Prenatal exome sequencing for fetuses with structural abnormalities: the next step

Fetal gene therapy

Fetal gene therapy was first proposed toward the end of the 1990s when the field of gene therapy was, to quote the Gartner hype cycle, at its "peak of inflated expectations." Gene therapy was still an immature field but over the ensuing decade, it matured and is now a clinical and market reality. The trajectory of treatment for several genetic diseases is toward earlier intervention. The ability, capacity, and the will to diagnose genetic disease early-in utero-improves day by day. A confluence of clinical trials now signposts a trajectory toward fetal gene therapy. In this review, we recount the history of fetal gene therapy in the context of the broader field, discuss advances in fetal surgery and diagnosis, and explore the full ambit of preclinical gene therapy for inherited metabolic disease.

Application of array comparative genomic hybridization (aCGH) for identification of chromosomal aberrations in the recurrent pregnancy loss

Spontaneous abortion occurs in 8–20% of recognized pregnancies and usually takes place in the first trimester (7–11 weeks). There are many causes of pregnancy loss, but the most important (about 75%) is the presence of chromosomal aberrations. We present the results of oligonucleotide array application in a cohort of 62 miscarriage cases. The inclusion criteria for the study were the loss after 8th week of pregnancy and the appearance of recurrent miscarriages. DNA was extracted from trophoblast or fetal skin fibroblasts. In the 62 tested materials from recurrent miscarriages, the detection rate was 56.5% (35/62). The most commonly found were aneuploidies (65%) (chromosomal trisomy 14, 16, 18, 21, and 22), Turner syndrome, and triploidy (17.1%). Other chromosomal abnormalities included pathogenic and likely pathogenic structural aberrations: 1) pathogenic: deletion 7p22.3p12.3 and duplication 9p24.3p13.2 inherited from the normal father, deletion 3q13.31q22.2 and deletion 3q22.3q23 of unknown inheritance and duplication of 17p12 inherited from father with foot malformation; 2) likely pathogenic variants: deletion 17p13.1 inherited from normal mother, deletion 5q14.3 of unknown inheritance and de novo deletion 1q21.1q21.2. Among these aberrations, six CNVs (copy number variants) were responsible for the miscarriage: deletion 7p22.3p12.3 and duplication 9p24.3p13.2, deletion 3q13.31q22.2 and deletion 3q22.3q23, and deletion 17p13.1 and deletion 1q21.1q21.2. Other two findings were classified as incidental findings (deletion 5q14.3 and 17p12 duplication). Our research shows that 17% of the aberrations (6/35 abnormal results) that cannot be identified by the routine kariotype analysis are structural aberrations containing genes important for fetal development, the mutations of which may cause spontaneous abortion.

What's out there for parents? A systematic review of online information about prenatal microarray and exome sequencing

Objective

To identify what online patient information (presented in English) is available to parents about prenatal microarray (CMA) and exome sequencing (ES), and evaluate its content, quality, and readability.

Method

Systematic searches (Google and Bing) were conducted, and websites were categorised according to their purpose. Websites categorised as patient information were included if they were: in English, directed at patients, or were a text, video, or online version of an information leaflet. Author‐developed content checklists, the DISCERN Genetics tool, and readability tests (the Flesch Reading Ease Score, the Gunning Fog Index, and the Simple Measure of Gobbledygook Index) were then used to assess those sources of patient information.

Results

Of the 665 websites screened, 18 met the criteria. A further 8 sources were found through a targeted search of professional organisations, resulting in 26 sources available for further evaluation. In general, this was found to be low in quality, omitted details recommended by national or international guidance, and was written at a level too advanced for average readers.

Conclusion

Improvements should be made to the content, quality, and readability of online information so that it both reinforces and complements the discussions between parents and clinicians about testing options during pregnancy.

What's already known about this topic?

The Internet is an important source of information for parents during pregnancy

Little is known about the availability and standard of online information about newer prenatal genetic tests like chromosomal microarray (CMA) and prenatal exome sequencing (ES)

What does this study add?

Our results revealed limited online information aimed at parents about CMA and ES

The information we did identify was lacking the details recommended by professional guidelines, had low quality scores, and was written at an advanced level

Improvements to online information for parents are needed to support informed decision‐making regarding prenatal genetic tests

Isolated Increased Nuchal Translucency in First Trimester Ultrasound Scan: Diagnostic Yield of Prenatal Microarray and Outcome of Pregnancy

Background: Increased nuchal translucency (NT) is associated with aneuploidy. When the karyotype is normal, fetuses are still at risk for structural anomalies and genetic syndromes. Our study researched the diagnostic yield of prenatal microarray in a cohort of fetuses with isolated increased NT (defined as NT ≥ 3.5 mm) and questioned whether prenatal microarray is a useful tool in determining the adverse outcomes of the pregnancy. Materials and Methods: A prospective study was performed, in which 166 women, pregnant with a fetus with isolated increased NT (ranging from 3.5 to 14.3 mm with a mean of 5.4 mm) were offered karyotyping and subsequent prenatal microarray when karyotype was normal. Additionally, all ongoing pregnancies of fetuses with normal karyotype were followed up with regard to postnatal outcome. The follow-up time after birth was maximally 4 years. Results: Totally, 149 of 166 women opted for prenatal testing. Seventy-seven fetuses showed normal karyotype (52%). Totally, 73 of 77 fetuses with normal karyotype did not show additional anomalies on an early first trimester ultrasound. Totally, 40 of 73 fetuses received prenatal microarray of whom 3 fetuses had an abnormal microarray result: two pathogenic findings (2/40) and one incidental carrier finding. In 73 fetuses with an isolated increased NT, 21 pregnancies showed abnormal postnatal outcome (21/73, 28.8%), 29 had a normal outcome (29/73, 40%), and 23 were lost to follow-up (23/73, 31.5%). Seven out of 73 live-born children showed an adverse outcome (9.6%). Conclusions: Prenatal microarray in fetuses with isolated increased NT had a 5% (2/40) increased diagnostic yield compared to conventional karyotyping. Even with a normal microarray, fetuses with an isolated increased NT had a 28.8% risk of either pregnancy loss or an affected child.

Prenatal Exome Sequencing in Recurrent Fetal Structural Anomalies: Systematic Review and Meta-Analysis

To determine the diagnostic yield of exome sequencing (ES), a microarray analysis was carried out of fetuses with recurrent fetal structural anomalies (with similar anomalies in consecutive pregnancies). This is a systematic review conducted in accordance with Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) criteria. The selected studies describing ES in fetuses with recurrent fetal malformation were assessed using the Standards for Reporting of Diagnostic Accuracy Studies (STARD) criteria for risk of bias. Incidence was used as the pooled effect size by single-proportion analysis using random-effects modeling (weighted by inverse of variance). We identified nine studies on ES diagnostic yield that included 140 fetuses with recurrent structural anomalies. A pathogenic or likely pathogenic variant was found in 57 fetuses, resulting in a 40% (95%CI: 26% to 54%) incremental performance pool of ES. As expected, the vast majority (86%: 36/42) of the newly identified diseases had a recessive inheritance pattern, and among these, 42% (15/36) of variants were found in homozygosity. Meckel syndrome was the monogenic disease most frequently found, although the genes involved were diverse. The ES diagnostic yield in pregnancies with recurrent fetal structural anomalies was 40% (57/140). Homozygous disease-causing variants were found in 36% (15/57) of the newly identified monogenic disorders.

KH domain containing 3 like (KHDC3L) frame-shift mutation causes both recurrent pregnancy loss and hydatidiform mole

OBJECTIVE

Recurrent pregnancy loss (RPL) is a common infertility-related complication that affects approximately 1-3 % of women worldwide. Known causes of etiology are found in approximately half the cases but the other half remain unexplained. It is estimated that several thousands of genes contribute to reproductive success in mammals and the genetic causes of RPL cannot be fully addressed through targeted genetic tests. In recent years, massive parallel sequencing technologies has helped discovering many causal mutations in hereditary diseases such as RPL.

STUDY DESIGN

Using whole-exome sequencing (WES), we studied a large multiplex consanguineous family with multiple cases of RPL and hydatidiform moles (HM). In addition, targeted Sanger sequencing was applied to 40 additional non-related individuals with RPL.

RESULTS

The use of WES permitted to identify the pathogenic variant in KHDC3L (c.322_325delGACT) in related who experienced RPL with or without HM. Sanger sequencing confirmed the segregation of the mutation throughout the pedigree and permitted to establish this variant as the genetic cause responsible for RPL and HM in this family.

CONCLUSION

KHDC3L is well established as a susceptibility gene for HM but we confirmed here that KHDC3L deleterious variants can also induce RPL. In addition, we observed a genotype-phenotype correlation, demonstrating that women with a truncating KHDC3L homozygous variant could not sustain a pregnancy and often had pregnancy losses mainly due to HM while those with the same heterozygous variant could have children but often endured RPL with no HM.

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.

The potential diagnostic yield of whole exome sequencing in pregnancies complicated by fetal ultrasound anomalies

INTRODUCTION

The aim of this retrospective cohort study was to determine the potential diagnostic yield of prenatal whole exome sequencing in fetuses with structural anomalies on expert ultrasound scans and normal chromosomal microarray results.

MATERIAL AND METHODS

In the period 2013-2016, 391 pregnant women with fetal ultrasound anomalies who received normal chromosomal microarray results, were referred for additional genetic counseling and opted for additional molecular testing pre- and/or postnatally. Most of the couples received only a targeted molecular test and in 159 cases (40.7%) whole exome sequencing (broad gene panels or open exome) was performed. The results of these molecular tests were evaluated retrospectively, regardless of the time of the genetic diagnosis (prenatal or postnatal).

RESULTS

In 76 of 391 fetuses (19.4%, 95% CI 15.8%-23.6%) molecular testing provided a genetic diagnosis with identification of (likely) pathogenic variants. In the majority of cases (91.1%, 73/76) the (likely) pathogenic variant would be detected by prenatal whole exome sequencing analysis.

CONCLUSIONS

Our retrospective cohort study shows that prenatal whole exome sequencing, if offered by a clinical geneticist, in addition to chromosomal microarray, would notably increase the diagnostic yield in fetuses with ultrasound anomalies and would allow early diagnosis of a genetic disorder irrespective of the (incomplete) fetal phenotype.

Evaluation of Diagnostic Yield in Fetal Whole-Exome Sequencing: A Report on 45 Consecutive Families

Prenatal ultrasound (US) abnormalities often pose a clinical dilemma and necessitate facilitated investigations in the search of diagnosis. The strategy of pursuing fetal whole-exome sequencing (WES) for pregnancies complicated by abnormal US findings is gaining attention, but the reported diagnostic yield is variable. In this study, we describe a tertiary center's experience with fetal WES from both terminated and ongoing pregnancies, and examine the clinical factors affecting the diagnostic rate. A total of 45 consecutive families of Jewish descent were included in the analysis, for which clinical fetal WES was performed under either single (fetus only), trio (fetus and parents) or quatro (two fetuses and parents) design. Except one, all families were non-consanguineous. In 41 of the 45 families, WES was sought following abnormal fetal US findings, and 18 of them had positive relevant family history (two or more fetuses with US abnormalities, or single fetus with US abnormalities and an affected parent). The overall diagnostic yield was 28.9% (13/45 families), and 31.7% among families with fetal US abnormalities (13/41). It was significantly higher in families with prenatal US abnormalities and relevant family history (10/18, 55.6%), compared to families with prenatal US abnormal findings and lack of such history (3/23, 13%) (p = 0.004). WES yield was relatively high (42.9-60%) among families with involvement of brain, renal or musculoskeletal US findings. Taken together, our results in a real-world setting of genetic counseling demonstrates that fetal WES is especially indicated in families with positive family history, as well as in fetuses with specific types of congenital malformation.

Prenatal Diagnosis by Whole Exome Sequencing in Fetuses with Ultrasound Abnormalities

Whole-exome sequencing (WES) has been used as a standard of care for postnatal diagnosis in the clinical setting in the past few years for children and adults with undiagnosed disease. Many rare disorders have been diagnosed through WES, which is less expensive than the traditional serial genetic testing where patients had previously spent years on an uninformative diagnostic odyssey. Seeking a diagnosis often entails enduring time consuming, and sometimes invasive procedures which may be associated with medical risks that are stressful for families and impose a heavy burden on the health-care system. However, the use of WES is considered impractical in the prenatal and neonatal testing period because of the technical and computational challenges of performing genomic sequencing from small amounts of genetic material, and the need for faster turnaround time (TAT) than the current 6-8 weeks TAT provided by most clinical labs offering postnatal testing. With the rapidly evolving methods of sequence analysis, there are clinical challenges such as the constantly increasing number of genes being identified which are not yet fully phenotypically characterized, especially when ascertained prenatally or neonatally before all the clinical features may be evident. Despite these challenges, there are many clinical benefits to acquiring genomic information in the prenatal and neonatal period. These include superior prognostic information which allows for prenatal planning of mode of delivery and hospital for delivery and optimized neonatal management. We have developed a clinical WES assay using small amounts of DNA with a TAT of 10 days for use in the prenatal or neonatal setting. This test is used to detect small nucleotide variants and indels in fetuses and neonates with structural abnormalities.

Novel mutation in CCBE 1 as a cause of recurrent hydrops fetalis from Hennekam lymphangiectasia-lymphedema syndrome-1

Whole exome sequencing (WES) was used to determine the etiology of recurrent hydrops fetalis in this case of Hennekam lymphangiectasia-lymphedema syndrome-1. WES is a useful approach for diagnosing rare single-gene conditions with nonspecific phenotypes and should be considered early in the diagnostic process of investigating fetal abnormalities.

A Reappraisal of Circulating Fetal Cell Noninvasive Prenatal Testing

New tools for higher-resolution fetal genome analysis including microarray and next-generation sequencing have revolutionized prenatal screening. This article provides commentary on this rapidly advancing field and a future perspective emphasizing circulating fetal cell (CFC) utility. Despite the tremendous technological challenges associated with their reliable and cost-effective isolation from maternal blood, CFCs have a strong potential to bridge the gap between the diagnostic sensitivity of invasive procedures and the desirable noninvasive nature of cell-free fetal DNA (cffDNA). Considering the rapid advances in both rare cell isolation and low-input DNA analysis, we argue here that CFC-based noninvasive prenatal testing is poised to be implemented clinically in the near future.

Clinical utility of exome sequencing in the prenatal diagnosis of congenital anomalies: A Review

Advances in prenatal genomics have enabled the assessment of not only the sub-microscopic structure of chromosomes using chromosomal microarray analysis, but also the detection of "pathogenic variants" to the resolution of a single base pair with the use of next generation sequencing. Research is emerging on the additional prenatal diagnostic yield that exome sequencing offers when structural fetal anomalies are detected on ultrasound examination, in particular the identification of monogenic abnormalities defining prognosis and recurrence of anomalies. Primarily assessed using fetal DNA obtained by invasive techniques (amniocytes or chorionic villi), this technology is progressing into a non-invasive approach using maternal plasma. There are several challenges, to be addressed before this technology can be introduced into routine clinical practice. These are primarily technical and interpretational but also relate to service provision; cost-effectiveness; turn-around time; patient acceptability and ethical dilemmas. With adequate pre- and post-test counselling many of these challenges may be overcome and such counselling has to be multi-disciplinary, involving clinical geneticists, genetic scientists, paediatricians, perinatal pathologists and fetal medicine subspecialists. There is therefore a need for obstetricians to have an understanding of the clinical utility, application, advantages and challenges of such technologies before introduction into routine clinical practice.

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.

Introducing new and emerging genetic tests into prenatal care

Given the rapid advances in genomics, translating new genomic tests effectively into prenatal clinical practice remains challenging. We discuss emerging genetic tests, considerations for their use, how tests should ideally be validated prior to use in clinical practice, and the role of the Federal Drug Administration, Clinical Laboratory Improvement Amendments (CLIA) laboratories, commercial laboratories, insurers, and professional societies such as the American College of Obstetricians and Gynecologists (ACOG), and the Society for Maternal-Fetal Medicine (SMFM) in the introduction of new prenatal genetic tests. After the introduction of new tests into the prenatal clinic, it is critical to utilize shared databases with measured outcomes to improve clinical care as well as to advance science.

Early Detection of Structural Anomalies in a Primary Care Setting in the Netherlands

OBJECTIVE

This study assessed the percentage and type of congenital anomalies diagnosed at first-trimester ultrasound (US) scan in a primary care setting without following a standardized protocol for fetal anatomical assessment.

MATERIALS AND METHODS

US scans performed between 11+0 and 13+6 weeks of gestation in pregnancies with estimated date of delivery between January 1, 2012 and January 1, 2016 were searched. Data were supplemented with results of 20-week scans and pregnancy outcome.

RESULTS

Of all scans, 38.6% were dating scans and 61.4% were part of first-trimester screening. Anomalies were diagnosed prenatally in 200 (1.8%) fetuses; 81 (0.7%) were chromosomal and 119 (1.1%) were structural. Of all prenatally detected anomalies, 27% (n = 32) were detected at first-trimester scan, with a false-positive rate of 0.04%. All cases of anencephaly (n = 4), encephalocele (n = 2), exomphalos (n = 9), megacystis (n = 4), and limb reduction (n = 1) were diagnosed. First-trimester detection of gastroschisis and congenital heart defects was 67 and 19%, respectively.

CONCLUSION

In a primary care setting, global fetal anatomical assessment at first-trimester scan without following a standardized protocol detects about 30% of all structural anomalies and most of the severe anomalies, with an extremely low false-positive rate. We hypothesize that additional training and use of a systematic protocol would improve early detection of structural anomalies.

Prenatal exome sequencing in anomalous fetuses: new opportunities and challenges

PurposeWe investigated the diagnostic and clinical performance of exome sequencing in fetuses with sonographic abnormalities with normal karyotype and microarray and, in some cases, normal gene-specific sequencing.MethodsExome sequencing was performed on DNA from 15 anomalous fetuses and from the peripheral blood of their parents. Parents provided consent to be informed of diagnostic results in the fetus, medically actionable findings in the parents, and their identification as carrier couples for significant autosomal recessive conditions. We assessed the perceptions and understanding of exome sequencing using mixed methods in 15 mother-father dyads.ResultsIn seven (47%) of 15 fetuses, exome sequencing provided a diagnosis or possible diagnosis with identification of variants in the following genes: COL1A1, MUSK, KCTD1, RTTN, TMEM67, PIEZO1 and DYNC2H1. One additional case revealed a de novo nonsense mutation in a novel candidate gene (MAP4K4). The perceived likelihood that exome sequencing would explain the results (5.2 on a 10-point scale) was higher than the approximately 30% diagnostic yield discussed in pretest counseling.ConclusionExome sequencing had diagnostic utility in a highly select population of fetuses where a genetic diagnosis was highly suspected. Challenges related to genetics literacy and variant interpretation must be addressed by highly tailored pre- and posttest genetic counseling.

Opening Pandora's box?: ethical issues in prenatal whole genome and exome sequencing

OBJECTIVE

The development of genomic approaches to prenatal testing such as whole genome and exome sequencing offers the potential for a better understanding of prenatal structural anomalies in the fetus and ultimately for improved patient care and more informed reproductive decision making. In addition to the scientific and clinical challenges of achieving this, the introduction of new reproductive technologies also presents a number of ethical problems. The successful and appropriate development and introduction of prenatal genomics into clinical practice require these problems to be identified, understood and carefully analysed in the development of models of good ethical practice.

METHOD

We conducted a critical review of the existing literature on ethical issues in prenatal genomics.

RESULTS

We identified and discussed five areas of particular concern: valid consent, management and feed-back of information, responsibilities of health professionals, priority setting and resources and duties towards the future child.

CONCLUSION

There is a need for further discussion of the issues we have outlined here, and we hope that this brief summary of ethical arguments in the literature encourages researchers, clinicians, patients and scientists to engage in further discussion of these and other important issues raised by prenatal genomics. © 2017 The Authors. Prenatal Diagnosis published by John Wiley & Sons, Ltd.

Prenatal diagnosis of upper extremity malformations with ultrasonography: Diagnostic features and perinatal outcome

OBJECTIVE

The aim of this study was to assess the sonographic (US) characteristics, associated malformations, chromosomal status, and perinatal outcomes of fetuses with an upper extremity malformation (UEM) detected by US examination.

METHODS

The data of all patients evaluated in the Department of Obstetrics and Gynecology, Prenatal Diagnosis Unit between 2010 and 2015 were searched for UEM.

RESULTS

A total of 51 cases with UEM were detected. Eighteen cases (35.2%) had defects in the formation of body parts (absence of hand/forearm/digits); 25 cases (49%) had defects in differentiation (contractures, syndactyly), and 8 cases (15.6%) had duplication defects (polydactyly). The specificity of prenatal US for UEM was 96.2%. Ten cases (19.7%) had isolated UEM, and 41 cases (80.3%) had additional anomalies, most of which were cardiac, central nervous system, or facial malformations. Although chromosomal structure in isolated cases was normal in 9 of 10 cases (90%), 15 of 41 cases (36.5%) with multiple defects showed abnormal karyotypes. The chromosomal constituents of nine cases (17.6%) were not available. Although the postnatal outcome of isolated cases was favorable except for the presence of orthopedic problems, complex UEMs with or without abnormal karyotypes were always lethal (97.5%).

CONCLUSIONS

UEMs associated with other malformations are usually a sign of underlying severe chromosomal abnormalities, and the prognosis is poor. In contrast, chromosomal structure in isolated cases is normal, and the perinatal and postnatal outcomes are good. In general, US is an effective tool in differentiating fetuses with isolated UEM from those with UEM associated with additional malformations. © 2016 Wiley Periodicals, Inc. J Clin Ultrasound 45:267-276, 2017.

Prenatal and pre-implantation genetic diagnosis

The past decade has seen the development of technologies that have revolutionized prenatal genetic testing; that is, genetic testing from conception until birth. Genome-wide single-cell arrays and high-throughput sequencing analyses are dramatically increasing our ability to detect embryonic and fetal genetic lesions, and have substantially improved embryo selection for in vitro fertilization (IVF). Moreover, both invasive and non-invasive mutation scanning of the genome are helping to identify the genetic causes of prenatal developmental disorders. These advances are changing clinical practice and pose novel challenges for genetic counselling and prenatal care.

Combined ultrasound and exome sequencing approach recognizes Opitz G/BBB syndrome in two malformed fetuses

Orofacial clefts are the most common congenital craniofacial anomalies and can occur as an isolated defect or be associated with other anomalies such as posterior fossa anomalies as a part of several genetic syndromes. We report two consecutive voluntary pregnancy interruptions in a nonconsanguineous couple following the fetal ultrasound finding of cleft lip and palate and posterior fossa anomalies confirmed by means of post-termination examination on the second fetus. The quantitative fluorescent PCR, the karyotype, and the comparative genomic hybridization-array analysis after amniocentesis were normal. Exome sequencing on abortive material from both fetuses detected a missense mutation in MID1, resulting in a clinical diagnosis of Opitz G/BBB syndrome. The same mutation was found in the mother and in her brother, who both revealed cerebellar anomalies at an MRI examination. Our study supports the efficacy of exome sequencing in the presence of both a family history suggestive of an inherited disorder and well-documented ultrasound findings. It reveals the importance of a synergistic effort between gynecologists and geneticists aimed at the integration of the most sophisticated ultrasound techniques with the next-generation sequencing tools to provide a definite diagnosis essential to orient the final decision and to estimate a proper recurrence risk.

Recent advances in prenatal genetic screening and testing

The introduction of new technologies has dramatically changed the current practice of prenatal screening and testing for genetic abnormalities in the fetus. Expanded carrier screening panels and non-invasive cell-free fetal DNA-based screening for aneuploidy and single-gene disorders, and more recently for subchromosomal abnormalities, have been introduced into prenatal care. More recently introduced technologies such as chromosomal microarray analysis and whole-exome sequencing can diagnose more genetic conditions on samples obtained through amniocentesis or chorionic villus sampling, including many disorders that cannot be screened for non-invasively. All of these options have benefits and limitations, and genetic counseling has become increasingly complex for providers who are responsible for guiding patients in their decisions about screening and testing before and during pregnancy.

Whole exome sequencing and array-based molecular karyotyping as aids to prenatal diagnosis in fetuses with suspected Simpson-Golabi-Behmel syndrome

OBJECTIVE

Simpson-Golabi-Behmel (SGBS) syndrome type 1 and type 2 represent rare X-linked prenatal overgrowth disorders. The aim of our study is to describe the prenatal sonographic features as well as the genetic work-up.

METHOD

Retrospective analysis of four cases with a pre- or postnatal diagnosis of SGBS in a single tertiary referral center within a period of 4 years.

RESULTS

In the study period, four male fetuses with SGBS were detected. The final diagnosis was made prenatally in three cases. In all cases the second trimester anomaly scan revealed left sided congenital diaphragmatic hernia (CDH) with additional anomalies; three fetuses with SGBS type 1 showed fetal overgrowth. In two of these, whole exome sequencing showed a possible frameshift mutation and a point mutation in the gene GPC3, respectively. In the third case, multiplex ligation-dependent probe amplification (MLPA) revealed a hemizygous duplication of exon 3-7 in the gene GPC3. In the fourth case, SGBS type 2 was confirmed by array comparative genomic hybridization (CGH) of amniotic fluid cells showing a deletion of the gene OFD1.

CONCLUSION

We could demonstrate, that in the presence of a CDH, syndromes of the fetus can be increasingly differentiated by detailed sonography followed by a selective and graded molecular diagnostic using microarray techniques and whole exome sequencing. © 2016 John Wiley & Sons, Ltd.

Prenatal Testing for Adult-Onset Conditions: the Position of the National Society of Genetic Counselors

Advances in genetic testing and the availability of such testing in pregnancy allows prospective parents to test their future child for adult-onset conditions. This ability raises several complex ethical issues. Prospective parents have reproductive rights to obtain information about their fetus. This information may or may not alter pregnancy management. These rights can be in conflict with the rights of the future individual, who will be denied the right to elect or decline testing. This paper highlights the complexity of these issues, details discussions that went into the National Society of Genetic Counselors (NSGC) Public Policy Task Force's development of the Prenatal testing for Adult-Onset Conditions position statement adopted in November 2014, and cites relevant literature on this topic through December 2015. Issues addressed include parental rights and autonomy, rights of the future child, the right not to know, possible adverse effects on childhood and the need for genetic counseling. This paper will serve as a reference to genetic counselors and healthcare professionals when faced with this situation in clinical practice.

Chromosomal microarray in prenatal diagnosis: case studies and clinical challenges

Chromosomal microarray analysis (CMA) is a diagnostic tool used in the evaluation of pediatric patients with congenital anomalies or developmental and intellectual disability. In both the pediatric and prenatal patient population, CMA has been shown to have a higher detection rate of chromosomal abnormalities than conventional karyotype alone. Currently, the diagnostic yield of prenatal CMA is highest when applied to the evaluation of a fetus with multiple ultrasound anomalies. Challenges arise when CMA yields isolated findings not associated with a phenotype on ultrasound or variants of uncertain significance, which warrants evaluation of the risks, benefits, limitations and optimal incorporation of CMA into prenatal care. The clinical cases presented here will be used to illustrate these issues.

"Something Extra on Chromosome 5": Parents' Understanding of Positive Prenatal Chromosomal Microarray Analysis (CMA) Results

This study aims to explore how couples' understanding of the nature and consequences of positive prenatal chromosomal microarray analysis (CMA) results impacts decision-making and concern about pregnancy. We interviewed 28 women and 12 male partners after receiving positive results and analyzed the transcripts to assess their understanding and level of concern about the expected clinical implications of results. Participant descriptions were compared to the original laboratory interpretation. When diagnosed prenatally, couples' understanding of the nature and consequences of copy number variants (CNVs) impacts decision-making and concern. Findings suggest women, but less so partners, generally understand the nature and clinical implications of prenatal CMA results. Couples feel reassured, perhaps sometimes falsely so, when a CNV is inherited from a "normal" parent and experience considerable uncertainty when a CNV is de novo, frequently precipitating a search for additional information and guidance. Five factors influenced participants' concern including: the pattern of inheritance, type of possible phenotypic involvement, perceived manageability of outcomes, availability and strength of evidence about outcomes associated with the CNV, and provider messages about continuing the pregnancy. A good understanding of results is vital as couples decide whether or not to continue with their pregnancy and seek additional information to assist in pregnancy decision-making.

Whole exome sequencing in recurrent early pregnancy loss

STUDY HYPOTHESIS

Exome sequencing can identify genetic causes of idiopathic recurrent pregnancy loss (RPL).

STUDY FINDING

We identified compound heterozygous deleterious mutations affecting DYNC2H1 and ALOX15 in two out of four families with RPL. Both genes have a role in early development. Bioinformatics analysis of all genes with rare and putatively pathogenic mutations in miscarriages and couples showed enrichment in pathways relevant to pregnancy loss, including the complement and coagulation cascades pathways.

WHAT IS KNOWN ALREADY

Next generation sequencing (NGS) is increasingly being used to identify known and novel gene mutations in children with developmental delay and in fetuses with ultrasound-detected anomalies. In contrast, NGS is rarely used to study pregnancy loss. Chromosome microarray analysis detects putatively causative DNA copy number variants (CNVs) in ∼2% of miscarriages and CNVs of unknown significance (predominantly parental in origin) in up to 40% of miscarriages. Therefore, a large number of miscarriages still have an unknown cause.

STUDY DESIGN, SAMPLES/MATERIALS, METHODS

Whole exome sequencing (WES) was performed using Illumina HiSeq 2000 platform on seven euploid miscarriages from four families with RPL. Golden Helix SVS v8.1.5 was used for data assessment and inheritance analysis for deleterious DNA variants predicted to severely disrupt protein-coding genes by introducing a frameshift, loss of the stop codon, gain of the stop codon, changes in splicing or the initial codon. Webgestalt (http://bioinfo.vanderbilt.edu/webgestalt/) was used for pathway and disease association enrichment analysis of a gene pool containing putatively pathogenic variants in miscarriages and couples in comparison to control gene pools.

MAIN RESULTS AND THE ROLE OF CHANCE

Compound heterozygous mutations in DYNC2H1 and ALOX15 were identified in miscarriages from two families with RPL. DYNC2H1 is involved in cilia biogenesis and has been associated with fetal lethality in humans. ALOX15 is expressed in placenta and its dysregulation has been associated with inflammation, placental, dysfunction, abnormal oxidative stress response and angiogenesis. The pool of putatively pathogenic single nucleotide variants (SNVs) and small insertions and deletions (indels) detected in the miscarriages showed enrichment in 'complement and coagulation cascades pathway', and 'ciliary motility disorders'. We conclude that CNVs, individual SNVs and pool of deleterious gene mutations identified by exome sequencing could contribute to RPL.

LIMITATIONS, REASONS FOR CAUTION

The size of our sample cohort is small. The functional effect of candidate mutations should be evaluated to determine whether the mutations are causative.

WIDER IMPLICATIONS OF THE FINDINGS

This is the first study to assess whether SNVs may contribute to the pathogenesis of miscarriage. Furthermore, our findings suggest that collective effect of mutations in relevant biological pathways could be implicated in RPL.

STUDY FUNDING AND COMPETING INTERESTS

The study was funded by Canadian Institutes of Health Research (grant MOP 106467) and Michael Smith Foundation of Health Research Career Scholar salary award to ERS.

Deficiency of the myogenic factor MyoD causes a perinatally lethal fetal akinesia

Background

Lethal fetal akinesia deformation sequence (FADS) describes a clinically and genetically heterogeneous phenotype that includes fetal akinesia, intrauterine growth retardation, arthrogryposis and developmental anomalies. Affected babies die as a result of pulmonary hypoplasia. We aimed to identify the underlying genetic cause of this disorder in a family in which there were three affected individuals from two sibships.

Methods

Autosomal-recessive inheritance was suggested by a family history of consanguinity and by recurrence of the phenotype between the two sibships. We performed exome sequencing of the affected individuals and their unaffected mother, followed by autozygosity mapping and variant filtering to identify the causative gene.

Results

Five autozygous regions were identified, spanning 31.7 Mb of genomic sequence and including 211 genes. Using standard variant filtering criteria, we excluded all variants as being the likely pathogenic cause, apart from a single novel nonsense mutation, c.188C>A p.(Ser63*) (NM_002478.4), in MYOD1. This gene encodes an extensively studied transcription factor involved in muscle development, which has nonetheless not hitherto been associated with a hereditary human disease phenotype.

Conclusions

We provide the first description of a human phenotype that appears to result from MYOD1 mutation. The presentation with FADS is consistent with a large body of data demonstrating that in the mouse, MyoD is a major controller of precursor cell commitment to the myogenic differentiation programme.

Reproductive genetic counseling challenges associated with diagnostic exome sequencing in a large academic private reproductive genetic counseling practice

OBJECTIVE

Diagnostic whole exome sequencing (WES) is rapidly entering clinical genetics, but experience with reproductive genetic counseling aspects is limited. The purpose of this study was to retrospectively review and report on our experience with preconception and prenatal genetic counseling for diagnostic WES.

METHOD

We performed a retrospective chart review over 34 months in a large private prenatal genetic counseling practice and analyzed data for referral indications, findings, and results of genetic counseling related to diagnostic WES.

RESULTS

Ten of 14 patients counseled about diagnostic WES for ongoing pregnancies pursued the test, resulting in identification of three pathogenic variants (30%). Five of 15 patients seeking counseling about familial WES results in an affected proband pursued prenatal diagnosis, resulting in identification of one affected fetus and five unaffected fetuses. We experienced challenges related to complexity and uncertainty of results, turnaround time, cost and insurance overage, and multidisciplinary fetal care coordination.

CONCLUSION

Despite having experienced complexity and identified challenges of the reproductive genetic counseling, availability of diagnostic WES contributed important information that aided in prenatal care planning and decision-making. Future enhanced provider education and larger studies to systematically study the integration of WES in reproductive genetic counseling and prenatal care will be important.

Genome-Wide Sequencing for Prenatal Detection of Fetal Single-Gene Disorders

New sequencing methods capable of rapidly analyzing the genome at increasing resolution have transformed diagnosis of single-gene or oligogenic genetic disorders in pediatric and adult medicine. Targeted tests, consisting of disease-focused multigene panels and diagnostic exome sequencing to interrogate the sequence of the coding regions of nearly all genes, are now clinically offered when there is suspicion for an undiagnosed genetic disorder or cancer in children and adults. Implementation of diagnostic exome and genome sequencing tests on invasively and noninvasively obtained fetal DNA samples for prenatal genetic diagnosis is also being explored. We predict that they will become more widely integrated into prenatal care in the near future. Providers must prepare for the practical, ethical, and societal dilemmas that accompany the capacity to generate and analyze large amounts of genetic information about the fetus during pregnancy.

Exome sequencing positively identified relevant alterations in more than half of cases with an indication of prenatal ultrasound anomalies

OBJECTIVE

Exome sequencing is a successful option for diagnosing individuals with previously uncharacterized genetic conditions, however little has been reported regarding its utility in a prenatal setting. The goal of this study is to describe the results from a cohort of fetuses for which exome sequencing was performed.

METHODS

We performed a retrospective analysis of the first seven cases referred to our laboratory for exome sequencing following fetal demise or termination of pregnancy. All seven pregnancies had multiple congenital anomalies identified by level II ultrasound. Exome sequencing was performed on trios using cultured amniocytes or products of conception from the affected fetuses.

RESULTS

Relevant alterations were identified in more than half of the cases (4/7). Three of the four were categorized as 'positive' results, and one of the four was categorized as a 'likely positive' result. The provided diagnoses included osteogenesis imperfecta II (COL1A2), glycogen storage disease IV (GBE1), oral-facial-digital syndrome 1 (OFD1), and RAPSN-associated fetal akinesia deformation sequence.

CONCLUSION

This data suggests that exome sequencing is likely to be a valuable diagnostic testing option for pregnancies with multiple congenital anomalies detected by prenatal ultrasound; however, additional studies with larger cohorts of affected pregnancies are necessary to confirm these findings.

Prenatal whole-exome sequencing: parental attitudes

OBJECTIVE

The aim of this study was to survey the opinions of expectant parents regarding prenatal whole-exome sequencing.

METHODS

The study used a questionnaire that focused on acceptability of prenatal whole-exome sequencing to individuals who pursued first-trimester prenatal screening in a tertiary academic medical center. A total of 186 expectant individuals completed the questionnaire. The results of the questionnaire were analyzed using descriptive statistics and logistic regression models.

RESULTS

Eighty-three percent of the participants answered that prenatal whole-exome sequencing should be offered, 14.8% were neutral, and only 2.2% disagreed. Fifty-four percent of the participants were interested in having prenatal whole-exome sequencing for their fetus, 40.1% were neutral, and 6.6% disagreed. The majority of participants expressed a desire to know about treatable (96.2%) and non-treatable (86.3%) childhood conditions, and most said the same for treatable (76.0%) and non-treatable (74.3%) adult-onset conditions. Over half of the participants (59.7%) indicated a maximum acceptable turnaround time of 3 weeks or less for prenatal whole-exome sequencing.

CONCLUSIONS

The majority of respondents felt prenatal whole-exome sequencing should be offered. Moreover, the majority wanted to know prenatally about treatable and non-treatable childhood and adult conditions.

Comparing genetic counselor's and patient's perceptions of needs in prenatal chromosomal microarray testing

OBJECTIVE

Chromosome microarray analysis is poised to take a significant place in the prenatal setting given its increased yield over standard karyotyping, but concerns regarding ethical and counseling challenges remain, especially associated with the risk of uncertain and incidental findings. Guidelines recommend patients receiving prenatal screening to undergo genetic counseling prior to testing, but little is known about women's specific pre-testing and post-testing informational needs, as well as their preference for return of various types of results.

METHODS

The present study surveys 199 prenatal genetic counselors who have counseled patients undergoing chromosome microarray analysis testing and 152 women who have undergone testing on the importance of understanding pre-test information, return of various types of results, and resources made available following an abnormal finding.

RESULTS

Counselors and patients agree on many aspects, although findings indicate patients consider all available information very important, while genetic counselors give more varying ratings.

CONCLUSION

Counseling sessions would benefit from information personalized to a patient's particular needs and a shared decision-making model, to reduce informational overload and avoid unnecessary anxiety. Additionally, policies regarding the return of various types of results are needed. © 2015 John Wiley & Sons, Ltd.