胎儿侧脑室增宽与拷贝数变异的研究进展

侧脑室增宽(ventriculomegaly,VM)是一种常见的超声异常,与感染、染色体异常及结构畸形相关。目前,传统的核型分析技术是检测胎儿侧脑室增宽遗传学病因的主要手段。近年来,由于染色体微阵列分析技术(chromosomal microarray analysis,CMA)在产前诊断领域的广泛应用,VM被发现与拷贝数变异(copy number variations,CNVs)密切相关。最近研究表明,除了染色体数目异常和大片段结构异常外,致病性CNVs是胎儿VM的另一个重要遗传学原因,并且可能参与胎儿VM的病理过程以及出生后神经发育障碍。此外,VM胎儿致病性CNVs的检出率与是否合并其他结构异常有关,但与VM的严重程度无关。然而,由于CNVs是胎儿VM的重要原因,因此,应建议所有VM胎儿进行CMA检测,无论VM的严重程度或是否合并其他结构异常。     

77例室间隔缺损胎儿产前超声及遗传学检查结果分析

目的 探讨室间隔缺损(VSD)胎儿常见超声异常表型及遗传学结果,为产前咨询及预后评估提供资料。方法 对2016年11月至2018年12月我院超声心动图诊断VSD胎儿进行染色体核型分析、染色体微阵列分析(CMA)、低深度全基因组测序方法(CNV-seq)、全外显子测序(WES)等遗传学检测。以遗传学检测资料完整并随访至妊娠终止的77例VSD胎儿作为研究对象,回顾性分析其心脏及心外超声结构异常表型、遗传学检查结果。结果 1.77例VSD胎儿中：孤立性VSD胎儿41例(53.2%),VSD同时合并心脏及心外畸形16例(20.8%)、VSD只合并心脏畸形14例(18.2%)、VSD只合并心外畸形6例(7.8%)。2.超声表型异常：合并心外畸形22例(28.6%),以超声微小结构异常最常见;合并心脏异常30例(39%),均为圆锥动脉干畸形。3.遗传学异常共16例,检出率20.8%(16/77)：VSD同时合并心脏及心外畸形胎儿遗传学异常率最高,为43.8%(7/16), 其次为VSD只合并心脏畸形胎儿35.7%(5/14)、VSD只合并心外畸形胎儿33.3%(2/6)、孤立性VSD胎儿4.9%(2/41)。在核型正常VSD胎儿中额外检出12例异常：致病性CNVs 8例(6例微缺失、2例微重复)、4例单基因病,分子诊断率分别提高了15.1%、7.5%。结论 产前超声发现胎儿存在VSD时,应仔细扫查是否合并心脏及心外异常,并进行遗传学检测;综合合理应用包括核型,CMA及高通量测序(WES, CNV-seq)等方法能提高VSD胎儿遗传学异常检出率,对VSD胎儿的产前评估和预后咨询能提供更多信息。     

染色体微阵列分析在脉络丛囊肿胎儿产前诊断中的应用

目的 探讨染色体微阵列分析(CMA)在脉络丛囊肿(CPC)胎儿产前诊断中的应用价值。方法 回顾性选取2017年4月至2020年11月在安徽省妇幼保健院于孕中期超声诊断为胎儿CPC的孕妇187例,分别采用CMA技术和核型分析技术检测胎儿染色体异常情况,并进行统计学分析。结果 187例CPC胎儿中,核型分析技术检出12例染色体非整倍体异常,检出率为6.42%(12/187),其中18-三体9例。CMA技术检出染色体非整倍体异常与核型分析结果一致,但额外检出异常CNVs 16例,额外检出率为8.56%(16/187)。孤立性CPC胎儿、CPC合并超声软指标胎儿和CPC合并超声结构异常胎儿pCNVs的检出率分别为5.10%、11.11%和58.33%,3组间的差异有统计学意义(χ²=38.33,P=0.000)。结论 采用CMA技术检测CPC胎儿染色体异常具有更高的敏感性,可以提高对CPC胎儿异常CNVs的检出率,为临床医生进行产前遗传咨询及胎儿预后评估提供依据。     

产前超声诊断先天性心脏病胎儿的基因特征

目的 观察产前超声诊断先天性心脏病（CHD）胎儿的基因特征。方法 回顾性分析613胎经产前超声诊断CHD的单胎胎儿资料,并将其分为8类心脏结构异常;其中40胎因染色体核型分析和/或染色体微阵列分析（CMA）提示良性拷贝数变异（CNV）或临床意义不明确的CNV（VUS）而接受全外显子测序（WES）。结果 613胎CHD中,479胎接受染色体核型分析及CMA,基因检测显示60胎（60/479,12.53%）存在异常;134胎仅接受CMA,基因检测显示4胎（4/134,2.99%）存在异常。568胎为孤立性、45胎为非孤立性CHD,分别有40胎（40/568,7.04%）及15胎（15/45,33.33%）染色体核型分析和/或CMA显示异常。复合型CHD（10/41,24.39%）染色体核型分析和/或CMA异常检出率高于非复合型（54/572,9.44%）。复合型CHD中,染色体核型分析和/或CMA异常检出率在圆锥动脉干畸形（CTD）合并静脉系统畸形胎儿中最高,达30.77%（4/13）;非复合型CHD中,染色体核型分析和/或CMA异常检出率在内脏反位胎儿中最高,为25.00%（1/4）。染色体核型分析和/或CMA结果提示良性CNV或VUS的40胎中,WES提示3胎为致病性/可能致病性CNV（P/LP）、3胎为VUS、34胎为良性CNV。结论 CHD胎儿、尤其合并心外畸形者可能存在基因异常;CTD胎儿合并其他类型心脏结构异常时,基因异常可能性更大。相比单纯CMA,染色体核型分析联合CMA更有助于发现基因异常。     

多种分子遗传技术应用于2例小额外标记染色体胎儿的产前筛查与诊断

目的运用多种分子遗传技术对小额外标记染色体(small supernumerary marker chromosome,sSMC)胎儿进行产前筛查和诊断,探讨各分子遗传技术的优缺点。方法对2例无创产前基因检测(non-invasive prenatal tests, NIPT)高风险胎儿的孕妇进行羊膜腔穿刺术,采集羊水标本,运用多重连接依赖探针扩增技术(multiplex ligation-dependent probe amplification,MLPA)对2例胎儿进行染色体非整倍体快速诊断,同时进行细胞培养和G显带核型分析;采用染色体微阵列技术(chromosome microarray, CMA)对胎儿1(18三体高风险)进行验证,采用MLPA技术对胎儿2(性染色体异常高风险)进行Y染色体微缺失检测。2例胎儿双亲均进行外周血G显带核型分析。结果 MLPA技术快速诊断结果为:胎儿1的18号染色体短臂部分三倍体,胎儿2携带2条正常X染色体和1条短臂缺失的Y染色体;胎儿1羊水G显带核型结果为47,XY,+Mar(胎儿1),胎儿2为47,XX,+Mar;胎儿1的CMA检测结果为arr[hg19]18p11.32p11.21 (136,227-15,099)×4;胎儿2的Y染色体微缺失结果为SRY基因和生精区AZFc区缺失。2例胎儿父母双亲的外周血染色体核型均正常。结论 NIPT检测适用于sSMC胎儿的产前筛查,不同的分子遗传产前诊断技术检测sSMC胎儿各有优缺点,相互补充验证的结果可为sSMC胎儿临床遗传咨询提供更详细的信息。     

SNP-array分析在超声波检测颈项透明层增厚胎儿的遗传学诊断中的应用

目的探讨染色体核型分析与单核苷酸多态性微阵列芯片技术(single nucleotide polymorphism array,SNP-array)在颈项透明层(nuchal translucency,NT)增厚胎儿遗传学检查中的应用价值。方法回顾分析130例妊娠早期(11～13~(+6)周)NT≥3.0 mm为NT增厚,行介入性产前诊断绒毛标本的临床资料,统计并分析胎儿染色体核型分析与染色体微阵列芯片检测情况。染色体微阵列分析采用Illumina Human Cyto SNP12微阵列芯片进行全基因组拷贝数变异(copy number variations,CNVs)检测,结合查询国际病理性CNVs数据库(ClinGen,ClinVar,DECIPHER,OMIM)、正常人基因组变异数据库(database of genomic variants,DGV)以及PubMed文献数据库等对检出的CNVs的致病性进行分析。结果 130例胎儿NT增厚的胎儿样本中,检出染色体核型异常35例,检出率26.9%(35/130),检出SNP-array异常44例,检出率33.8%(44/130),SNP-array异常检出率明显高于染色体核型异常检出率,并且差异具有统计学意义(χ~2=6.23,P0.05)。且染色体微阵列技术检出了染色体核型分析未能检出的8例微缺失,4例微重复以及1例单亲二倍体。结论对超声检测胎儿NT增厚的胎儿样本,行SNP-array检测有助于发现染色体核型分析无法检出的染色体亚显微结构异常,且SNP-array有利于提高对颈项透明层增厚胎儿遗传病因的诊断。     

染色体微阵列检测技术在NT增厚胎儿中的应用

目的探讨染色体微阵列(CMA)检测技术在颈项透明层(NT)增厚胎儿中检测基因组拷贝数变异(CNVs)的临床应用价值。方法收集2018年1月至12月郑州大学第三附属医院妊娠早期NT筛查异常(≥2.5 mm)并接受CMA检查的胎儿305例,分析胎儿染色体数目异常及拷贝数异常发生情况;并根据NT值分为以下5组:2.5～2.9 mm、3.0～3.4 mm、3.5～3.9 mm、4.0～4.9 mm、≥5 mm组,分析各组胎儿染色体数目异常及微缺失、微重复发生情况;根据是否合并其他超声异常,分为合并超声异常组和单纯组,分析并比较两组染色体异常发生情况。结果 NT值2.5～2.9 mm、3.0～3.4 mm、3.5～3.9 mm、4.0～4.9 mm、≥5 mm组染色体异常率分别为5.6%、14.4%、22.4%、25.0%和42.3%;305例NT增厚的胎儿采用CMA技术共检出59例(19.3%)染色体异常;且与常规的染色体核型分析相比,CMA多检出5例致病性CNVs(5/246)及12例临床意义不明(VOUS)变异;此外,合并超声异常的NT增厚胎儿和单纯NT增厚的胎儿染色体异常率分别为44.2%和17.2%。结论 CMA检测可检出常规的染色体核型分析无法检出的CNVs及临床意义不明的微缺失、微重复。     

孕11～27周胎儿鼻骨发育不良的CNV-seq联合染色体核型诊断结果分析

目的 分析孕11～27周胎儿鼻骨发育不良的染色体拷贝数变异测序(CNV-seq)联合染色体核型诊断结果。方法 回顾性纳入2021年1月至2022年12月于广州市妇女儿童医疗中心柳州医院产科就诊的并行孕期超声诊断为胎儿鼻骨发育不良的432例孕妇作为研究对象,对其进行染色体核型分析和CNV-seq分析,并对其检测结果进行分析。结果 432例病例中,核型分析共检出染色体核型异常36例(8.3%),其中非整倍体31例(7.2%),包括21-三体26例(6.0%),18-三体3例(0.69%),其他2例(0.46%);另有结构异常5例(1.2%);CNV-seq分析另检出15例CNVs(3.47%),包括5例(1.2%)致病性CNVs、10例(2.3%)临床意义未明CNVs。结论 孕11～27周鼻骨发育不良是重要的染色体异常的重要依据,染色体核型和CNV-seq联合检测可有效提高染色体异常的检出率,可作为产前诊断的一线方法,有助于对染色体畸变及早诊断和干预,为遗传学咨询和生育指导提供一定的依据,减少出生缺陷的发生。     

全基因组低覆盖度测序技术检测胎儿先天性心脏病拷贝数变异

目的采用全基因组低覆盖度测序技术检测先天性心脏畸形(CHD)胎儿染色体基因拷贝数变异(CNVs),探讨胎儿期CHD遗传学特征。方法采集CHD胎儿脐带组织,用全基因组低覆盖度测序技术检测CNVs,分析其与临床参数的关系。结果22例CHD胎儿共检出CNVs异常8例,异常率为36.4%。其中致病性CNVs异常4例(18三体综合征、13三体综合征、Di George综合征、猫叫综合征各1例),致病性未知的CNVs异常(VOUS)5例,包括3q29del 1.66M、3q28del 0.24Mb、15q77.1q11.2dup 2.38Mb、Xdup 0.4M、Xq26.3dup 0.4Mb各1例。结论胎儿期CHD与CNVs关系密切,全基因组低覆盖度测序技术有助于发现与CHD遗传易感相关的CNVs。     

马蹄内翻足产前超声诊断及其与染色体异常的关系

目的探讨马蹄内翻足(TE)合并其他畸形的产前超声诊断及其与染色体异常的关系。方法 104例产前超声诊断为TE并经产后或引产后证实的胎儿,分析其足内翻合并畸形的超声图像、染色体核型分析及染色体微阵列分析(CMA)的结果。结果单侧、双侧TE组分别为44、60例,两组染色体核型分析及CMA异常检出率均无显著差异(P0.05)。单纯TE组68例,复杂TE组(TE合并其他畸形)36例,两组染色体核型异常的检出率分别为2.9%、11.1%,无显著差异(P0.05);复杂TE组CMA异常检出率27.8%明显高于单纯TE组7.3%(P0.05)。TE的CMA异常检出率14.4%明显高于染色体核型分析的异常检出率5.8%(P0.05)。结论胎儿TE合并其他畸形,染色体异常的概率增高,需行CMA检查。单纯TE组胎儿超声随访观察仍提示TE,建议CMA检查。     

Prenatal genetic testing in 19 fetuses with corpus callosum abnormality

BackgroundCorpus callosum abnormality (CCA) can lead to epilepsy, moderate severe neurologic or mental retardation. The prognosis of CCA is closely related to genetic etiology. However, copy number variations (CNVs) associated with fetal CCA are still limited and need to be further identified. Only a few scattered cases have been reported to diagnose CCA by whole exome sequencing (WES).MethodsKaryotyping analysis, copy number variation sequencing (CNV‐seq), chromosomal microarray analysis (CMA) and WES were parallelly performed for prenatal diagnosis of 19 CCA cases.ResultsThe total detection rate of karyotyping analysis, CMA (or CNV‐seq) and WES were 15.79% (3/19), 21.05% (4/19) and 40.00% (2/5), respectively. Two cases (case 11 and case 15) were diagnosed as aneuploidy (47, XY, + 13 and 47, XX, + 21) by karyotyping analysis and CNV‐seq. Karyotyping analysis revealed an unknown origin fragment (46,XY,add(13)(p11.2)) in case 3, which was further confirmed to originate from p13.3p11.2 of chromosome 17 by CNV‐seq. CMA revealed arr1q43q44 (238923617–246964774) × 1(8.04 Mb) in case 8 with a negative result of chromosome karyotype. WES revealed that 2 of 5 cases with negative results of karyotyping and CNV‐seq or CMA carried pathogenic genes ALDH7A1 and ARID1B.ConclusionParallel genetic tests showed that CNV‐seq and CMA are able to identify additional, clinically significant cytogenetic information of CCA compared to karyotyping; WES significantly improves the detection rate of genetic etiology of CCA. For the patients with a negative results of CNV‐seq or CMA, further WES test is recommended.     

胎儿超声微小异常的产前遗传学分析

目的探讨胎儿微小异常的产前超声表现及遗传咨询要点。 方法对2014年至2017年在北京协和医院经超声检查发现微小异常、核型分析正常但染色体微阵列分析显示拷贝数变异的胎儿17例,综合产前超声表现、遗传学检查结果、病理检查结果或出生后表现进行回顾分析。 结果超声检查显示不同种类和数目的微小异常,10例为单发异常,其余7例为多发异常。17例主要超声表现：测值小于孕周（7例）、脉络丛囊肿（2例）、心室强回声（1例）、肠管增宽或回声增强（4例）、肾盂增宽（2例）、侧脑室增宽（2例）、单脐动脉（2例）、永存右脐静脉（2例）、永存左上腔静脉（1例）、鼻骨缺失（4例）、手异常（3例）、足异常（1例）、羊水量异常（2例）及脐带异常（1例）。17例胎儿均进行了遗传学检查,核型分析及快速荧光原位杂交检测正常,通过染色体微阵列分析（CMA）检出不同片段大小的拷贝数变异,7例（41.18%）为致病性拷贝数变异,10例（58.82%）为意义不明的拷贝数变异（VOUS）。参考胎儿父母CMA诊断结果对10例VOUS进行了解释和区分,4例为偏致病性（VOUS-LP）,3例为偏良性（VOUS-LB）,3例意义不明确（VOUS-unknown）。经产前咨询后9例孕妇选择继续妊娠,胎儿出生后1例显示并趾及喂养困难,其余8例均生长发育正常;8例孕妇选择终止妊娠,其中2例引产胎儿行病理检查。 结论产前超声筛查未发现重大结构异常、但发现胎儿微小异常时应积极进行随诊,并行遗传学检查。与传统核型分析比较,CMA更有助于早期检出少见遗传学异常,为产前诊断和预后评估提供重要参考信息。     

Microarray application in prenatal diagnosis: a position statement from the cytogenetics working group of the Italian Society of Human Genetics (SIGU), November 2011

A precise guideline establishing chromosomal microarray analysis (CMA) applications and platforms in the prenatal setting does not exist. The controversial question is whether CMA technologies can or should soon replace standard karyotyping in prenatal diagnostic practice. A review of the recent literature and survey of the knowledge and experience of all members of the Italian Society of Human Genetics (SIGU) Committee were carried out in order to propose recommendations for the use of CMA in prenatal testing. The analysis of datasets reported in the medical literature showed a considerable 6.4% incidence of pathogenic copy number variations (CNVs) in the group of pregnancies with sonographically detected fetal abnormalities and normal karyotype. The reported CNVs are likely to have a relevant role in terms of nosology for the fetus and in the assessment of reproductive risk for the couple. Estimation of the frequency of copy number variations of uncertain significance (VOUS) varied depending on the different CMA platforms used, ranging from 0-4%, obtained using targeted arrays, to 9-12%, obtained using high-resolution whole genome single nucleotide polymorphism (SNP) arrays. CMA analysis can be considered a second-tier diagnostic test to be used after standard karyotyping in selected groups of pregnancies, namely those with single (apparently isolated) or multiple ultrasound fetal abnormalities, those with chromosomal rearrangements, even if apparently balanced, and those with supernumerary marker chromosomes.     

Prenatal genetic diagnosis of omphalocele by karyotyping,chromosomal microarray analysis and exome sequencing

ObjectivesThe aim of this study is to share our experience in the prenatal diagnosis of omphalocele by karyotyping, chromosomal microarray analysis (CMA) and whole exome sequencing (WES).MethodsIn this retrospective study, 81 cases of omphalocele were identified from 2015 to 2020. Associated anomalies and prenatal diagnosis based on karyotyping, CMA and WES were analysed.ResultsFifty-eight (71.6%) of the 81 foetuses had other ultrasound anomalies. Giant omphalocele was present in 11 cases (13.6%) and small omphalocele was present in 70 cases (86.4%). Chromosomal abnormalities were found in 24 foetuses (29.6%, 24/81), the most common of which were trisomy 18 (58.8%, 11/24) and trisomy 13 (29.2%, 7/24). Compared to isolated omphalocele, non-isolated omphalocele was accompanied by an increased prevalence of chromosomal abnormalities (4.3% (1/23) vs. 39.7% (23/58), χ² = 8.226, p = .004). All chromosomal abnormalities were found in small omphalocele. Aside from aneuploidy, CMA showed one pathogenic copy number variants (CNVs) for a detection rate of 1.2%, one variants of unknown significance (VOUS) and one instance of loss of heterozygosity (LOH). WES was performed on 3 non-isolated cases, and one was found to have pathogenic variants.ConclusionsThe most common genetic cause of omphalocele is aneuploidy and the prevalence of chromosomal abnormalities is increased with non-isolated and small omphalocele. CMA and WES can be useful for providing further genetic information to assist in prenatal counselling and pregnancy management.     

Chromosomal microarray in postnatal diagnosis of congenital anomalies and neurodevelopmental disorders in Serbian patients

BackgroundArray‐based genomic analysis is a gold standard for the detection of copy number variations (CNVs) as an important source of benign as well as pathogenic variations in humans. The introduction of chromosomal microarray (CMA) has led to a significant leap in diagnostics of genetically caused congenital malformations and neurodevelopmental disorders, with an average diagnostic yield of 15%. Here, we present our experience from a single laboratory perspective in four years’ postnatal clinical CMA application.MethodsDNA samples of 430 patients with congenital anomalies and/or neurodevelopmental disorders were analyzed by comparative genome hybridization using oligonucleotide‐based microarray platforms. Interpretation of detected CNVs was performed according to current guidelines. The detection rate (DR) of clinically significant findings (pathogenic/likely pathogenic CNVs) was calculated for the whole cohort and isolated or combined phenotypic categories.ResultsA total of 140 non‐benign CNVs were detected in 113/430 patients (26.5%). In 70 patients at least one CNV was considered clinically significant thus reaching a diagnostic yield of 16.3%. The more complex the phenotype, including developmental delay/intellectual disability (DD/ID) as a prevailing feature, the higher the DR of clinically significant CNVs is obtained. Isolated congenital anomalies had the lowest, while the “dysmorphism plus” category had the highest diagnostic yield.ConclusionIn our study, CMA proved to be a very useful method in the diagnosis of genetically caused congenital anomalies and neurodevelopmental disorders. DD/ID and dysmorphism stand out as important phenotypic features that significantly increase the diagnostic yield of the analysis.     

Detection of Copy Number Variants by Short Multiply Aggregated Sequence Homologies

Chromosomal microarray testing is indicated for patients with diagnoses including unexplained developmental delay or intellectual disability, autism spectrum disorders, and multiple congenital anomalies. The short multiply aggregated sequence homologies (SMASH) genomic assay is a novel next-generation sequencing technology that performs copy number analysis at resolution similar to high-coverage whole genome sequencing but requires far less capacity. We benchmarked the performance of SMASH on a panel of genomic DNAs containing known copy number variants (CNVs). SMASH was able to detect pathogenic copy number variants of ≥10 kb in 77 of 77 samples. No pathogenic events were seen in 32 of 32 controls, indicating 100% sensitivity and specificity for detecting pathogenic CNVs >10 kb. Repeatability (interassay precision) and reproducibility (intra-assay precision) were assessed with 13 samples and showed perfect concordance. We also established that SMASH had a limit of detection of 20% for detection of large mosaic CNVs. Finally, we analyzed seven blinded specimens by SMASH analysis and successfully identified all pathogenic events. These results establish the efficacy of the SMASH genomic assay as a clinical test for the detection of pathogenic copy number variants at a resolution comparable to chromosomal microarray analysis.

Certain types of clinical genetic testing, including chromosome analysis and chromosomal microarray analysis (CMA), are standard practice for patients with suspected genetic diseases, including developmental delay/intellectual disability, autism spectrum disorders, and multiple congenital anomalies. These categories of disorders account for the largest proportion of cytogenetic testing because of their high prevalence in the population.¹ Most patients lack sufficient specific histories or features from physical examination to suggest specific genetic (or nongenetic) causes. Published guidelines for testing such patients have emphasized screening for chromosomal abnormalities by karyotyping and CMA as well as testing for single-gene disorders and panel or whole exome sequencing.The utility of detecting constitutional genomic copy number gains and losses in patients with intellectual disabilities, autism, and other congenital anomalies has been well documented. CMA is now recommended as a first-tier test for neuropsychiatric and neurodegenerative indications. The short multiply aggregated sequence homologies (SMASH) genomic assay is a powerful new approach for detecting copy number variation in the human genome by next-generation sequencing. SMASH performs a similar function to CMA but at a higher resolution for genomic imbalances, comparable to that obtained by read-depth analysis of high-coverage whole genome sequencing (WGS).²SMASH utilizes a combination of low-coverage WGS and a novel mapping algorithm to find copy number variants (CNVs) in the human genome. CMA testing yields a diagnosis in approximately 20% of sporadic disease cases, which supports its use as a diagnostic test for patients with suspected copy number disorders or simplex disease presentations of possible genetic cause and for patients with clinical diagnoses of heterogeneous genetic conditions.^1,3,4 Compared with CMA (the current American College of Medical Genetics and Genomics first-tier diagnostic test for identifying CNVs), SMASH can directly interrogate a far more diverse range of nucleotides within a human haplotype than is possible with oligonucleotide-based probes. Because it has a much higher signal/noise ratio than hybridization-based technologies, SMASH has superior sensitivity for calling CNVs relative to clinical CMA and can effectively call CNVs as small as 4 kb.⁵ This is a substantial increase in resolution over what is typically possible with CMA. Although current microarray platforms can detect smaller CNVs, which range from 25 to 50 kb in size, this detection is dependent on the probe distribution in the genomic region and a requirement of certain number of probes in the genomic region. Because of this limitation, clinically significant CNVs may be missed in genomic regions with inadequate number and distribution of the probes.To benchmark the performance of SMASH relative to CMA, we analyzed a set of cell lines and anonymous patient samples with known pathogenic CNVs. The CNVs were first detected by CMA or Sanger sequencing, and effectively represent the spectrum of events detectable by clinical CMA. We present herein our assay validation data for detection of constitutional copy number variation by SMASH.     

Prenatal chromosomal microarray analysis in foetuses with isolated absent or hypoplastic nasal bone

ObjectivesTo evaluate the efficiency of chromosomal microarray analysis (CMA) in the prenatal diagnosis of foetuses with isolated absent or hypoplastic nasal bone (NB) in the first and second trimester.MethodsFrom January 2015 to April 2021, foetuses with isolated absent or hypoplastic NB who received invasive prenatal diagnosis were enrolled. The results of CMA were analysedResultsThere were 221 foetuses, including 166 cases with isolated absent NB and 55 cases with isolated hypoplastic NB. Twenty-four foetuses (10.9%, 24/221) had an ultrasonic diagnosis in the first trimester and 197 (89.1%, 197/221) had a ultrasonic diagnosis in the second trimester. The overall diagnostic yield of CMA was 9.0% (20/221). Aneuploidies were detected in 13 (5.9%, 13/221) foetuses, including 10 Down syndrome, 2 Klinefelter''s syndrome and 1 trisomy 18. Pathogenic copy number variations (CNVs) were detected in seven foetuses (3.2%, 7/221). In addition, variants of unknown significance (VOUS) were detected in four foetuses. The foetuses with isolated absent NB had a higher detection rate of chromosome abnormality than the isolated hypoplastic NB, but the difference was not significant in the statistical analysis (10.2% vs. 5.5%, χ² =0.642, p = .423). No significant difference was observed in the detection rate between the first trimester and the second trimester (16.6% vs. 8.1%, χ² = 1.002, p = .317, Chi-square test).ConclusionCMA can increase the diagnostic yield of chromosome abnormality, especially pathogenic CNVs for foetuses with isolated absent or hypoplastic NB. CMA should be recommended when isolated absent or hypoplastic NB is suspected antenatally.7