孤立型室间隔缺损胎儿的基因组拷贝数变异分析及文献回顾

目的评估拷贝数变异(CNVs)检测对于孤立型室间隔缺损(VSD)胎儿遗传学病因的诊断价值。方法选取2017年12月至2020年12月郑州大学第一附属医院超声检查发现的69例孤立型VSD胎儿, 同时检索万方、万方医学、中国知网等数据库, 2016年1月1日至2021年1月1日以"室间隔缺损""拷贝数变异"以及"产前"为关键词, 连同文献报道的839例胎儿, 共计908例孤立型VSD胎儿作为研究对象。对69例胎儿进行低深度全基因组测序, 并合并文献数据进行回顾性分析。结果在908例样本中, 共检出33例致病性异常, 总体检出率为3.63%。其中包括11例(1.21%)非整倍体以及22例(2.42%)致病性CNVs。后者涉及12种综合征, 具体包括5例22q11.21缺失、2例4q末端缺失以及1例9q亚端粒缺失, 均与心脏发育相关。22例致病性CNVs胎儿中, 15例具有已知的妊娠结局, 12例为自主终止妊娠, 3例出生后室间隔自然闭合, 但其中1例具有其他异常。结论孤立型VSD的胎儿具有较高的染色体异常检出率, 因此建议对其进行CNV-seq检测。     

微阵列比较基因组杂交技术检测先天性心脏畸形胎儿的隐藏基因组拷贝数变异

目的 检测1例先天性主动脉弓离断和室间隔缺损胎儿的基因组拷贝数变异(copy number variations,CNVs),寻找其致病的遗传学证据,探讨微阵列比较基因组杂交技术(array-based comparative genomic hybridization,array-CGH)在分子细胞遗传诊断中应用的可行性.方法 对该患儿脐血及其父母外周血进行常规G显带核型分析,发现胎儿核型为46,XX,t(7;9)(q12;q21),双亲核型正常.进而应用array-CGH芯片对患儿进行全基因组高分辨率扫描分析,采用荧光原位杂交技术(fluorescence in situ hybridization,FISH)对新发现的CNVs进行实验验证.结果 array-CGH分析发现胎儿基因组存在1个病理性亚显微结构的拷贝数变异:del(22)(q11.2)(17 370 128～19 790 009,2.42 Mb).FISH实验结果验证了此22q11.2微缺失的存在.结论 隐藏的22q11.2微缺失可能是此胎儿致病的原因;染色体平衡易位的先天缺陷胎儿可能会含有位于重排断裂点区域之外的亚显微结构基因组拷贝数变异;微阵列比较基因组杂交具有高分辨率、高通量和高准确性等优点,适用于亚显微基因组拷贝数变异的检测.     

微阵列比较基因组杂交技术检测先天性心脏畸形胎儿的隐藏基因组拷贝数变异

目的 检测1例先天性主动脉弓离断和室间隔缺损胎儿的基因组拷贝数变异(copy number variations,CNVs),寻找其致病的遗传学证据,探讨微阵列比较基因组杂交技术(array-based comparative genomic hybridization,array-CGH)在分子细胞遗传诊断中应用的可行性.方法 对该患儿脐血及其父母外周血进行常规G显带核型分析,发现胎儿核型为46,XX,t(7;9)(q12;q21),双亲核型正常.进而应用array-CGH芯片对患儿进行全基因组高分辨率扫描分析,采用荧光原位杂交技术(fluorescence in situ hybridization,FISH)对新发现的CNVs进行实验验证.结果 array-CGH分析发现胎儿基因组存在1个病理性亚显微结构的拷贝数变异:del(22)(q11.2)(17 370 128～19 790 009,2.42 Mb).FISH实验结果验证了此22q11.2微缺失的存在.结论 隐藏的22q11.2微缺失可能是此胎儿致病的原因;染色体平衡易位的先天缺陷胎儿可能会含有位于重排断裂点区域之外的亚显微结构基因组拷贝数变异;微阵列比较基因组杂交具有高分辨率、高通量和高准确性等优点,适用于亚显微基因组拷贝数变异的检测.     

一例手足裂胎儿的临床特征及病因学分析

目的分析一例手足裂胎儿的临床特征以及基因组拷贝数变异(copy number variations,CNVs)的情况。方法收集孕期胎儿超声以及引产儿X线检查资料并进行总结。应用二代测序(next generation sequencing,NGS)检测引产儿的CNVs。用NGS及荧光原位杂交(fluorescence in situ hybridization,FISH)对其亲代进行分析,用实时荧光定量PCR对胎儿染色体异常区域的基因表达量进行检测。结果超声及X线检查提示胎儿右手及双足均呈"V"形开裂。NGS检测提示胎儿染色体7q21.3区存在约0.36 Mb的缺失。NGS及FISH检测提示其双亲均未携带相同的变异。实时荧光定量PCR结果提示胎儿DYNC1I1基因存在杂合缺失,而SEM1、DLX5、DLX6基因的拷贝数则未见异常。结论胎儿手足裂畸形的致病原因为7q21.3区微缺失,后者为新发变异。     

三个17q12微缺失综合征家系的临床表型及遗传学分析

目的明确3个有胎儿肾脏发育异常史的家系的遗传学病因,并分析其与表型的相关性。方法采集先证者的外周血或引产胎儿的皮肤样本,应用二代测序技术对全基因组染色体拷贝数变异进行检测。结果家系1患者曾反复发生胎儿肾脏发育异常,且合并多囊肾及糖尿病,家系2和3均于孕期发现胎儿肾脏发育异常。3个家系的样本均发现在17q12区存在1.4~1.48 Mb的杂合性缺失,其范围均涉及HNF1B基因。结论17q12微缺失综合征患者的肾脏表现尤为广泛,不易确诊。对染色体拷贝数进行检测有助于明确相关肾脏异常的遗传学病因。     

产前诊断胎儿泌尿系统畸形与染色体1q21.1微缺失

目的 应用微阵列比较基因组杂交技术探讨胎儿先天性泌尿系统畸形的遗传学病因.方法 选取32例经产前超声检查提示发生不同程度泌尿系统畸形并且常规G显带核型分析方法未发现异常的胎儿病例及其父母的DNA,按照标准的Affymetrix cytogenetic 2.7M芯片的操作手册进行杂交、洗涤及全基因组扫描,应用配套的CHAS软件分析结果.结果 微阵列比较基因组杂交技术检测发现9例胎儿基因组发生了不平衡的拷贝数变异(copy number variations,CNVs),检出率为28％.其中4例CNVs遗传自亲代(12.5％);2例CNVs在相关数据库中提示在正常人基因组中存在(6％);3例是新发的致病性CNVs(9％),并且这3例胎儿样本均发生了染色体1q21.1微缺失和微重复,异常片段内包含与泌尿生殖系统功能密切相关的PDZK1基因.结论 先天性泌尿系统畸形胎儿基因组发生不平衡畸变的几率约为28％,其中致病性的基因组不平衡异常约占9％.染色体1q21.1区带DNA拷贝数改变是导致先天性泌尿系统畸形的病因之一,其致病机制可能与PDZK1基因的异常表达有关.     

先天性心脏病患者22q11微缺失检测及相关分析

目的探讨5个短串联重复（short tandem repeat，STR）标记用于检测22q11微缺失的可行性，了解中国汉族未经挑选的先天性心脏畸形患者中22q11微缺失的发生情况。方法选择位于22q11缺失区域的5个STR标记，对163例中国汉族先天性心脏畸形（congenital heart defect，CHD）息者及双亲进行单倍型分析，对检出的阳性病例及部分阴性病例进行荧光原位杂交（fluorescence in situ hybridization，FISH）验证。结果5个标记均具有较好的信息量，22D_4_1和22D_4_2杂合率分别为0．65和0．52，22D_4_3、22D_4_4和D22S873杂合率均在0．7以上，可用于汉族人群多态性分析；163例先天性心脏畸形患者用STR标记检出12例22q11微缺失，其中9例得到FISH检测证实，2例微小缺失和1例远端缺失FISH检测为阴性；CHD患者22q11微缺失检出率为7．36％，室间隔缺损微缺失检出率为8．18％（9／110），法乐氏四联征检出率为14．3％（3／21），其它类型的CHD未检出缺失。结论5个STR标记可用于汉族人群22q11微缺失的检测，且有快速、成本低的优点；中国汉族CHD患者中存在一定比率的22q11微缺失，尤其是室间隔缺损和法乐氏四联征较为常见。     

全基因组芯片产前诊断母源性中间缺失型22q11.2微缺失胎儿一例

目的对1例无创产前检测提示22号染色体长臂q11.21位置存在1.62 Mb缺失的胎儿进行产前诊断,为其家系提供遗传咨询。方法行羊水穿刺术后,通过常规染色体核型分析和全基因组芯片技术对胎儿进行产前诊断。应用全基因组芯片技术对胎儿父母进行比对分析,以明确胎儿基因组变异的来源。结果羊水常规染色体核型分析结果显示胎儿染色体核型为46,XX,胎儿全基因组芯片结果为arr[hg19]22q11.21(20,723,685-21,800,471)x1,即胎儿22q11.21区段存在1.08 Mb的缺失,该区域覆盖CRKL基因,TBX1、COMT、HIRA及MAPK1基因并不包含在内。经基因组定位分析发现,该缺失属于22q11.2微缺失综合征中间缺失型。父母外周血全基因组芯片比对结果显示,胎儿父亲染色体为正常男性核型:arr(1-22)×2,(X,Y)×1,胎儿母亲为女性核型,含有2处染色体异常:arr[hg19]22q11.21(20,716,876-21,800,471)x1,即22q11.21区段存在约1.08 Mb缺失;arr[hg19]22q13.31(45,071,900-45,305,325)x1,即22q13.31区段存在约233 kb缺失。结论胎儿22号染色体长臂上存在的微缺失遗传自母亲,为罕见的母源性22q11.2微缺失中间缺失型。     

微阵列比较基因组杂交技术检测先天性心脏畸形胎儿的隐藏基因组拷贝数变异

目的 检测1例先天性主动脉弓离断和室间隔缺损胎儿的基因组拷贝数变异(copy number variations,CNVs),寻找其致病的遗传学证据,探讨微阵列比较基因组杂交技术(array-based comparative genomic hybridization,array-CGH)在分子细胞遗传诊断中应用的可行性.方法 对该患儿脐血及其父母外周血进行常规G显带核型分析,发现胎儿核型为46,XX,t(7;9)(q12;q21),双亲核型正常.进而应用array-CGH芯片对患儿进行全基因组高分辨率扫描分析,采用荧光原位杂交技术(fluorescence in situ hybridization,FISH)对新发现的CNVs进行实验验证.结果 array-CGH分析发现胎儿基因组存在1个病理性亚显微结构的拷贝数变异:del(22)(q11.2)(17 370 128～19 790 009,2.42 Mb).FISH实验结果验证了此22q11.2微缺失的存在.结论 隐藏的22q11.2微缺失可能是此胎儿致病的原因;染色体平衡易位的先天缺陷胎儿可能会含有位于重排断裂点区域之外的亚显微结构基因组拷贝数变异;微阵列比较基因组杂交具有高分辨率、高通量和高准确性等优点,适用于亚显微基因组拷贝数变异的检测.

Abstract：

Objective To detect the copy number variation (CNV) of a fetus with interrupted aortic arch and ventricular septal defect, in order to explore the underlying genetic causes of the congenital malformation, and investigate the feasibility of array-based comparative genomic hybridization (array-CGH)in molecular cytogenetic diagnosis. Methods The whole genome of the fetus with de novo apparently balanced translocations [46, XX, t ( 7 ; 9 ) ( q12 ; q21 ) ] diagnosed by G-banding was scanned and analyzed by array-CGH, and the copy number variation was confirmed by fluorescence in situ hybridization (FISH).Results A pathologic submicroscopic CNV ldel(22) (q11. 2) (17 370 128-19 790 009,-2. 42 Mb)] was identified and mapped by array-CGH. FISH test confirmed the microdeletion detected by array-CGH.Conclusion The cryptic 22q11.2 deletion might be the reason leading to the congenital malformation of the fetus. This study provides evidence that apparently balanced translocations classified by conventional cytogenetic techniques may host additional submicroscopic CNVs which are not located at the breakpoints.Due to the high-resolution, high-throughput and high-accuracy, array-CGH is considered to be a powerful tool for submicroscopic CNVs detection.     

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。     

Identification of a new familial case of 3q29 deletion syndrome associated with cleft lip and palate via whole-exome sequencing

Many unbalanced large copy number variants reviewed in the paper are associated with syndromic orofacial clefts, including a 1.6 Mb deletion on chromosome 3q29. The current report presents a new family with this recurrent deletion identified via whole-exome sequencing and confirmed by array comparative genomic hybridization. The proband exhibited a more severe clinical phenotype than his affected mother, comprising right-sided cleft lip/alveolus and cleft palate, advanced dental caries, heart defect, hypospadias, psychomotor, and speech delay, and an intellectual disability. Data analysis from the 3q29 registry revealed that the 3q29 deletion increases the risk of clefting by nearly 30-fold. No additional rare and pathogenic nucleotide variants were identified that could explain the clefting phenotype and observed intrafamilial phenotypic heterogeneity. These data suggest that the 3q29 deletion may be the primary risk factor for clefting, with additional genomic variants located outside the coding sequences, methylation changes, or environmental exposure serving as modifiers of this risk. Additional studies, including whole-genome sequencing or methylation analyses, should be performed to identify genetic factors underlying the phenotypic variation associated with the recurrent 3q29 deletion.     

BMPR1A is a candidate gene for congenital heart defects associated with the recurrent 10q22q23 deletion syndrome

Congenital heart defects (CHD) are associated with the recurrent 10q22q23 deletion syndrome and with partially overlapping distal 10q23.2.q23.31 microdeletions. We report on a de novo intragenic deletion of the BMPR1A gene in a normally developing adolescent boy with short stature, delayed puberty, facial dysmorphism and an atrioventricular septal defect. Based on this finding, complemented with computational prioritization data and molecular evidence in literature, the critical region for CHD on 10q23 can be downsized to a single gene, BMPR1A. Although loss-of-function mutations in BMPR1A typically result in juvenile polyposis syndrome, none of the patients with the typical 10q22q23 microdeletion syndrome, comprising this gene, were reported to have juvenile polyposis thus far. We reason that, even in the absence of juvenile polyposis syndrome, sequencing and copy number analysis of BMPR1A should be considered in patients with (atrioventricular) septal defects, especially when associated with facial dysmorphism and anomalous growth.     

Congenital anomalies and rhabdoid tumor associated with 22q11 germline deletion and somatic inactivation of the SMARCB1 tumor suppressor

The most common microdeletion in humans involves the 22q11 region. Congenital anomalies associated with 22q11 loss include cardiac and facial defects. Less frequent is the co-presentation of malignant rhabdoid tumors that are highly aggressive childhood malignancies typically found in renal or extra-renal soft tissues and central nervous system. A newborn patient presented with multiple congenital anomalies consistent with 22q11 deletion syndrome including cleft lip and palate, ear tags and ventricular septal defects co-presenting with an axillary rhabdoid tumor. Comparative genomic hybridization revealed a 2.8 Mb germline deletion in the 22q11.2 region containing genes required for normal fetal development and the SMARCB1 tumor suppressor gene. Analysis of tumor DNA revealed a somatic deletion of exon 7 in the second allele of SMARCB1. Expression of SMARCB1 was absent, while tumor markers including MYC, GFAP, and CLAUDIN-6 were upregulated. The presence of tandem oriented BCRL modules located within interspersed low copy repeat elements throughout the 22q11 distal region may predispose this area for microdeletions through nonalleleic homologous recombination.     

Congenital heart defect in a patient with deletion of chromosome 7q

We describe a premature male infant with a terminal deletion of 7q [del(7) (pter----q34:)]. Manifestations include low birth weight, hypertelorism, bilateral cleft lip and palate, cryptorchidism, and a complex congenital heart defect. The latter consisted of hypoplasia of the main pulmonary artery, absent pulmonary valve, ventricular septal defect, and anomalous right pulmonary artery. We briefly review the spectrum of heart defects seen with chromosome 7 deletions, and comment on the incidence of this unusual heart lesion.     

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。