Fetal de novo heterozygous variant in the isocitrate dehydrogenase 1 gene associated with growth restriction,skeletal, cerebral and vascular anomalies

Germline pathogenic variants in isocitrate dehydrogenase 1 (IDH1) can lead to a rare neurodevelopmental disorder called metaphyseal chondromatosis with D-2-hydroxyglutaric aciduria, including severe skeletal and cerebral anomalies. To the best of our knowledge, no prenatal case of an IDH1 pathogenic variant has been reported in literature. Somatic sequence variants in IDH1/2 genes are described in distinct cancers, premalignant diseases and rare inherited metabolic disorders. Amniocentesis and further genetic testing including trio exome sequencing were performed due to suspicious findings on a second trimester routine prenatal ultrasound examination. The fetus was found to have growth restriction, cerebral abnormalities (ex vacuo hydrocephalus, cerebellar and vermian hypoplasia, corpus callosum dysgenesis), brachycephaly, narrow chest, persistent left superior vena cava, liver calcifications, hyperechogenic bowel, short tubular bones and joint contractures. A de novo heterozygous variant in the IDH1 gene was detected via trio exome sequencing. The prenatal diagnosis of a de novo pathogenic variant in IDH1 in a fetus with the described phenotype, obtained through trio exome sequencing, helped parents and providers with an informed decision making about pregnancy management.     

Likely pathogenic variant in the BICD2 gene in fetus presenting with non-immune hydrops

Trio exome sequencing was performed on a fetus presenting with severe hydrops fetalis at 21 + 0 weeks gestation. A novel de novo BICD2 missense variant was identified in the fetus. Pathogenic variants in the BICD2 gene are associated with lower extremity-predominant spinal muscular atrophy. The variant was initially classified as a variant of uncertain clinical significance (VUS) as at the time of analysis and initial report, pathogenic variants in the BICD2 gene specifically had not been associated with fetal hydrops and no other abnormalities had been detected. It was agreed in multidisciplinary team discussions to include the variant in the report as a VUS recommending phenotypic follow-up. The pregnancy was terminated and post-mortem findings were in keeping with a BICD2-pathogenic variant. In addition, a paper was published reporting another case with a pathogenic BICD2 variant presenting with fetal hydrops. The variant classification was then upgraded to class 4 likely pathogenic and reported as consistent with the diagnosis. This case demonstrates the importance of reporting these new gene/phenotypes in enabling others in the classification of variants, staying up-to-date with literature and following up phenotype for class 3 variants of interest.     

Prenatal diagnosis of CLCN4-related neurodevelopmental disorder in fetuses with congenital brain anomalies

We report two male fetuses born to a healthy unrelated couple, with agenesis of the corpus callosum identified on detailed 20-week ultrasound scans and confirmed by in-utero MRI. Whole-genome sequencing identified a likely pathogenic missense variant in the CLCN4 gene, establishing this as the causative gene in the family. Pathogenic variants in the CLCN4 gene cause a neurodevelopmental disorder (also called Raynaud-Claes syndrome) inherited in an X-linked pattern. The disorder is characterised by developmental delay, intellectual disability, autism spectrum disorder, epilepsy, mental health conditions, and significant feeding difficulties, predominantly, but not exclusively, affecting males. This is the first report of a prenatal phenotype associated with variants in the CLCN4 gene. The diagnosis of the CLCN4-related neurodevelopmental disorder in this family allowed accurate genetic counseling and discussion of reproductive choices. This leaves uncertainty about the possibility of a postnatal neurodevelopmental phenotype in heterozygous females, which we discuss.     

A novel L1CAM mutation with L1 spectrum disorders

X-linked hydrocephalus, HSAS (hydrocephalus due to stenosis of aqueduct of Sylvius), MASA (mental retardation, aphasia, shuffling gait, and adducted thumbs), and CRASH (corpus callosum hypoplasia, retardation, adducted thumbs, spastic paraplegia, and hydrocephalus) syndromes are allelic disorders. X-linked hydrocephalus and associated phenotypes are due to mutations in the L1CAM gene, which has been identified as a coding neural cell adhesion molecule. We report two cases of L1 spectrum disorders within the same family. The first case was diagnosed by ultrasonographic examination prenatally and the second case was diagnosed postnatally. Both patients and their mothers carry a novel mutation of the L1CAM gene. In this family, nine X-linked hydrocephalus and five female carriers were found in three generations, and molecular genetic analysis was performed to detect the asymptomatic carriers. Copyright © 2005 John Wiley & Sons, Ltd.     

Molecular prenatal diagnosis of Smith–Lemli–Opitz syndrome is reliable and efficient

Smith–Lemli–Opitz (RSH) syndrome (SLOS, OMIM 270400) is a relatively common, autosomal recessive disorder of cholesterol biosynthesis with a broad spectrum of phenotypic abnormalities caused by mutations of the 7-dehydrocholesterol reductase gene (DHCR7) on chromosome 11. Prenatal diagnosis can be established by detection of elevated 7-dehydrocholesterol or of SLOS-causing mutations in the DHCR7 gene. We report here our experience with molecular prenatal diagnosis of SLOS. Mutation analysis of the DHCR7 gene was performed in chorionic villus samples of 13 pregnancies of couples with a family history of SLOS and known SLOS genotypes. This approach is accurate and reliable. If facilities for biochemical analysis are not available, or in cases with ambiguous biochemical patterns, molecular prenatal diagnosis is an attractive, alternative option. Copyright © 2002 John Wiley & Sons, Ltd.     

Problems in prenatal diagnosis of β-thalassaemia by fetal blood analysis: β-chain variant comigrating with gamma chains

This report describes a couple at risk for β thalassaemia in which one spouse was heterozygous for classical high Hb A2 β-thalassaemia while the other had the compound heterozygous state for β⁺-thalassaemia and a β-chain variant. This variant comigrates on carboxymethyl-cellulose columns (CMC) with γ-chains, indicating that globin separation on CMC columns could not have been used for fetal diagnosis. The β-chain variant migrates separately from the other globin chains on HPLC and the respective abnormal haemoglobin can be separated by isoelectrofocusing. Oligonucleotide hybridization showed that both parents were carriers of the β⁺ IVS-1, nt 6 mutation. Prenatal diagnosis was successfully accomplished by oligo-nucleotide analysis on trophoblast DNA. This case indicates that an Antenatal Service should have alternative methods to CMC columns so as to carry out prenatal diagnosis of β-thalassaemia in uncommon cases.     

A prospective study on rapid exome sequencing as a diagnostic test for multiple congenital anomalies on fetal ultrasound

Objective

Conventional genetic tests (quantitative fluorescent-PCR [QF-PCR] and single nucleotide polymorphism-array) only diagnose ~40% of fetuses showing ultrasound abnormalities. Rapid exome sequencing (rES) may improve this diagnostic yield, but includes challenges such as uncertainties in fetal phenotyping, variant interpretation, incidental unsolicited findings, and rapid turnaround times. In this study, we implemented rES in prenatal care to increase diagnostic yield.

Methods

We prospectively studied 55 fetuses. Inclusion criteria were: (a) two or more independent major fetal anomalies, (b) hydrops fetalis or bilateral renal cysts alone, or (c) one major fetal anomaly and a first-degree relative with the same anomaly. In addition to conventional genetic tests, we performed trio rES analysis using a custom virtual gene panel of ~3850 Online Mendelian Inheritance in Man (OMIM) genes.

Results

We established a genetic rES-based diagnosis in 8 out of 23 fetuses (35%) without QF-PCR or array abnormalities. Diagnoses included MIRAGE (SAMD9), Zellweger (PEX1), Walker-Warburg (POMGNT1), Noonan (PTNP11), Kabuki (KMT2D), and CHARGE (CHD7) syndrome and two cases of Osteogenesis Imperfecta type 2 (COL1A1). In six cases, rES diagnosis aided perinatal management. The median turnaround time was 14 (range 8-20) days.

Conclusion

Implementing rES as a routine test in the prenatal setting is challenging but technically feasible, with a promising diagnostic yield and significant clinical relevance.     

Prenatal diagnosis of X-linked hydrocephalus in a Chinese family with four successive affected pregnancies

We report on a woman with four successive pregnancies affected with X-linked hydrocephalus (XLH). The first child had prenatal craniocentesis and died in utero. The second child had a postnatal shunting operation, but suffers from severe growth and mental retardation at 5 years of age. In the third pregnancy, prenatal ultrasound detected hydrocephalus at the 16th and 20th weeks of gestation and the pregnancy was terminated. In the fourth pregnancy, ultrasound scanning at the 17th and 20th weeks of gestation revealed no remarkable findings, but hydrocephalus was detected at the 24th week. Autopsy confirmed the prenatal diagnosis. DNA polymorphism analysis of the Bell site of exons 17–18 of factor VIII gene of the woman and her last two fetuses seemed to be compatible with a linkage between the XLH locus and factor VIII gene. Although XLH has a variable presentation of ventriculomegaly, ultrasound scanning is still a useful tool for prenatal diagnosis at present. Earlier and more accurate prenatal diagnosis will be feasible with molecular analysis of the XLH locus or its flanking regions.     

Fetal hydrops caused by a novel pathogenic MECOM variant

We report a fetus with hydrops, congenital heart disease and bilateral radioulnar synostosis caused by a novel pathogenic MECOM variant. The female fetus was referred for post-mortem examination after fetal hydrops and intrauterine death was diagnosed at 20 weeks gestation. Post-mortem examination confirmed fetal hydrops, pallor, truncus arteriosus and bilateral radioulnar synostosis. Trio whole genome sequencing analysis detected a novel de novo heterozygous pathogenic loss-of-function variant in MECOM (NM_004991), associated with a diagnosis of Radioulnar Synostosis with Amegakaryocytic Thrombocytopenia 2 (RUSAT-2). RUSAT-2 is a variable condition associated postnatally with bone marrow failure, radioulnar synostosis and congenital anomalies. RUSAT-2 is not currently associated with a prenatal phenotype or fetal demise, and was not present on diagnostic NHS prenatal gene panels at time of diagnosis. This case highlights the diagnostic value of detailed phenotyping with post-mortem examination, and of using a broad sequencing approach.     

First application of preimplantation genetic diagnosis to neurofibromatosis type 2 (NF2)

Neurofibromatosis type 2 (NF2) is a dominantly inherited cancer predisposition syndrome that is caused bymutations in the NF2 gene. We report here the first clinical preimplantation genetic diagnosis (PGD) forNF2. A protocol was developed to simultaneously amplify the mutation and a single nucleotide polymorphism (SNP) located within the gene. The mutation and polymorphism were analysed by simultaneous fluorescent single-strand conformation polymorphism (SSCP) on an automated DNA sequencer. The mutation, carried by the male partner, was a single base pair substitution affecting a splice site in intron 4 of the gene. The female partner was infertile due to polycystic ovary syndrome and would require IVF to conceive. The couple was found to be informative at a linked intragenic SNP situated in the 5′ untranslated region of the gene. The SNP was included in the assay to reduce the risk of misdiagnosis due to allele dropout (ADO). The couple underwent three cycles of treatment during which a total of 43 blastomeres were biopsied from 31 embryos. Amplification at both loci was obtained in 35 cells (81%). A total of five embryos were transferred, two in the first cycle, two in the second and one in the third. No pregnancy ensued. The results of the diagnoses indicated that, in this couple, the inheritance of the mutation may be non-Mendelian. Out of a total of 32 embryos tested only four were found not to carry the mutation. The reasons for this apparent skew remain unknown. Copyright © 2002 John Wiley & Sons, Ltd.     

Prenatal diagnosis of multiple acyl-CoA dehydrogenase deficiency: association with elevated α-fetoprotein and cystic renal changes

We report the occurrence of multiple acyl-CoA dehydrogenase deficiency (MADD) in two consecutive pregnancies in a young, Caucasian, non-consanguineous couple. In the first pregnancy, the maternal serum α-fetoprotein was elevated. A sonogram showed growth delay, cystic renal disease, and oligohydramnios; the parents decided to terminate the pregnancy. Postmortem examination confirmed the cystic renal disease and showed hepatic steatosis, raising the suspicion of a metabolic disorder. The diagnosis of MADD was made by immunoblot studies on cultured fibroblasts. In the subsequent pregnancy, a sonogram at 15 weeks' gestation showed an early growth delay but normal kidneys. The maternal serum and amniotic fluid concentrations of α-fetoprotein were elevated, and the amniotic fluid acylcarnitine profile was consistent with MADD. In vitro metabolic studies on cultured amniocytes confirmed the diagnosis. A follow-up sonogram showed cystic renal changes. These cases provide additional information regarding the evolution of renal changes in affected fetuses and show a relationship with elevated α-fetoprotein, which may be useful in counseling the couple at risk. MADD should be considered in the differential diagnosis of elevated α-fetoprotein and cystic renal disease. Early growth delay may be an additional feature. Copyright © 2001 John Wiley & Sons, Ltd.     

Prenatal diagnosis in a family with X-linked hydrocephalus

The neural cell adhesion molecule L1 is a transmembrane glycoprotein belonging to the immunoglobulin superfamily of cell adhesion molecules (CAMs). Its expression is essential during embryonic development of the nervous system and it is involved in cognitive function and memory. Mutations in the L1CAM gene are responsible for four related L1 disorders; X-linked hydrocephalus/HSAS (H ydrocephalus as a result of S tenosis of the A queduct of S ylvius), MASA (M ental retardation, A phasia, S huffling gait, and A dducted thumbs) syndrome, X-linked complicated spastic paraplegia type I (SPG1) and X-linked A genesis of the C orpus C allosum (ACC). These four disorders represent a clinical spectrum that varies both between and within families. The main clinical features of this spectrum are C orpus callosum hypoplasia, mental R etardation, A dducted thumbs, S pastic paraplegia and H ydrocephalus (CRASH syndrome). Since there is no biochemically assayed disease marker, molecular analysis of the L1CAM gene is the only means of confirming a clinical diagnosis. Most L1CAM mutations reported to date are point mutations (missense, nonsense, splice site) and only a few patients with larger rearrangements have been documented. We have characterised a rare intragenic deletion of the L1CAM gene in a sample of DNA extracted from a chorionic villus biopsy (CVB) performed at 12 weeks' gestation. Copyright © 2005 John Wiley & Sons, Ltd.     

Prenatal diagnosis of fetal glioblastoma multiforme

Intracerebral tumours of the fetus are very rare conditions, most often presenting clinically as polyhydramnios and hydrocephalus. These conditions can be diagnosed with ultrasound and clearly differentiated from hydrocephalus and other intracranial lesions. The following report is of a case of an intracerebral tumour (glioblastoma multiforme) diagnosed at 33 weeks in utero using ultrasound. The prognosis for this condition is universally poor.     

Prenatal molecular diagnosis in RASA1-related disease

RASA1-related disease is a rare autosomal dominant disease characterized by capillary malformations, arteriovenous malformations (AVMs), and/or arteriovenous fistulas (AFVs). Penetrance is nearly complete and vascular malformations may cause serious complications such as organ injury due to oxygenation disorder, brain abscess, hemorrhage, and stroke. Early diagnosis is useful in order to discuss optimal management, including AVMs/AVFs embolization or surgical procedures, and try to prevent some of the complications. In this context, molecular testing of RASA1 gene mutation in relatives may help to better manage the family. All arteriovenous malformations are however not accessible to such procedures. In addition, these therapeutic procedures may result in potential side effects and complications. A couple was referred to our genetics unit and asked us for prenatal genetic testing about a RASA1 mutation. Here, we discuss about arguments that led our team to accept prenatal testing. To the best of our knowledge, no molecular prenatal diagnosis was reported until now in RASA1-related diseases. This first report of prenatal diagnosis in RASA1-related diseases may also offer perspectives for a more general discussion in the field of inherited arteriovenous malformations.     

Two unrelated fetuses with ITPR1 missense variants and fetal hydrops

We describe two fetuses from unrelated families with likely pathogenic variants in ITPR1 that presented with nonimmune fetal hydrops. Trio exome sequencing revealed a de novo heterozygous likely pathogenic missense variant c.7636G > A (p.Val2531Met) in ITPR1 (NM_001378452.1) in proband 1 and a de novo heterozygous likely pathogenic missense variant c.34G > A [p.Gly12Arg] in proband 2. Variants in ITPR1 have been associated with several genetic conditions, including spinocerebellar ataxia 15, spinocerebellar ataxia 29, and Gillespie syndrome. Our report on two patients details a previously undescribed severe fetal presentation of nonimmune hydrops fetalis associated with missense variants in the ITPR1 gene.     

Microalgae cultivation using an aquaculture wastewater as growth medium for biomass and biofuel production

Microalgae as a main feedstock has attracted much attention in recent years but is still not economically feasible due to high algal culture cost. The objective of this study was to develop a comprehensive eco-friendly technology for cultivating microalgae Platymonas subcordiformis using aquaculture wastewater as growth medium for biomass and biofuel production. Platymonas subcordiformis was grown in pretreated flounder aquaculture wastewaters taken from different stages. Each of wastewater contained different levels of nutrients. The biomass yield of microalgae and associated nitrogen and phosphorous removal were investigated. The results showed that algal cell density increased 8.9 times than the initial level. Platymonas subcordiformis removed nitrogen and phosphorus from wastewater with an average removal efficiency of 87%-95% for nitrogen and 98%-99% for phosphorus. It was feasible to couple the removal of nitrogen and phosphorus from wastewater to algal biomass and biofuel production. However, further studies are required to make this technologies economically viable for algae biofuel production.     

Prenatal diagnosis of a craniopharyngioma using ultrasonography and magnetic resonance imaging

We report an infant with a craniopharyngioma which was detected in utero. Maternal uterine ultrasonography, done at 27 weeks because of polyhydramnios, revealed a 4 cm midline mass near the base of the fetal skull. At 31 weeks, magnetic resonance imaging of the maternal abdomen confirmed the presence of a mass in the region of the third ventricle and revealed hydrocephalus. Two days post-partum a computed tomography (CT)-guided needle biopsy of the mass was performed and recovered tissue which was histologically consistent with a craniopharyngioma. The infant' s postnatal period was complicated by seizures, which were treated with phenobarbital, and by progressive hydrocephalus, necessitating placement of a ventriculo-peritoneal shunt. He also received therapy for central hypothyroidism and diabetes insipidus. The infant' s parents refused permission for attempted resection of the tumour and he died at 8 weeks of age. This represents the second reported case of an antenatally detected craniopharyngioma. Four other cases of different intracranial tumours have been detected in utero using ultrasound, with no reported survivors past 3 days of age. There is a uniformly poor prognosis of such infants, but earlier diagnosis and intervention may change this result.     

Non-invasive prenatal testing (NIPT): Combination of copy number variant and gene analyses using an “in-house” target enrichment next generation sequencing—Solution for non-centralized NIPT laboratory?

Objective

Recent studies have integrated copy number variant (CNV) and gene analysis using target enrichment. Here, we transferred this concept to our routine genetics laboratory, which is not linked to centralized non-invasive prenatal testing (NIPT) facilities.

Method

From a cohort of 100 pregnant women, 22 were selected for the analysis of maternal genomic DNA (gDNA) along with fetal cell-free DNA. Using targeted enrichment, 135 genes were analyzed, combined with aberrations of chromosomes 21, 18, 13, X, and Y. The data were subjected to specificity and sensitivity analyses, and correlated with the results from invasive testing methods.

Results

The sensitivity/specificity was determined for the CNV analysis of chromosomes: 21 (80%/75%), 18 (-/82%), 13 (100%/67%), and Y (100%/100%). The gene detection was valid for maternal gDNA. However, for cell-free fetal DNA, it was not possible to determine the boundary between an artifact and a real sequence variant.

Conclusion

The target enrichment method combining CNV and gene detection seems feasible in a regular laboratory. However, this method can only be responsibly optimized with a sufficient number of controls and further validation on a strong bioinformatic background. The present results showed that NIPT should be performed in specialized centers, and that its introduction to isolated laboratories may not provide valid data.     

Prenatal diagnosis of SMPD4 loss - A neurodevelopmental disorder with microcephaly,arthrogryposis and structural brain anomalies

SMPD4 loss is a rare neurodevelopmental disorder that leads to severe mental and physical disability and early death in infancy. Most cases of this genetic condition have been diagnosed postnatally. This article focuses on the prenatal findings of affected fetuses. The phenotypes can include growth restriction, arthrogryposis (clenched hands, foot deformity), as well as cerebral abnormalities (simplified gyral pattern/lissencephaly, cerebellar hypoplasia, corpus callosum deformity). SMPD4 loss is detectable via exome sequencing. Here, two fetuses displayed a homozygotic pathogen variant in the SMPD4 gene, encoding for the enzyme Sphingomyelinase-4. Both parents were heterozygous carriers of the pathogenic variant. On detection of the above mentioned signs exome sequencing is indicated, with focus on the SMPD4 gene.     

Prenatal diagnosis of GM2-gangliosidosis B1 variant

Prenatal diagnosis in a pregnancy at risk for a juvenile B1 variant of GM₂-gangliosidosis was carried out. The biochemical study of the cultured amniocytes and the affected fetal brain is reported. The results obtained show that the sulphated artificial substrate can be used in the diagnosis of B1 variant, but not the neutral one. The accumulation of GM₂-ganglioside in the fetal brain of the B1 juvenile form and an infantile form of GM₂-gangliosidosis (0 variant) was compared.