Integrated CNV-seq, karyotyping and SNP-array analyses for effective prenatal diagnosis of chromosomal mosaicism

Abstract Background Emerging studies suggest that low‐coverage massively parallel copy number variation sequencing (CNV-seq) more sensitive than chromosomal microarray analysis (CMA) for detecting low-level mosaicism. However, a retrospective back-to-back comparison evaluating accuracy, efficacy, and incremental yield of CNV-seq compared with CMA is warranted. Methods A total of 72 mosaicism cases identified by karyotyping or CMA were recruited to the study. There were 67 mosaic samples co-analysed by CMA and CNV-seq, comprising 40 with sex chromosome aneuploidy, 22 with autosomal aneuploidy and 5 with large cryptic genomic rearrangements. Results Of the 67 positive mosaic cases, the levels of mosaicism defined by CNV-seq ranged from 6 to 92% compared to the ratio from 3 to 90% by karyotyping and 20% to 72% by CMA. CNV-seq not only identified all 43 chromosomal aneuploidies or large cryptic genomic rearrangements detected by CMA, but also provided a 34.88% (15/43) increased yield compared with CMA. The improved yield of mosaicism detection by CNV-seq was largely due to the ability to detect low level mosaicism below 20%. Conclusion In the context of prenatal diagnosis, CNV-seq identified additional and clinically significant mosaicism with enhanced resolution and increased sensitivity. This study provides strong evidence for applying CNV-seq as an alternative to CMA for detection of aneuploidy and mosaic variants.

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Integrated CNV-seq, Karyotyping and SNP-array Analyses for Effective Prenatal Diagnosis of Chromosomal Mosaicism

10.21203/rs.3.rs-80004/v1 ◽

2020 ◽

Author(s):

Na Ma ◽

Hui Xi ◽

Jing Chen ◽

Ying Peng ◽

Zhengjun Jia ◽

...

Keyword(s):

Prenatal Diagnosis ◽

Sex Chromosome ◽

Snp Array ◽

Chromosomal Mosaicism ◽

Chromosomal Microarray ◽

Chromosomal Microarray Analysis ◽

Significant Information ◽

Prenatal Diagnostic ◽

Autosomal Aneuploidy ◽

Number Variation

Abstract Background: Emerging studies suggest that low‐coverage massively parallel copy number variation sequencing (CNV-seq) provide advantage in detecting low-level mosaicism compared with chromosomal microarray analysis (CMA). However, a prospective back-to-back comparison evaluating accuracy, efficacy, and incremental yield of CNV-seq compared with CMA is warranted. Methods: A total of 72 mosaicism cases identified by karyotyping or CMA were recruited in this study, and 67 samples (40 sex chromosome aneuploidy, 22 autosomal aneuploidy and 5 submicroscopic CNVs) were eventually analyzed by CNV-seq. Results: CNV-seq not only identified all 43 chromsomal aneuploidies or submicroscopic CNVs detected by CMA, but also provided a 34.88% (15/43) increased yield compared with CMA. Besides, the level of mosaicism defined by CNV-seq range from 6% to 92%. Conclusion: In the context of prenatal diagnosis, CNV-seq identified additional and clinically significant information with enhanced resolution and increased sensitivity of detecting mosaicism as compared with the CMA platform we used. This study provides strong evidence for applying CNV-seq as an alternative prenatal diagnostic test.

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Chromosomal microarray analysis allows prenatal detection of low level mosaic autosomal aneuploidy

Prenatal Diagnosis ◽

10.1002/pd.4333 ◽

2014 ◽

Vol 34 (5) ◽

pp. 505-507 ◽

Cited By ~ 3

Author(s):

Georgina K. Hall ◽

Fiona L. Mackie ◽

Susan Hamilton ◽

Alison Evans ◽

Dominic J. McMullan ◽

...

Keyword(s):

Microarray Analysis ◽

Chromosomal Microarray ◽

Chromosomal Microarray Analysis ◽

Low Level ◽

Prenatal Detection ◽

Autosomal Aneuploidy

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Rapid Diagnosis of Imprinting Disorders Involving Copy Number Variation and Uniparental Disomy Using Genome-Wide SNP Microarrays

Cytogenetic and Genome Research ◽

10.1159/000435847 ◽

2015 ◽

Vol 146 (1) ◽

pp. 9-18 ◽

Cited By ~ 10

Author(s):

Weiqiang Liu ◽

Rui Zhang ◽

Jun Wei ◽

Huimin Zhang ◽

Guojiu Yu ◽

...

Keyword(s):

Copy Number ◽

Snp Array ◽

Uniparental Disomy ◽

Copy Number Variations ◽

Chromosomal Microarray ◽

Chromosomal Microarray Analysis ◽

Imprinting Disorders ◽

Genome Wide ◽

Number Variation ◽

Efficient Alternative

Imprinting disorders, such as Beckwith-Wiedemann syndrome (BWS), Prader-Willi syndrome (PWS) and Angelman syndrome (AS), can be detected via methylation analysis, methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA), or other methods. In this study, we applied single nucleotide polymorphism (SNP)-based chromosomal microarray analysis to detect copy number variations (CNVs) and uniparental disomy (UPD) events in patients with suspected imprinting disorders. Of 4 patients, 2 had a 5.25-Mb microdeletion in the 15q11.2q13.2 region, 1 had a 38.4-Mb mosaic UPD in the 11p15.4 region, and 1 had a 60-Mb detectable UPD between regions 14q13.2 and 14q32.13. Although the 14q32.2 region was classified as normal by SNP array for the 14q13 UPD patient, it turned out to be a heterodisomic UPD by short tandem repeat marker analysis. MS-MLPA analysis was performed to validate the variations. In conclusion, SNP-based microarray is an efficient alternative method for quickly and precisely diagnosing PWS, AS, BWS, and other imprinted gene-associated disorders when considering aberrations due to CNVs and most types of UPD.

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Prenatal Diagnosis of BACs-on-Beads Assay in 3647 Cases of Amniotic Fluid Cells

Reproductive Sciences ◽

10.1177/1933719118804416 ◽

2018 ◽

Vol 26 (7) ◽

pp. 1005-1012 ◽

Cited By ~ 5

Author(s):

Chunyan Li ◽

Biliang Chen ◽

Jiao Zheng ◽

Lu Cheng ◽

Tingting Song ◽

...

Keyword(s):

Prenatal Diagnosis ◽

Amniotic Fluid ◽

Sex Chromosome ◽

Trisomy 13 ◽

Chromosomal Microarray ◽

Chromosomal Microarray Analysis ◽

Microdeletion Syndromes ◽

Structural Abnormalities ◽

Chromosomal Aneuploidies

Objective: To evaluate the diagnostic accuracy of the BACs-on-Beads (BoBs) assay for the rapid diagnosis of common aneuploidies and microdeletion syndromes. Methods: BACs-on-Beads and chromosomal karyotyping were used for detecting 3647 cases of amniotic fluid samples with indications for prenatal diagnosis, which were collected from January 2015 to June 2017 in Xijing Hospital. Fluorescence in situ hybridization (FISH) or chromosomal microarray analysis (CMA) provided further validation. Results: The overall abnormality detection rate (BoBs combined with karyotyping) was 7.73% (282/3647). A total of 209 chromosomal aneuploidies, 10 mosaic cases, 11 microdeletion/microduplication syndromes, and 52 structural abnormalities were observed. Both assays were concordant for trisomy 21 (4.22%, 154/3647), trisomy 18 (0.69%, 25/3647), trisomy 13 (0.05%, 2/3647), and sex chromosome aneuploidies (0.77%, 28/3647). Meanwhile, DiGeorge syndrome (0.05%, 2/3647), 22q11.2 microduplication (0.08%, 3/3647), Smith-Magenis syndrome (0.03%, 1/3647), 17p11.2 microduplication (0.03%, 1/3647), Wolf-Hirschhorn syndrome (0.03%, 1/3647), Williams-Beuren syndrome (0.03%, 1/3647), Cri du Chat syndrome (0.03%, 1/3647), and Miller-Dieker syndrome (0.03%, 1/3647) were identified by BoBs assay, thus giving the incidence of the detection of these syndromes of 0.30% (11/3647). Conclusion: BACs-on-Beads assay is a reliable test for rapid detection of common aneuploidies and microdeletion syndromes, combining with karyotyping, FISH, and CMA, to improve the efficiency and accuracy of prenatal diagnosis to alleviate maternal emotional anxiety.

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Prenatal diagnosis of cri-du-chat syndrome by SNP array: report of twelve cases and review of the literature

Molecular Cytogenetics ◽

10.1186/s13039-019-0462-0 ◽

2019 ◽

Vol 12 (1) ◽

Cited By ~ 1

Author(s):

Jiasun Su ◽

Huayu Fu ◽

Bobo Xie ◽

Weiliang Lu ◽

Wei Li ◽

...

Keyword(s):

Prenatal Diagnosis ◽

Snp Array ◽

Nasal Bone ◽

Hydrops Fetalis ◽

Terminal Deletion ◽

Chromosomal Microarray ◽

Chromosomal Microarray Analysis ◽

Cri Du Chat Syndrome ◽

Definitive Method ◽

Hypoplastic Nasal Bone

Abstract Background Cri-du-chat syndrome (CdCS; OMIM#123450) is a classic contiguous gene syndrome caused by chromosome 5p terminal deletion (5p-), which characterized by a high-pitched cat-like cry, developmental delay, severe psychomotor, mental retardation, and dysmorphic features in infancy. Prenatal diagnosis of CdCS is difficult due to the non-specific ultrasound features. And reports using array analysis are rare. This study presented the first retrospective analysis of prenatal series of CdCS fetuses diagnosed by single nucleotide polymorphism (SNP) array in China. Case presentation A total of 35,233 pregnant women were enrolled from Jan 2014 to April 2019 in our center, there are twelve 5p- cases with abnormal sonographic signs revealed by SNP array, giving an incidence of 0.034% (12/35,233). Clinical information and molecular basis included: maternal demographics, indications for invasive testing, sonographic findings and SNP array results. Among all the 5p- cases revealed, nine cases were diagnosed by both karyotyping and SNP array, three cases were detected only by SNP array. Half of our cases (6/12) had an isolated 5p terminal deletion, which sizes ranged from 9.0 Mb to 30 Mb. The other half of cases (6/12) characterized by unbalanced translocation, with sex ratio 7:5 (female: male), when combine the clinical features observed from this study and available literature, the most frequent anomaly observed in prenatal ultrasound examination of CdCS was cerebral abnormalities, accounted for 44.4% (16/36) of the existing cases. Features that are less consistent included: choroid plexus cyst (13.8%, 5/36), single umbilical artery (13.3%, 4/30), ventricular septal defect (11.1%, 4/36), hydrops fetalis (8.3%, 3/36), ascites (8.3%, 3/36), increased NT/NF (8.3%, 3/36), absent/severely hypoplastic nasal bone (5.5%, 2/36), in order. Conclusion Prenatal findings such as cerebral abnormalities, absent/hypoplastic nasal bone, hydrops fetalis, ascites or encephalocele may act as suggestive signs of CdCS or other microdeletion/duplication syndromes. Combining typical karyotyping with chromosomal microarray analysis (CMA) is a definitive method for a precise diagnosis of CdCS and provides more accurate results in order to offer genetic counseling to families which need to deal with cryptic aberrations.

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Application of Chromosome Microarray Analysis and Karyotype Analysis in Diagnostic Assessment of Abnormal Down's Syndrome Screening Results

10.21203/rs.3.rs-846353/v1 ◽

2021 ◽

Author(s):

Han Kang ◽

Lingxi Wang ◽

Xingyu Li ◽

Chonglan Gao ◽

Yamei Xie ◽

...

Keyword(s):

Prenatal Diagnosis ◽

Pregnant Women ◽

Microarray Analysis ◽

Sex Chromosome ◽

Karyotype Analysis ◽

Down's Syndrome ◽

Down’S Syndrome ◽

Chromosomal Microarray ◽

Chromosomal Microarray Analysis ◽

Balanced Translocation

Abstract Background: Although screening for fetal aneuploidy with the use of cell-free DNA obtained from maternal plasma is highly effective, biomarkers screening is in extensive use in economically underdeveloped areas and poor population. This study aims to explore the application value of chromosomal microarray analysis (CMA) and karyotype analysis in prenatal diagnosis for pregnant women with abnormal Down’s syndrome (DS) screening results.Methods: The study recruited 813 pregnant women with abnormal DS screening results from Chengdu Women’s and Children’s Central Hospital. They underwent amniocentesis to obtain fetal amniotic fluid for CMA and G-band karyotype analysis. An Affymetrix CytoScan 750 K Array chip was used for CMA analysis according to the manufacturer’s instructions.Results: In total, CMA identified 21/813 abnormal results, which was more efficient than karyotype analysis(10/813, P<0.001.) CMA is equivalent to traditional karyotype analysis for the prenatal diagnosis of aneuploidies. However, CMA identified 1.60% more copy number variants(CNVs) than karyotype analysis. These pathogenic/likely pathogenic(P/LP) CNVs ranged from 159Kb deletion to 3616Kb deletion. 53.8% of them were recurrent pathogenic CNVs associated with risk of neurodevelopmental disorders. CMA identified 7 variants of uncertain significance (VUS) results, including 6 microduplication and 1 microdeletion, with the size ranged from 840kb-1484kb. Karyotype analysis identified 2 mosaic sex chromosome aneuploidy, 2 balanced translocation and 1 mosaic balanced translocation, which could not be identified by CMA. Conclusions: Performing both CMA and karyotype analysis simultaneously is more beneficial to pregnant women with abnormal DS screening results.

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Chromosomal mosaicism detected by karyotyping and chromosomal microarray analysis in prenatal diagnosis

Journal of Cellular and Molecular Medicine ◽

10.1111/jcmm.16080 ◽

2020 ◽

Author(s):

Yi Zhang ◽

Mei Zhong ◽

Dezhong Zheng

Keyword(s):

Prenatal Diagnosis ◽

Microarray Analysis ◽

Chromosomal Mosaicism ◽

Chromosomal Microarray ◽

Chromosomal Microarray Analysis

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The Necessity of Prenatal Diagnosis by CMA for the Women with NIPS-Positive Results

International Journal of Genomics ◽

10.1155/2020/2145701 ◽

2020 ◽

Vol 2020 ◽

pp. 1-7

Author(s):

Jun Xu ◽

Ying Xue ◽

Jing Wang ◽

Qin Zhou ◽

Bin Zhang ◽

...

Keyword(s):

Prenatal Diagnosis ◽

Sex Chromosome ◽

Karyotype Analysis ◽

Single Nucleotide Polymorphism Array ◽

Chromosomal Microarray ◽

Chromosomal Microarray Analysis ◽

Chromosome Aneuploidy ◽

Prenatal Diagnostic ◽

Uncertain Significance ◽

Positive Results

Objective. To retrospectively analyze the results of prenatal diagnoses of noninvasive prenatal screening- (NIPS) positive pregnant women and discuss whether there is a need for chromosomal microarray analysis (CMA). Methods. The study recruited 1,019 NIPS-positive women from two prenatal diagnostic centers. Based on clinical advice, they opted for traditional karyotype analysis or CMA. Single nucleotide polymorphism array testing was performed on a commercial 750K microarray chip (Affymetrix CytoScan 750K Array). Results. Of the NIPS-positive women, 761 (74.7%) accepted the prenatal diagnosis. There were 418 (54.9%) abnormal results, and most (99.5%) were chromosome aneuploidy or structural abnormalities. Only three cases were confirmed as pathogenic copy number variation (CNVs), which were found only with CMA and not by karyotype analysis. Fifteen women were variants of uncertain significance (VUS) CNV. In addition, 300 women selected opted for both karyotype analysis and CMA for prenatal diagnosis: in 275 (91.7%) cases, the results of the two modalities were consistent, while in the remaining 25, they were not. In three cases, the additional positive results obtained with CMA were potentially clinically significant. Conclusions. CMA may not be useful for many women positive for trisomy 21/18/13 based on NIPS results, because traditional karyotype analysis can identify most problems. However, it can yield important additional findings in women positive for fetal sex chromosome aneuploidy (SCA). Further clinical studies are needed to confirm these findings.

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Prenatal diagnosis of chromosomal aberrations by chromosomal microarray analysis in foetuses with ventriculomegaly

Scientific Reports ◽

10.1038/s41598-020-77400-8 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Jiamin Wang ◽

Zhu Zhang ◽

Qinqin Li ◽

Hongmei Zhu ◽

Yi Lai ◽

...

Keyword(s):

Prenatal Diagnosis ◽

Microarray Analysis ◽

Chromosomal Aberrations ◽

Copy Number Variants ◽

Snp Array ◽

Chromosomal Microarray ◽

Chromosomal Microarray Analysis ◽

Increased Risk ◽

Long Term Follow Up

AbstractVentriculomegaly is considered to be linked to abnormal neurodevelopment outcome. The aim of this retrospective study was to investigate the current applications of chromosomal microarray analysis (CMA) in foetuses with ventriculomegaly. A total of 548 foetuses with ventriculomegaly detected by prenatal ultrasound underwent single nucleotide polymorphism (SNP) array testing and were subjected to long-term follow-up. The overall prevalence of chromosomal aberrations was 7.30% (40/548), including 4.20% (23/548) with pathogenic/likely pathogenic copy number variants. The incidence of chromosomal aberrations was significantly higher in foetuses with bilateral ventriculomegaly than in those with unilateral ventriculomegaly (10.56% vs. 5.71%, P = 0.040), in foetuses with non-isolated ventriculomegaly than in those with isolated ventriculomegaly (12.99% vs. 2.38%, P < 0.0001), and in foetuses with severe ventriculomegaly than in those with mild-to-moderate ventriculomegaly (23.08% vs. 6.51%, P = 0.005). The outcome in foetuses with mild ventriculomegaly was significantly better than in those with moderate ventriculomegaly (95.60% vs. 84.00%, P = 0.003). Thus, CMA should be regarded as the first-tier test for prenatal diagnosis of foetal ventriculomegaly, especially in foetuses with bilateral or non-isolated ventriculomegaly. The outcome of foetuses with mild ventriculomegaly is favourable; however, there is an increased risk of neurodevelopmental disabilities in foetuses with moderate ventriculomegaly.

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