ASD of strong European and African ancestries. Rare CNVs were detected in 39 patients: 41 of unknown significance (VUS), four pathogenic and one likely pathogenic CNVs (clinical yield of 4.1%; 5/122). Based on gene content and recurrence in three large cohorts [a Brazilian neurodevelopmental disorder cohort, the autism MSSNG cohort, and the Canadian-based Centre for Applied Genomics microarray database], this work strengthened the pathogenicity of 14 genes (FAT1, CAMK4, BIRC6, DPP6, CSMD1, CTNNA3, CDH8/CDH11, CDH13, OR1C1, CNTN6, CNTNAP4, FGF2 and PTPRN2) within 14 CNVs. Notably, enrichment of cell adhesion proteins to ASD etiology was identified (p < 0.05), highlighting the importance of these gene families in the etiology of ASD.     

Copy number variation in patients with cervical artery dissection

Cervical artery dissection (CeAD) occurs in healthy young individuals and often entails ischemic stroke. Skin biopsies from most CeAD-patients show minor connective tissue alterations. We search for rare genetic deletions and duplication that may predispose to CeAD. Forty-nine non-traumatic CeAD-patients with electron microscopic (EM) alterations of their dermal connective tissue (EM+ patients) and 21 patients with normal connective tissue in skin biopsies (EM− patients) were analyzed. Affymetrix 6.0 microarrays (Affymetrix) from all patients were screened for copy number variants (CNVs). CNVs absent from 403 control subjects and from 2402 published disease-free individuals were considered as CeAD-associated. The genetic content of undentified CNVs was analyzed by means of the Gene Ontology (GO) Term Mapper to detect associations with biological processes. In 49 EM+ patients we identified 13 CeAD-associated CNVs harboring 83 protein-coding genes. In 21 EM− patients we found five CeAD-associated CNVs containing only nine genes (comparison of CNV gene density between the groups: Mann–Whitney P=0.039). Patients'' CNVs were enriched for genes involved in extracellular matrix organization (COL5A2, COL3A1, SNTA1, P=0.035), collagen fibril organization COL5A2, COL3A1, (P=0.0001) and possibly for genes involved in transforming growth factor beta (TGF)-beta receptor signaling pathway (COL3A1, DUPS22, P=0.068). We conclude that rare genetic variants may contribute to the pathogenesis of CeAD, in particular in patients with a microscopic connective tissue phenotype.     

Segregating patterns of copy number variations in extended autism spectrum disorder (ASD) pedigrees

Autism spectrum disorder (ASD) is a relatively common childhood onset neurodevelopmental disorder with a complex genetic etiology. While progress has been made in identifying the de novo mutational landscape of ASD, the genetic factors that underpin the ASD's tendency to run in families are not well understood. In this study, nine extended pedigrees each with three or more individuals with ASD, and others with a lesser autism phenotype, were phenotyped and genotyped in an attempt to identify heritable copy number variants (CNVs). Although these families have previously generated linkage signals, no rare CNV segregated with these signals in any family. A small number of clinically relevant CNVs were identified. Only one CNV was identified that segregated with ASD phenotype; namely, a duplication overlapping DLGAP2 in three male offspring each with an ASD diagnosis. This gene encodes a synaptic scaffolding protein, part of a group of proteins known to be pathologically implicated in ASD. On the whole, however, the heritable nature of ASD in the families studied remains poorly understood.     

孤独症谱系障碍的遗传学研究进展

孤独症谱系障碍(autism spectrum disorder,ASD)是一组复杂的神经系统发育障碍性疾病的统称,患者通常表现出不同程度的社会沟通交往障碍,并伴有语言发育异常和重复刻板的行为或兴趣。随着测序技术的不断发展,ASD相关的变异、基因、功能通路,以及脑区基因表达模式在不断被发现。本文就ASD相关的各个层面的...     

Copy number variations in neurodevelopmental disorders

Common neurodevelopmental disorders (including autism, speech and language delay, schizophrenia, epilepsy and intellectual disability) have complex aetiology, which is predominantly genomic, but also environmental in origin. They share a paradox, in that high heritability is matched by lowered fecundity, placing them under negative genetic selection. This implicates variants of recent origin, such as de novo mutations or common, very low-risk polymorphisms that escape negative selection. High or moderate risk variants have been discovered by chromosome analysis, genome sequencing and copy number variant (CNV) detection, including a 3Mb deletion causing 22q11.2 deletion syndrome (Velo-Cardio-Facial Syndrome) that has penetrance of up to 50% for schizophrenia. More recently, rare, recurrent and often de novo pathogenic CNVs, including deletions at NRXN1, 1q21.2, 15q11.2 and 15q13.3, 16p11.2 and duplications at VIPR2 and 16p13.11, have also been discovered. These have several unique features that differentiate them from Mendelian disease mutations in that they have incomplete penetrance, with moderate-to-high odds ratios for risk, and show diagnostic pleiotropy, increasing risk across the neurodevelopmental disorder spectrum. Some are also syndromic, with characteristic features such as facial dysmorphology, and other specific risks such as aortic dissection or obesity, implying that they might be better classified as distinct diagnoses. The discovery of pathogenic CNVs provide new opportunities for translation leading to patent benefit, including improvements in clinical genetic diagnosis and genetic counselling, the possibility of clinician decision-making tools for risk prediction, and the identification of drug targets and implementation of personalised medicine using stratification by genotype.