Detection of copy number variation associated with ventriculomegaly in fetuses using single nucleotide polymorphism arrays

Xue, Huili; Yu, Aili; Lin, Ning; Lin, Min; Wang, Yan; Huang, Hailong; Xu, Liangpu

doi:10.1038/s41598-021-83147-7

Cited by 14 publications

(19 citation statements)

References 39 publications

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“…Other studies have demonstrated similar results. For example, Shaffer et al (2012) found that the rate of pathogenic CNVs in fetuses with isolated VM and non-isolated VM was 4.0 and 6.6%, respectively; Donnelly et al (2014) reported that the rate of CNVs in fetuses with isolated VM and non-isolated VM was 8.7 and 17.2%, respectively; Wadt et al (2012) reported on two familial submicroscopic terminal 6q deletions in fetuses with isolated VM; Fu et al (2014) found MECP2 microduplication in four fetuses with VM; Xue et al (2021) reported that detections of clinical significant CNVs were higher in non-isolated VM than in isolated VM (16.81% vs. 10.7%, P = 0.19). In the future, large-scale studies are required to determine the relationship between the incidence of genomic abnormalities and the severity of VM in fetuses.…”

Section: Discussionmentioning

confidence: 99%

Classifying and Evaluating Fetuses With Ventriculomegaly in Genetic Etiologic Studies

Cai

Huang

et al. 2021

Front. Genet.

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The association between genetics and fetuses with ventriculomegaly (VM) is unknown. This study aimed to classify and evaluate abnormal copy number variations (CNVs) in fetuses with VM. From December 2016 to September 2020, amniotic fluid or umbilical cord blood from 293 pregnant women carrying fetuses with VM was extracted for single-nucleotide polymorphism microarray (SNP array). Among 293 fetuses with VM, 31 were detected with abnormal CNVs, including 22 with pathogenic CNVs (7.51%) and nine with variation of uncertain clinical significance (VUS) CNVs (3.07%). Of the 22 fetuses with pathogenic CNVs, 13 had known disease syndromes. Among the 293 fetuses, 133 had mild isolated VM [pathogenic CNVs, 7/133 (5.26%)]; 142 had mild non-isolated VM [pathogenic CNVs, 13/142 (9.15%)]; 12 had severe isolated VM [pathogenic CNVs, 2/12 (16.67%)]; and six had severe non-isolated VM (no abnormal CNVs was detected). There was no statistical significance in the rate of pathogenic CNVs among the four groups (P = 0.326, P > 0.05). Among the 267 fetuses with successful follow-up, 38 were terminated (of these, 21 had pathogenic CNVs). Of the 229 fetuses, two had developmental delay and the remaining 227 had a good prognosis after birth. Overall, the results are useful for the detection of fetal microdeletion/microduplication syndrome and for the accurate assessment of fetal prognosis in prenatal consultation.

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Section: Discussionmentioning

confidence: 99%

Classifying and Evaluating Fetuses With Ventriculomegaly in Genetic Etiologic Studies

Cai

Huang

et al. 2021

Front. Genet.

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“…However, 17 (5.1%) cases in the VOUS group feared the uncertainties and stubbornly decided to terminate the pregnancy. Thus, for VOUS foetuses, further long-term follow-up studies, experience accumulation and sharing are necessary [ 40 ].…”

Section: Discussionmentioning

confidence: 99%

Detection rates of abnormalities in over 10,000 amniotic fluid samples at a single laboratory

Kakongoma

et al. 2023

BMC Pregnancy Childbirth

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Background A growing number of cytogenetic techniques have been used for prenatal diagnosis. This study aimed to demonstrate the usefulness of karyotyping, BACs-on-Beads (BoBs) assay and single nucleotide polymorphism (SNP) array in prenatal diagnosis during the second trimester based on our laboratory experience. Methods A total of 10,580 pregnant women with a variety of indications for amniocentesis were enrolled in this retrospective study between January 2015 and December 2020, of whom amniotic fluid samples were analysed in 10,320 women. The main technical indicators of participants in the three different technologies were summarized, and cases of chromosome abnormalities were further evaluated. Results The overall abnormality detection rate of karyotyping among all the amniotic fluid samples was 15.4%, and trisomy 21 was the most common abnormality (20.9%). The total abnormality detection rate of the BoBs assay was 5.6%, and the diagnosis rate of microdeletion/microduplication syndromes that were not identified by karyotyping was 0.2%. The detection results of the BoBs assay were 100.0% concordant with karyotyping analysis in common aneuploidies. Seventy (87.5%) cases of structural abnormalities were missed by BoBs assay. The total abnormality detection rate of the SNP array was 21.6%. The detection results of common aneuploidies were exactly the same between SNP array and karyotyping. Overall, 60.1% of structural abnormalities were missed by SNP array. The further detection rate of pathogenic significant copy number variations (CNVs) by SNP was 1.4%. Conclusions Karyotyping analysis combined with BoBs assay or SNP array for prenatal diagnosis could provide quick and accurate results. Combined use of the technologies, especially with SNP array, improved the diagnostic yield and interpretation of the results, which contributes to genetic counselling. BoBs assay or SNP array could be a useful supplement to karyotyping.

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“…CMA was carried out using Affymetrix CytoScan 750 K array (Affymetrix Inc., Santa Clara, CA), and data was analyzed via Affymetrix Chromosome Analysis Suite Software (version 3.1.0.15) as previously described 19 . The reporting threshold was set at gains ≥ 1 Mb, losses ≥ 500 Kb and loss of heterozygosity (LOH) ≥ 10 Mb.…”

Section: Methodsmentioning

confidence: 99%

Prenatal genetic analysis of fetal aberrant right subclavian artery with or without additional ultrasound anomalies in a third level referral center

Xue

Zhang

et al. 2023

Sci Rep

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To evaluate the correlation between chromosomal abnormalities and fetal aberrant right subclavian artery (ARSA) with or without additional ultrasound anomalies (UAs). A total of 340 fetuses diagnosed with ARSA by ultrasound between December, 2015, and July, 2021, were included. All cases were subdivided into three groups: (A) 121 (35.6%) cases with isolated ARSA, (B) 91 (26.8%) cases with soft markers, and (C) 128 (37.6%) cases complicated with other UAs. Invasive testing was performed via amniotic fluid or cord blood karyotyping and chromosomal microarray analysis (CMA) in parallel, and pregnancy outcomes were followed. Karyotype abnormalities were identified in 18/340 (5.3%) patients. Karyotype abnormalities in Groups A, B, and C were 0/121 (0.0%), 7/91 (7.7%), and 11/128 (8.6%), respectively. CMA abnormalities with clinically significant variants were detected in 37/340 (10.9%) cases, of which 22q11.2 deletion syndrome and trisomy 21 accounted for 48.6% (18/37). The overall abnormal CMA with clinically significant variant detection rates in Groups A, B, and C were 3/121(2.5%), 13/91 (14.3%), and 21/128 (16.4%), respectively. There were significant difference in clinically significant CMA anomalies detection rate between Groups A and C (p < 0.05), as well as Groups A and B (p < 0.05). Comparing CMA to karyotyping showed a clinically significant incremental yield in Group C (7.8%, 10/128) compared to Groups A (2.5%, 3/121) and B (6.6%, 6/91) (p > 0.05). Fetal ARSA with additional UAs, concurred with cardiac and extra-cardiac anomalies, constitutes a high-risk factor for chromosomal aberrations, especially for pathogenic or likely pathogenic copy number variants.

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Detection of copy number variation associated with ventriculomegaly in fetuses using single nucleotide polymorphism arrays

Cited by 14 publications

References 39 publications

Classifying and Evaluating Fetuses With Ventriculomegaly in Genetic Etiologic Studies

Classifying and Evaluating Fetuses With Ventriculomegaly in Genetic Etiologic Studies

Detection rates of abnormalities in over 10,000 amniotic fluid samples at a single laboratory

Prenatal genetic analysis of fetal aberrant right subclavian artery with or without additional ultrasound anomalies in a third level referral center

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