Current controversies in prenatal diagnosis 2: should a fetal exome be used in the assessment of a dysmorphic or malformed fetus?

Women's responses to prenatal genetic diagnosis and attitudes to termination of pregnancy after non-invasive prenatal testing: An online survey of Western Australian women

BACKGROUND

Non-invasive prenatal testing (NIPT) using cell-free DNA (cfDNA) has expanded from detecting chromosome aneuploidy to testing for a variety of genetic conditions, including some select single gene disorders. As next generation sequencing/whole exome sequencing technology develops, it may be possible to expand NIPT of cfDNA to identify hundreds of single gene and chromosomal disorders in a fetus, thereby increasing the complexity of pretest counselling and parental decision-making.

AIM

The aim of this study was to assess the views of women on the phenotypes of genetic conditions potentially detectable with expanded NIPT that they would consider severe enough to warrant pregnancy termination.

MATERIALS AND METHODS

Using multiple clinical scenarios, we asked women via an online survey about the early detection of several well-described genetic phenotypes in pregnancy that in theory could be detected by expanded NIPT.

RESULTS

Two hundred and nineteen women participated in this study. There was high support for early diagnosis and the option for termination of pregnancy in conditions perceived as severe (52-71%). Women expressed a preference for testing to be provided by general practitioners and assigned a high value to genetic counselling support (75-90%). In the case of a continuing pregnancy, women recognised the essential role of ongoing psychosocial counselling for family members and childhood early intervention programs.

CONCLUSION

Women expressed clear preferences for termination of pregnancy for severe conditions and as early in gestation as feasible. Information and support from genetic counsellors are a highly valued resource in decision-making following a prenatal diagnosis of a fetal genetic abnormality.

Simpson-Golabi-Behmel syndrome in one of the Dichorionic-diamniotic twin: a case report and literature review

Background

Simpson-Golabi-Behmel syndrome (SGBS) is a rare X-linked overgrowth syndrome. The main clinical manifestations are overgrowth and multiple malformations.

Case presentation

A 38-year-old Chinese woman was pregnant with dichorionic-diamniotic (DCDA) twins after in-vitro fertilization. Series of ultrasound examinations indicated that the measurements (abdominal circumference and estimated foetal weight) of one twin were significantly greater than those of the other one. The genetic testing results of the larger baby indicated of Simpson-Golabi-Behmel syndrome.

Conclusion

SGBS is difficult to diagnose due to different clinical manifestations. Clinicians need to be more aware of typical SGBS’s clinical findings and choose genetic testing methods individually to improve its prenatal diagnosis.

Fetal Exome Sequencing on the Horizon

Prenatal whole exome sequencing has recently been introduced. It is evolving and although not currently ready for everyday clinical practice, it will likely become part of the diagnostic arsenal available to clinicians caring for couples carrying a pregnancy for which fetal anomalies have been identified. This commentary discusses what it is, its indications, its benefits, and its limitations.

Next-Generation Sequencing Using a Cardiac Gene Panel in Prenatally Diagnosed Cardiac Anomalies

OBJECTIVE

Most prenatally identified congenital heart defects (CHDs) are the sole structural anomaly detected; however, there is a subgroup of cases where the specific genetic cause will impact prognosis, including chromosome abnormalities and single-gene causes. Next-generation sequencing of all the protein coding regions in the genome or targeted to genes involved in cardiac development is currently possible in the prenatal period, but there are minimal data on the clinical utility of such an approach. This study assessed the outcome of a CHD gene panel that included single-gene causes of syndromic and non-syndromic CHDs.

METHOD

Sixteen cases with a fetal CHD identified on prenatal ultrasound were studied using a 108 CHD gene panel. DNA was extracted from cultured amniocytes.

RESULTS

There was no diagnostic pathogenic variant identified in these cases. There was an average of 2.9 reportable variants identified per case and the majority of them were variants of uncertain significance.

CONCLUSION

Next-generation sequencing has the potential for increased genetic diagnosis for fetal anomalies. However, the large number of variants and the absence of an examinable patient make the interpretation of these variants challenging.

Laboratory considerations for prenatal genetic testing

New genetic tests have rapidly entered clinical care with little consistency in laboratory testing and reporting. Non-invasive prenatal screening using cell free DNA (cfDNA) may either screen for common aneuploidies alone or include chromosomal microdeletions. All cfDNA screening tests have false positives and false negatives, and accordingly laboratories should report positive and negative predictive values. In addition, since fetal fraction plays a significant role in the reliability of results, this should also be reported with all test results. Chromosomal microarray addresses significant clinically relevant information beyond that detected with standard karyotype testing but may, in less than one percent of cases, result in a variant of uncertain significance (VUS). Laboratories should indicate their policies for reporting these VUS findings. In addition, physicians using this testing should be aware of the advantages and disadvantages of the laboratory platforms. Whole-exome and whole-genome sequencing are just entering clinical care and issues of VUS, incidental findings, and phenotype/genotype correlations need to be investigated before these techniques enter routine clinical care.

Prenatal diagnosis of X-linked myopathy associated with a VMA21 gene mutation afforded through a novel targeted exome sequencing strategy applied in fetuses with abnormal ultrasound findings

Fetal malformations detected through routine prenatal ultrasound examination comprise a heterogeneous group potentially associated with genetic disorders where the underlying cause is difficult to establish. We present the prenatal diagnosis of a rare X‐linked myopathy involving a new VMA21 gene mutation, detected through a novel prenatal exome sequencing‐based approach.

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.

First applications of a targeted exome sequencing approach in fetuses with ultrasound abnormalities reveals an important fraction of cases with associated gene defects

Background. Fetal malformations and other structural abnormalities are relatively frequent findings in the course of routine prenatal ultrasonographic examination. Due to their considerable genetic and clinical heterogeneity, the underlying genetic cause is often elusive and the resulting inability to provide a precise diagnosis precludes proper reproductive and fetal risk assessment. We report the development and first applications of an expanded exome sequencing-based test, coupled to a bioinformatics-driven prioritization algorithm, targeting gene disorders presenting with abnormal prenatal ultrasound findings.

Methods. We applied the testing strategy to14 euploid fetuses, from 11 on-going pregnancies and three products of abortion, all with various abnormalities or malformations detected through prenatal ultrasound examination. Whole exome sequencing (WES) was followed by variant prioritization, utilizing a custom analysis pipeline (Fetalis algorithm), targeting 758 genes associated with genetic disorders which may present with abnormal fetal ultrasound findings.

Results. A definitive or highly-likely diagnosis was made in 6 of 14 cases (43%), of which 3 were abortuses (Ellis-van Creveld syndrome, Ehlers-Danlos syndrome and Nemaline myopathy 2) and 3 involved on-going pregnancies (Citrullinemia, Noonan syndrome, PROKR2-related Kallmann syndrome). In the remaining eight on-going pregnancy cases (57%), a ZIC1 variant of unknown clinical significance was detected in one case, while in seven cases testing did not reveal any pathogenic variant(s). Pregnancies were followed-up to birth, resulting in one neonate harboring the PROKR2 mutation, presenting with isolated minor structural cardiac abnormalities, and in seven apparently healthy neonates.

Discussion. The expanded targeted exome sequencing-based approach described herein (Fetalis), provides strong evidence suggesting a definite and beneficial increase in our diagnostic capabilities in prenatal diagnosis of otherwise chromosomally balanced fetuses with troubling ultrasound abnormalities. Furthermore, the proposed targeted exome sequencing strategy, designed primarily as a diagnostic rather than a research discovery tool, overcomes many of the problems and limitations associated with clinical wide-scale WES testing in a prenatal setting.