Prenatal diagnosis of a 12q22q23.2 interstitial deletion by array CGH in a malformed fetus

We report the prenatal diagnosis of a 12q22q23.2 de novo interstitial deletion performed by array based comparative genomic hybridization (array CGH) in a fetus with cystic hygroma colli, intrauterine growth retardation, microcephaly and micrognathism. Haploinsufficiency for insuline-like growth factor 1 gene (IGF1), which is mapped in the deleted region, is suggested because of its implication in prenatal and postnatal growth and in neuronal maturation. This case demonstrates the contribution of array CGH in prenatal diagnosis for detecting small unbalanced chromosomal abnormalities in malformed fetuses and, subsequently, for genetic counselling.     

Experience of chromosomal microarray applied in prenatal and postnatal settings in Hong Kong

Chromosomal microarray (CMA) is recommended as a first tier investigation for patients with developmental delay (DD), intellectual disability (ID), autistic spectrum disorder (ASD), and multiple congenital anomalies (MCA). It is widely used in the prenatal and postnatal settings for detection of chromosomal aberrations. This is a retrospective review of all array comparative genomic hybridization (aCGH/ array CGH) findings ascertained in two major prenatal and postnatal genetic diagnostic centers in Hong Kong from June 2012 to December 2017. Medical records were reviewed for cases with pathogenic and variants of uncertain clinical significance (VUS). Classification of copy number variants (CNVs) was based on current knowledge and experience by August 2018. The aims of this review are to study the diagnostic yield of array CGH application in prenatal and postnatal settings in Hong Kong and to describe the spectrum of abnormalities found. Prenatal indications included abnormal ultrasound findings, positive Down syndrome screening, abnormal noninvasive prenatal test results, advanced maternal age and family history of chromosomal or genetic abnormalities. Postnatal indications included unexplained DD, ID, ASD, and MCA. A total of 1,261 prenatal subjects and 3,096 postnatal patients were reviewed. The prenatal diagnostic yield of pathogenic CNV and VUS (excluding those detectable by karyotype) was 3.5%. The postnatal diagnostic yield of pathogenic CNV was 15.2%. The detection rates for well‐defined microdeletion and microduplication syndromes were 4.6% in prenatal and 6.1% (1 in 16 index patients) in postnatal cases, respectively. Chromosomes 15, 16, and 22 accounted for over 21 and 25% of pathogenic CNVs detected in prenatal and postnatal cohorts, respectively. This review provides the first large scale overview of genomic imbalance of mostly Chinese patients in prenatal and postnatal settings.     

Array—CGH技术用于产前诊断可疑胎儿染色体异常

目的探讨微阵列比较基因组杂交技术（array—based comparative genomic hybridization,array—CGH）在产前诊断胎儿染色体异常中的应用价值。方法产前诊断发现4例常规G显带染色体核型分析不能明确的胎儿染色体异常,按照标准的array—CGH操作分析对这些病例进行全基因组检测。结果通过array—CGH技术分析,明确了4例胎儿可疑染色体异常的诊断并且进行精确定位,1例染色体部分缺失,1例正常,1例染色体部分重复,1例不平衡易位。结论array—CGH技术对产前诊断胎儿染色体异常具有高分辨率,能够精确定位异常片段,明确胎儿预后,对产前诊断具有重要应用价值。     

Detection of genomic imbalances by array based comparative genomic hybridisation in fetuses with multiple malformations

Background: Malformations are a major cause of morbidity and mortality in full term infants and genomic imbalances are a significant component of their aetiology. However, the causes of defects in many patients with multiple congenital malformations remain unexplained despite thorough clinical examination and laboratory investigations.

Methods: We used a commercially available array based comparative genomic hybridisation method (array CGH), able to screen all subtelomeric regions, main microdeletion syndromes, and 201 other regions covering the genome, to detect submicroscopic chromosomal imbalances in 49 fetuses with three or more significant anomalies and normal karyotype.

Results: Array CGH identified eight genomic rearrangements (16.3%), all confirmed by quantitative multiplex PCR of short fluorescent fragments. Subtelomeric and interstitial deletions, submicroscopic duplications, and a complex genomic imbalance were identified. In four de novo cases (15qtel deletion, 16q23.1–q23.3 deletion, 22q11.2 deletion, and mosaicism for a rearranged chromosome 18), the genomic imbalance identified clearly underlay the pathological phenotype. In one case, the relationship between the genotype and phenotype was unclear, since a subtelomeric 6q deletion was detected in a mother and her two fetuses bearing multiple malformations. In three cases, a subtelomeric 10q duplication, probably a genomic polymorphism, was identified.

Conclusions: The detection of 5/49 causative chromosomal imbalances (or 4/49 if the 6qtel deletion is not considered as causative) suggests wide genome screening when standard chromosome analysis is normal and confirms that array CGH will have a major impact on pre and postnatal diagnosis as well as providing information for more accurate genetic counselling.

     

产前诊断中胎儿新发生染色体异常的临床结局与遗传咨询

目的 分析在产前诊断中胎儿新发生染色体异常的检测结果和临床结局,为胎儿新发生染色体异常的遗传咨询积累有价值的临床资料.方法 2006年1月至2009年12月,在2583例产前诊断的细胞染色体核型分析中,共发现12例新发生的胎儿染色体异常,回顾性分析这12例胎儿的细胞和(或)分子细胞遗传学检测结果、产前超声检查结果、妊娠结局和出生后的随访结果.结果 12例新发生染色体异常的胎儿有10例是非平衡性染色体异常,2例平衡性染色体异常.10例非平衡染色体异常的胎儿中有8例引产终止妊娠,有2例足月顺娩,其中1例是标记染色体异常出生后随访未见异常,另1例出生后随访至2周岁发现语言功能发育迟缓.2例平衡性染色体异常的胎儿均足月顺娩,出生后随访未发现异常.结论 新发生染色体异常的胎儿表型可通过详细的染色体核型分析以及进一步的分子细胞遗传学检测所提供的染色体成分进行预测,产前超声结构畸形检查可为妊娠结局的评估提供有力的参考依据.

Abstract：

Objective To analyze the chromosome rearrangements and clinical outcome in fetus detected at prenatal diagnosis, and provide information for genetic counseling about de novo chromosomal aberrations. Methods From January 2006 to December 2009, we found 12 cases of de novo chromosomal aberrations in 2 583 cases of prenatal cytogenetic analyses and reviewed the karyotypes, other experimental analyses data, fetal ultrasound findings and clinical outcomes. Results Out of the 12 de novo chromosomal aberrations, 10 had unbalanced translocations and 2 had balanced reciprocal translocations. Eight of the 10unbalanced translocation cases were terminated therapeutically, and 2 were delivered with full term.Neonates were phenotypically normal in the 2 cases with unbalanced translocations, but 1 had language retardation when followed up. The two balanced translocation cases were delivered with full term, and the neonates were phenotypically normal and clinical examinations were normal too. Conclusion Detailed cytogenetic and molecular study will be adjunctive tools for predicting the phenotype of fetus with de novo chromosomal aberrations. Fetal ultrasound examination will provide convincible demonstration to determine the outcome of pregnancy.     

Pre- and postnatal genetic testing by array-comparative genomic hybridization: genetic counseling perspectives

Recently, a new genetic test has been developed that allows a more detailed examination of the genome when compared with a standard chromosome analysis. Array comparative genomic hybridization (CGH microarray; also known as chromosome microarray analysis) in effect, combines chromosome and fluorescence in situ hybridization analyses allowing detection not only of aneuploidies, but also of all known microdeletion and microduplication disorders, including telomere rearrangements. Since 2004, this testing has been available in the Medical Genetics Laboratory at Baylor College of Medicine for postnatal evaluation and diagnosis of individuals with suspected genomic disorders. Subsequently, to assess the feasibility of offering CGH microarray for prenatal diagnosis, a prospective study was conducted on 98 pregnancies in a clinical setting comparing the results obtained from array CGH with those obtained from a standard karyotype. This was followed by the availability of prenatal testing on a clinical basis in 2005. To date, we have analyzed over 8000 cases referred to our clinical laboratory, including approximately 300 prenatal cases. With the clinical introduction of any new testing strategy, and particularly one focused on genetic disorders, issues of patient education, result interpretation, and genetic counseling must be anticipated and strategies adopted to allow the implementation of the testing with maximum benefit and minimum risk. In this article, we describe our experience with over 8000 clinical prenatal and postnatal cases of CGH microarray ordered by our clinical service or referred to the Baylor Medical Genetics Laboratory and describe the strategies used to optimize patient and provider education, facilitate clinical interpretation of results, and provide counseling for unique clinical circumstances.     

Supernumerary marker chromosomes derived from chromosome 6: cytogenetic, molecular cytogenetic, and array CGH characterization

Supernumerary marker chromosomes (SMC) are relatively common in prenatal diagnosis. As the clinical outcomes vary greatly, a better understanding of the karyotype-phenotype correlation for different SMCs will be important for genetic counseling. We present two cases of prenatally detected de novo, small SMCs. The markers were present in 80% of amniocyte colonies in Case 1 and 38% of the colonies in Case 2. The SMCs were determined to be derived from chromosome 6 during postnatal confirmation studies. Although the sizes and the chromosomal origin of the SMCs in these two cases appeared to be similar, the clinical outcomes varied. The clinical manifestations observed in Case 1 included small for gestational age, feeding difficulty at birth, hydronephrosis, deviated septum and dysmorphic features, while the phenotype is apparently normal in Case 2. Array comparative genomic hybridization (CGH) was performed and showed increase in dosage for approximately 26 Mb of genetic material from the proximal short and long arms of chromosome 6 in Case 1. Results of array CGH were uninformative in Case 2, either due to mosaicism or lack of detectable euchromatin. The difference in the clinical presentation in these two patients may have resulted from the difference in the actual gene contents of the marker chromosomes and/or the differential distribution of the mosaicism.     

Genetic diagnoses and associated anomalies in fetuses prenatally diagnosed with esophageal atresia

Esophageal atresia (EA) is a congenital anomaly occurring in 2.3 per 10,000 live births. Due to advances in prenatal imaging, EA is more readily diagnosed, but data on the associated genetic diagnoses, other anomalies, and postnatal outcome for fetuses diagnosed prenatally with EA are scarce. We collected data from two academic medical centers (n = 61). Our data included fetuses with suspected EA on prenatal imaging that was confirmed postnatally and had at least one genetic test. In our cohort of 61 cases, 29 (49%) were born prematurely and 19% of those born alive died in the first 9 years of life. The most commonly associated birth defects were cardiac anomalies (67%) and spine anomalies (50%). A diagnosis was made in 61% of the cases; the most common diagnoses were vertebral defects, anal atresia, cardiac anomalies, tracheoesophageal fistula with esophageal atresia, radial or renal dysplasia, and limb anomalies association (43%, although 12% met only 2 of the criteria), trisomy 21 (5%), and CHARGE syndrome (5%). Our findings suggest that most fetuses with prenatally diagnosed EA have one or more additional major anomaly that warrants a more comprehensive clinical genetics evaluation. Fetuses diagnosed prenatally appear to represent a cohort with a worse outcome.     

De novo chromosomal aberrations in the fetus; genetic counseling and clinical outcome

The aim of this study was to examine the incidence and clinical outcome of de novo chromosomal aberrations retrospectively and provide useful data for genetic counseling in the prenatal cytogenetic diagnosis. We found 17 cases of de novo chromosomal aberrations in 5501 cases of prenatal cytogenetic analysis and reviewed the karyotype, further study, medical records, fetal ultrasound findings and clinical outcomes. Out of the 17 de novo chromosomal aberrations, 5 had balanced reciprocal translocations and 12 had unbalanced translocations characterized as deletion, addition, or marker. In the case of the five balanced reciprocal translocations, 3 cases without abnormal ultrasound findings were carried to term after comprehensive genetic counseling. Neonates were phenotypically normal and clinical examinations were normal. Two cases with abnormal ultrasound findings were terminated therapeutically. Twelve cases of unbalanced translocations were terminated except one case with a mosaic marker chromosome. High resolution fetal ultrasound and detailed cytogenetic and molecular study will be adjunctive tools for predicting the karyotype/phenotype correlations of fetuses with de novo chromosomal aberrations, although they have limitation to find all phenotypic effects.     

Prenatal detection of unbalanced chromosomal rearrangements by array CGH

Background

Karyotype analysis has been the standard method for prenatal cytogenetic diagnosis since the 1970s. Although highly reliable, the major limitation remains the requirement for cell culture, resulting in a delay of as much as 14 days to obtaining test results. Fluorescent in situ hybridisation (FISH) and quantitative fluorescent PCR (QF‐PCR) rapidly detect common chromosomal abnormalities but do not provide a genome wide screen for unexpected imbalances. Array comparative genomic hybridisation (CGH) has the potential to combine the speed of DNA analysis with a large capacity to scan for genomic abnormalities. We have developed a genomic microarray of approximately 600 large insert clones designed to detect aneuploidy, known microdeletion syndromes, and large unbalanced chromosomal rearrangements.

Methods

This array was tested alongside an array with an approximate resolution of 1 Mb in a blind study of 30 cultured prenatal and postnatal samples with microscopically confirmed unbalanced rearrangements.

Results

At 1 Mb resolution, 22/30 rearrangements were identified, whereas 29/30 aberrations were detected using the custom designed array, owing to the inclusion of specifically chosen clones to give increased resolution at genomic loci clinically implicated in known microdeletion syndromes. Both arrays failed to identify a triploid karyotype. Thirty normal control samples produced no false positive results.

Conclusions

Analysis of 30 uncultured prenatal samples showed that array CGH is capable of detecting aneuploidy in DNA isolated from as little as 1 ml of uncultured amniotic fluid; 29/30 samples were correctly diagnosed, the exception being another case of triploidy. These studies demonstrate the potential for array CGH to replace conventional cytogenetics in the great majority of prenatal diagnosis cases.     

Application of a target array Comparative Genomic Hybridization to prenatal diagnosis

Background  

While conventional G-banded karyotyping still remains a gold standard in prenatal genetic diagnoses, the widespread adoption of array Comparative Genomic Hybridization (array CGH) technology for postnatal genetic diagnoses has led to increasing interest in the use of this same technology for prenatal diagnosis. We have investigated the value of our own designed DNA chip as a prenatal diagnostic tool for detecting submicroscopic deletions/duplications and chromosome aneuploidies.     

792例血清学高危行无创产前基因检测研究

目的探讨无创产前基因检测联合血清学产前筛查在产前诊断胎儿染色体非整倍体中的应用价值。方法选择2013年5月至2013年12月血清学筛查高危单胎孕妇792例,采用无创产前基因检测的方法评估胎儿染色体非整倍体的患病风险率,对患病风险率提示高危的孕妇进行核型分析以确诊结果。结果检出高风险14例,占调查资料总数1.77%,其中21-三体6例,18-三体3例,性染色体5例,染色体核型分析确认6例21-三体,3例18-三体,1例47,XXY。结论无创产前基因检测的方法能早期、快速、准确、无创地检测21-三体、18-三体,可避免很多不必要的介入性有创检查。无创产前基因检测联合血清学筛查是目前产前筛查最为实用和有效的方法之一。     

柳州地区6876例产前诊断羊水细胞染色体核型分析

目的分析妊娠中期进行产前诊断的高危孕妇羊水细胞染色体核型,了解此期异常核型出现的频率及类型。方法6887例具备产前诊断指征的妊娠妇女,在知情选择的情况下行羊膜腔穿刺术及染色体核型检测。结果6876例羊水细胞培养成功,成功率为99．84％（6876／6887）。在6876例羊水细胞培养成功的染色体核型中,检出异常核型107例,异常率为1．56％,常见核型为三体型,占异常核型47．66％。结论羊水细胞学检查作为一项产前诊断技术对于指导优生优育,降低缺陷儿的出生具有重要意义。     

Natural outcome of trisomy 13, trisomy 18, and triploidy after prenatal diagnosis

Trisomy 13, trisomy 18, and triploidy belong to the chromosomal abnormalities which are compatible with life, but which are also associated with a high rate of spontaneous abortion, intrauterine death, and a short life span. This study was conducted to analyze natural outcome after prenatal diagnosis of these disorders. Between January 1, 1999 and December 31, 2009, we investigated all amniocenteses and chorionic villus biopsies carried out at our department. All cases with fetal diagnosis of triploidy, trisomy 13, and 18 were analyzed, with a focus on cases with natural outcome. Overall, 83 (78%) cases of pregnancy termination and 24 (22%) patients with natural outcome (NO) were identified. The NO group included 15 cases of trisomy 18, six cases of triploidy, and three cases of trisomy 13. No case of triploidy was born alive. The live birth rate was 13% for trisomy 18 and 33% for trisomy 13. The three live-born infants with trisomy 13 and 18 died early after a maximum of 87 hr postpartum. Our data are consistent with the literature concerning outcome of triploidy, with none or only a few live births. Analyzes of trisomy 13 and 18 indicate a very short postnatal life span. Different study designs and diverse treatment strategies greatly affect the fetal and neonatal outcome of fetuses with triploidy, trisomy 13, and 18. More studies analyzing natural outcome after prenatal diagnosis of these chromosomal abnormalities are needed. Non-termination of these pregnancies remains an option, and specialists advising parents need accurate data for counseling.     

Application of chromosomal microarray in the evaluation of abnormal prenatal findings

We performed karyotype and array comparative genomic hybridization (aCGH) analyses on 177 prenatal samples, including 162 (92%) samples from fetuses with sonographic anomalies. Overall 12 fetuses (6.8%) had abnormal karyotype and 42 (23.7%) fetuses had abnormal microarray results: 20 (11.3%) with pathogenic copy number variations (CNVs), 16 with CNVs of uncertain clinical significance, 4 with CNVs establishing carrier status for recessive, X‐linked, or susceptibility to late onset dominant disease, and two CNVs with pseudomosaicism due to in vitro cultural artifacts. For 23 pregnancies (13%), aCGH contributed important new information. Our results highlight the interpretation challenges associated with CNVs of unclear significance, incidental findings, as well as technical aspects. Array CGH analysis significantly improved the detection of genomic imbalances in prenatal diagnosis of pregnancies with structural birth defects.     

235例维吾尔族胎儿孤立性轻度侧脑室增宽临床预后研究

目的探讨超声诊断235例维吾尔族胎儿孤立性侧脑室增宽的妊娠结局及临床预后。方法回顾性分析我院产前超声诊断235例维吾尔族胎儿孤立性轻度侧脑室增宽的资料,并进行追踪随访.重点观察临床预后。结果 235例胎儿侧脑室增宽10-15mm,其中200例侧脑室增宽10-12mm,35例增宽12-15mm。随访中有7例侧脑室增宽至16-18mm,诊断为脑积水,其中5胎选择引产（其中1胎证实18一三体综合症）,2胎出生后10天内死亡。其余28胎活产病例中（男胎16例,女胎12例）,1例于出生一月内死亡,27例存活,其中1例发生神经系统发育迟滞,余26例发育正常。其余于妊娠晚期及出生后复查IMV自然消退。结论超声检查是胎儿IMV产前诊断的有效方法,IMV胎儿总体预后较好,但应重视出生后随诊。     

Whole-genome array CGH identifies pathogenic copy number variations in fetuses with major malformations and a normal karyotype

Despite a wide range of clinical tools, the etiology of mental retardation and multiple congenital malformations remains unknown for many patients. Array-based comparative genomic hybridization (aCGH) has proven to be a valuable tool in these cases, as its pangenomic coverage allows the identification of chromosomal aberrations that are undetectable by other genetic methods targeting specific genomic regions. Therefore, aCGH is increasingly used in clinical genetics, both in the postnatal and the prenatal settings. While the diagnostic yield in the postnatal population has been established at 10-12%, studies investigating fetuses have reported variable results. We used whole-genome aCGH to investigate fetuses presenting at least one major malformation detected on ultrasound, but for whom standard genetic analyses (including karyotype) failed to provide a diagnosis. We identified a clinically significant chromosomal aberration in 8.2% of tested fetuses (4/49), and a result of unclear clinical significance in 12.2% of tested fetuses (6/49). Our results document the value of whole-genome aCGH as a prenatal diagnostic tool and highlight the interpretation difficulties associated with copy number variations of unclear significance.     

三例22号染色体异常胎儿的产前遗传学分析

目的应用超声以及多种遗传学检测技术对3例产前筛查提示染色体可能异常的胎儿进行分析,为遗传咨询提供依据。方法对3例孕妇进行胎儿超声检查、核型分析、单核苷酸多态性微阵列芯片(single nucleotide polymorphism-based microarray,SNP-Array)检测,并通过荧光原位杂交(fluorescence in situ hybridization,FISH)对结果进行验证。结果三例胎儿均发现22号染色体存在异常。例1在22q13.2q13.33区存在7.1 Mb的杂合缺失,涉及SHANK3、FBLN1等54个OMIM基因;例2为嵌合体核型,约12%的细胞22q13.31q13.33区存在6.6 Mb的杂合缺失,覆盖SHANK3、PPARA等48个OMIM基因,另有5%的细胞22q11.1q13.2区存在26.1 Mb的拷贝重复,覆盖285个OMIM基因;例3在22q11.1q11.21区存在1.7 Mb的二次重复,涉及CECR1、CECR2、ATP6V1E1等10个OMIM基因。三例胎儿父母的核型及SNP-Array检测结果均未见异常,提示胎儿为新发变异。结论22号染色体微缺失/微重复所致疾病的严重性不仅与其范围有关,还与染色体结构、基因剂量及环境等密切相关。在产前诊断中综合运用超声和多种遗传学检测技术可以显著提高表型变异较大的遗传学异常的检出率。     

Familial deletion 11q14.3-q22.1 without apparent phenotypic consequences: a haplosufficient 8.5 Mb region

We present the prenatal diagnosis of a chromosome 11q14.3-q22.1 deletion identified in three generations without apparent phenotypic consequences. A 25-year-old G2, P1 woman underwent amniocentesis at 15 weeks' gestation because of a positive result for Down syndrome maternal serum-screening test (1/70). The fetal karyotype revealed an interstitial deletion of the long arm of chromosome 11 confirmed by CGH and FISH: 46,XX,del(11)(q14.3q22.1). The mother and grandfather of the fetus presented the same interstitial deletion with a little if any phenotype effect. The pregnancy was carried to term and resulted in the birth of a normal girl. To our knowledge, only one case of a chromosome 11q14.3-q21 deletion without phenotypic anomalies has been reported. Our study allows the initially described haplosufficient region to be extended from 3.6 Mb to at least 8.5 Mb. This large deletion was compatible with fertility and apparently normal phenotype. Identification of such chromosomal regions is important for prenatal diagnosis and genetic counseling.     

1318例发育异常和高危胎儿产前诊断及处理的结局分析

目的分析1318例发育异常和高危胎儿产前诊断及处理的结局,总结异常和高危胎儿产前诊断、围产期监护和处理、出生后衔接治疗流程,以探讨适合目前国内医疗水平的胎儿医学模式。方法对在本院和外院转送经常规产检筛查:发现孕期孕母高龄或血清唐氏风险高、TORCH感染、RH(-)、父母双方地贫携带者等孕期胎儿高危因素者1123例和B超影象发现结构异常的胎儿195例进行①介入性产前诊断检查染色体、TORCH等;②预后评估;③围产期监护;④分娩后衔接处理;⑤新生儿期跟踪处理;⑥定期随访与总结。结果产前诊断结果胎儿重型a地贫39/276,重型B地贫18/236;TORCH感染11/229例;母RH(-)5例,1/5例胎儿严重水肿引产,1/5例胎儿黄疸;染色体异常19例,其中7/377例为母高龄或血清筛查唐氏风险高,11/195例为胎儿结构异常;单纯胎儿结构异常62例引产放弃,2/195 TORCH感染,引产;120例期待观察,其中68例手术治疗,7例治疗失败,其余胎儿均获得良好愈后。结论异常和高危胎儿可通过产前诊断、医学评估、宫内监护、出生后治疗处理获得良好和合理结局。