The use of chromosomal microarray for prenatal diagnosis

doi:10.1016/j.ajog.2016.07.016

American Journal of Obstetrics and Gynecology

Volume 215, Issue 4, October 2016, Pages B2-B9

https://doi.org/10.1016/j.ajog.2016.07.016 Get rights and content

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).

Section snippets

What are the different types of microarray?

There are 2 major microarray platforms used in prenatal diagnosis: single-nucleotide polymorphism (SNP) arrays and comparative genomic hybridization (CGH) arrays. With SNP and CGH arrays, DNA from a fetal sample, such as CVS or amniocentesis, is hybridized to an array platform consisting of DNA probes on a solid surface, such as a microscope slide or a silicon chip.

CGH compares the fetal DNA sample with a normal reference DNA sample (Figure 1). The test DNA and the reference DNA samples are

What can CMA detect? How does it differ from a karyotype?

A standard karyotype can detect aneuploidies (abnormalities in chromosome number), relatively large structural abnormalities such as deletions or duplications that are microscopically visible down to a resolution of approximately 5−10 Mb, and balanced or unbalanced translocations and inversions. CMA has a greater resolution than conventional karyotyping, allowing for the detection of much smaller, submicroscopic deletions, and duplications typically down to a 50- to 100-kb level.² CMA also can

What are the limitations of CMA?

Because CMA looks for genomic imbalance, this technique is not able to detect totally balanced chromosomal rearrangements, such as translocations or inversions. The large majority of balanced rearrangements, however, result in a normal outcome. In addition, CMA does not provide information about the chromosomal mechanism of a genetic imbalance.⁶ For example, if there is a gain of an entire chromosome 13, CMA cannot distinguish between trisomy 13 and an unbalanced Robertsonian translocation,

What are the risks of using CMA? What are variants of uncertain significance and how should they be managed?

A disadvantage of CMA is the inability to precisely interpret the clinical significance of a previously unreported CNV or to accurately predict the phenotype of some CNVs that are associated with variable outcomes. CNVs are characterized as benign, clinically significant (ie, pathogenic), and as a variant of uncertain significance (VUS). The overall prevalence of VUS is approximately 1−2%.3, 8, 9 The NICHD-sponsored multicenter trial reported a 0.9% prevalence of pathogenic CNVs and a 1.5%

When should array be offered, and what are the indications?

The American College of Obstetricians and Gynecologists (ACOG) and the Society for Maternal-Fetal Medicine (SMFM) recommend that “[A]ll pregnant women should be offered prenatal assessment for aneuploidy by screening or diagnostic testing regardless of maternal age or other risk factors…The differences between screening and diagnostic testing also should be discussed.”¹² CMA in particular is recommended when genetic analysis is performed in cases with fetal structural anomalies and/or fetal

When is it appropriate to perform just a karyotype? Is it necessary to do a karyotype if a microarray is being done?

Conventional karyotype and/or rapid FISH testing may be more appropriate when a common aneuploidy such as trisomy 21, 18, 13 or monosomy X is strongly suspected based on prenatal ultrasound findings. In these circumstances, conventional karyotype and fluorescence in situ hybridization (FISH) analysis might provide a more rapid turn-around, allow for more sensitive detection of low-level mosaicism and rule out a translocation-associated trisomy. A CMA can be performed in the event that the FISH

How should patients be counseled before CMA?

Pre- and posttest counseling should be performed by trained genetic counselors, geneticists, or other providers with expertise in the complexities of interpreting CMA results (Box 1). We recommend that pre- and posttest counseling be performed by trained genetic counselors, geneticists or other providers with expertise in the complexities of interpreting CMA results (Best practice). Providers should be familiar with the microarray platform used by their laboratory, including the rate of VUS.

What samples can be used?

CMA may be performed on DNA obtained from amniocentesis, CVS, fetal cord blood, and stillbirth specimens. DNA obtained from the mesenchymal core cells of the chorionic villi and uncultured amniocytes is preferable to DNA from cultured cells to allow for quicker turnaround and to avoid the possibility of culture artifacts.¹¹ Some labs require that a maternal blood specimen be sent with the original CMA specimen while other labs only request parental samples when a CNV is detected, to distinguish

Are there differences between prenatal and postnatal microarray?

In the postnatal setting, CMAs are used to explain existing abnormalities, whereas in the prenatal setting CMAs are obtained to predict fetal outcomes. In many prenatal cases, patients opt to have CMA for reassurance that a significant finding is absent.17, 18 CMAs are recommended as the first-tier diagnostic test for the postnatal evaluation of individuals with multiple congenital anomalies, developmental delay/intellectual disability, and/or autism spectrum disorders, with clinically

What guidelines exist from other societies regarding the use of CMA?

Recent guidelines from several international and national societies have advocated the selective use of CMAs for pregnancies undergoing prenatal testing. ACOG and SMFM published joint recommendations on the use of microarray in prenatal diagnosis in 2013.¹³ CMA is recommended when genetic analysis is performed in cases with fetal structural abnormalities and/or stillbirth. In these circumstances, CMA replaces the need for karyotype. In cases with a structurally normal fetus, either CMA or

What are the issues of cost and insurance coverage of CMA?

The cost of chromosomal microarray is currently greater than conventional karyotyping but is expected to decrease with increasing volumes and technical advances. Insurance coverage in the United States largely conforms to the recommendations of the joint ACOG and SMFM Committee Opinion. Two major carriers currently consider CMA medically necessary for all patients undergoing invasive prenatal diagnostic testing as well as the evaluation of a fetal demise in cases with structural abnormalities.26

References (28)

C.L. Martin et al.
Copy number variants, aneuploidies and human disease
Clin Perinatal
(2015)
G. Fruhman et al.
Applications of array comparative genomic hybridization in obstetrics
Obstet Gynecol Clin North Am
(2010)
S.T. South et al.
ACMG Standards and Guidelines for constitutional cytogenomic microarray analysis, including postnatal and prenatal applications: revision 2013
Genet Med
(2013)
M.I. Evans et al.
Genetics: update on prenatal screening and diagnosis
Obstet Gynecol Clin North Am
(2015)
D.T. Miller et al.
Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies
Am J Hum Genet
(2010)
S. Darilek et al.
Pre- and postnatal genetic testing by array-comparative genomic hybridization: genetic counseling perspectives
Genet Med
(2008)
L. Hui et al.
Recent advances in the prenatal interrogation of the human fetal genome
Trends Genet
(2013)
A. Duncan et al.
Use of array genomic hybridization technology in prenatal diagnosis in Canada
J Obstet Gynaecol Can
(2011)
R.J. Wapner et al.
Chromosomal microarray versus karyotyping for prenatal diagnosis
N Engl J Med
(2012)
J.L. Callaway et al.
The clinical utility of microarray technologies applied to prenatal cytogenetics in the presence of a normal conventional karyotype: a review of the literature
Prenat Diagn
(2013)

U.M. Reddy et al.

NICHD Stillbirth Collaborative Research Network. Karyotype versus microarray testing for genetic abnormalities after stillbirth

N Engl J Med

(2012)

L.K. Conlin et al.

Mechanisms of mosaicism, chimerism and uniparental disomy identified by single nucleotide polymorphism array analysis

Hum Mol Genet

(2010)

S.C. Hillman et al.

Use of prenatal chromosomal microarray: prospective cohort study and systematic review and meta-analysis

Ultrasound Obstet Gynecol

(2013)

L.G. Shaffer et al.

Experience with microarray-based comparative genomic hybridization for prenatal diagnosis in over 5000 pregnancies

Prenat Diagn

(2012)

Cited by (124)

The role of a multidisciplinary team in managing variants of uncertain clinical significance in prenatal genetic diagnosis
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Although in general prenatal exome sequencing only reports (likely) pathogenic variants, in some cases a variant of uncertain significance (VUS) is disclosed. The aims of this retrospective study were to evaluate the types of VUS that have been reported to prospective parents, possible reclassification and to design a standard flow chart to determine which types of VUS could be considered for reporting in prenatal settings. Furthermore, we investigated what the crucial elements are to facilitate rapid management of uncertain results in a prenatal setting.
We reviewed exome results from 451 pregnancies performed in 2019–2021. We analyzed which factors that were taken into account by the multidisciplinary team (MDT) contributed towards decision making on reporting VUS after prenatal exome sequencing.
In 9/451 (2%) pregnancies tested with exome sequencing using a broad panel analysis a VUS was reported. After birth 3/9 VUS could be reclassified to likely pathogenic variants based on new clinical follow up data. We considered reporting VUS in genes: 1) matching the fetal phenotype, 2) associated with a severe disorder when a functional test is available or 3) possibly associated with a disorder where early post-partum diagnosis and treatment are crucial for a better prognosis. Two flowcharts were designed to guide first the laboratory specialist and then the MDT in decisions on reporting VUS. The crucial elements that enabled timely decisions on VUS disclosure were regular meetings, appropriate expertise, professional connections with other experts and psychological safety within the MDT.
In this study three out of nine VUS could be re-classified as likely pathogenic after clinical follow-up. In order to protect pregnant couples from the burden of uncertain results, the genetic professionals have to take the responsibility to limit the reporting of VUS. This can be done not only by automated filtering of data, by following professional guidelines and by building standardized decision flows, but also by discussing individual cases considering personal situations and the involved disease and by sharing professional experience and responsibility in a multidisciplinary prenatal team setting.
How to choose a test for prenatal genetic diagnosis: a practical overview
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Rapid advances in genetic technology in recent years have substantially enhanced our ability to identify diseases in utero.1–9
Establishing the diagnosis of a fetal genetic disease in utero expands decision-making opportunities for individuals during pregnancy and enables providers to tailor prenatal care and surveillance to disease-specific risks. The selection of prenatal genetic tests is guided by key details from fetal imaging, family and obstetrical history, suspected diagnoses and mechanisms of disease, an accurate understanding of what abnormalities each test is designed to detect, and, at times, the gestational age at which testing is initiated. Pre- and posttest counseling, by or in conjunction with providers trained in genetics, ensure an accurate understanding of genetic tests, their potential results and limitations, estimated turnaround time for results, and the clinical implications of their findings. As prenatal diagnosis and testing options continue to expand rapidly, it is increasingly important for obstetrical providers to understand how to choose appropriate genetic testing and contextualize the clinical implications of their results.
Management of Myelomeningocele and Related Disorders of the Newborn
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Open spina bifida aperta (myelomeningocele [MMC]) is the most frequent nonlethal congenital birth defect of the central nervous system, seen in 3 to 4 per 10,000 live births in the United States every year. It is a midline vertebral defect that exposes the contents of the spinal column to the outside environment. The cause of spina bifida is not fully clear and may involve genetic, metabolic, and environmental influences. Many infants with MMC also have the Chiari II malformation due to ongoing loss of cerebral spinal fluid from the lesion and herniation of the brainstem through the foramen magnum, resulting in obstructive hydrocephalus. The widespread availability of prenatal sonographic diagnosis has facilitated the diagnosis of systemic genetic abnormalities, and in some patients, timely fetal surgery may reduce the need for postnatal ventriculoperitoneal shunt placement. These patients need multidisciplinary management to reduce the morbidity and optimize outcomes.
Next-generation sequencing for gene panels, clinical exome, and whole-genome analysis
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Next-generation sequencing for the diagnosis of genetic disorders has become an invaluable tool in both genetics research and clinical practice. The ability to rapidly sequence large amounts of DNA molecules at high resolution enables the analysis of many genes simultaneously, which is especially useful for atypical or incompletely defined phenotypes, or genetically heterogeneous conditions. Genome sequencing analyzes all the DNA that can be feasibly sequenced, whereas exome analysis focuses only on the coding regions of genes. A more targeted approach via gene panel testing can be efficient when there is already a more narrow differential diagnosis. Applications in reproductive medicine include the discovery of causative genes for reproductive disorders and for prenatally diagnosed structural fetal anomalies. Gene panels and exome sequencing are already being integrated into preconception, preimplantation, and prenatal genetic screening and diagnosis. Prenatal genome sequencing trials are currently ongoing. This chapter reviews current experience, benefits, and challenges associated with sequence variant interpretation, its clinical utility, genetic counseling considerations, and ethical and societal issues of fetal genome-wide sequencing.
Chromosomal microarrays and next-generation sequencing for diagnosis of fetal abnormalities
2023, Human Reproductive and Prenatal Genetics
The G-banded karyotype has been the mainstay of prenatal diagnostic analysis for over half a century. Two new approaches to genomic evaluation of the fetus have recently been introduced into prenatal testing. Chromosome microarray analysis has a diagnostic resolution about 100 times that of karyotyping and has revealed submicroscopic clinically significant copy number variants in approximately 6% of fetuses with structural anomalies and in 1.2%–1.7% of structurally normal pregnancies sampled for advanced maternal age, positive screening or maternal anxiety. Next-generation sequencing (NGS) assays like whole-exome sequencing can identify a single altered base pair and adds an incremental diagnostic rate of about 14% in fetuses with structural anomalies when karyotype and CMA are normal. Interpretation of CMA and NGS data requires considerable experience and reporting of results needs to be done in the context of Professional Society guidelines. Genetic counseling is an integral part of offering these two new technologies.
Fetal Megacystis in the first trimester: Comparing management and outcomes between longitudinal bladder length groups
2023, Journal of Gynecology Obstetrics and Human Reproduction
Citation Excerpt :
In our center, we only had access to microarray from 2016 onwards, which explains why karyotyping was the most performed test. Microarray was performed, instead of karyotype, in almost all cases after 2016, even if no other fetal malformations were present, to further detect submicroscopic delections or duplications that could explain our findings of fetal abnormalities [13]. We still performed PCR for the most common aneuploidies.
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.

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: All authors and Committee members have filed a conflict of interest disclosure delineating personal, professional, and/or business interests that might be perceived as a real or potential conflict of interest in relation to this publication. Any conflicts have been resolved through a process approved by the Executive Board. The Society for Maternal-Fetal Medicine has neither solicited nor accepted any commercial involvement in the development of the content of this publication.

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Society for Maternal-Fetal Medicine (SMFM) Consult Series | #41The use of chromosomal microarray for prenatal diagnosis

Section snippets

What are the different types of microarray?

What can CMA detect? How does it differ from a karyotype?

What are the limitations of CMA?

What are the risks of using CMA? What are variants of uncertain significance and how should they be managed?

When should array be offered, and what are the indications?

When is it appropriate to perform just a karyotype? Is it necessary to do a karyotype if a microarray is being done?

How should patients be counseled before CMA?

What samples can be used?

Are there differences between prenatal and postnatal microarray?

What guidelines exist from other societies regarding the use of CMA?

What are the issues of cost and insurance coverage of CMA?

Clin Perinatal

Obstet Gynecol Clin North Am

Genet Med

Obstet Gynecol Clin North Am

Am J Hum Genet

Genet Med

Trends Genet

J Obstet Gynaecol Can

Chromosomal microarray versus karyotyping for prenatal diagnosis

N Engl J Med

The clinical utility of microarray technologies applied to prenatal cytogenetics in the presence of a normal conventional karyotype: a review of the literature

Prenat Diagn

NICHD Stillbirth Collaborative Research Network. Karyotype versus microarray testing for genetic abnormalities after stillbirth

N Engl J Med

Mechanisms of mosaicism, chimerism and uniparental disomy identified by single nucleotide polymorphism array analysis

Hum Mol Genet

Use of prenatal chromosomal microarray: prospective cohort study and systematic review and meta-analysis

Ultrasound Obstet Gynecol

Experience with microarray-based comparative genomic hybridization for prenatal diagnosis in over 5000 pregnancies

Prenat Diagn

Society for Maternal-Fetal Medicine (SMFM) Consult Series | #41
The use of chromosomal microarray for prenatal diagnosis