5p部分单体3例全基因组拷贝数变异分析

目的应用全基因组微阵列芯片平台,对染色体核型提示为Cri du chat综合征的新生儿进行全基因组拷贝数变异（CNVs）的检测,以帮助解释基因型与表型的相关性。方法 2009年6月至2010年5月复旦大学附属儿科医院收治的染色体核型提示为Cri du chat综合征的3例新生儿进入研究。采用Cytogenetic Whole-Genome芯片筛查全基因组CNVs,针对发现的所有CNVs进行分析,参照国际基因组拷贝数变异多态性数据库除外正常人群多态性CNVs。结合本研究3例与DECIPHER数据库已报道的Cri du chat综合征患儿的临床表型,行5p缺失大小及范围分析,对重复区域行候选基因分析。结果 3例患儿经微阵列芯片检测,均证实并更为精确的定位了5p的缺失范围。例15p缺失位于5p15.33-p13.3,例2缺失位于5p15.33-5p15.1,例3缺失位于5p15.33-p14.3;此外例2发现9p部分重复,例3发现7p部分重复。结合DECIPHER数据库已报道的5例Cri du chat综合征临床表型,重复区域和候选基因分析显示,临床表型为猫叫样哭声或声音异常：缺失片段重叠区域为5p15.33-15.31内3.86Mb,覆盖（IRX1和IRX2与胚胎形成相关的基因）;临床表型为面容异常：缺失片段重叠区域为5p15.2-15.1内2.51Mb（覆盖ANKH与颅骨干骺端发育相关的基因）。例3合并有先天性巨结肠。因纳入病例均为新生儿,无法评价是否存在智力低下和生长发育迟缓,无法对相应的关键区域进行分析。结论本研究提供了微阵列平台罕见潜在致病可能CNVs的分析方法,进一步为建立5p部分缺失表型基因型关联性提供了依据。     

以先天性甲状腺功能减退为表现的14q12q13.3微缺失综合征患儿1例的临床及遗传学分析

目的分析1例以先天性甲状腺功能减退症(CH)为表现的14q12q13.3微缺失综合征患儿的临床表型与遗传学病因。方法以1例因先天性甲状腺功能减退就诊于临沂市人民医院的新生儿作为研究对象, 对其进行全外显子组测序(WES)、深度基因组拷贝数变异(CNV)和染色体微阵列分析(CMA), 分析其临床资料并进行文献复习。结果患儿于新生儿期起病, 主要表现为特殊面容、外阴水肿、肌张力低下、精神运动发育迟缓、反复呼吸道感染伴喉喘鸣和喂养困难等, 实验室检测显示甲状腺功能减退。WES和深度基因组CNV分析检测提示患儿染色体14q12q13.3区可能存在拷贝数缺失, CMA证实其14q12q13.3区(32649595₃6769800)存在4.12 Mb的片段缺失, 共涉及22个基因, 包含CH的致病基因NKX2-1, 患儿父母均未发现同样的片段缺失。结论综合其临床表型及基因检测的结果, 确诊患儿为14q12q13.3微缺失综合征。     

一例先天性唇腭裂胎儿的产前诊断

目的分析1例先天性唇腭裂胎儿的遗传学病因。方法应用染色体微阵列分析技术(chromosomal microarray analysis,CMA)检测胎儿及其家系成员染色体拷贝数变异(copy number variation,CNVs)。结果CMA检测显示胎儿为男性,其染色体Xp11.22区域存在228 kb的DNA片段缺失,染色体9p21.1区域存在721 kb的DNA片段重复,两个CNVs均遗传自亲代。其中染色体Xp11.22区域的CNV为可疑致病性CNV,致病基因为PHF8,9p21.1区域的CNV为良性CNV。结论染色体Xp11.22区域DNA片段缺失可能为胎儿唇腭裂的原因。     

10p末端三体致多发畸形的临床表型及遗传学分析

目的分析1例多发畸形患儿的遗传学原因,探讨其染色体变异与表型的相关性。方法应用常规G显带分析患儿外周血染色体核型,采用低覆盖度全基因组高通量测序技术(low-coverage massively parallel copy number variation sequencing,CNV-seq)进行DNA拷贝数变异分析,并通过荧光原位杂交对患儿及父母进行验证,以判断变异区域的结构变化和遗传学来源。结果G带检测患儿核型为46,XX,3pter+?。CNV-seq分析结果显示患儿10pl3pl5.3区存在约13.5 Mb重复(60466〜13556655)和3p26.3区存在636 kb微缺失(60064〜695821)0对患儿及父母进行FISH验证,明确患儿核型为46,XX,ish der(3)t(3;10)(10p+,3p dim),父母荧光原位杂交验证结果未见异常,提示患儿为新发变异。结论患儿的10pl3pl5.3重复与智力缺陷、生长迟缓、畸形表型、胃食管返流等临床表型相关。3p末端缺失涉及CHL1基因,该基因在大脑的构建和功能中起重要作用,可能同时协作影响患儿的智力发育。     

3p26.3p25.3缺失患儿1例的临床表型与遗传学分析

目的探讨1例特殊面容合并多发畸形患儿的遗传学病因并分析其与临床表型的相关性。方法选取2020年11月4日因"孕妇胎膜早破、双胎妊娠(双绒毛膜双羊膜囊)、妊娠期糖尿病"于孕34+6周自然分娩出生的1例患儿作为研究对象, 应用常规G显带方法分析患儿的染色体核型, 再用高通量测序法分析患儿拷贝数变异(CNVs)的情况。结果患儿为男性, 顺产出生, 表现为特殊面容、尿道下裂、隐睾、四肢肌张力低等。患儿染色体核型为46, XY, del(3)(p26), 高通量测序结果提示染色体3p26.3-p25.3 (60 000-9 860 000)存在约9.80 Mb的缺失, 共涉及33个蛋白编码基因。结论 3p26.3p25.3缺失可能是患儿的致病原因, 需对其进行持续随访, 提高生存质量。     

一例表现为主动脉瓣狭窄的非典型Williams-Beuren综合征患儿的遗传学诊断及分析

目的对1例主动脉瓣狭窄的患儿进行遗传学诊断,分析其发病机制。方法采用常规G显带染色体分析、微阵列比较基因组杂交(array comparative genomic hybridization,aCGH)及多重连接探针扩增(multiplex ligation-dependent probe amplification,MLPA)技术分析患儿及其父母的染色体核型和基因组拷贝数变异。结果患儿及其父母的外周血染色体核型均未见异常。aCGH检测显示患儿7q11.23区存在278 kb杂合缺失,与Williams-Beuren综合征(Williams-Beuren syndrome,WBS)关键区部分重叠,涉及WBS的关键致病基因之一ELN。MLPA检测证实患儿存在上述缺失,患儿父母未发现染色体微重复/微缺失。结论患儿7q11.23区杂合缺失为新发突变。ELN基因单倍剂量不足可能是其发生主动脉瓣狭窄的原因,诊断为非典型WBS。     

一例合并6q21-q22．31微缺失的锁骨颅骨发育不良患者的遗传学分析CSCD

目的对1例发育迟缓伴多发畸形患儿进行遗传学检测,分析其预后及发生机制,为临床咨询提供依据。 方法采用常规G显带和微阵列比较基因组杂交（array comparative genomic hybridization, aCGH）技术分析患儿及其父母的外周血染色体核型和DNA。结果G显带分析结果显示,患儿染色体核型为46,XX,del（6）（q22）,inv（6）（p21.1q21）,其父母染色体核型未见异常。aCGH检测结果显示患儿6p21.1区存在800 kb杂合缺失,包含RUNX2基因,6q21-q22.31区存在11.79 Mb杂合缺失,其父母未检测到染色体微重复/微缺失。 结论患儿为染色体新发倒位,两处微缺失均为新发突变,具有致病性。6p21.1区域RUNX2基因微缺失导致锁骨颅骨发育不良,6q21-q22.31区域微缺失可能与患儿脑部结构发育异常相关。     

一例8q21.11缺失综合征患儿的临床表型与遗传学诊断

目的对1例角膜混浊新生儿进行染色体拷贝数变异分析,明确其遗传学病因。方法应用常规G显带染色体核型分析技术分析患儿及其父母的外周血染色体核型,用全基因组低深度测序及单核苷酸多态性微阵列芯片(single nucleotide polymorphism array,SNP array)对患儿及其父母进行基因组拷贝数变异分析。结果G显带结果显示患儿及其父母染色体核型均未见异常,全基因组低深度测序结果显示患儿染色体8q21.11-q21.13区存在5.5 Mb杂合缺失,为新发突变,缺失区域包含ZFHX4、PEX2等基因,该结果在SNP array平台得到验证。结论患儿诊断为8q21.11缺失综合征,ZFHX4可能是该综合征的关键基因之一。     

1例3p部分三体综合征患儿的临床表型与遗传学分析

目的 明确1例体格发育异常合并多发畸形患儿染色体拷贝数变异的性质和来源，并分析基因与表型相关性。方法 采用G显带染色体核型分析及单核甘酸多态性微阵列芯片（SNP-array）技术对患儿进行检测，并用荧光原位杂交（FISH）进行验证。患儿父母外周血样本进行染色体核型分析及其母亲外周血样本进行荧光原位杂交（FISH）分析。结果 G显带染色体核型结果为：46,XY,der(2)t(2;3)(p25.3;p24.1),SNP-array分析结果显示患儿染色体3p26.3p24.1存在30.4Mb重复，2p25.3存在1.39Mb缺失。结论 患儿3p26.3p24.1重复与3p部分三体综合征（partialtrisomy3p syndrome）相关，该重复是导致患儿多发畸形及发育异常的主要遗传学病因。3p部分三体综合征临床表型差异较大，患儿临床特征与基因型有一定关联，临床诊断时应结合临床表型及遗传学检测技术进行综合诊断。     

一例Miller-Dieker综合征胎儿的产前诊断及遗传学分析

目的对1例无脑回畸形胎儿进行遗传学诊断,分析其可能的发生机制,为临床诊断和遗传咨询提供依据。方法应用拷贝数变异分析(copy number variation,CNV)技术检测分析胎儿羊水细胞DNA。结果CNV检测结果显示胎儿染色体17p13.3p13.2区存在5.02 Mb杂合缺失,该缺失片段完全覆盖Miller-Dieker综合征所在区域(chr17:1~2588909)。结论胎儿诊断为Miller-Dieker综合征,17号染色体短臂末端PAFAH1B1基因缺失可能是造成胎儿无脑回畸形的关键基因。     

Haploinsufficiency of XPO1 and USP34 by a de novo 230 kb deletion in 2p15, in a patient with mild intellectual disability and cranio-facial dysmorphisms

2p15p16.1-deletion syndrome was first described in 2007 based on the clinical presentation of two patients. The syndrome is characterized by intellectual disability, autism spectrum disorders, microcephaly, dysmorphic facial features and a variety of congenital organ defects. The precise genotype–phenotype correlation in 2p15-deletion syndrome is not understood. However, greater insight can be obtained by thorough clinical investigation of patients carrying deletions, especially those of small size. We report a 21-year-old male patient with features overlapping the clinical spectrum of the 2p15p16.1-deletion syndrome, such as intellectual disability, dysmorphic facial features, and congenital defects. He carried a 230 kb de novo deletion (chr2:61500346-61733075 bp, hg19), which affects the genes USP34, SNORA70B and XPO1. While there is a lack of functional data on SNORA70B, the involvement of USP34 and XPO1 in the regulation of fundamental developmental processes is well known. We suggest that haploinsufficiency of one or both of these genes is likely to be responsible for the disease in our patient.     

染色体核型分析联合染色体微阵列分析对于产前诊断的价值

目的评估染色体核型分析联合染色体微阵列分析(chromosomal microarray analysis,CMA)对于产前诊断的价值。方法对546例孕妇的羊水同时进行G显带染色体核型分析和CMA检测。结果共检出82例异常,其中43例两种方法的检测结果一致,包括21三体14例、18三体6例、13三体1例、性染色体数目异常14例、染色体缺失4例、染色体重复3例以及嵌合体1例。核型分析漏检15例,包括染色体微缺失9例和染色体微重复6例。CMA漏检16例,包括染色体易位15例,性染色体嵌合1例。有7例核型分析与CMA检测结果不一致。1例核型分析为标记染色体,经CMA检测为9号染色体p13.1p21.1重复。结论染色体核型分析联合CMA技术可以提高染色体异常的检出率,对产前诊断具有重要的意义。     

Clinical and genetic analysis of three children patients with Kleefstra syndromeCSCD

Objective To explore the genetic basis of three children with unexplained developmental delay/intellectual disability (DD/ID). Methods Peripheral blood samples were collected from the patients and subjected to chromosomal microarray analysis (CMA). Results Patient 1 was found to harbor a 190 kb deletion at 9q34.3, which encompassed most of EHMT1 (OMIM 607001), the key gene for Kleefstra syndrome (OMIM 610253). Patients 2 and 3 were siblings. CMA showed that they have shared four chromosomal copy number variations (CNVs) including a deletion at 9q34.3 which spanned 154 kb and 149 kb, respectively, and encompassed the EHMT1 and CACNA1B (OMIM 601012) genes. The remaining 3 CNVs were predicted to be with no clinical significance. Conclusion Microdeletions at 9q33.4 probably underlay the pathogenesis of DD/ID in the three children, for which EHMT1 may be the key gene. © 2022 West China University of Medical Sciences. All rights reserved.     

Combined G-banded karyotyping and multiplex ligation-dependent probe amplification for the detection of chromosomal abnormalities in fetuses with congenital heart defects北大核心CSCD

Objective To assess the value of G-banded karyotyping in combination with multiplex ligation-dependent probe amplification (MLPA) as a tool for the detection of chromosomal abnormalities in fetuses with congenital heart defects. Methods The combined method was used to analyze 104 fetuses with heart malformations identified by ultrasonography. Abnormal findings were confirmed with chromosomal microarray analysis (CMA). Results Nineteen (18%) fetuses were found to harbor chromosomal aberrations by G-banded karyotyping and MLPA. For 93 cases, CMA has detected abnormalities in 14 cases including 10 pathogenic copy number variations (CNVs) and 4 CNVs of uncertain significance (VOUS). MLPA was able to detect all of the pathogenic CNVs and 1 VOUS CNV. Conclusion Combined use of G-banded karyotyping and MLPA is a rapid, low-cost and effective method to detect chromosomal abnormalities in fetuses with various heart malformations.     

染色体微阵列分析对于胎儿十二指肠梗阻的检测价值

目的探讨染色体微阵列分析(chromosome microarray analysis,CMA)对于胎儿十二指肠梗阻(duodenal obstruction,DO)的检测价值。方法选取51例超声提示存在DO的胎儿,将其分为单纯组和合并其他异常组。对其进行CMA检测,并随访所有病例的妊娠结局。结果在51例胎儿中共发现8例异常,检出率为15.7%,包括3例染色体数目异常,5例致病性拷贝数变异(copy number variations,CNVs),分别为17q12微重复综合征、13q21.33q31.1微缺失、13q21.32q22.3缺失、13q21.2q31.1缺失和1q43q44重复。13q的EDNRB及17q12的HNF1B为胎儿DO的候选基因。单纯DO组于合并其他结构异常组致病性CNVs的检出率差异无统计学意义(9.5%vs.11.1%,P>0.05)。39例活产,1例死胎,引产的11例中包括8例CMA结果异常者。结论DO与基因组拷贝数异常存在一定的相关性,须进行产前诊断。CMA不仅可以检测微缺失/微重复变异,同时具有发现可疑致病基因的能力,可为DO胎儿的产前诊断、咨询以及预后评估提供依据。     

染色体微阵列产前诊断8q13.3微缺失一例

目的应用染色体微阵列分析(chromosome microarray analysis,CMA)技术对1例超声结构异常胎儿进行全基因组拷贝数变异(copy number variations,CNVs)检测,探讨CMA在超声结构异常胎儿产前诊断中的意义。方法应用常规G显带染色体核型分析胎儿及其父母的染色体核型,应用CMA技术分析胎儿及其父母的CNVs。结果G显带核型分析显示胎儿核型与母亲一致,为46,XN,t(8;11)(q21.2;q13)mat,父亲核型正常;父母CMA检测结果均未见异常;胎儿的检测结果为arr[GRCh37]8q13.3(71314082-73322915)×1,提示一条8号染色体的8q13.3区域发生2.00 Mb缺失。结论超声结构异常胎儿染色体核型分析检出的平衡易位,需借助CMA等技术进一步确定是否存在微缺失微重复。     

无创产前筛査对于检测胎儿16号染色体非整倍体的价值

目的通过多种技术验证及追踪随访妊娠结局,探讨无创产前筛査(non-invasive prenatal screening,NIPS)对于检测胎儿16号染色体非整倍体的价值。方法选取7972例孕周>10周的单胎妊娠孕妇,经知情同意后对其进行NIPS检测。对结果提示16号染色体异常者进行侵入性产前诊断,对羊水进行染色体核型和染色体微阵列分析(chromosomal microarray analysis,CMA).结果16例孕妇NIPS检测提示胎儿存在16号染色体异常,检出率为0.2%。孕妇平均年龄为(33.5±5.24)岁,平均孕周为(19.88±2.47)周。羊水核型分析显示3例胎儿为染色体嵌合体,1例为9号染色体臂间倒位,阳性预测值(positive predictive value,PPV)为1&8%;CMA检测的PPV则高达43.8%o 16例孕妇中有11人分娩出正常婴儿,占68.8%.结论对于NIPS提示16号染色体非整倍体高风险的孕妇,应结合多种技术对结果进行评估。CMA等分子检测手段优于传统的核型分析,在临床诊断时应首选。     

染色体微阵列分析在超声异常胎儿产前诊断中的应用价值

目的探讨染色体微阵列分析技术(chromosomal microarray analysis,CMA)在超声异常胎儿产前诊断中的应用价值。方法选取B超提示异常的胎儿293例,包括结构异常168例及非结构异常125例。在排除常见的染色体异常核型后,对其羊水行CMA检测。结果CMA共检出致病性拷贝数变异(pathogenic copy number variants,pCNVs)16例,检出率为5.46%。在168例结构异常胎儿中检出pCNVs 10例,检出率为5.95%。在125例非结构异常胎儿中检出pCNVs 6例,检出率为4.80%。结论与传统的染色体核型分析相比,CMA可以提高超声异常胎儿染色体异常的检出率,可作为有效的产前诊断方法。     

2p15-p16.1 microdeletion syndrome: molecular characterization and association of the OTX1 and XPO1 genes with autism spectrum disorders

Reports of unrelated individuals with autism spectrum disorder (ASD) and similar clinical features having overlapping de novo interstitial deletions at 2p15-p16.1 suggest that this region harbors a gene(s) important to the development of autism. We molecularly characterized two such deletions, selecting two genes in this region, exportin 1 (XPO1) and orthodenticle homolog 1 (OTX1) for association studies in three North American cohorts (Autism Spectrum Disorder - Canadian American Research Consortium (ASD-CARC), New York, and Autism Genetic Resource Exchange (AGRE)) and one Italian cohort (Società Italiana per la Ricerca e la Formazione sull'Autismo (SIRFA)) of families with ASD. In XPO1, rs6735330 was associated with autism in all four cohorts (P<0.05), being significant in ASD-CARC cohorts (P-value following false discovery rate correction for multiple testing (P(FDR))=1.29 × 10(-5)), the AGRE cohort (P(FDR)=0.0011) and the combined families (P(FDR)=2.34 × 10(-9)). Similarly, in OTX1, rs2018650 and rs13000344 were associated with autism in ASD-CARC cohorts (P(FDR)=8.65 × 10(-7) and 6.07 × 10(5), respectively), AGRE cohort (P(FDR)=0.0034 and 0.015, respectively) and the combined families (P(FDR)=2.34 × 10(-9) and 0.00017, respectively); associations were marginal or insignificant in the New York and SIRFA cohorts. A significant association (P(FDR)=2.63 × 10(-11)) was found for the rs2018650G-rs13000344C haplotype. The above three SNPs were associated with severity of social interaction and verbal communication deficits and repetitive behaviors (P-values <0.01). No additional deletions were identified following screening of 798 ASD individuals. Our results indicate that deletion 2p15-p16.1 is not commonly associated with idiopathic ASD, but represents a novel contiguous gene syndrome associated with a constellation of phenotypic features (autism, intellectual disability, craniofacial/CNS dysmorphology), and that XPO1 and OXT1 may contribute to ASD in 2p15-p16.1 deletion cases and non-deletion cases of ASD mapping to this chromosome region.     

Prediction of osteoporosis candidate genes by computational disease-gene identification strategy

Osteoporosis is a complex disease with a strong genetic component. To date, more than 20 genome-wide linkage scans across multiple populations have been launched to hunt for osteoporosis susceptibility genes. Some significant or suggestive chromosomal regions of linkage to bone mineral density have been identified and replicated in genome-wide linkage screens. However, identification of key candidate genes within these confirmed regions is challenging. We used five freely available bioinformatics tools (Prioritizer, GeneSeeker, PROSPECTR and SUSPECTS, Disease Gene Prediction, and Endeavor) to analyze the 13 well-replicated osteoporosis susceptibility loci: 1p36, 1q21-25, 2p22-24, 3p14-25, 4q25-34, 6p21, 7p14-21, 11q14-25, 12q23-24, 13q14-34, 20p12, 2q24-32, and 5q12-21. Pathways and regulatory network analyses were performed using the Ingenuity Pathways Analysis (IPA) software. We identified a subset of most likely candidate osteoporosis susceptibility genes that are largely involved in transforming growth factor (TGF)-beta signaling, granulocyte-macrophage colony-stimulating factor (GM-CSF) signaling, axonal guidance signaling, peroxisome proliferator-activated receptor (PPAR) signaling, and Wnt/beta-catenin signaling pathway. Six nonoverlapping networks were generated by IPA 5.0 from 88 out of the 91 candidate genes. The list of most likely candidate genes and the associated pathway identified will assist researchers in prioritizing candidate disease genes for further empirical analysis and understanding the pathogenesis of osteoporosis.