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.     

X染色体倾斜失活人胚胎干细胞的拷贝数变异

背景：倾斜性与随机X染色体失活的人胚胎干细胞拷贝数变异是否存在差异不清楚。 目的：在全基因组水平分析倾斜性X染色体失活的人胚胎干细胞的拷贝数变异情况,分析其涵盖基因及其对细胞功能产生的影响。 方法：3株倾斜性X染色体失活细胞为研究组,两株随机X染色体失活细胞为对照组。运用美国Affymetrix公司Cytogenetics Whole-Genome 2.7M 芯片对其进行全基因组拷贝数变异分析,数据经ChAS软件、OMIM等工具分析,在3株倾斜性X染色体失活细胞中寻找相同拷贝数变异区域及其涵盖基因。 结果与结论：①研究组中大于50 kb的拷贝数变异数均超过130个,高于对照组的平均36个,两组中拷贝数变异改变均以重复为主(> 70%)。②研究组中共发现9个共同拷贝数变异区域,分布于1q22、1p34.1、6q16.3、7q31.32、11q13.1、16q12.2、19p13.12、Xp22.33及Xq26.2,均为3个拷贝的重复,总共涵盖19个基因。对照组中这些区域及基因均为正常2个拷贝。③拷贝数变异涵盖基因多与DNA及核苷酸结合等功能相关,Xq26.2区域的GPC3基因突变与倾斜性X染色体失活可能有关联。结果表明倾斜性X染色体失活细胞相对随机失活细胞具有更多的微小基因组改变,拷贝数变异涵盖的重要基因可能对人胚胎干细胞功能产生不利影响。     

Enrichment of rare copy number variation in children with developmental language disorder

Developmental language disorder (DLD) is a common neurodevelopmental disorder with largely unknown etiology. Rare copy number variants (CNVs) have been implicated in the genetic architecture of other neurodevelopmental disorders (NDDs), which have led to clinical genetic testing recommendations for these disorders; however, the evidence is still lacking for DLD. We analyzed rare and de novo CNVs in 58 probands with severe DLD, their 159 family members and 76 Swedish typically developing children using high‐resolution microarray. DLD probands had larger rare CNVs as measured by total length (P = .05), and average length (P = .04). In addition, the rate of rare CNVs overlapping coding genes was increased (P = .03 and P = .01) and in average more genes were affected (P = .006 and P = .03) in the probands and their siblings, respectively. De novo CNVs were found in 4.8% DLD probands (2/42) and 2.4% (1/42) siblings. Clinically significant CNVs or chromosomal anomalies were found in 6.9% (4/58) of the probands of which 2 carried 16p11.2 deletions. We provide further evidence that rare CNVs contribute to the etiology of DLD in loci that overlap with other NDDs. Based on our results and earlier literature, families with DLD should be offered molecular genetic testing as a routine in their clinical follow‐up.     

The behavioral profile of children aged 1–5 years with sex chromosome trisomy (47,XXX, 47,XXY, 47,XYY)

Children with SCT have an increased risk of suboptimal neurodevelopment. Previous studies have shown an elevated risk for neurobehavioral problems in individuals with SCT. However, not much is known about neurobehavioral problems in very young children; knowledge that could help with early identification of children at risk for suboptimal development, and that could help establish targets for early intervention. This study addressed the question of what the behavioral profile of children with SCT aged 1–5 years looks like. In total, 182 children aged 1–5 years participated in this study (N_SCT=87, N_{nonclinical controls} = 95). Recruitment and assessment took place in the Netherlands and the United States. The SCT group was recruited through prospective follow‐up (50%), information seeking parents (31%), and clinical referral (18%). Behavioral profiles were assessed with the child behavior checklist and the ages‐and‐stages social–emotional questionnaire. Levels of parent‐rated problem behavior were higher in children with SCT. Difficulties with overall social–emotional functioning were already present in 1‐year‐olds, and elevated scores were persistent across the full age range. Affective and pervasive developmental behaviors were seen in late toddlerhood and prominent at preschool age. Anxiety, attention deficit, and oppositional defiant behaviors were seen in preschool‐aged children. Within this cross‐sectional study, the developmental trajectory of affective, pervasive developmental, and oppositional defiant behaviors seemed to be different for SCT children than nonclinical controls. Collectively, these results demonstrate the importance of behavioral screening for behavioral problems in routine clinical care for children with SCT from a young age. Social–emotional problems may require special attention, as these problems seem most prominent, showing increased risk across the full age range, and with these problems occurring regardless of the timing of diagnosis, and across all three SCT karyotypes.     

Patterns of chromosome 18 loss of heterozygosity in multifocal ileal neuroendocrine tumors

Ileal neuroendocrine tumors (NETs) represent the most common neoplasm of the small intestine. Although up to 50% of patients with ileal NETs are diagnosed with multifocal disease, the mechanisms by which multifocal ileal NETs arise are not yet understood. In this study, we analyzed genome‐wide sequencing data to examine patterns of copy number variation in 40 synchronous primary ileal NETs derived from three patients. Chromosome (chr) 18 loss of heterozygosity (LOH) was the most frequent copy number alteration identified; however, not all primary tumors from the same patient had evidence of this LOH. Our data revealed three distinct patterns of chr18 allelic loss, indicating that primary tumors from the same patient can present different LOH patterns including retention of either parental allele. In conclusion, our results are consistent with the model that multifocal ileal NETs originate independently. In addition, they suggest that there is no specific germline allele on chr18 that is the target of somatic LOH.     

Copy number variation and association analysis of SHANK3 as a candidate gene for autism in the IMGSAC collection

SHANK3 is located on chromosome 22q13.3 and encodes a scaffold protein that is found in excitatory synapses opposite the pre-synaptic active zone. SHANK3 is a binding partner of neuroligins, some of whose genes contain mutations in a small subset of individuals with autism. In individuals with autism spectrum disorders (ASDs), several studies have found SHANK3 to be disrupted by deletions ranging from hundreds of kilobases to megabases, suggesting that 1% of individuals with ASDs may have these chromosomal aberrations. To further analyse the involvement of SHANK3 in ASD, we screened the International Molecular Genetic Study of Autism Consortium (IMGSAC) multiplex family sample, 330 families, for SNP association and copy number variants (CNVs) in SHANK3. A collection of 76 IMGSAC Italian probands from singleton families was also examined by multiplex ligation-dependent probe amplification for CNVs. No CNVs or SNP associations were found within the sample set, although sequencing of the gene was not performed. Our data suggest that SHANK3 deletions may be limited to lower functioning individuals with autism.     

Analysis copy number variation of Chinese children in early‐onset epileptic encephalopathies with unknown cause

Copy number variations (CNVs) play an important role in the genetic etiology of unknown cause early‐onset epileptic encephalopathies (EOEEs), but the genomic CNVs analysis of Chinese EOEEs children was rare. Here, we identified CNVs by single nucleotide polymorphism array in 116 patients with different subtypes of EOEEs. Of 116 patients 17 (14.66%) carried 19 large CNVs. A total of 14 CNVs in 12 patients were further validated: four of the CNVs were classified as de novo, seven were maternal, and three were paternal. Follow‐up of those 12 patients showed that 5 had been seizure‐free for at least 9 months, 5 had seizures several times per month or per year, and 2 had seizures everyday. But eight patients have profound developmental delay. In this study, we found at least 3.4% of patients had pathogenic CNVs. For the patients, our study laid the foundation for prenatal interventions for their families. Further, we identified potential candidate gene involved in EOEEs. The association of CNVs and clinical features will contribute to the understanding of EOEEs.     

Clinical application of SNP array analysis in first‐trimester pregnancy loss: a prospective study

Chromosomal microarray analysis (CMA) has been used routinely in pediatric and prenatal genetic diagnosis in clinical practice, but it has rarely been applied to miscarriage analysis. In this study, we conducted a prospective study to evaluate the feasibility of CMA for genetic diagnosis of first‐trimester miscarriage specimens. We successfully analyzed 551 fresh miscarriage specimens using single‐nucleotide polymorphism (SNP) array. Among the specimens, 2.9% (16/551) had significant maternal cell contamination and were excluded from the study. Clinically significant chromosomal abnormalities were identified in 295 (55.1%) cases, including 214 (40%) with aneuploidy, 40 (7.5%) with polyploidy, 19 (3.6%) with partial aneuploidy, 12 (2.2%) with pathogenic microdeletion/microduplication, and 10 (1.9%) with uniparental isodisomy (isoUPD). Variants of uncertain significance were obtained in 15 cases (2.8%). Notably, isoUPD involving a single chromosome (chromosome 22) and two recurrent copy number variations, 22q11.2 microdeletion and 7q11.23 microdeletion, were identified as probably to be associated with miscarriage. The frequency and distribution of genetic aberrations in the spontaneous abortion group was not significantly different from those in the recurrent miscarriage group. Our study suggests SNP array is a reliable, robust, and high‐resolution technology for genetic diagnosis of miscarriage in clinical practice.     

Y chromosome gene copy number and lack of autism phenotype in a male with an isodicentric Y chromosome and absent NLGN4Y expression

We describe a unique male with a dicentric Y chromosome whose phenotype was compared to that of males with 47,XYY (XYY). The male Y‐chromosome aneuploidy XYY is associated with physical, behavioral/cognitive phenotypes, and autism spectrum disorders. We hypothesize that increased risk for these phenotypes is caused by increased copy number/overexpression of Y‐encoded genes. Specifically, an extra copy of the neuroligin gene NLGN4Y might elevate the risk of autism in boys with XYY. We present a unique male with the karyotype 46,X,idic(Y)(q11.22), which includes duplication of the Y short arm and proximal long arm and deletion of the distal long arm, evaluated his physical, behavioral/cognitive, and neuroimaging/magnetoencephalography (MEG) phenotypes, and measured blood RNA expression of Y genes. The proband had tall stature and cognitive function within the typical range, without autism features. His blood RNA showed twofold increase in expression of Yp genes versus XY controls, and absent expression of deleted Yq genes, including NLGN4Y. The M100 latencies were similar to findings in typically developing males. In summary, the proband had overexpression of a subset of Yp genes, absent NLGN4Y expression, without ASD findings or XYY‐MEG latency findings. These results are consistent with a role for NLGN4Y overexpression in the etiology of behavioral phenotypes associated with XYY. Further investigation of NLGN4Y as an ASD risk gene in XYY is warranted. The genotype and phenotype(s) of this subject may also provide insight into how Y chromosome genes contribute to normal male development and the male predominance in ASD.     

Whole exome sequencing in a patient with uniparental disomy of chromosome 2 and a complex phenotype

Whole exome sequencing and chromosomal microarrays are two powerful technologies that have transformed the ability of researchers to search for potentially causal variants in human disease. This study combines these tools to search for causal variants in a patient found to have maternal uniparental isodisomy of chromosome 2. This subject has a complex phenotype including skeletal and renal dysplasia, immune deficiencies, growth failure, retinal degeneration and ovarian insufficiency. Eighteen non‐synonymous, rare homozygous variants were identified on chromosome 2. Additionally, five genes with compound heterozygous mutations were detected on other chromosomes that could lead to a disease phenotype independent of the uniparental disomy found in this case. Several candidate genes with potential connection to the phenotype are described but none are definitively proven to be causal. This study highlights the potential for detection of a large number of candidate genes using whole exome sequencing complicating interpretation in both the research and clinical settings. Forums must be created for publication and sharing of detailed phenotypic and genotypic reports to facilitate further biological discoveries and clinical counseling.