Rapid and novel prenatal molecular assay for detecting aneuploidies and microdeletion syndromes

Analysis of a preimplantation genetic test for aneuploidies in 893 screened blastocysts using KaryoLite BoBs: a single-centre experience

INTRODUCTION

Does euploidy of trophectoderm (TE) biopsies correlate with conventional blastocyst morphological, maternal age and implantation potential?

METHODS

This is a one-centre, retrospective, observational study.

RESULTS

Eight hundred and ninety-three blastocysts were biopsied; 57.73% were euploid. The euploidy rate was found to be significantly higher for the embryos with good morphology of inner cell mass (ICM) and TE. Between ICM and TE morphology variables, TE was more predictive of the euploidy rate. When broken down into different age groups, the percentage of good morphology embryos remained similar across all age groups, while the percentage of euploid embryos dropped with increasing age. These results suggest that the correlation between blastocyst morphology and ploidy status was present but poor. Faster growing day 5 blastocysts showed a significantly higher euploidy rate than slower growing day 6 or 7 blastocysts. The number of good-quality blastocysts per cycle, euploid blastocysts per cycle and the euploidy rate were strongly associated with maternal age. A trend towards an increased implantation rate was found with euploid embryo transfers compared to the control group without preimplantation genetic test for aneuploidies (PGT-A).

CONCLUSIONS

Blastocyst morphology, rate of development and maternal age were found to be significantly associated with euploidy rate. There is a trend that suggests PGT-A may help to improve the pregnancy rate, but it is not statistically different, and therefore, PGT-A remains an unproven hypothesis. Due to the limitation of a small size of the control group, further studies with more data are needed.

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

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.

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.

Prenatal diagnosis of BACs-on-Beads assay in 1520 cases from Fujian Province, China

Background

The aim of this study was to evaluate the application of BACs‐on‐Beads (BoBs™) assay for rapid detection of chromosomal abnormalities for prenatal diagnosis (PND).

Methods

A total of 1520 samples, including seven chorionic villi biopsy samples, 1328 amniotic fluid samples, and 185 umbilical cord samples from pregnant women were collected to detect the chromosomal abnormalities using BoBs™ assay and karyotyping. Furthermore, abnormal specimens were verified by chromosome microarray analysis (CMA) and fluorescence in situ hybridization (FISH).

Results

The results demonstrated that the success rate of karyotyping and BoBs™ assay in PND was 98.09% and 100%, respectively. BoBs™ assay was concordant with karyotyping for Trisomy 21, Trisomy 18, and Trisomy 13, sex chromosomal aneuploidy, Wolf–Hirschhorn syndrome, and mosaicism. BoBs™ assay also detected Smith–Magenis syndrome, Williams–Beuren syndrome, DiGeorge syndrome, Miller–Dieker syndrome, Prader–Willi syndrome, Xp22.31 microdeletions, 22q11.2, and 17p11.2 microduplications. However, karyotyping failed to show these chromosomal abnormalities. A case of 8q21.2q23.3 duplication which was found by karyotyping was not detected by BoBs™ assay. Furthermore, all these chromosomal abnormalities were consistent with CMA and FISH verifications. According to the reports, we estimated that the detection rates of karyotyping, BoBs™, and CMA in the present study were 4.28%, 4.93%, and 5%, respectively, which is consistent with the results of a previous study. The respective costs for the three methods were about $135–145, $270–290, and $540–580.

Conclusion

BoBs™ assay is considered a reliable, rapid test for use in PND. A variety of comprehensive technological applications can complement each other in PND, in order to maximize the diagnosis rate and reduce the occurrence of birth defects.

The Prenatal Diagnosis of Seven Fetuses with 7q11.23 Microdeletion or Microduplication

Objective: There is scant information available about fetuses with 7q11.23 copy number variants (CNVs) found during pregnancy. We studied the clinical significance of 7q11.23 CNVs in prenatal diagnosis. Materials and methods: The amniocentesis was performed on pregnant women who underwent ultrasound (US) of fetal abnormalities. After karyotype analysis, CNVs were detected using BACs-on-Beads (BoBs) technique and chromosome microarray analysis (CMA). Results: Of seven fetuses with CNV of 7q11.23, five had microdeletions and two had microduplications. Case 1 had a 7q11.23 microdeletion along with other CNVs. Case 7 was a newborn with a normal phenotype and 7q11.23 microduplication. Conclusion: The CNVs in 7q11.23 results in many clinical manifestations, but the specificity of clinical features is not high. This study demonstrated that BoBs combined with CMA allows prenatal diagnosis of CNVs involving 7q11.23, and provide a clinical basis for prenatal diagnosis and genetic counseling of such CNVs.

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.

Combined use of bacterial artificial chromosomes-on-beads with karyotype detection improves prenatal diagnosis

Background

This study evaluated the individual and combined diagnostic performance of the bacterial artificial chromosomes (BACs)-on-Beads (BoBs™) assay and conventional karyotyping for the prenatal detection of chromosomal abnormalities in pregnant women who were 35 or more years-old.

Method

The primary outcome was concordance of any numerical, structural, or submicroscopic chromosomal abnormalities between BoBs™ and conventional karyotyping of amniotic fluid specimens from pregnant women at 17 to 22 weeks gestation.

Results

We examined samples from 4852 pregnant women. BoBs™ indicated that 4708 samples were normal (97.03%), and 144 were abnormal (2.97%); conventional karyotyping indicated that 4656 (95.96%) samples were normal and 196 (4.04%) were abnormal. The combined use of both methods indicated that 4633 of 4852 samples were normal (95.49%) and 219 of 4852 samples (4.51%) were abnormal. The kappa coefficient of the combined test was 0.70, indicating substantial consistency between BoBs™ and conventional karyotyping (95% CI = 0.65–0.76, P < 0.001).

Conclusions

Our results indicate that the combined use of BoBs™ and conventional karyotyping detected more fetal abnormalities than either test alone.

Utility and performance of bacterial artificial chromosomes-on-beads assays in chromosome analysis of clinical prenatal samples, products of conception and blood samples

AIM

Chromosome analysis of prenatal samples and products of conception (POC) has conventionally been done by karyotyping (KT). Shortcomings of KT like high turnaround time and culture failure led to technology innovations, such as the bacterial artificial chromosomes (BAC)s-on-Beads (BoBs)-based tests, Prenatal BoBs (prenatal samples) and KaryoLite BoBs (POC samples). In the present study, we validated and evaluated the utility of each test on prenatal, POC and blood samples.

METHODS

Study A (n = 305; 259 prenatal + 46 blood/POC) and Study B (n = 176; 146 POC/chorionic vill + 30 blood/amniotic fluid) samples were analyzed using Prenatal and KaryoLite BoBs kits, respectively. KT, array-based Comparative Genomic Hybridization (arrayCGH) and fluorescence in situ hybridization (FISH) were used for comparison of results. Ability of KaryoLite BoBs to identify ring chromosomes was tested.

RESULTS

Prenatal BoBs had zero test failure rate and results of all samples were concordant with KT results. Totally four microdeletions were identified by Prenatal BoBs but not by KT. In Study B, all but two POC samples (one triploid and one tetraploid) were concordant with KT and arrayCGH. Partial chromosomal imbalance detection rate was ~64% and KaryoLite BoBs indicated the presence of a ring chromosome in all four cases. The failure rate of KaryoLite BoBs was 3%.

CONCLUSION

We conclude that Prenatal BoBs (common aneuploidies and nine microdeletions) together with KT constitutes more comprehensive prenatal testing compared to FISH and KT. KaryoLite BoBs for aneuploidies of all chromosomes is highly successful in POC analysis and the ability to indicate presence of ring chromosomes improves its clinical sensitivity. Both tests are robust and could also be used for different specimens.

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

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.

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

Prenatal diagnosis focuses on the detection of anatomic and physiologic problems with a foetus before birth. Karyotyping is currently considered the gold standard for prenatal diagnosis of chromosomal abnormalities, but this method can be time consuming. This study evaluated the diagnostic accuracy of the BACs-on-Beads^TM (BoBs™) assay for the rapid diagnosis of aneuploidies and microdeletions. A total of 625 samples from pregnant women in Fujian province, in southeastern China-including three chorionic villus biopsies, 523 amniotic fluid samples, and 99 umbilical-cord centesis samples-were assessed for chromosomal abnormalities by karyotyping and by the BoBs™ assay. A diagnosis was successfully achieved by karyotyping for 98.8% (618/625) and by the BoBs™ assay for 100% (625/625) of the samples. Both assays were concordant for trisomy 21 (2.72%, 17/625), trisomy 18 (1.12%, 7/625), trisomy 13 (0.48%, 3/625), and sex chromosome aneuploidies (0.8%, 5/625). Unlike karyotyping, the BoBs™ assay detected 22q11.2 microdeletion (0.64%, 4/625), 22q11.2 microduplication (0.16%, 1/625), Smith-Magenis syndrome microdeletion (0.16%, 1/625), and Miller-Dieker syndrome microdeletion (0.16%, 1/625). Thus, the BoBs™ assay is a reliable and rapid test for detecting common aneuploidies and microdeletions for prenatal diagnosis, and could be used instead of karyotyping for detection of common aneuploidies as well as to provide additional information regarding microdeletions.

Chromosomal Microarrays for the Prenatal Detection of Microdeletions and Microduplications

Chromosomal microarray analysis has replaced conventional G-banded karyotype in prenatal diagnosis as the first-tier test for the cytogenetic detection of copy number imbalances in fetuses with/without major structural abnormalities. This article reviews the basic technology of microarray; the value and clinical significance of the detection of microdeletions, microduplications, and other copy number variants; as well as the importance of genetic counseling for prenatal diagnosis. It also discusses the current status of noninvasive screening for some of these microdeletion and microduplication syndromes.

Prevalence of recurrent pathogenic microdeletions and microduplications in over 9500 pregnancies

OBJECTIVES

The implementation of chromosomal microarray analysis (CMA) in prenatal testing for all patients has not achieved a consensus. Technical alternatives such as Prenatal BACs-on-Beads(TM) (PNBoBs(TM) ) have thus been applied. The aim of this study was to provide the frequencies of the submicroscopic defects detectable by PNBoBs(TM) under different prenatal indications.

METHODS

A total of 9648 prenatal samples were prospectively analyzed by karyotyping plus PNBoBs(TM) and classified by prenatal indication. The frequencies of the genomic defects and their 95%CIs were calculated for each indication.

RESULTS

The overall incidence of cryptic imbalances was 0.7%. The majority involved the DiGeorge syndrome critical region (DGS). The additional diagnostic yield of PNBoBs(TM) in the population with a low a priori risk was 1/298. The prevalences of DGS microdeletion and microduplication in the low-risk population were 1/992 and 1/850, respectively.

CONCLUSIONS

The constant a priori risk for common pathogenic cryptic imbalances detected by this technology is estimated to be ~0.3%. A prevalence higher than that previously estimated was found for the 22q11.2 microdeletion. Their frequencies were independent of maternal age. These data have implications for cell-free DNA screening tests design and justify prenatal screening for 22q11 deletion, as early recognition of DGS improves its prognosis.

Expanding the scope of noninvasive prenatal testing: detection of fetal microdeletion syndromes

OBJECTIVE

The purpose of this study was to estimate the performance of a single-nucleotide polymorphism (SNP)-based noninvasive prenatal test for 5 microdeletion syndromes.

STUDY DESIGN

Four hundred sixty-nine samples (358 plasma samples from pregnant women, 111 artificial plasma mixtures) were amplified with the use of a massively multiplexed polymerase chain reaction, sequenced, and analyzed with the use of the Next-generation Aneuploidy Test Using SNPs algorithm for the presence or absence of deletions of 22q11.2, 1p36, distal 5p, and the Prader-Willi/Angelman region.

RESULTS

Detection rates were 97.8% for a 22q11.2 deletion (45/46) and 100% for Prader-Willi (15/15), Angelman (21/21), 1p36 deletion (1/1), and cri-du-chat syndromes (24/24). False-positive rates were 0.76% for 22q11.2 deletion syndrome (3/397) and 0.24% for cri-du-chat syndrome (1/419). No false positives occurred for Prader-Willi (0/428), Angelman (0/442), or 1p36 deletion syndromes (0/422).

CONCLUSION

SNP-based noninvasive prenatal microdeletion screening is highly accurate. Because clinically relevant microdeletions and duplications occur in >1% of pregnancies, regardless of maternal age, noninvasive screening for the general pregnant population should be considered.

BACs-on-Beads™ (BoBs™) assay for the genetic evaluation of prenatal samples and products of conception

BACs-on-Beads™ (BoBs™) is a new emerging technology, a modification of comparative genomic hybridization that can be used to detect DNA copy number gains and losses. Here, we describe the application of two different types of BoBs™ assays: (1) Prenatal BoBs (CE-IVD) to detect the most frequent syndromes associated with chromosome microdeletions, as well as the trisomy 13, 18 and 21, and (2) KaryoLite BoBs (RUO) which can detect aneuploidy in all chromosomes by quantifying proximal and terminal regions of each chromosomal arm. The interpretation of the results by BoBsoft™ software is also described. Although BoBs™ may not have the breadth and scope to replace chromosomal microarrays (array comparative genomic hybridization and single nucleotide polymorphism array) in the prenatal setting, particularly when a fetal anomaly has been detected, it is a well suited alternative for FISH or QF-PCR because BoBs™ is comparable, if not superior in terms of cost, turnaround time (TAT) and throughput and accuracy. BoBs™ also has the ability to detect significant fetal mosaicism (≥30% with Prenatal BoBs and ≥50% with KaryoLite BoBs). However, perhaps the greatest strength of this new technology is the fact that unlike FISH or QF-PCR, it has the ability to detect common microdeletion syndromes or additional aneuploidies, both of which may be easily missed despite excellent prenatal sonography. Thus, when BoBs™ is applied in the correct clinical setting and run and analyzed in appropriate laboratories this technique can improve and augment best practices with a personalization of prenatal care.

BACs-on-beads: a new robust and rapid detection method for prenatal diagnosis

Karyotyping, the gold standard used for diagnosis of chromosomal abnormalities, is being progressively replaced by rapid aneuploidy testing (RAT) techniques such as quantitative fluorescence-PCR, FISH and multiplex ligation-dependent probe amplification for diagnosing the common aneuploidies or chromosomal microarray analysis for comprehensive genome-wide testing. However, due to technical limitations, current RATs are confined to the detection of common aneuploidies 13, 18, 21 and sex chromosomes. To overcome the limitations of RATs, a bacterial artificial chromosomes-on-beads (BoBs™) assay technology has been introduced for the detection of the common aneuploidies as well as specific microdeletion syndromes. The BoBs assay is a bead-based multiplex assay using polystyrene beads impregnated with two spectrally distinct infrared fluorochromes to create a liquid array of up to 100 unique spectral signatures that supports the analysis of that scale of simultaneous hybridization assays on a minute DNA sample. This review gives an overview on the collective experiences of BoBs applications in prenatal diagnosis.

Prenatal diagnosis of 24 cases of microduplication 22q11.2: an investigation of phenotype-genotype correlations

OBJECTIVE

Microduplication 22q11.2 is primarily characterized by a highly variable clinical phenotype, which ranges from apparently normal or slightly dysmorphic features (in the presence or absence of learning disorders) to severe malformations with profound mental retardation. Hence, genetic counseling is particularly challenging when microduplication 22q11.2 is identified in a prenatal diagnosis. Here, we report on 24 prenatal cases of microduplication 22q11.2.

METHODS

Seventeen of the cases were also reanalyzed by microarray analysis, in order to determine copy number variations (CNVs, which are thought to influence expressivity). We also searched for possible correlations between fetal phenotypes, indications for invasive prenatal diagnosis, inheritance, and pregnancy outcomes.

RESULTS

Of the 24 cases, 15 were inherited, six occurred de novo, and three were of unknown origin. Termination of pregnancy occurred in seven cases and was mainly decided on the basis of ultrasound findings. Moreover, additional CNVs were found in some patients and we try to make a genotype-phenotype correlation.

CONCLUSION

We discuss the complexity of genetic counseling for microduplication 22q11.2 and comment on possible explanations for the clinical heterogeneity of this syndrome. In particular, we assessed the co-existence of additional CNVs and their contribution to phenotypic variations in chromosome 22q11.2 microduplication syndrome.

Diagnostic accuracy of the BACs-on-Beads™ assay versus karyotyping for prenatal detection of chromosomal abnormalities: a retrospective consecutive case series

OBJECTIVE

To evaluate the diagnostic performance of the BACs-on-Beads(™) (BoBs(™)) assay for prenatal detection of chromosomal abnormalities.

DESIGN

Retrospective study.

SETTING

Tertiary prenatal diagnosis centre.

POPULATION

Women referred for prenatal diagnosis.

METHODS

We retrieved 2153 archived DNA samples collected between January 2010 and August 2011 for the BoBs(™) assay. These samples had previously been tested by quantitative fluorescence polymerase chain reaction (QF-PCR) and karyotyping. In the BoBs(™) assay a sample was defined as normal disomic when the ratio of the fluorescence intensities in a chromosome locus lay within the threshold (mean ratio ± 2SD), and as deleted or duplicated when the ratio was below the lower threshold (0.6-0.8) or above the upper threshold (1.3-1.4), respectively. The BoBs(™) results were further validated by microarray and compared in a blinded manner with the original QF-PCR and karyotyping results.

MAIN OUTCOME MEASURES

Concordance of any numerical, structural, and submicroscopic chromosomal abnormalities between the methods.

RESULTS

BACs-on-Beads(™) was similar to karyotyping and QF-PCR in detecting trisomy 13, trisomy 18, trisomy 21, and sex chromosomal aneuploidies, and superior to QF-PCR in detecting major structural abnormalities (53.3 versus 13.3%) and mosaicism (28.6 versus 0%) involving chromosomal abnormalities other than the common aneuploidies. BoBs(™) detected six microdeletion syndromes missed by karyotyping and QF-PCR; however, BoBs(™) missed two cases of triploidy identified by QF-PCR. Therefore, the sensitivity of BoBs(™) is 96.7% (95% CI 92.6-98.7%), and its specificity is 100% (95% CI 99.8-100%).

CONCLUSIONS

BACs-on-Beads(™) can replace QF-PCR for triaging in prenatal diagnosis, and gives a better diagnostic yield than current rapid aneuploidy tests.

Bacterial artificial chromosomes (BACs)-on-Beads™ as a diagnostic platform for the rapid aneuploidy screening of products of conception

The aim of the present study was to evaluate the use of KaryoLite™ bacterial artificial chromosomes (BACs)‑on‑Beads™ (BoBs) technology for the rapid screening of products of conception (POC). Validation and prospective studies were carried out on 85 and 95 patient samples, respectively. Validation studies had previously been analyzed using routine culture and G-banded karyotyping. BoBs resulted in an abnormality detection frequency of 27%, with a failure rate of <3%. The time required for processing was significantly lower compared with that of tissue culture. In conclusion, BoBs technology decreased the failure rate, while increasing the analytical sensitivity compared with G-banded karyotype analysis alone. Additionally, significant cost savings may be achieved with regard to the time of processing and analysis of specimens.

The detection of mosaicism by prenatal BoBs™

OBJECTIVE

The objective of the study was to evaluate the ability of a new prenatal diagnostic platform - prenatal BACs-on-Beads™ (BoBs™) in detecting mosaicism by comparison to quantitative fluorescence-polymerase chain reaction (QF-PCR).

METHODS

A validation study of prenatal BoBs™ was firstly performed using 18 artificially constructing mosaic samples involving various aneuploidies and microdeletion conditions. Additionally, we compared the accuracy between prenatal BoBs™ and QF-PCR for 18 archived clinical mosaic cases and nine chromosomally abnormal cell lines with reference to conventional karyotype results.

RESULTS

In the validation study, BoBs™ allowed the detection of mosaicism at a level of 20-40%. Among the clinical mosaic cases, 14/18 cases were within the detection of BoBs™, 8/14 (57.1%) could be identified by BoBs™ and 6/9 (66.7%) by QF-PCR, but 6/14 (42.9%) were missed by both tests. Three cases (16.7%) were detected by prenatal BoBs™ but missed by QF-PCR, whereas QF-PCR detected one case that was missed by BoBs™. The overall sensitivity of BoBs™ in detecting mosaicism is 44.4% (8/18), which is slightly higher than that of QF-PCR (33.3%; 6/18).

CONCLUSION

Prenatal BoBs™ has a sensitivity of 57.1% in the detection clinical mosaic cases. According to the validation test, mosaicism of 20% or greater is detectable by the BoBs™ assay.

Prenatal diagnosis of 17p13.1p13.3 duplication

We present here the first prenatal diagnosis of 17p13.1p13.3 duplication. 17p13.3 duplication has recently been defined as a new distinctive syndrome with several diagnosed patients. In the current case prenatal chromosome analysis (G-banding) performed on cultured amniocytes revealed additional material in chromosome 19p. This was further defined as a chromosome 17p13.1p13.3 duplication by FISH and genomic microarray analysis (GMA). In addition Prenatal BACs-on-Beads (PN_BoBs) assay was performed, which detected the duplication clearly. This enables rapid prenatal diagnosis of the duplication for this family in the future.

Prenatal BACs-on-Beads™: the prospective experience of five prenatal diagnosis laboratories

OBJECTIVE

We previously reported on the validation of Prenatal BACs-on-Beads™ on retrospectively selected and prospective prenatal samples. This bead-based multiplex assay detects chromosome 13, 18, 21 and X/Y aneuploidies and the nine most frequent microdeletion syndromes. We demonstrated that Prenatal BACs-on-Beads(TM) is a new-generation, prenatal screening tool. Here, we describe the experience of five European prenatal diagnosis laboratories concerning the ongoing use of Prenatal BACs-on-Beads™ .

METHODS

Some 1653 samples were analyzed. All results were confirmed by conventional karyotyping or another appropriate technique. All indications for invasive prenatal diagnosis were included. Amniotic fluid and chorionic villus samples were analyzed in equivalent proportions.

RESULTS

The failure rate was 3.3% and the overall abnormality detection rate was ~1/10. Eighty-five percent of the detected abnormalities were common aneuploidies. Eleven microdeletions and duplications were identified, thus giving an overall yield for microdeletion and microduplication detection of 1/145. Compared with QF-PCR, Prenatal BACs-on-Beads™ provides an additional detection rate of ~1/250 for low-risk pregnancies. The false positive and negative rates were both <1%.

CONCLUSION

When associated with conventional karyotyping, the Prenatal BACs-on-Beads™ assay combines a short turnaround time (typical of rapid aneuploidy detection tests) with valuable detection of the most frequent microdeletion syndromes that cannot be detected in cytogenetic analyses.

Referral patterns for microarray testing in prenatal diagnosis

OBJECTIVE

To understand the prenatal referral patterns from the United States, Canada, and Israel for two whole-genome microarray platforms, each with a different resolution.

METHOD

Physicians selected one of the two array designs to be performed on 1483 prenatal specimens for a 1-year period. We retrospectively examined detection rates, indications for study, and physician array selection.

RESULTS

The lower resolution array (55 K) showed an ~32% decrease in the detection of results of unclear clinical significance while retaining the ability to detect all but one significant abnormality identified by the higher resolution array (135 K). A majority of samples were referred for abnormal ultrasound findings. Whereas the United States and Canada utilized the higher resolution array more often for this indication, Israel preferred the 55 K array. Referral patterns for parental anxiety were similar for the United States and Israel, with most cases being tested on the 55 K array. Few cases were referred for advanced maternal age or family history of a genetic condition from either Canada or Israel.

CONCLUSION

Referral patterns varied between the countries and between indications for study. Understanding these differences will provide laboratories the critical information needed to develop array designs to meet the medical needs and patient desires for prenatal testing.