New genetic testing in prenatal diagnosis

Survey on patients' organisations' knowledge and position paper on screening for inherited neuromuscular diseases in Europe

BACKGROUND

The development of new genetic testing methods and the approval of the first treatments raises questions regarding when and how to perform screening for inherited neuromuscular conditions. Screening directives and access to the different techniques is not uniform across Europe. The patient advisory board of the European reference network for rare neuromuscular diseases (NMD) conducted a qualitative study to understand the state of play of screening for inherited NMD in Europe and patients' needs.

RESULTS

We collected answers from 30 patient organisations (POs) from 18 European countries. Fifteen acknowledge the existence of pre-implantation genetic diagnosis in their country. Regarding prenatal screening, we had 25 positive answers and 5 negative ones. Twenty-four POs mentioned that newborn screening was available in their country. We had some contradictory answers from POs from the same country and in some cases; diseases said to be part of the screening programmes were not hereditary disorders. Twenty-eight organisations were in favour of screening tests. The reasons for the two negative answers were lack of reimbursement and treatment, religious beliefs and eventual insurance constrains. Most POs (21) were in favour of systematic screening with the option to opt-out. Regarding the timing for screening, "at birth", was the most consensual response. The main priority to perform screening for NMDs was early access to treatment, followed by shorter time to diagnostic, preventive care and genetic counselling.

CONCLUSIONS

This is the first study to assess knowledge and needs of POs concerning screening for NMDs. The knowledge of POs regarding screening techniques is quite uneven. This implies that, even in communities highly motivated and knowledgeable of the conditions they advocate for, there is a need for better information. Differences in the responses to the questions "how and when to screen" shows that the screening path depends on the disease and the presence of a disease modifying treatment. The unmet need for screening inherited NMDs should follow an adaptive pathway related to the fast moving medical landscape of NMDs. International coordination leading to a common policy would certainly be a precious asset tending to harmonize the situation amongst European countries.

Prenatal Exome Sequencing: Background, Current Practice and Future Perspectives-A Systematic Review

The introduction of Next Generation Sequencing (NGS) technologies has exerted a significant impact on prenatal diagnosis. Prenatal Exome Sequencing (pES) is performed with increasing frequency in fetuses with structural anomalies and negative chromosomal analysis. The actual diagnostic value varies extensively, and the role of incidental/secondary or inconclusive findings and negative results has not been fully ascertained. We performed a systematic literature review to evaluate the diagnostic yield, as well as inconclusive and negative-result rates of pES. Papers were divided in two groups. The former includes fetuses presenting structural anomalies, regardless the involved organ; the latter focuses on specific class anomalies. Available findings on non-informative or negative results were gathered as well. In the first group, the weighted average diagnostic yield resulted 19%, and inconclusive finding rate 12%. In the second group, the percentages were extremely variable due to differences in sample sizes and inclusion criteria, which constitute major determinants of pES efficiency. Diagnostic pES availability and its application have a pivotal role in prenatal diagnosis, though more homogeneity in access criteria and a consensus on clinical management of controversial information management is envisageable to reach widespread use in the near future.

A novel method for noninvasive diagnosis of monogenic diseases from circulating fetal cells

OBJECTIVE

To establish a method for noninvasive fetal cell isolation from maternal blood and prenatal testing of monogenic diseases by a combination of direct sequencing and targeted NGS-based SNP haplotyping from single fetal cells.

METHOD

Peripheral blood of pregnant women in two families (congenital deafness and ichthyosis) was collected. After density-based separation and immunostaining with multiple biomarkers, candidate fetal cells were identified by high-throughput imagine analysis and picked up by automation. Individual fetal cells were subjected to STR-genotyping to identify their origin. Pathogenic mutations were identified by direct Sanger sequencing, and a combination of targeted NGS and SNP haplotyping using a custom panel. All the results were compared with amniotic fluid DNA.

RESULTS

Fetal trophoblasts were successfully harvested from maternal blood. STR-genotyping confirmed the fetal origin. Direct sequencing of pathogenic genetic mutations in fetal cells showed consistent results with amniotic fluid samples. For congenital deafness family, NGS-based SNP haplotyping also correctly identified the fetal haplotype. This single cell haplotyping method can be used to diagnose various genetic diseases.

CONCLUSION

We have established a method for noninvasive prenatal testing of monogenic diseases from circulating trophoblast cells. This cell-based NIPT can be further applied to the prenatal diagnosis of various monogenic diseases.

Non‑invasive prenatal diagnosis of thalassemia through multiplex PCR, target capture and next‑generation sequencing

Prenatal clinical detection of thalassemia involves gap-PCR and reverse dot blot (RDB) analysis of fetal DNA acquired through invasive methods. The present study aimed to develop a non-invasive prenatal diagnostic method for thalassemia based on next-generation sequencing (NGS). A total of eight families with proband children with thalassemia were recruited for the study during a subsequent pregnancy. The sequence of the thalassemia genes of the parents and proband were determined using NGS, based on a thalassemia AmpliSeq panel. Cell-free plasma DNA from pregnant women related to the aforementioned proband was analyzed using an NGS panel, based on thalassemia-associated capture probes. Heterozygous single nucleotide polymorphisms within the 10 kb regions flanking exons of the targeted thalassemia genes were acquired using probes or AmpliSeq and employed for parental haplotype construction using Trio-based panel sequencing. The fetal haplotype was deduced from the parental haplotypes and relative haplotype dosage, and subsequently validated using gap-PCR and RDB, based on invasively sampled amniotic fluid. A non-invasive prenatal diagnosis procedure from maternal plasma fetal DNA was successfully developed based on haplotype analysis. The deduced haplotypes of eight fetuses were identical to the results of invasive prenatal diagnosis procedures, with an accuracy rate of 100%. Taken together, the present study demonstrated the potential for non-invasive prenatal diagnosis of α- and β-thalassemia using NGS and haplotype-assisted analysis.

Couples experiences of receiving uncertain results following prenatal microarray or exome sequencing: A mixed-methods systematic review

Background

Tests in pregnancy such as chromosomal microarray analysis and exome sequencing are increasing diagnostic yield for fetal structural anomalies, but have greater potential to result in uncertain findings. This systematic review investigated the experiences of prospective parents about receiving uncertain results from these tests.

Methods

A systematic search of three electronic databases was conducted. Data extraction was performed for studies that met the eligibility and quality criteria. Results were synthesised following the principles of thematic analysis.

Results

Fourteen studies (10 qualitative, 4 quantitative) were included. Findings were grouped into three overarching themes. Sources of uncertainty included the testing procedure, the diagnosis and prognosis, and health professionals' own uncertainty. The clinical impact of the uncertainty included parents struggling to make clinical decisions with the information available, the emotional impact included decisional‐regret, shock, worry and feeling overwhelmed. To manage the uncertainty, parents sought support from healthcare professionals, friends, family, the internet and other parents as well as remaining hopeful.

Conclusions

Prospective parents experience a myriad of uncertainties in the prenatal setting, which must be handled sensitively. Future research should explore optimal ways of managing uncertainty to minimise harm. Recommendations are made for discussing uncertainty during pre‐ and post‐test counseling.

The frequency of CNVs in a cohort population of consecutive fetuses with congenital anomalies after the termination of pregnancy

BACKGROUND

The implementation of molecular karyotyping has resulted in an improved diagnostic yield in the genetic diagnostics of congenital anomalies, detected prenatally or after the termination of pregnancy. However, the systematic epidemiologic ascertainment of copy number variations in the etiology of congenital anomalies has not yet been sufficiently explored.

METHODS

Consecutive fetuses, altogether 204, with major single or multiple congenital anomalies were ascertained by using the SLOCAT registry for the period from 2011 to 2015. After excluding aneuploidies by using conventional karyotyping or Quantitative Fluorescence-Polymerase Chain Reaction, array comparative genomic hybridization was performed for the detection of copy number variations.

RESULTS

We identified pathogenic or likely pathogenic copy number variations in 14 fetuses (6.8%); 2.9% in fetuses with isolated, and 3.9% in fetuses with multiple congenital anomalies. Additionally, aneuploidies and major structural chromosomal abnormalities were detected in 40.2%.

CONCLUSION

Our systematic approach of ascertaining congenital anomalies resulted in explaining the etiology of congenital anomalies in 47% of fetuses after the termination of pregnancy. By using array comparative genomic hybridization, we found that copy number variations represent an important part in the etiology of multiple, as well as isolated congenital anomalies, which indicates the importance of analyzing copy number variations in the diagnostic approach of fetuses with congenital anomalies after the termination of pregnancy.

The challenges of the expanded availability of genomic information: an agenda-setting paper

Rapid advances in microarray and sequencing technologies are making genotyping and genome sequencing more affordable and readily available. There is an expectation that genomic sequencing technologies improve personalized diagnosis and personalized drug therapy. Concurrently, provision of direct-to-consumer genetic testing by commercial providers has enabled individuals' direct access to their genomic data. The expanded availability of genomic data is perceived as influencing the relationship between the various parties involved including healthcare professionals, researchers, patients, individuals, families, industry, and government. This results in a need to revisit their roles and responsibilities. In a 1-day agenda-setting meeting organized by the COST Action IS1303 "Citizen's Health through public-private Initiatives: Public health, Market and Ethical perspectives," participants discussed the main challenges associated with the expanded availability of genomic information, with a specific focus on public-private partnerships, and provided an outline from which to discuss in detail the identified challenges. This paper summarizes the points raised at this meeting in five main parts and highlights the key cross-cutting themes. In light of the increasing availability of genomic information, it is expected that this paper will provide timely direction for future research and policy making in this area.

Ethical considerations in prenatal testing: Genomic testing and medical uncertainty

Prenatal diagnostic testing has recently progressed from karyotype to routinely available chromosomal microarray, and the potential for fetal whole exome sequencing, both through invasive diagnostic testing and, in some cases, non-invasive prenatal testing. These tests bring beneficence through providing a higher diagnostic yield, often with lower risks of miscarriage than previously available testing, but also raise the question of harms related to an increase in uncertain and unknown results. Some parents-to-be report a desire to learn as much information as possible prenatally, and there may be beneficence in providing them with this information. However, the potential uncertainty these tests may create may raise anxiety and may complicate pregnancy decision-making for both patients and providers. This article reviews current prenatal technologies and the growing research on the clinical and ethical aspects of uncertainty as it relates to expanding prenatal testing options.

Unsolved challenges in pediatric whole-exome sequencing: A literature analysis

Whole-exome sequencing (WES) has been instrumental in the discovery of novel genes and mechanisms causing Mendelian diseases. While this technology is now being successfully applied in a number of clinics, particularly to diagnose patients with rare diseases, it also raises a number of ethical, legal and social issues. In order to identify what challenges were directly foreseen by technology users, we performed a systematic review of the literature. In this paper, we focus on recent publications related to the use of WES in the pediatric context and analyze the most prominent challenges raised by technology users. This is particularly relevant considering that a) most patients currently undergoing testing using WES to identify the genetic basis for rare diseases are children and b) their lack of capacity to consent for themselves makes them a vulnerable population and generates the need for specific ethical, legal and regulatory procedures. We identified key challenges that related to four main categories: (1) intake; (2) sequence production and analysis; (3) reporting of results and counseling considerations and (4) collaborative data interpretation and data sharing. We then contextualize these challenges in light of the recent recommendations and guidelines, published by professional societies that have significant potential to impact the field.

Unsolved challenges of clinical whole-exome sequencing: a systematic literature review of end-users' views

BACKGROUND

Whole-exome sequencing (WES) consists in the capture, sequencing and analysis of all exons in the human genome. Originally developed in the research context, this technology is now increasingly used clinically to inform patient care. The implementation of WES into healthcare poses significant organizational, regulatory, and ethical hurdles, which are widely discussed in the literature.

METHODS

In order to inform future policy decisions on the integration of WES into standard clinical practice, we performed a systematic literature review to identify the most important challenges directly reported by technology users.

RESULTS

Out of 2094 articles, we selected and analyzed 147 which reported a total of 23 different challenges linked to the production, analysis, reporting and sharing of patients' WES data. Interpretation of variants of unknown significance, incidental findings, and the cost and reimbursement of WES-based tests were the most reported challenges across all articles.

CONCLUSIONS

WES is already used in the clinical setting, and may soon be considered the standard of care for specific medical conditions. Yet, technology users are calling for certain standards and guidelines to be published before this technology replaces more focused approaches such as gene panels sequencing. In addition, a number of infrastructural adjustments will have to be made for clinics to store, process and analyze the amounts of data produced by WES.

High-resolution melting analysis for noninvasive prenatal diagnosis of IVS-II-I (G-A) fetal DNA in minor beta-thalassemia mothers

OBJECTIVES

The high-resolution melting (HRM) technique is fast, effective and successful method for mutation detection. The aim of this study was to determine the sensitivity and specificity of the HRM method for detection of a paternally inherited mutation in a fetus as a noninvasive prenatal diagnosis of β-thalassemia.

METHODS

Genomic DNAs were prepared from 50 β-thalassemia minor couples whose pregnancy was at risk for homozygous β-thalassemia. Ten milliliters of the maternal blood from each pregnant woman were collected and after separating plasma stored at -80 °C until analysis. The extracted DNAs were analyzed by HRM real-time PCR for detection of IVS-II-I (G-A) as a paternally inherited mutation. The gold standard was the result of a chorionic villus sampling by a standard reverse dot blotting test.

RESULTS

The sensitivity and specificity of HRM real-time PCR were 92.6% and 82.6%, respectively. Also, the positive and negative predictive values were 86.2% and 90.47%, respectively.

CONCLUSIONS

HRM real-time PCR was a sensitive and specific method for determining the paternally inherited mutation in the fetus at risk with thalassemia major.

Prenatal diagnosis: do prospective parents have the right not to know?

Prenatal diagnosis (PND) challenges the issue of parental autonomy. Two ethical aspects of the parental decision making process with reference to PND have been taken into consideration: the duty to know and the right not to know. Whilst the first approach has been widely discussed in literature, the latter seems to be overlooked. In order to find good moral reasons supporting the right not to know, firstly the duty to know approach was critically analysed. Subsequently, the emphasis was put on the unconditional parental love and the issue of child's best interests as the features supporting parental right not to know. The clarification of what is good parenthood was presented as the best normative approach supporting the parental right not to know in case of PND. Apart from parental autonomy, raising the question of the right not to know is important in the debate about the place and role of people with disabilities in society.