Application of the BACs-on-Beads™ assay for rapid prenatal detection application of BoBs™ for PND of aneuploidies and microdeletions

Application of the prenatal BACs-on-Beads™ assay for rapid prenatal detection of sex chromosome mosaicism

The prenatal BACs-on-Beads™ (BoBs) assay was introduced for rapid detection of abnormalities of chromosomes 13, 18, 21, X, and Y and specific nine significant microdeletion syndromes. The ability of prenatal BoBs to detect mosaicism ranged from 20 to 40%. However, there have been no prenatal studies of sex chromosome mosaicism in prenatal BoBs. Therefore, the present study was performed with an aim to uncover the detection level of sex chromosome mosaicism that application of prenatal BoBs assay, and then to assess the sensitivity of prenatal BoBs assay, thereby improving the prenatal diagnostic accuracy. A total of 31 samples of amniotic fluid (AF) and umbilical cord blood (UCB) for prenatal diagnosis were collected, and the results were confirmed through karyotyping, single nucleotide polymorphism microarray (SNP-array) and copy number variation sequencing (CNV-seq). 23 cases of sex chromosome mosaicism were prompted abnormal by prenatal BoBs, the minimum detection level of mosaicism was about 6% as detected by karyotype. The overall sensitivity of prenatal BoBs in the detection of sex chromosome mosaicism was 74.2% (23/31). This study evaluated the effectiveness of prenatal BoBs for detecting sex chromosome mosaicism in prenatal diagnosis, and the results will provide valuable information for genetic counseling.

Clinical Utility of the Prenatal BACs-on-Beads™ Assay in Invasive Prenatal Diagnosis

Background: The prenatal BACs-on-Beads™ (PNBoBs™) assay has been applied worldwide for prenatal diagnosis. However, there are neither guidelines nor consensus on choosing patients, sample types, or clinical pathways for using this technique. Moreover, different perspectives have emerged regarding its clinical value. This study aimed to evaluate its clinical utility in the context of clinical practice located in a prenatal diagnostic center in Xiamen, a city in southeast China. Methods: We tested 2,368 prenatal samples with multiple referral indications using both conventional karyotyping and PNBoBs™. Positive results from PNBoBs™ were verified using current gold-standard approaches. Results: The overall rates for the detection of pathogenic copy number variation (pCNV) by karyotyping and PNBoBs™ were 1.9% (46/2,368) and 2.0% (48/2,368), respectively. The overall detection rate of karyotyping combined with PNBoBs™ for pCNV was 2.3% (54/2,368). A total of 13 cases of copy number variation (CNV)with a normal karyotype were detected by PNBoBs™. Another case with a normal karyotype that was detected as a CNV of sex chromosomes by PNBoBs™ was validated to be maternal cell contamination by short tandem repeat analysis. Conclusion: Karyotyping combined with PNBoBs™ can improve both the yield and efficiency of prenatal diagnosis and is appropriate in the second trimester in all patients without fetal ultrasound anomalies who undergo invasive prenatal diagnosis.

17p13.3 Microduplication Syndrome: Further Delineating the Clinical Spectrum

17p13.3 microduplication syndrome has been associated with a clinical spectrum of phenotypes, and depending on the genes involved in the microduplication, it is categorized into two classes (Class I and Class II). We herein, describe two patients diagnosed with Class I 17p13.3 microduplication by BACs-on-Beads (BoBs) assay and further confirmed by fluorescence in situ hybridization (FISH). Our patients (Patient 1: 4-year-old male; Patient 2: 2-year-old male) presented with developmental delay, intellectual disability, and dysmorphic facial features. When compared with the literature, our patients manifested distinctive features (Patient 1: primary hypothyroidism; Patient 2: bilateral cryptorchidism) that were not previously described in the duplication 17p13.3 spectrum.

BACs-on-Beads Assay for the Prenatal Diagnosis of Microdeletion and Microduplication Syndromes

OBJECTIVE

To evaluate the clinical value of BACs-on-Beads (BoBs) assay in detection of microdeletion and microduplication syndromes.

METHODS

A total of 6,814 cases of amniotic fluid cells collected from January 2015 to July 2020 in our hospital were analyzed by chromosomal karyotyping and BoBs assay. Fluorescence in situ hybridization (FISH) or chromosomal microarray analysis (CMA) provided further validation for the cases of microdeletion and microduplication.

RESULTS

Thirty microdeletion and microduplication syndromes were identified by BoBs with an incidence of ~1/227, including 22q11.2 microduplication (0.044%, 3/6814), DiGeorge I syndrome (0.044%, 3/6814), 17p11.2 microduplication (0.015%, 1/6814), Smith-Magenis syndrome (0.015%, 1/6814), 17p11.2p11.3 microduplication (0.015%, 1/6814), Williams-Beuren syndrome (0.088%, 6/6814), 7q11.2 microduplication (0.029%, 2/6814), DiGeorge II syndrome (0.015%, 1/6814), 18p11.32p11.21 microduplication (0.015%, 1/6814), Wolf-Hirschhorn syndrome (0.029%, 2/6814), 4p16.3 microduplication (0.015%, 1/6814), Langer-Giedion syndrome (0.015%, 1/6814), Miller-Dieker syndrome (0.015%, 1/6814), Cri du Chat syndrome (0.015%, 1/6814), Xp22.31 microdeletion (0.059%, 4/6814), Prader-Willi syndrome (0.015%, 1/6814). High concordance was obtained between BoBs and FISH or CMA. However, only four cases were detected by chromosomal karyotyping.

CONCLUSION

BoBs assay can rapidly detect microdeletion and microduplication syndromes, which compensates the shortcomings of conventional chromosomal karyotyping and greatly improves the efficiency and accuracy of prenatal diagnosis.

Application of the BACs-on-Beads assay for the prenatal diagnosis of chromosomal abnormalities in Quanzhou, China

BACKGROUND

An increasing number of techniques have been used for prenatal diagnosis of genetic abnormalities. Our initial objective was to explore the value of the BACs-on-Beads (BoBs) assay for the prenatal diagnosis of aneuploidies and microdeletion/microduplication syndromes in Quanzhou, Southeast China.

METHODS

A total of 1409 pregnant women with high-risk factors for chromosomal abnormalities admitted to Quanzhou Women's and Children's Hospital were enrolled in this study. BoBs assays and karyotype analyses were conducted for all subjects. Subsequently, chromosome microarray analysis (CMA) or fluorescence in situ hybridization (FISH) was performed to validate the findings.

RESULTS

In this study, karyotype analysis and BoBs assay failed in 4 cases, and 2 cases, respectively. A total of 1403 cases were successfully analyzed, with success rates of 99.72% (1405/1409) and 99.85% (1407/1409) for karyotype analysis and Bobs assay, respectively. BoBs assay rapidly detected chromosomal aneuploidies in line with the karyotyping data. Additionally, 23 cases of microdeletions/microduplications were detected by BoBs assay but missed by karyotyping, including 22q11.2 microdeletions/microduplications, 5p15.32p15.33 microdeletion, Xp22.31 microdeletions/microduplications, Xq27.3 microdeletion, and Yp11.2 and Yq11.22q11.222 microduplication. In comparison with karyotyping, fewer mosaicisms were identified by BoBs assay. A high detection rate of chromosomal abnormalities was observed in the high-risk group during noninvasive prenatal testing (NIPT) (41.72%) and the abnormal ultrasound group (13.43%).

CONCLUSIONS

BoBs assay can be used for the rapid and efficient prenatal diagnosis of common aneuploidies and microdeletion/microduplication syndromes. Moreover, the combined use of BoBs assay and karyotyping in prenatal diagnosis may allow for a more effective detection of chromosomal abnormalities.

Evaluation of interpretation methods to improve accuracy of the prenatal BACs-on-Beads™ assay in prenatal diagnosis

Prenatal BACs-on-Beads™ (PNBoBs™) technology has been approved for use in routine clinical prenatal diagnosis in numerous countries. However, the influence of data interpretation on the accuracy of the results remains to be evaluated. The present study aimed to determine the accuracy of existing data interpretation approaches and develop an optimization method to improve the performance of the PNBoBs™ assay in prenatal diagnosis. A total of 2,289 prenatal cases with known karyotypes and raw ratio data from PNBoBs™ assays were recruited for the present study. Positive results, according to the data interpretation methods used for the PNBoBs™ test, were validated against current gold-standard approaches. Statistical analyses were then performed to evaluate the accuracy of existing methods in data interpretation to provide a basis for the optimization of a follow-up approach. Among the existing methods, the ‘trimmed standard deviation threshold’ approach had the highest sensitivity and false-positive rates, with 98.1 and 4.2%, respectively. The ‘n-1 or greater probes’ rule had the highest specificity (99.7%) and the second-highest false-negative rate (11.5%). The method optimized in the present study provided a reasonable balance between sensitivity (98.1%) and specificity (99.6%) with regards to the interpretation of the data obtained from the PNBoBs™ assay. The results indicated that the present optimization method outperforms existing approaches in data interpretation for the PNBoBs™ assay, and as a result, may reduce unnecessary verification turnaround time and cost in prenatal diagnosis.

The Comprehensive Comparison of Bacterial Artificial Chromosomes (BACs)-on-Beads Assay and Copy Number Variation Sequencing in Prenatal Diagnosis of Southern Chinese Women

Bacterial artificial chromosomes (BACs)-on-Beads (BoBs) assay and copy number variation sequencing (CNV-seq) are two frequently used methods in today's prenatal diagnosis. Several studies were conducted to investigate the performance of each approach, but they were never compared side by side. In this article, a comprehensive comparison of BoBs and CNV-seq was conducted using 1876 amniotic fluid and umbilical cord blood samples collected from Fujian Maternity and Child Health Hospital between 2015 and 2019. Karyotyping was used as the gold standard for chromosome structure variation, and chromosomal microarray analysis was performed to validate inconsistent results. Overall, 174 cases of confirmed chromosome anomalies were detected, including 73 chromosomal aneuploidies, 10 mosaics, 30 pathogenic CNVs, and 61 other structural anomalies. BoBs and CNV-seq achieved a 100% concordance in all 55 pathogenic euchromosome aneuploidies, but CNV-seq had a higher detection rate in sex chromosome aneuploidy and mosaic identification. For CNV detection, all of the 20 pathogenic CNVs discovered by the BoBs assay also were identified by CNV-seq and 10 additional pathogenic CNVs were observed by CNV-seq. The results of this study showed that CNV-seq was a reliable and more favorable method in terms of detection rate, costs, and disease range. In combination with karyotyping, CNV-seq could improve the efficiency and accuracy of a prenatal diagnosis to alleviate maternal emotional anxiety and deduce birth defects.

Rapid prenatal aneuploidy detection of BACs-on-Beads assay in 4961 cases of amniotic fluid samples

Objective: To evaluate the diagnostic value of the BACs-on-Beads (BoBs) assay for the rapid diagnosis of common aneuploidies and microdeletions.Methods: A total of 4961 pregnant women admitted to the Wuxi Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University from January 2017 to March 2019 were enrolled. BoBs assay and conventional karyotyping were applied to detect amniotic fluid samples with various indications for prenatal diagnosis. Chromosomal microarray analysis (CMA) and maternal cell contamination (MCC) tests were used for further validation.Results: The overall abnormality detection rates (BoBs associated with karyotyping) were 4.25% (211/4961). The prenatal diagnosis success rate of karyotyping was 99.4% (4933/4961), compared to 100% (4961/4961) using the BoBs assays. The BoBs assay was similar to karyotyping for the detection of trisomy 21 (1.01%, 50/4961), trisomy 18 (0.40%, 20/4961), trisomy 13 (0.04%, 2/4961), and sex chromosomal aneuploidies (0.15%, 12/4961). The BoBs assay also identified sex chromosomal microduplications/microdeletions (1.73%, 86/4961), 22q11.2 microdeletions/microduplications (0.1%, 5/4961), and Cri du Chat syndrome (0.02%, 1/4961) which were missed by karyotyping. The sensitivity for the detection of numerical chromosomal abnormalities of the BoBs assay and karyotyping analysis was 100% (95/95, 95% CI: 1.0-1.0) and 98.9% (94/95, 95% CI: 0.969-1.010), respectively. The sensitivity of detecting structural chromosomal abnormalities in the BoBs assay was significantly higher than those of karyotyping (79.3%, 92/116, 95% CI: 0.718-0.868) versus 21.6% (25/116, 95% CI: 0.140-0.291) (p < .01).Conclusions: The BoBs assay is a reliable and rapid test for the detection of common aneuploidies and nine microdeletion syndromes with high sensitivity and accuracy in prenatal diagnosis. The assay can compensate for the limitations of karyotyping analysis.

BACs-on-Beads™ assay, a rapid aneuploidy test, improves the diagnostic yield of conventional karyotyping

BACs-on-Beads (BoBs™) assay is a rapid aneuploidy test (RAT) that detects numerical chromosomal aneuploidies and multiple microdeletion/microduplication syndromes. This study was conducted to appraise the usefulness of the BoB™ assay as a complementary diagnostic tool to conventional karyotyping for the rapid detection of chromosomal aneuploidies. A total of 485 prenatal (amniotic fluid and chorionic villi) and blood/products of conception samples were collected between July 2013 and August 2018, and analyzed by the BoBs™ assay and cytogenetic karyotyping and further validated by fluorescence in situ hybridization (FISH). Forty-three of 484 qualifying samples (8.9%) were identified as abnormal by the BoBs™ assay. The assay was comparable to karyotyping in the detection of common structural abnormalities (trisomy 21, trisomy 18, X, and Y), with a sensitivity of 96.0% and a specificity of 100%. BoBs™ assay detected 20 microdeletion and microduplication syndromes that were missed by karyotyping. BoBs™, however, missed 10 cases of polyploidies and chromosomal rearrangements which were identified by conventional karyotyping. Our findings suggest that BoBs™ is a reliable RAT which is suitable in combination with conventional karyotyping for the detection of common aneuploidies. The assay also improves the diagnostic yield by recognizing clinically relevant submicroscopic copy number gains and losses.