Microarray comparative genomic hybridization in prenatal diagnosis: a review

Fetal Megacystis in the first trimester: Comparing management and outcomes between longitudinal bladder length groups

Fetal megacystis is a sonographic sign, defined in first trimester as a longitudinal bladder length (LBD)>7 mm. Different causes may be associated with megacystis and outcomes vary with many factors. There are no international guidelines on how to manage megacystis cases, and invasive testing is controversial when no other abnormalities are found. The main objective of this study is to compare etiologies, management and outcomes of fetuses with first trimester megacystis, specifically between groups of LBD≤15 mm and >15 mm. This is a retrospective cohort study of megacystis cases managed in a Prenatal Diagnosis Center, between January 2009 and September 2020. Descriptive and bivariate analysis were performed. We studied 43 fetuses: 67.4% with LBD≤15 mm and 32.6% with LBD>15 mm. We found an association between LBD and isolated Low Urinary Tract Obstruction (LUTO) (3.4% vs 64.3%; p<0.001) and with isolated megacystis (44.8% vs 0.0%; p = 0.001). No differences were seen regarding the presence of aneuploidies (31.0% vs 14.3%; p = 0.213). Invasive testing was performed in 93.0% of cases. Overall, we report 41.9% of live births, 39.5% of pregnancy termination and 18.6% of intrauterine fetal demise. We found a higher rate of live births in fetuses with LBD≤15 mm (55.2% vs 14.3%; p = 0.011). For a mean follow-up time of 20.6 months, we report one neonatal death and one case of renal insufficiency. In conclusion, isolated LUTO is more frequent if LBD>15 mm whereas isolated megacystis is more frequently found if LBD≤15 mm. If LBD≤15 mm, live birth rates and long-term outcomes seem to be enhanced.

Chromosomal Microarray Analysis in Fetuses Detected with Isolated Cardiovascular Malformation: A Multicenter Study, Systematic Review of the Literature and Meta-Analysis

Cardiovascular malformations (CVM) represent the most common structural anomalies, occurring in 0.7% of live births. The CVM prenatal suspicion should prompt an accurate investigation with fetal echocardiography and the assessment through genetic counseling and testing. In particular, chromosomal microarray analysis (CMA) allows the identification of copy number variations. We performed a systematic review and meta-analysis of the literature, studying the incremental diagnostic yield of CMA in fetal isolated CVM, scoring yields for each category of heart disease, with the aim of guiding genetic counseling and prenatal management. At the same time, we report 59 fetuses with isolated CVM with normal karyotype who underwent CMA. The incremental CMA diagnostic yield in fetuses with isolated CVM was 5.79% (CI 5.54–6.04), with conotruncal malformations showing the higher detection rate (15.93%). The yields for ventricular septal defects and aberrant right subclavian artery were the lowest (2.64% and 0.66%). Other CVM ranged from 4.42% to 6.67%. In the retrospective cohort, the diagnostic yield was consistent with literature data, with an overall CMA diagnostic yield of 3.38%. CMA in the prenatal setting was confirmed as a valuable tool for investigating the causes of fetal cardiovascular malformations.

Molecular Approaches in Fetal Malformations, Dynamic Anomalies and Soft Markers: Diagnostic Rates and Challenges-Systematic Review of the Literature and Meta-Analysis

Fetal malformations occur in 2-3% of pregnancies. They require invasive procedures for cytogenetics and molecular testing. "Structural anomalies" include non-transient anatomic alterations. "Soft markers" are often transient minor ultrasound findings. Anomalies not fitting these definitions are categorized as "dynamic". This meta-analysis aims to evaluate the diagnostic yield and the rates of variants of uncertain significance (VUSs) in fetuses undergoing molecular testing (chromosomal microarray (CMA), exome sequencing (ES), genome sequencing (WGS)) due to ultrasound findings. The CMA diagnostic yield was 2.15% in single soft markers (vs. 0.79% baseline risk), 3.44% in multiple soft markers, 3.66% in single structural anomalies and 8.57% in multiple structural anomalies. Rates for specific subcategories vary significantly. ES showed a diagnostic rate of 19.47%, reaching 27.47% in multiple structural anomalies. WGS data did not allow meta-analysis. In fetal structural anomalies, CMA is a first-tier test, but should be integrated with karyotype and parental segregations. In this class of fetuses, ES presents a very high incremental yield, with a significant VUSs burden, so we encourage its use in selected cases. Soft markers present heterogeneous CMA results from each other, some of them with risks comparable to structural anomalies, and would benefit from molecular analysis. The diagnostic rate of multiple soft markers poses a solid indication to CMA.

Development and validation of a novel 26-plex system for prenatal diagnosis with forensic markers

Short tandem repeat (STR) loci are commonly used in forensic casework, such as personal identification and paternity testing. In recent years, STR has also been widely used for rapid, accurate and automated prenatal diagnosis, known as quantitative fluorescent PCR (QF-PCR). Despite their usefulness, the current systems often lack the power to detect mosaicism for Turner syndrome. In this study, we developed a novel 26-plex system that combined the 22 STRs in chromosome 21/18/13/X, 3 sex loci and 1 quality control marker (TAF9L). The system was generated to achieve greater diagnostic power of trisomy 21/18/13 and sex chromosome abnormalities. Studies of the sensitivity, specificity, stability and accuracy were performed according to the Scientific Working Group on DNA Analysis Methods (SWGDAM) guidelines. Compared with the results of the chromosomal microarray analysis (CMA)/copy number variation sequencing (CNV-seq), the detection ratio of non-mosaic chromosome abnormalities of this system in the identification of chromosome 21/18/13/X/Y aneuploidies reached 100%, and the rate of negative results was consistently 100% based on 203 prenatal diagnosis sample analyses. In addition, our results suggested that this panel was a useful tool for mosaicism for Turner syndrome cases. Interestingly, we found one case with large segment loss of chromosome X, which indicated that we should be alert to this situation when the STR genotype of the parent-child is inconsistent in forensic genetics. In summary, this study demonstrated that our system is an accurate, cost-effective and rapid approach for the detection of chromosome numerical abnormalities in prenatal diagnosis.

Chromosomal microarray vs. NIPS: analysis of 5541 low-risk pregnancies

PURPOSE

To evaluate the diagnostic yield of chromosomal microarray (CMA) in pregnancies with normal ultrasound.

METHODS

This retrospective cohort analysis included all pregnancies with normal ultrasound undergoing CMA testing between the years 2010 and 2016. We calculated the rate of detection of clinically significant CMA findings in the whole cohort and according to various indications.

RESULTS

Of 5541 CMA analyses, clinically significant findings were yielded in 78 cases (1.4%). Of these, 31 (39.7%) variants could have theoretically been detected by karyotyping (e.g., sized above 10 Mb), and 28 (35.9%) by noninvasive prenatal screening aimed at five common aneuploidies. Of the 47 submicroscopic findings detectable by CMA only, the majority (37 cases, 78.7%) represented known recurrent syndromes. Detection of clinically significant CMA findings in women with no indication for invasive testing was 0.76% (21/2752), which was significantly lower compared with 1.8% in advanced maternal age group (41/2336), 2.8% in abnormal biochemical serum screening (6/211), and 4.1% (10/242) in fetuses with sonographic soft markers.

CONCLUSION

Clinically significant CMA aberrations are detected in 1 of 71 pregnancies with normal ultrasound, and in 1 of 131 women with no indication for invasive testing. Thus, CMA might be recommended a first-tier test in pregnancies with normal ultrasound.

Next Generation Sequencing of Prenatal Structural Chromosomal Rearrangements Using Large-Insert Libraries

Precise tests for genomic structural variation (SV) are essential for accurate diagnosis of prenatal genome abnormalities. The two most ubiquitous traditional methods for prenatal SV assessment, karyotyping and chromosomal microarrays, do not provide sufficient resolution for some clinically actionable SVs. Standard whole-genome sequencing (WGS) overcomes shortcomings of traditional techniques by providing base-pair resolution of the entire accessible genome. However, while sequencing costs have continued to decline in recent years, conventional WGS costs remain high for most routine clinical applications. Here, we describe a specialized WGS technique using large inserts (liWGS; also known as "jumping libraries") to resolve large (>5000-10,000 nucleotides) SVs at kilobase-resolution in prenatal samples, and at a fraction of the cost of standard WGS. We explicate the protocols for generating liWGS libraries and supplement with an overview for processing and analyzing liWGS data.

The use of chromosomal microarray for prenatal diagnosis

Chromosomal microarray analysis is a high-resolution, whole-genome technique used to identify chromosomal abnormalities, including those detected by conventional cytogenetic techniques, as well as small submicroscopic deletions and duplications referred to as copy number variants. Because chromosomal microarray analysis has a greater resolution than conventional karyotyping, it can detect deletions and duplications down to a 50- to 100-kb level. The purpose of this document is to discuss the technique, advantages, and disadvantages of chromosomal microarray analysis and its indications and limitations. We recommend the following: (1) that chromosomal microarray analysis be offered when genetic analysis is performed in cases with fetal structural anomalies and/or stillbirth and replaces the need for fetal karyotype in these cases (GRADE 1A); (2) that providers discuss the benefits and limitations of chromosomal microarray analysis and conventional karyotype with patients who are considering amniocentesis and chorionic villus sampling (CVS), and that both options should be available to women who choose to undergo diagnostic testing (GRADE 1B); (3) that pre- and posttest counseling should be performed by trained genetic counselors, geneticists, or other providers with expertise in the complexities of interpreting chromosomal microarray analysis results (Best Practice); (4) that patients be informed that chromosomal microarray analysis does not detect every genetic disease or syndrome and specifically does not detect autosomal-recessive disorders associated with single gene point mutations, as well as that chromosomal microarray analysis can detect consanguinity and nonpaternity in some cases (Best Practice); (5) that patients in whom a fetal variant of uncertain significance is detected by prenatal diagnosis receive counseling from experts who have access to databases that provide updated information concerning genotype-phenotype correlations (Best Practice).

Estimation of Detection Rates of Aneuploidy in High-Risk Pregnancy Using an Approach Based on Nuchal Translucency and Non-Invasive Prenatal Testing: A Cohort Study

OBJECTIVES

The aim was to investigate aneuploidy detection using an approach based on nuchal translucency (NT) and non-invasive prenatal testing (NIPT).

METHODS

This was a cohort study including 5,306 high-risk pregnancies with NT measurements and chorionic villus samples (CVS) tested for full karyotype.

RESULTS

The fetal karyotype was normal in 4,172 (78.6%) cases and abnormal in 1,134 (21.4%), including 1,009 with a likely clinically significant adverse outcome. Universal CVS with full karyotyping would lead to the diagnosis of all clinically significant abnormalities. A policy of relying solely on NIPT would have led to the diagnosis of 88.9% of clinically significant abnormalities. A strategy whereby NIPT is the main method, with CVS reserved for cases with NT ≥3.0 mm, would require CVS in 21.7% of cases, identify 94.8% of significant abnormalities and avoid miscarriage in 41 pregnancies compared to CVS for all.

CONCLUSIONS

A policy of NIPT for increased-risk cases and CVS with full karyotype if the NT was ≥3.0 mm reduced the risk of miscarriage yet still identified 95% of clinically significant aneuploidy.

Subtelomeric multiplex ligation-dependent probe amplification as a supplement for rapid prenatal detection of fetal chromosomal aberrations

Background

Pregnant women with high-risk indications are highly suspected of fetal chromosomal aberrations. To determine whether Multiplex Ligation-dependent Probe Amplification (MLPA) using subtelomeric probe mixes (P036-E2 and P070-B2) is a reliable method for rapid detection of fetal chromosomal aberrations. The subtelomeric MLPA probe mixes were used to evaluate 50 blood samples from healthy individuals. 168 amniocytes and 182 umbilical cord blood samples from high-risk fetuses were analyzed using the same subtelomeric MLPA probe sets. Karyotyping was also performed in all cases of high-risk pregnancies, and single nucleotide polymorphism array analysis was used to confirm submicroscopic and ambiguous results from MLPA/karyotyping.

Results

Subtelomeric MLPA analysis of normal samples showed normal result in all cases by use of P036-E2 probe mix, while P070-B2 probe mix gave normal results for all but one case. In one normal control case P070-B2 produced a duplicated signal of probe for 13q34. In the high-risk group, totally 44 chromosomal abnormalities were found by karyotyping and MLPA, including 23 aneuploidies and 21 rearrangements or mosaics. MLPA detected all 23 aneuploidies, 12 rearrangements and 1 mosaic. Importantly, MLPA revealed 4 chromosomal translocations, 2 small supernumerary marker chromosomes (sSMCs), and 3 subtelomeric imbalances that were not well characterized or not detectable by karyotyping. However, MLPA showed negetive results for the remaining 8 rearrangements or mosaics, including 3 low mosaic aneuploidies, 1 inherited sSMC, and 4 paracentric inversions.

Conclusions

Results suggest that combined use of subtelomeric MLPA and karyotyping may be an alternative method for using karyotype analyses alone in rapid detection of aneuploidies, rearrangements, and sSMCs.

Electronic supplementary material

The online version of this article (doi:10.1186/s13039-014-0096-1) contains supplementary material, which is available to authorized users.

High-resolution microarray in the assessment of fetal anomalies detected by ultrasound

AIMS

The main aim of this study was to determine the feasibility of using high-resolution microarray to assist with prenatal diagnosis of ultrasound-detected fetal abnormality and to describe the frequency of abnormal results in different categories of fetal anomalies.

METHODS

Prospective cross-sectional study was conducted on women diagnosed with a fetal anomaly (ies) between February 2009 and December 2011 who were offered testing by microarray analysis (Affymetrix 2.7M SNP) and fluorescent in situ hybridisation (FISH) instead of standard karyotyping. Fetal anomalies were categorised according to organ system involvement.

RESULTS

One hundred and eighteen women consented to testing with microarray. Eleven of one hundred eighteen (9.3%) cases had aneuploidy detected by FISH. Of the remaining 107, 23 (21.5%) had an abnormality detected on microarray, only three of which would have been detected using the combination of six-probe FISH and banded karyotype. The maximum expected yield for six-probe FISH and karyotype was thus 14/118 (11.8%), compared to 34/118 (28.8%), P < 0.0001. Of the 23 abnormalities detected with microarray, 10 (43%) were pathogenic, six (26%) were long continuous stretches of homozygosity and seven (30%) were of uncertain significance. The maximum yield was in cases with cardiovascular (100%); multiple (40%); central nervous system (CNS) (25%) and skeletal (9%) abnormalities.

CONCLUSION

This study has confirmed the feasibility of translation of microarray into clinical practice. 11.8% (14/118) of the cases would have a genetic basis of an abnormality with a FISH and banded karyotype. This figure is approximately tripled to 28.8% (34/118) if we offer FISH and microarray. High yield for imbalances are multiple, cardiovascular, CNS and skeletal abnormalities.

Is high fetal nuchal translucency associated with submicroscopic chromosomal abnormalities on array CGH?

OBJECTIVE

To examine the possible association between high fetal nuchal translucency thickness (NT) and pathogenic chromosomal copy number variants (CNVs) detected by array comparative genomic hybridization (CGH) in pregnancies with normal fetal karyotype.

METHODS

Array CGH was carried out in stored samples of chorionic villi from 215 singleton pregnancies resulting in live births in which chorionic villus sampling at 11-13 weeks' gestation for high fetal NT (≥ 3.5 mm) had demonstrated normal karyotype.

RESULTS

Median fetal NT was 4.0 (range, 3.5-9.5) mm. Array CGH detected additional CNVs in 1.4% (95% CI, 0.5-4.0) of the cases, but none of these was a known pathogenic CNV.

CONCLUSION

High fetal NT in the absence of sonographically detectable defects may not be associated with pathogenic CNVs.

High-resolution chromosomal microarrays in prenatal diagnosis significantly increase diagnostic power

OBJECTIVE

The objective of this study was to determine for the first time the reliability and the diagnostic power of high-resolution microarray testing in routine prenatal diagnostics.

METHODS

We applied high-resolution chromosomal microarray testing in 464 cytogenetically normal prenatal samples with any indication for invasive testing.

RESULTS

High-resolution testing revealed a diagnostic yield of 6.9% and 1.6% in cases of fetal ultrasound anomalies and cases of advanced maternal age (AMA), respectively, which is similar to previous studies using low-resolution microarrays. In three (0.6%) additional cases with an indication of AMA, an aberration in susceptibility risk loci was detected. Moreover, one case (0.2%) showed an X-linked aberration in a female fetus, a finding relevant for future family planning. We found the rate of cases, in which the parents had to be tested for interpretation of unreported copy number variants (3.7%), and the rate of remaining variants of unknown significance (0.4%) acceptably low. Of note, these findings did not cause termination of pregnancy after expert genetic counseling. The 0.4% rate of confined placental mosaicism was similar to that observed by conventional karyotyping and notably involved a case of placental microdeletion.

CONCLUSION

High-resolution prenatal microarray testing is a reliable technique that increases diagnostic yield by at least 17.3% when compared with conventional karyotyping, without an increase in the frequency of variants of uncertain significance.

Genomic microarrays in prenatal diagnosis

The application of microarray-based techniques for the diagnosis of genomic rearrangements has been steadily growing in popularity since its introduction in 2004. Given the many advantages of these techniques over conventional cytogenetics, there is increasing pressure towards their application in prenatal diagnosis. However, there remain several important issues that must be addressed. For example, microarray-based techniques (comparative genomic hybridization-based arrays and single nucleotide polymorphism-based arrays) allow detection of even very small genomic imbalances that can determine pathological clinical conditions. In addition, there are other copy number variations which represent normal variation, with no detectable effects on phenotype. Given the still incomplete knowledge of the changes in our genome and the associated phenotypes, microarray-based diagnosis is likely to find variants of uncertain and unknown clinical significance. The interpretation of these variants is now a major challenge for the medical geneticist, who often find it difficult to establish precise correlations between genotype and phenotype. There is sufficient available evidence to justify the use of microarray-based diagnostics for a select number of specific conditions, but there is also an inevitable trend towards ever wider application. It is very important that this drift does not progress in an unchecked and uncontrolled manner under the thrust of commercial interests. Therefore, we recommend that scientific societies be vigilant and take an advisory role in the adopting of these technologies as new scientific knowledge becomes available.

The future of prenatal diagnosis: karyotype, microarray or both? Technical and ethical considerations

Prenatal diagnosis is now offered to high-risk pregnancies, including advanced maternal age, ultrasound anomalies and positive Down's syndrome screening, and karyotype on cultured fetal material is the test of choice to screen these pregnancies. However, microscope analysis can only detect gross chromosome abnormalities, highlighting the need for more sensitive techniques. It has recently been established that the higher resolution of microarray-based platforms can increase the diagnostic yield, offering more information to couples, and it is being discussed as a replacement to the standard karyotype. Conversely, the very high sensitivity of microarray-based analysis allows us to detect small microdeletions/microduplications (copy number variations) with unknown functional role and difficult genotype/phenotype correlation. In addition, the new copy number variation syndromes are often associated with variable outcomes, ranging from normal to severely affected individuals. This means that the microarray-based analysis introduced routinely in prenatal diagnosis needs to answer the question: are laboratory staff, clinical geneticists and counselors really experienced enough to manage these new scenarios?

DepthTools: an R package for a robust analysis of gene expression data

Background

The use of DNA microarrays and oligonucleotide chips of high density in modern biomedical research provides complex, high dimensional data which have been proven to convey crucial information about gene expression levels and to play an important role in disease diagnosis. Therefore, there is a need for developing new, robust statistical techniques to analyze these data.

Results

depthTools is an R package for a robust statistical analysis of gene expression data, based on an efficient implementation of a feasible notion of depth, the Modified Band Depth. This software includes several visualization and inference tools successfully applied to high dimensional gene expression data. A user-friendly interface is also provided via an R-commander plugin.

Conclusion

We illustrate the utility of the depthTools package, that could be used, for instance, to achieve a better understanding of genome-level variation between tumors and to facilitate the development of personalized treatments.

Prenatal diagnosis using combined quantitative fluorescent polymerase chain reaction and array comparative genomic hybridization analysis as a first-line test: results from over 1000 consecutive cases

OBJECTIVES

First, to assess the performance of a prenatal diagnostic service using quantitative fluorescent polymerase chain reaction (QF-PCR) and array comparative genomic hybridization (aCGH) as first-line investigations. Second, to determine the incidence of copy number variants (CNVs) by indication for testing, with particular reference to ultrasound and biochemical parameters measured in combined first-trimester screening.

METHODS

All patients undergoing invasive prenatal testing at a specialist prenatal screening service in Sydney, Australia, were included in the study. All samples underwent QF-PCR and targeted aCGH.

RESULTS

Of 1049 cases, CNVs were reported in 156 (14.9%). Preliminary QF-PCR identified abnormalities in 104 of these cases. Of the remaining 52 cases, 20 could have been detected on karyotype testing, leaving 32 cases (3.1%) with CNVs only detectable by aCGH, of which 13 (1.2%) were pathogenic. Variants of unknown significance (VOUS) were seen in only three cases. Fetal structural abnormalities identified in the first trimester were the group most likely to be associated with pathogenic CNVs (11.8%).

CONCLUSIONS

Combining QF-PCR and aCGH is an effective first-tier prenatal testing regime that does not require conventional karyotyping. The incidence of VOUS in this study was very low owing to appropriate aCGH targeting and specific reporting criteria that reduced the number of potentially difficult counseling encounters. Pathogenic CNVs are positively correlated with the presence of fetal structural abnormalities, but not with enlarged nuchal translucency or abnormal first-trimester serology results.