Applications of array comparative genomic hybridization in obstetrics

The current state of prenatal detection of genetic conditions in congenital heart defects

The incidence of congenital heart defect (CHD) has increased over the past fifty years, partly attributed to routine fetal anatomical examination by sonography during obstetric care and improvements in ultrasound technology and technique. Fetal findings on ultrasound in addition to maternal biomarkers are the backbone of first- and second-trimester screening for common genetic conditions, namely aneuploidy. Since the introduction of non-invasive prenatal testing (NIPT) using next-generation sequencing to sequence cell-free fetal DNA, the detection rate of common trisomies as well as sex chromosomal aneuploidies have markedly increased. As the use of NIPT continues to broaden, the best means of incorporating NIPT into prenatal care is less clear and complicated by misunderstanding of the limitations and non-diagnostic role of NIPT by clinicians and families. In other advancements in prenatal genetic testing, recommendations on the role of chromosomal microarray (CMA) for prenatal diagnosis has led to its increasing use to identify genetic conditions in fetuses diagnosed with CHD. Lastly, as whole exome sequencing (WES) becomes more available and affordable, the next clinical application of next-generation sequencing in prenatal diagnostic testing is on the horizon. While newer genetic tests may provide answers in terms of genetic diagnosis, even more questions will likely ensue for clinicians, researchers, and parents. The objective of this review is to provide the perspective of the evolution of maternal and fetal obstetric care against the backdrop of advancing genetic technology and its impact on families and clinicians.

Exome Sequencing and Its Emerging Role in Prenatal Genetic Diagnosis

Importance

Prenatal genetic diagnosis can guide pregnancy management and decision making. Genetic diagnosis has advanced rapidly, and chromosomal microarray has become widely used, in addition to conventional karyotype. Exome sequencing may provide an even higher detection rate of genetic anomalies and may be more commonly applied in the future.

Objectives

The objectives of this manuscript are to review current practices in prenatal genetic diagnosis, define exome sequencing, identify scenarios in which exome sequencing may be indicated, identify potential concerns regarding exome sequencing, and review the importance for the general obstetrician-gynecologist to understand exome sequencing technology and its uses.

Evidence Acquisition

A MEDLINE search of "prenatal genetic testing," "chromosomal microarray," "conventional karyotype," or "exome sequencing" in the review was performed.

Results

The evidence cited in this review includes 6 medical society committee opinions and 17 additional peer-reviewed journal articles that were original research or expert opinion summaries.

Conclusions and Relevance

Exome sequencing may be a useful prenatal genetic diagnostic tool in cases with ultrasound anomalies with previously normal chromosomal microarray and/or karyotype. As more data become available, technology improves, and costs fall, exome sequencing may become more widely used in prenatal genetic diagnosis.

Genetic testing on products of conception and its relationship with body mass index

PURPOSE

The study aimed to investigate the relationship between elevated maternal body mass index (BMI) and foetal chromosomal aberrations by performing single-nucleotide polymorphism (SNP) array-based genetic testing on products of conception (POC).

METHODS

We retrospectively reviewed the data for 1068 assisted reproductive technology (ART)-conceived POC originated from 1068 patients with early spontaneous miscarriage. First, all types of chromosomal abnormalities were defined. Then, the baseline characteristics, including maternal age, BMI, thyroid-stimulating hormone (TSH), gestational age, fertilization method, reasons for fertility treatment, embryo transfer (ET) cycle, stage of embryo development and the embryo morphology grade, were compared between chromosomally normal and abnormal POC groups. Finally, a multivariate logistic regression model was used to analyse various factors affecting the foetal chromosomal abnormality rate.

RESULTS

The SNP array results showed that 45.3% (484/1068) of POC were chromosomally normal and that 54.7% (584/1068) of POC presented chromosomal abnormalities. Of these 584 chromosomally abnormal POC, 388 (66.4%) were trisomy, 42 (7.2%) had a monosomy, 68 (11.6%) were found with segmental aneuploidy, 46 (7.9%) were mosaic, 28 (4.8%) were identified as polyploidy and 12 (2.1%) were euploid samples with uniparental disomy (UPD). Multivariate logistic regression results showed that the risk of miscarrying chromosomally abnormal POC increased 1.424-fold in women with normal BMI compared to women with an elevated BMI (≥ 25 kg/m²) (OR = 1.424, 95% CI = 1.074-1.888, p = 0.014).

CONCLUSION

Women with an elevated BMI (≥ 25 kg/m²) are more likely to miscarry chromosomally normal POC.

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).

Microarrays as a diagnostic tool in prenatal screening strategies: ethical reflection

Genomic microarray analysis is increasingly being applied as a prenatal diagnostic tool. Microarrays enable searching the genome at a higher resolution and with higher sensitivity than conventional karyotyping for identifying clinically significant chromosomal abnormalities. As yet, no clear guidelines exist on whether microarrays should be applied prenatally for all indications or only in selected cases such as ultrasound abnormalities, whether a targeted or genome-wide array should be used, and what these should include exactly. In this paper, we present some ethical considerations on the prenatal use of microarrays. There is a strong consensus, at least in Western countries, that the aim of prenatal screening for foetal abnormalities should be understood as facilitating autonomous reproductive choice for prospective parents. The tests offered should be valid and useful to reach that purpose. Against this background, we address several ethical issues raised by the prenatal application of microarrays. First, we argue that the general distinction between a targeted and a genome-wide microarray needs to be scrutinised. Then we examine whether microarrays are 'suitable tests' to serve either a screening or a diagnostic purpose. Given the wide range of findings possibly generated by microarrays, the question arises whether microarrays actually promote or interfere with autonomous reproductive decision-making. Moreover, if variants of unknown clinical significance are identified, this adds to the burden and complexity of reproductive decision-making. We suggest a qualified use of microarrays in the prenatal context.

22q11.2 deletions in patients with conotruncal defects: data from 1,610 consecutive cases

The 22q11.2 deletion syndrome is characterized by multiple congenital anomalies including conotruncal cardiac defects. Identifying the patient with a 22q11.2 deletion (22q11del) can be challenging because many extracardiac features become apparent later in life. We sought to better define the cardiac phenotype associated with a 22q11del to help direct genetic testing. 1,610 patients with conotruncal defects were sequentially tested for a 22q11del. The counts and frequencies of primary lesions and cardiac features were tabulated for those with and those without a 22q11del. Logistic regression models investigated cardiac features that predicted deletion status in tetralogy of Fallot (TOF). Deletion frequency varied by primary anatomic phenotype. Regardless of the cardiac diagnosis, a concurrent aortic arch anomaly (AAA) was strongly associated with deletion status [odds ratio (OR), 5.07; 95 % confidence interval (CI), 3.66-7.04]. In the TOF subset, the strongest predictor of deletion status was an AAA (OR, 3.14; 95 % CI 1.87-5.27; p < 0.001), followed by pulmonary valve atresia (OR, 2.03; 95 % CI 1.02-4.02; p = 0.04). Among those with double-outlet right ventricle and transposition of the great arteries, only those with an AAA had a 22q11del. However, 5 % of the patients with an isolated conoventricular ventricular septal defect and normal aortic arch anatomy had a 22q11del, whereas no one with an interrupted aortic arch type A had a 22q11del. A subset of patients with conotruncal defects are at risk for a 22q11del. A concurrent AAA increases the risk regardless of the intracardiac anatomy. These findings help to direct genetic screening for the 22q11.2 deletion syndrome in the cardiac patient.

Molecular genetic testing and the future of clinical genomics

Genomic technologies are reaching the point of being able to detect genetic variation in patients at high accuracy and reduced cost, offering the promise of fundamentally altering medicine. Still, although scientists and policy advisers grapple with how to interpret and how to handle the onslaught and ambiguity of genome-wide data, established and well-validated molecular technologies continue to have an important role, especially in regions of the world that have more limited access to next-generation sequencing capabilities. Here we review the range of methods currently available in a clinical setting as well as emerging approaches in clinical molecular diagnostics. In parallel, we outline implementation challenges that will be necessary to address to ensure the future of genetic medicine.

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.

The utility of chromosomal microarray analysis in developmental and behavioral pediatrics

Chromosomal microarray analysis (CMA) has emerged as a powerful new tool to identify genomic abnormalities associated with a wide range of developmental disabilities including congenital malformations, cognitive impairment, and behavioral abnormalities. CMA includes array comparative genomic hybridization (CGH) and single nucleotide polymorphism (SNP) arrays, both of which are useful for detection of genomic copy number variants (CNV) such as microdeletions and microduplications. The frequency of disease-causing CNVs is highest (20%-25%) in children with moderate to severe intellectual disability accompanied by malformations or dysmorphic features. Disease-causing CNVs are found in 5%-10% of cases of autism, being more frequent in severe phenotypes. CMA has replaced Giemsa-banded karyotype as the first-tier test for genetic evaluation of children with developmental and behavioral disabilities.

Genetic counselling and ethical issues with chromosome microarray analysis in prenatal testing

Molecular karyotyping using chromosome microarray analysis (CMA) detects more pathogenic chromosomal anomalies than classical karyotyping, making CMA likely to become a first tier test for prenatal diagnosis. Detecting copy number variants of uncertain clinical significance raises ethical considerations. We consider the risk of harm to a woman or her fetus following the detection of a copy number variant of uncertain significance, whether it is ethically justifiable to withhold any test result information from a woman, what constitutes an 'informed choice' when women are offered CMA in pregnancy and whether clinicians are morally responsible for 'unnecessary' termination of pregnancy. Although we are cognisant of the distress associated with uncertain prenatal results, we argue in favour of the autonomy of women and their right to information from genome-wide CMA in order to make informed choices about their pregnancies. We propose that information material to a woman's decision-making process, including uncertain information, should not be withheld, and that it would be paternalistic for clinicians to try to take responsibility for women's decisions to terminate pregnancies. Non-directive pre-test and post-test genetic counselling is central to the delivery of these ethical objectives.

Unintended diagnosis of Von Hippel Lindau syndrome using Array Comparative Genomic Hybridization (CGH): counseling challenges arising from unexpected information

Array Comparative Genomic Hybridization (array CGH) is a powerful tool for identifying genomic imbalances and providing a diagnosis in individuals with a normal karyotype. It has been particularly useful in the investigation of individuals with developmental delay +/-, dysmorphic features and/or multiple congenital abnormalities. However, this non-targeted method of scanning the whole genome can reveal unexpected information. We present a case where array CGH identified the cause of a proband's moderate mental retardation by discovery of a de novo deletion of chromosome 3p25.3. This deletion was shown to contain at least 25 genes including the VHL gene, the deletion or mutation of which leads to Von Hippel Lindau (VHL) syndrome. Presymptomatic testing for VHL is usually offered after appropriate genetic counseling about the implications of this condition. Therefore, scanning the genome by array CGH presents a number of challenges for the genetic counselor. We suggest that further understanding of the psychosocial effects of array CGH is needed in order for appropriate pre- and post-test counseling to be provided.

Copy number and SNP arrays in clinical diagnostics

The ability of chromosome microarray analysis (CMA) to detect submicroscopic genetic abnormalities has revolutionized the clinical diagnostic approach to individuals with intellectual disability, neurobehavioral phenotypes, and congenital malformations. The recognition of the underlying copy number variant (CNV) in respective individuals may allow not only for better counseling and anticipatory guidance but also for more specific therapeutic interventions in some cases. The use of CMA technology in prenatal diagnosis is emerging and promises higher sensitivity for several highly penetrant, clinically severe microdeletion and microduplication syndromes. Genetic counseling complements the diagnostic testing with CMA, given the presence of CNVs of uncertain clinical significance, incomplete penetrance, and variable expressivity in some cases. While oligonucleotide arrays with high-density exonic coverage remain the gold standard for the detection of CNVs, single-nucleotide polymorphism (SNP) arrays allow for detection of consanguinity and most cases of uniparental disomy and provide a higher sensitivity to detect low-level mosaic aneuploidies.

Evolving applications of microarray analysis in prenatal diagnosis

PURPOSE OF REVIEW

Evaluation of copy number variation by microarray analysis has significant advantages over standard metaphase karyotyping and is quickly becoming the primary means of postnatal genetic evaluation for neonates and infants with dysmorphic features or cognitive difficulties. Before this technology is routinely used for prenatal diagnosis, further evaluation of its value and the clinical dilemmas it may introduce requires further study. This article reviews the recent literature on array technology use in prenatal diagnosis.

RECENT FINDINGS

The use of microarray analysis for routine prenatal diagnosis is still being investigated. Use in certain prenatal situations such as the fetus with structural anomalies or those who are stillborn appears to add important, clinically relevant information. There are a broad range of array designs available and recent research has focused on the appropriate design for prenatal testing. Patient counseling may occasionally be difficult because of the uncertain phenotype associated with some array findings.

SUMMARY

We present a brief overview of microarray technology including benefits and limitations. Previous research regarding use of microarray in prenatal diagnosis including specific scenarios of anomalous fetuses and abnormal karyotype is reviewed. Current guidelines and the authors' recommendations are presented.

Prenatal diagnosis of fetal aneuploidies: post-genomic developments

Prenatal diagnosis of fetal aneuploidies and chromosomal anomalies is likely to undergo a profound change in the near future. On the one hand this is mediated by new technical developments, such as chromosomal microarrays, which allow a much more precise delineation of minute sub-microscopic chromosomal aberrancies than the classical G-band karyotype. This will be of particular interest when investigating pregnancies at risk of unexplained development delay, intellectual disability or certain forms of autism. On the other hand, great strides have been made in the non-invasive determination of fetal genetic traits, largely through the analysis of cell-free fetal nucleic acids. It is hoped that, with the assistance of cutting-edge tools such as digital PCR or next generation sequencing, the long elusive goal of non-invasive prenatal diagnosis for fetal aneuploidies can finally be attained.