The Psychological Challenges of Replacing Conventional Karyotyping with Genomic SNP Array Analysis in Prenatal Testing

Challenges and Pragmatic Solutions in Pre-Test and Post-Test Genetic Counseling for Prenatal Exome Sequencing

The yield of genetic prenatal diagnosis has been notably improved by introducing whole genome chromosomal microarray (CMA) and prenatal exome sequencing (pES). However, together with increased numbers of diagnoses made, the need to manage challenging findings such as variants of unknown significance (VUS) and incidental findings (IF) also increased. We have summarized the current guidelines and recommendations and we have shown current solutions used in our tertiary center in the Netherlands. We discuss four of the most common clinical situations: fetus with normal pES results, fetus with a pathogenic finding explaining the fetal phenotype, fetus with a variant of uncertain clinical significance fitting the phenotype and fetus with a variant leading to an incidental diagnosis. Additionally, we reflect on solutions in order to facilitate genetic counseling in an NGS-era.

Prenatal diagnosis of chromosomal aberrations by chromosomal microarray analysis in foetuses with ventriculomegaly

Ventriculomegaly is considered to be linked to abnormal neurodevelopment outcome. The aim of this retrospective study was to investigate the current applications of chromosomal microarray analysis (CMA) in foetuses with ventriculomegaly. A total of 548 foetuses with ventriculomegaly detected by prenatal ultrasound underwent single nucleotide polymorphism (SNP) array testing and were subjected to long-term follow-up. The overall prevalence of chromosomal aberrations was 7.30% (40/548), including 4.20% (23/548) with pathogenic/likely pathogenic copy number variants. The incidence of chromosomal aberrations was significantly higher in foetuses with bilateral ventriculomegaly than in those with unilateral ventriculomegaly (10.56% vs. 5.71%, P = 0.040), in foetuses with non-isolated ventriculomegaly than in those with isolated ventriculomegaly (12.99% vs. 2.38%, P < 0.0001), and in foetuses with severe ventriculomegaly than in those with mild-to-moderate ventriculomegaly (23.08% vs. 6.51%, P = 0.005). The outcome in foetuses with mild ventriculomegaly was significantly better than in those with moderate ventriculomegaly (95.60% vs. 84.00%, P = 0.003). Thus, CMA should be regarded as the first-tier test for prenatal diagnosis of foetal ventriculomegaly, especially in foetuses with bilateral or non-isolated ventriculomegaly. The outcome of foetuses with mild ventriculomegaly is favourable; however, there is an increased risk of neurodevelopmental disabilities in foetuses with moderate ventriculomegaly.

How do geneticists and prospective parents interpret and negotiate an uncertain prenatal genetic result? An analysis of clinical interactions

Variants of unknown significance (VUS) and susceptibility loci (SL) are a challenge in prenatal genetic counseling. The aim of this study was to explore how such uncertain genetic results are communicated, negotiated, and made meaningful by genetics healthcare providers and couples in the actual clinical setting where results are delivered. The study was based on an anthropological approach and the material consisted of observations and audio-recordings from 16 purposively sampled genetic counseling sessions where prenatal testing had identified an inherited or de novo VUS or SL result. Field notes and transcripts from audio-recordings were analyzed using thematic analysis. The analysis identified a number of specific interpretations and strategies that clinical geneticists and couples collectively used for dealing with the ambiguity of the result. Thus, the analysis resulted in a total of three themes, each with 3-4 subthemes. The theme 'Setting the scene' describes the three-stage structure of the consultation. The theme 'Dealing with uncertainty' includes 'normalizing strategies' that emphasized the inherent uncertainty in human life in general and 'contextualizing strategies' that placed the result in relation to the surrounding society, where technological developments lead to new and unforeseen challenges. The theme 'Regaining control' includes interpretations that made the knowledge useful by focusing on the value of being prepared for potential, future challenges. Other strategies were to book an extra scan-to reconfirm fetal structural health and to reconnect to the pregnancy. Finally, inquiring about the sex was clearly a way for the couple to signal their investment in the pregnancy. Based on the analysis, we propose that these interpretations served to transform and reduce ambiguity through a process of reconfiguring the biomedical information into knowledge that resonated with the couples' lifeworlds. In this process, both geneticist and couples drew on wider social and moral concerns about uncertainty and responsibility.

Detection of copy number variants with chromosomal microarray in 10 377 pregnancies at a single laboratory

Introduction

Invasive prenatal testing with chromosomal microarray analysis may be a relevant option for all pregnant women, but there is only moderate‐quality evidence for such an offer. We intended to study the prevalence of copy number variants (CNVs) in prenatal samples using a single SNP‐array platform stratified by indication.

Material and methods

A cross‐sectional study was performed based on a cohort. From January 2015 to December 2017, a total of 10 377 prenatal samples were received for prenatal single nucleotide polymorphism (SNP)‐array in the laboratory of the Genetics Generation Advancement Corporation. Indications for chromosomal microarray analysis studies included the confirmation of an abnormal karyotype, ultrasound abnormalities, advanced maternal age and parental anxiety. CNVs and region of homozygosity identified by the SNP‐array were analyzed.

Results

Of 10 377 cases, 689 had ultrasound abnormalities and 9688 were ascertained to have other indications. The overall prevalence of CNVs was 2.1% (n = 223/10 377, 95% confidence interval [CI] 1.9‐2.4), but the prevalence was 4.4% (95% CI 3.0‐6.1) for cases referred with abnormal ultrasound findings and 2.0% (95% CI 1.7‐2.3) for other indications. Of the 223 CNVs detected, 42/10 377 were pathogenic (0.4%, 95% CI 0.3‐0.6), 84 were susceptibility CNV (0.8%, 95% CI 0.6‐1.0) and 97 were variants of uncertain significance (0.9%, 95% CI 0.8‐1.1). Using an SNP‐based platform allowed for the detection of paternal uniparental disomy of chromosome 14 in a fetus with ultrasound abnormality.

Conclusions

With an indication of advanced maternal age but normal ultrasound scans, the prevalence of pathogenic CNVs was 0.4% and that of susceptibility CNV 0.7%. As CNVs are independent of maternal age, the prevalence is likely the same for younger women. Thus, this study provides further evidence that chromosomal microarray analysis should be available for all women who wish to receive diagnostic testing, as this risk is above the cut‐off of 1:300 for Down syndrome, leading to the suggestion of invasive testing. A chromosomal microarray analysis based on SNP‐array platform is preferable, as it can also detect uniparental disomy in addition to copy number variants.

"It's probably nothing, but…" Couples' experiences of pregnancy following an uncertain prenatal genetic result

INTRODUCTION

A common concern regarding the introduction of chromosomal microarray in prenatal testing is the concomitant identification of an uncertain copy number variant (CNV) where significance and clinical implication for the unborn child can be difficult or impossible to predict. Following the identification of an uncertain CNV, prospective parents may decide to continue the pregnancy. The aim of this study was to explore how prospective parents manage uncertainty and experience pregnancy in light of an uncertain CNV result.

MATERIAL AND METHODS

Qualitative interviews with 16 women and 10 partners who had received a prenatally diagnosed, uncertain CNV. Participants were recruited from the Aarhus University Hospital, Denmark and most were interviewed in their homes 1-14 weeks after birth. Data were analyzed using thematic analysis.

RESULTS

Following the CNV diagnosis, some couples focused on the severe syndromes ruled out by the result, whereas others were more concerned with the new potential risks, for example, learning disabilities. Most couples did not remember the actual diagnosis, but all described a number of attention points generated by the CNV result. During pregnancy, the couples used various strategies to limit worry and enjoy their pregnancy, such as limiting information seeking, reducing talk of the CNV, and deferring thoughts of potential consequences. Furthermore, ultrasound was considered a valuable resource for reducing worry as it provided reassurance about the development of the baby. Inherited CNVs caused relief on one hand, but also feelings of responsibility for the child's potential challenges. After birth, worry decreased considerably, but all couples paid some extra attention to the child's development, while also being alert to the risk of wrongfully interpreting the child's development in terms of the CNV. Eleven couples expressed satisfaction with knowing about the child's CNV, whereas five couples would rather not have known.

CONCLUSIONS

The results indicate that health professionals should be mindful of terminology, remember to point out what has been ruled out by the CNV result, and discuss potential coping strategies with the couple. Furthermore, these couples may have a higher need for ultrasound during pregnancy to help reduce worry. More research is needed on the families' long-term coping.

Implementing non-invasive prenatal testing (NIPT) in the Netherlands: An interview study exploring opinions about and experiences with societal pressure, reimbursement, and an expanding scope

The noninvasive prenatal test (NIPT) as the first trimester prenatal screening (FTS) for trisomies 21, 18, and 13 is offered to all pregnant women in the Netherlands. NIPT using genome sequencing allows for an expansion of the scope of FTS and the introduction of NIPT gives rise to ethical and societal concerns about deliberated decision‐making, pressure to engage in screening, and possible lack of equal access due to the financial contribution (€175) to NIPT. We explored the opinions and experiences of pregnant women, who were offered FTS, about these concerns, and the possibility of a broadened scope. Nineteen pregnant women representing a diversity of backgrounds were interviewed using a semi‐structured interview guide. Eight women did not opt for prenatal screening while 11 did (NIPT = 4, combined test = 7). Women experienced a free choice to accept or decline prenatal screening, despite sometimes receiving advice from others. Prior to pretest counseling, some women had already deliberated about what an abnormal test result would mean to them. Others accepted or declined FTS without deliberation. The current Dutch policy of requiring a co‐payment was acceptable to some, who believed that it functioned as a threshold to think carefully about FTS. Others were concerned that a financial threshold would lead to unequal access to screening. Finally, pregnant women found it difficult to formulate opinions on the scope of FTS, because of lack of knowledge. Life expectancy, severity, and treatability were considered important criteria for the inclusion of a condition in NIPT.

Fetal and neonatal neurogenetics

Disorders of the developing nervous system may be of genetic origin, comprising congenital malformations of spine and brain as well as metabolic or vascular disorders that affect normal brain development. Acquired causes include congenital infections, hypoxic-ischemic or traumatic brain injury, and a number of rare neoplasms. This chapter focuses on the clinical presentation and workup of neurogenetic disorders presenting in the fetal or neonatal period. After a summary of the most frequent clinical presentations, clues from history taking and clinical examination are illustrated with short case reports. This is followed by a discussion of the different tools available for the workup of neurogenetic disorders, including the various genetic techniques with their advantages and disadvantages. The implications of a molecular genetic diagnosis for the patient and family are addressed in the section on counseling. The chapter concludes with a proposed workflow that may help the clinician when confronted with a potential neurogenetic disorder in the fetal or neonatal period.

Prenatal diagnosis by chromosomal microarray analysis

Chromosomal microarray analysis (CMA) is performed either by array comparative genomic hybridization or by using a single nucleotide polymorphism array. In the prenatal setting, CMA is on par with traditional karyotyping for detection of major chromosomal imbalances such as aneuploidy and unbalanced rearrangements. CMA offers additional diagnostic benefits by revealing sub-microscopic imbalances or copy number variations that are too small to be seen on a standard G-banded chromosome preparation. These submicroscopic imbalances are also referred to as microdeletions and microduplications, particularly when they include specific genomic regions that are associated with clinical sequelae. Not all microdeletions/duplications are associated with adverse clinical phenotypes and in many cases, their presence is benign. In other cases, they are associated with a spectrum of clinical phenotypes that may range from benign to severe, while in some situations, the clinical significance may simply be unknown. These scenarios present a challenge for prenatal diagnosis, and genetic counseling prior to prenatal CMA greatly facilitates delivery of complex results. In prenatal diagnostic samples with a normal karyotype, chromosomal microarray will diagnose a clinically significant subchromosomal deletion or duplication in approximately 1% of structurally normal pregnancies and 6% with a structural anomaly. Pre-test counseling is also necessary to distinguish the primary differences between the benefits, limitations and diagnostic scope of CMA versus the powerful but limited screening nature of non-invasive prenatal diagnosis using cell-free fetal DNA.

Offering a choice between NIPT and invasive PND in prenatal genetic counseling: the impact of clinician characteristics on patients' test uptake

Testing options for pregnant women at increased risk of common aneuploidies are non-invasive prenatal testing (NIPT) and invasive prenatal diagnosis (PND). Clinicians are challenged to comprehensively discuss the complex information in a patient-centered and non-directive manner, to allow for patients' informed decision-making. This study explored the information-centeredness, patient-centeredness, and level of non-directivity of different clinicians and examined group differences between their patients. First, semi-structured interviews with four senior obstetricians and one senior nurse were held regarding their information provision, their adaptation of a patient-centered attitude, and their practice of non-directivity. Interviews were transcribed verbatim and rated by four independent researchers. Secondly, 181 pregnant women were included in the study, of whom 82% opted for NIPT and 18% chose PND. Between clinicians, we assessed the distribution of choice ratios, patients' impression of clinicians' test preferences, and patients' knowledge scores. The results indicate that clinicians do not differ in their information-centeredness, but do differ in their patient-centeredness and their level of non-directivity. Significant differences in patients' NIPT/PND ratios were observed between clinicians, with the largest difference being 35 vs. 4% opting for invasive PND. Between 9 and 22% of the patients had an impression of their clinician's preference and chose in accordance with this preference. Patients' overall knowledge scores did not differ across clinicians. In conclusion, the differences in NIPT/PND ratios between clinicians indicate that clinicians' differing counseling approaches affect the choices their patients make. The interviews indicate a possible framing effect which may unintentionally steer the decision-making process.

[Clinical value of genome-wide chromosome microarray technique in diagnosis of fetal cerebral ventriculomegaly]

OBJECTIVE

To investigate the clinical value of gnome-wide chromosome microarray (CMA) technique in genetic etiological diagnosis of fetal cerebral ventriculomegaly.

METHODS

A retrospective analysis was conducted in 109 women with singleton pregnancy, who were admitted in Nanfang Hospital with the diagnosis of cerebral ventriculomegaly in the fetuses by ultrasound between January, 2014 and December, 2016. Routine karyotype analysis and chromosome microarray analysis were performed to identify the chromosomal abnormalities in the fetuses.

RESULTS

Karyotype analysis detected chromosomal abnormalities at a rate of 12.84% in these fetuses, significantly lower than the rate of 26.60% with CMA technique (P=0.004); the combined detection rate of the two techniques was 28.44%. In 17 cases, karyotype analysis yielded normal results while CMA microarray showed abnormalities with an extra abnormal detection rate of 15.60%. Among the 17 fetuses with chromosomal abnormalities, 6 had micro-deletion, 9 had micro-duplication, 1 had both micro-deletion and micro-duplication, and 1 had heterozygous loss of single parent diploid.

CONCLUSION

CMA technique can be used to detect abnormal chromosomal copy numbers in fetuses with cerebral ventriculomegaly to increase the detection rate of chromosomal abnormalities and facilitate prenatal consultation and prognostic evaluation.

Expert Knowledge Influences Decision-Making for Couples Receiving Positive Prenatal Chromosomal Microarray Testing Results

To assess how participants receiving abnormal prenatal genetic testing results seek information and understand the implications of results, 27 US female patients and 12 of their male partners receiving positive prenatal microarray testing results completed semi-structured phone interviews. These interviews documented participant experiences with chromosomal microarray testing, understanding of and emotional response to receiving results, factors affecting decision-making about testing and pregnancy termination, and psychosocial needs throughout the testing process. Interview data were analyzed using a modified grounded theory approach. In the absence of certainty about the implications of results, understanding of results is shaped by biomedical expert knowledge (BEK) and cultural expert knowledge (CEK). When there is a dearth of BEK, as in the case of receiving results of uncertain significance, participants rely on CEK, including religious/spiritual beliefs, "gut instinct," embodied knowledge, and social network informants. CEK is a powerful platform to guide understanding of prenatal genetic testing results. The utility of culturally situated expert knowledge during testing uncertainty emphasizes that decision-making occurs within discourses beyond the biomedical domain. These forms of "knowing" may be integrated into clinical consideration of efficacious patient assessment and counseling.

Choosing between Higher and Lower Resolution Microarrays: do Pregnant Women Have Sufficient Knowledge to Make Informed Choices Consistent with their Attitude?

Developments in prenatal testing allow the detection of more findings. SNP arrays in prenatal diagnosis (PND) can be analyzed at 0.5 Mb resolution detecting more clinically relevant anomalies, or at 5 Mb resolution. We investigated whether women had sufficient knowledge to make informed choices regarding the scope of their prenatal test that were consistent with their attitude. Pregnant women could choose between testing at 5 or at 0.5 Mb array. Consenting women (N = 69) received pre-test genetic counseling by phone and filled out the Measure of Informed Choice questionnaire designed for this study. Choices based on sufficient knowledge and consistent with attitude were considered informed. Sixty-two percent of the women made an adequately informed choice, based on sufficient knowledge and attitude-consistent with their choice of microarray resolution. Women who made an informed choice, opted for 0.5 Mb array resolution more often. There were no differences between women making adequately informed or less informed choices regarding level of experienced anxiety or doubts. Over time on T0 and T1, anxiety and doubts significantly decreased. While previous studies demonstrated that knowledge is an important component in informed decision-making, this study underlines that a consistent attitude might be equally important for decision-making. We advocate more focus on attitude-consistency and deliberation as compared to only a strong focus on knowledge.

Committee Opinion No.682: Microarrays and Next-Generation Sequencing Technology: The Use of Advanced Genetic Diagnostic Tools in Obstetrics and Gynecology

Genetic technology has advanced dramatically in the past few decades, and its applications and use in caring for and counseling pregnant women has been transformational in the realm of prenatal diagnosis. Two of the newer genetic technologies in the prenatal setting are chromosomal microarray and whole-exome sequencing. Chromosomal microarray analysis is a method of measuring gains and losses of DNA throughout the human genome. It can identify chromosomal aneuploidy and other large changes in the structure of chromosomes as well as submicroscopic abnormalities that are too small to be detected by traditional modalities. Prenatal chromosomal microarray analysis is recommended for a patient with a fetus with one or more major structural abnormalities identified on ultrasonographic examination and who is undergoing invasive prenatal diagnosis. Whole-genome sequencing analyzes the entire genome, including noncoding regions (introns) and coding regions (exons). However, because the introns are typically of little clinical relevance, there has been a focus instead on whole-exome sequencing, which examines the coding regions (exons) of the genome. The exons generally have greater clinical relevance and applicability to patient care. However, the routine use of whole-genome or whole-exome sequencing for prenatal diagnosis is not recommended outside of the context of clinical trials.

Couple's Narratives of Communion and Isolation Following Abnormal Prenatal Microarray Testing Results

In 2% to 3% of cases, prenatal microarray testing detects deletions and duplications in a fetus' genome that are undetected by conventional cytogenetics. Many of these changes are associated with variable or uncertain symptomatology. Little is known about how couples experience uncertain results. This study analyzed 24 interviews with members of 12 heterosexual U.S. couples who received pathogenic or uncertain microarray prenatal testing results. Researchers used narrative analysis to examine couples' understanding and incorporation of findings into decision making regarding pregnancy termination. Couples felt unprepared for these findings and frustrated because scant information was available to aid interpretation. Women sought information and made decisions, and men marginalized their distress to support their wives. A shift in voice from first to second person indicated attempts to normalize emotional responses by making the process "common" to all couples. Families pursuing highly sensitive prenatal testing may need expert guidance to support decision making.

Is there a Role for Genetic Counselors in Prenatal Paternity Testing? - an Assessment Based on Audit of 13 years of Clinical Experience in South Australia

The role of genetic counselors in prenatal paternity testing has not been widely studied in the genetic counseling literature. In South Australia, the genetic counselors of the State's public sector clinical genetics service are the primary contact point for women seeking information and testing, also coordinating the testing process. This has provided the opportunity to review all prenatal paternity testing performed in the State over a 13 year period and to consider the role played by the genetic counselor. We explored the reasons why women requested prenatal paternity testing and whether the genetic counselor was an appropriate health professional to facilitate this testing for women. The study had two parts, an audit of the clinical genetics files of 160 women who requested prenatal paternity testing between March 2001 and March 2014, and qualitative interviews of genetic counselors, clinical geneticists, obstetricians and social workers with involvement in this area. The audit determined that in 69.9 % of cases the long-term partner was the father of the pregnancy, for 23.7 % the short-term or other partner was the father and for 6.4 % the paternity results were not known by the genetic counselor. For 45.5 % of women whose long-term partner was excluded as the father, the women chose to have a termination of pregnancy. The results of the qualitative interviews yielded five major themes: accessibility of testing, role of the genetic counselor, social and relationship issues, decision making in pregnancy and emotional issues. We conclude that the genetic counselor is an appropriate health professional to facilitate prenatal paternity testing. Genetic counselors did not view their role as significantly different from a request for prenatal testing for another indication.