Prenatal Genome Research Articles

Impact of Variation in Practice in the Prenatal Reporting of Variants of Uncertain Significance by Commercial Laboratories: Need for Greater Adherence to Published Guidelines

ABSTRACT Ultrasound will identify fetal structural anomalies in up to 2% to 3% of pregnancies; these can vary from minor isolated defects to severe multisystem abnormalities. As genetic investigations into the causes can assist with prenatal and perinatal decision-making, various tests exist to assist in this endeavor. Rapid aneuploidy detection and chromosomal microarray analysis are both used for detecting chromosomal aneuploidy and microdeletions or duplications (termed copy number variations) for pregnancies with fetal abnormalities. Approximately 6% of fetuses with identifiable structural abnormalities have pathogenic copy number variations, and 32% have an abnormal karyotype. In the last 8 years, whole exome sequencing (WES) has been used for making a genetic diagnosis in the remaining undiagnosed pregnancies, and a recent meta-analysis determined an exome sequencing diagnostic yield of 31% following nondiagnostic chromosomal microarray analysis or karyotype. Use of exome sequencing is complicated, however, by its association with possibly detecting variants of uncertain significance (VUSs) and pathogenic/likely pathogenic (P/LP) variants in genes possibly noncausal for the prenatal phenotypes. Thus, the value of reporting VUSs is under debate, with various policies worldwide. This study's purpose was to evaluate the clinical impact of WES and targeted panel implementation at the clinical level when fetal structural anomalies suggest a single underlying gene disorder or syndrome. The study focus was the frequency of reporting VUSs, the diagnostic yield, and the contribution of reported VUSs toward a final diagnosis. This retrospective chart review at the Provincial Medical Genetics Program at BC Women's Hospital in Vancouver included patients undergoing WES between January 2016 and December 2020. Amniocentesis was used for obtaining fetal samples, except for 4 cases of sample acquisition at the time of pregnancy termination. A total of 124 patients underwent prenatal WES or panel testing at different commercial laboratories following the identification of fetal structural anomalies by ultrasound. Patients had either WES (n = 90) or panel testing (n = 31), with 3 patients undergoing both, as decided by the ordering clinical geneticist. Genetic diagnoses of variants classified by the laboratory as P or LP were obtained in 20 of 93 patients (21.5%) via prenatal WES and in 9 of 34 patients (26%) who underwent panel testing. The 2 tests' overall diagnostic yield was 23%. Of these, 20 patients (69%) were diagnosed with autosomal dominant disorders. Overall, 32% of patients with panel testing and 42% of patients who had WES had at least 1 VUS, and 23% of WES and 15% of panels reported more than 1 VUS. There was great variation in the reporting of VUSs between laboratories. The study uncovered a lack of strict adherence to guidelines for reporting of prenatal VUSs among various laboratories. One weakness (and strength) of the study is its use of multiple commercial laboratories for the WES, panel testing, and VUS reporting. Although this is beneficial to gain various perspectives (such as the lack of adherence to guidelines), it also diminishes the consistency of the results across the entire study because of varied procedures for diagnoses. In conclusion, this study reports on 124 pregnancies with fetal anomalies at a large tertiary care center experiencing the provision of prenatal WES (or targeted gene panels) with variant interpretation and sequencing outsourced to various laboratories. A result of 23% diagnostic yield for WES and panel testing occurred based on the laboratory-reported LP and P variants. The large number of VUSs reported by laboratories implies significant resource implications due to the time to review evidence and further examine or investigate the fetus and/or parent. This is essential, and the authors emphasize the complex nature of the required posttest genetic counseling. Based on these results, the authors strongly encourage strict adherence to recommendations on VUS reporting in the prenatal setting, with the importance of a multidisciplinary approach bringing laboratory and clinical expertise of prenatal genomics and genetics together.

Decision-making process about prenatal genetic screening: how deeply do moms-to-be want to know from Non-Invasive Prenatal Testing?

BackgroundPrenatal information may be obtained through invasive diagnostic procedures and non-invasive screening procedures. Several psychological factors are involved in the decision to undergo a non-invasive prenatal testing (NIPT) but little is known about the decision-making strategies involved in choosing a specific level of in-depth NIPT, considering the increased availability and complexity of NIPT options. The main aim of this work is to assess the impact of psychological factors (anxiety about pregnancy, perception of risk in pregnancy, intolerance to uncertainty), and COVID-19 pandemic on the type of NIPT chosen, in terms of the number of conditions that are tested.MethodsA self-administered survey evaluated the decision-making process about NIPT. The final sample comprised 191 women (Mage = 35.53; SD = 4.79) who underwent a NIPT from one private Italian genetic company. Based on the test date, the sample of women was divided between “NIPT before COVID-19” and “NIPT during COVID-19”.ResultsAlmost all of the participants reported being aware of the existence of different types of NIPT and more than half reported having been informed by their gynecologist. Results showed no significant association between the period in which women underwent NIPT (before COVID-19 or during COVID-19) and the preferences for more expanded screening panel. Furthermore, regarding psychological variables, results showed a significant difference between perceived risk for the fetus based on the NIPT type groups, revealing that pregnant women who underwent the more expanded panel had a significantly higher level of perceived risk for the fetus than that reported by pregnant women who underwent the basic one. There was no statistically significant difference between the other psychological variables and NIPT type.ConclusionsOur findings indicate the paramount role of gynecologist and other health care providers, such as geneticists and psychologists, is to support decision-making process in NIPT, in order to overcome people’s deficits in genetic knowledge, promote awareness about their preferences, and control anxiety related to the unborn child. Decision-support strategies are critical during the onset of prenatal care, according to the advances in prenatal genomics and to parent’s needs.

Prospects for limiting access to prenatal genetic information about Down syndrome in light of the expansion of prenatal genomics

Down syndrome (Trisomy 21) is a mild to moderate intellectual disability. Historically, this condition has been a primary target for prenatal testing. However, Down syndrome has not been targeted for prenatal testing because it is an especially severe illness. The condition was just one that could be easily identified prenatally using the techniques first available decades ago. We are moving into an era in which we can prenatally test for a vast range of human traits. I argue that when we can test for anything, there is no longer any reason to continue targeting Down syndrome. I present an argument based on the value of nondiscrimination. It is justified to set limits on access to prenatal information if the information is going to be used for discriminatory purposes. I use the examples of (1) prenatal testing for misogynistic fetal sex selection, and (2) homophobia-motivated prenatal testing for potential homosexuality, as compelling analogies.

Decision-making for prenatal genetic screening: how will pregnant women navigate a growing number of aneuploidy and carrier screening options?

BackgroundPrenatal genetic screens, including carrier screening (CS) and aneuploidy screening (AS), comprise an important component of reproductive healthcare delivery. Clinical practice guidelines emphasize the importance of informed decision-making and patient’s preferences regarding the use of these screens. Yet, it is unclear how to achieve this ideal as prenatal genetic screening options rapidly become more complex and increasingly available to patients. With increased complexity and availability of reproductive testing options, decision-support strategies are critical to prepare patients to consider AS and/or CS.MethodsA self-administered survey evaluated knowledge and decision-making preferences for expanded carrier (CS) and aneuploidy (AS) prenatal screening. The survey was administered to participants before their first prenatal visit to assess baseline decision-making needs and preference at the initiation of prenatal care. Analysis was approached as a descriptive process.ResultsParticipants had similar familiarity with the concepts associated with AS compared to CS; mean knowledge scores for CS was 0.59 [possible range 0.00 to 1.00] and 0.55 for AS. Participants reported preferences to learn about a range of conditions, including those with severe or mild impact, childhood-onset, and adult-onset. Decision-making preference with respect to learning about the associated disease phenotypes for the contained on AS and CS panel shifted with the complexity of the panel, with a greater preference to learn about conditions post-test compared pre-test education as panels increased from 5 to 100 conditions.ConclusionPatients’ baseline knowledge of prenatal genetic screens coupled with evolving decision-making preferences presents challenges for the delivery of prenatal genetic screens. This calls for the development and implementation of innovative approaches to support pregnant patients’ decision-making commensurate with advances in prenatal genomics.

Ethical Issues Relating to Prenatal Genetic Testing

"Introduction: Non-invasive prenatal testing (NIPT) is a rapidly developing genomic technology that is constantly widening its scope and opening up new possibilities in reproductive medicine. Ten years after NIPT has been made commercially available, it is increasingly entering routine antenatal care as either a first- or second-tier test. In England, France and Germany, for example, NIPT has been made available free-of-charge as a second-tier test to women with a higher chance of common chromosomal anomalies. The clinical implementation of NIPT carries benefits but also raises important ethical questions. Our project analyses these questions within their specific contexts in England, France and Germany. Methods: As part of a wider research project, which will involve qualitative methods, we conducted a document analysis to compare arguments about, and regulations governing NIPT in the three countries in: law and policy document; public reports; medical press; academic literature; and media. Results: Despite the similarities between the three countries to offer NIPT as a second-tier screening tool, they exhibit differences with regard to their public discourses about prenatal genomics, screening policies, the risk-thresholds they use, professional regulations and laws. These differences have an impact on the way ethical issues emerge, and questions about the meaning of health, illness and disability, the scope of public health interventions, social inclusion and exclusion as well as reproductive choice are approached in each country. "

How to deal with uncertainty in prenatal genomics: A systematic review of guidelines and policies.

Exome sequencing (ES) enhanced the diagnostic yield of genetic testing, but has also increased the possibility of uncertain findings. Prenatal ES is increasingly being offered after a fetal abnormality is detected through ultrasound. It is important to know how to handle uncertainty in this particularly stressful period. This systematic review aimed to provide a comprehensive overview of guidelines available for addressing uncertainty related to prenatal chromosomal microarray (CMA) and ES. Ten uncertainty types associated with prenatal ES and CMA were identified and defined by an international multidisciplinary team. Medline (all) and Embase were systematically searched. Laboratory scientists, clinical geneticists, psychologists, and a fetal medicine specialist screened the papers and performed the data extraction. Nineteen papers were included. Recommendations generally emphasized the importance of trio analysis, clinical information, data sharing, validation and re‐analysis, protocols, multidisciplinary teams, genetic counselling, whether to limit the possible scope of results, and when to report particular findings. This systematic review helps provide a vocabulary for uncertainties, and a compass to navigate uncertainties. Prenatal CMA and ES guidelines provide a strong starting point for determining how to handle uncertainty. Gaps in guidelines and recommendations were identified and discussed to provide direction for future research and policy making.

Turner syndrome: New insights from prenatal genomics and transcriptomics.

In some parts of the world, prenatal screening using analysis of circulating cell-free (cf) DNA in the plasma of pregnant women has become part of routine prenatal care with limited professional guidelines and without significant input from the Turner syndrome community. In contrast to the very high positive predictive values (PPVs) achieved with cfDNA analysis for trisomy 21 (91% for high-risk and 82% for low-risk cases), the PPVs for monosomy X are much lower (~26%). This is because the maternal plasma sample contains both maternal cfDNA and placental DNA, which is a proxy for the fetal genome. Underlying biological mechanisms for false positive monosomy X screening results include confined placental mosaicism, co-twin demise, and maternal mosaicism. Somatic loss of a single X chromosome in the mother is a natural phenomenon that occurs with aging; this could explain many of the false positive cfDNA results. There is also increased awareness of women who have constitutional mosaicism for 45, X who are fertile. It is important to recognize that a positive cfDNA screen for 45, X does not mean that the fetus has Turner syndrome. A follow-up diagnostic test, either amniocentesis or neonatal karyotype/chromosome microarray, is recommended. Research studies on cell-free mRNA in second trimester amniotic fluid, which is almost exclusively fetal, demonstrate consistent dysregulation of genes involved in the hematologic, immune, and neurologic systems. This suggests that some of the pathophysiology of Turner syndrome occurs early in fetal life and presents novel opportunities for consideration of antenatal treatments.

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.

Health professionals' and researchers' perspectives on prenatal whole genome and exome sequencing: 'We can't shut the door now, the genie's out, we need to refine it'.

The Prenatal Assessment of Genome and Exomes (PAGE) project is a UK-wide study aiming to gain a better understanding of genetic variants causing developmental problems during pregnancy. A further aim of the study is to provide an evidence-base for the introduction of prenatal whole genome and exome sequencing (PWGES) into prenatal diagnostics provided by the NHS, which is expected in 2018. This paper presents the findings of a qualitative interview study undertaken with 20 health professionals and researchers involved in the PAGE project, and explores their implications for understandings of ‘good practice’ in the uses of prenatal genomics clinically. A number of critical issues are identified that will need to be addressed in the development of a model of good ethical practice for prenatal genomics: consent, management of expectations, return of results, and professional duties in the context of PWGES. The analysis presented identifies and illustrates a great deal of complexity and qualitative richness in these issues as they arise in the day-to-day work of genomics professionals. Inclusive, critical discussion of these findings, together with the findings from other empirical studies, normative analysis and scientific discoveries resulting from PAGE, will be required to inform the development of appropriate guidelines of good ethical practice that address the needs and concerns to be encountered in daily clinical practice.

Genetically Engineered Traits versus Virtuous Living

ABSTRACTIt is fruitless to attempt to genetically engineer virtuous living. Prenatal genome modification could, in principle, establish desired traits and predispose us to certain behaviors. But, traits given at birth are not the same thing as a virtuous character that can be acquired only by self-discipline. The ethicist further fears that free market eugenics—the sale of gene modification—may become one more expression of the social sin our culture inherits.

In Utero Gene Therapy and Genome Editing

The purpose of this review is to summarize the current status of in utero gene therapy and postnatal in vivo genome editing with an eye toward prenatal genome editing. The rational for gene therapy and genome editing in utero is described, specifically the small size of the fetus, fetal immunologic immaturity, prenatal accessibility of stem and progenitor cells, and the ability to treat target diseases prior to birth. We review studies in normal and disease small and large animal models which demonstrate the feasibility and safety of in utero gene therapy using a variety of viral vectors. Postnatal in vivo genome editing with CRISPR-Cas9 in a number of murine disease models is discussed including the preference for nonhomologous end-joining compared to homology-directed repair in non-proliferating adult cells as a potential benefit to application of CRISPR-Cas9 genome editing to the fetus. Finally, the ethical challenges of human in utero gene therapy are discussed in the context of the EVERREST trial that is currently being designed. In utero gene therapy and genome editing is a developing field with great potential to treat congenital monogenic diseases. More research in small and large animal models is required before clinical translation can occur.

NP Bookshelf

Graduate-level nursing curricula continue to bulge with content deemed new and essential for understanding and care of patients. Some new and complex content is increasingly introduced in classes but relies on texts assigned to students to study on their own for the detailed mastery of content and ongoing reference. One of the best examples of this practice is the integration of genomics into nurse practitioner (NP) programs. As more information is learned about how genomics affects the patients we care for, this information becomes more important for clinicians. Genomic Essentials for Gradate Level Nurses is written by advanced practice nurses, expert nurses, and physicians who have developed expertise in this area over many years. They have lectured widely and helped import the basic definitions and principles from genetics and genomics fields that every NP should master. This information is presented in a commonsense progression of chapters. The contributors emphasize that the science of genetics looked carefully at the fairly rare changes in an individual or single gene or chromosome. Genomics is a broader term that “considers the interactions between and within genes, regulatory sequences, and the environment.”p. 1 From the basics of DNA structure and replication and discussions of mutations to Mendelian patterns of inheritance and their alternations, foundational information is presented to help the reader understand the current advances in genomics. There is a detailed chapter about risk assessment, data collection, and interpretation for genomic clinical assessment. The various steps taken to conduct risk assessment, confirm diagnosis, and manage risk are presented in easy-to-understand steps. Significant attention is paid to testing and counseling for genetic and genomic conditions. This 445-page book has 18 chapters that explore almost every component possible related to genomics, including legal and social implications and essentials of pharmacogenomics that address important information essential to all clinicians. The book proceeds with content relevant to the life span—preconceptual and prenatal genomics, newborn screening, genetic considerations in childhood and aging—and then moves to a discussion of genomics related to specific cardiovascular, respiratory, hematology, neurologic, and endocrine disorders and to cancer. Specific chapters are also written about the role that genomics might play in nursing education, research, leadership and practice, genomic technologies, and symptomatology. Many experienced NPs attended NP programs before this content was available. This book is a useful, understandable, practical resource that all NPs would benefit from reading. It will empower readers to have a greater depth of understanding in their work with patients.

An empirical analysis of intention to use array-comparative genomic hybridisation method

Because of advancements in modern medical technology, array-Comparative Genomic Hybridisation (aCGH), a new type of prenatal genome detection technology, has a higher resolution than that of traditional chromosome inspection techniques and can rely on chromosome chip inspection to compensate for the deficiencies of traditional chromosome inspection techniques. This study mainly used the Health Belief Model (HBM) to evaluate the intention of pregnant women to use chromosome chip detection and to determine the factors that influence such intentions. The results showed that the public's knowledge on chromosome chip inspection, perceived susceptibility, and cues to action has positive effects on usage intention, whereas perceived barriers have negative effects on usage intention.

Current approaches on non-invasive prenatal diagnosis: Prenatal genomics, transcriptomics, personalized fetal diagnosis.

Recent developments in molecular genetics improved our knowledge on fetal genome and physiology. Novel scientific innovations in prenatal diagnosis have accelerated in the last decade changing our vision immensely. Data obtained from fetal genomic studies brought new insights to fetal medicine and by the advances in fetal DNA and RNA sequencing technology novel treatment strategies has evolved. Non-invasive prenatal diagnosis found ground in genetics and the results are widely studied in scientific arena. When Lo and colleges proved fetal genetic material can be extracted from maternal plasma and fetal DNA can be isolated from maternal serum, the gate to many exciting discoveries was open. Microarray technology and advances in sequencing helped fetal diagnosis as well as other areas of medicine. Today it is a very crucial prerequisite for physicians practicing prenatal diagnosis to have a profound knowledge in genetics. Prevailing practical use and application of fetal genomic tests in maternal and fetal medicine mandates obstetricians to update their knowledge in genetics. The purpose of this review is to assist physicians to understand and update their knowledge in fetal genetic testing from maternal blood, individualized prenatal counseling and advancements on the subject by sharing our experiences as İstanbul University Fetal Nucleic Acid Research Group.

Prenatal genome sequencing

Prenatal genome sequencing

Non-invasive prenatal measurement of the fetal genome

The vast majority of prenatal genetic testing requires invasive sampling. Since this poses a risk to the fetus, one must make a decision that weighs the desire for genetic information against the risk of an adverse outcome due to hazards of the testing process. These issues are not required to be coupled, and it would be desirable to discover genetic information about the fetus without incurring a health risk. Here we demonstrate that it is possible to noninvasively sequence the entire prenatal genome. Our results show that molecular counting of parental haplotypes in maternal plasma by shotgun sequencing of maternal plasma DNA allows the inherited fetal genome to be deciphered noninvasively. We also applied the counting principle directly to each allele in the fetal exome by performing exome capture on maternal plasma DNA prior to shotgun sequencing. This approach enables noninvasive exome screening of clinically relevant and deleterious alleles that were paternally inherited or had arisen as de novo germline mutations, and complements the haplotype counting approach to provide a comprehensive view of the fetal genome. Noninvasive determination of the fetal genome may ultimately facilitate the diagnosis of all inherited and de novo genetic disease.