Noninvasive prenatal screening for cystic fibrosis using circulating trophoblasts: Detection of the 50 most common disease-causing variants

Objectives

Cystic fibrosis (CF) is one of the most common severe autosomal recessive disorders. Prenatal or preconception CF screening is offered in some countries. A maternal blood sample in early pregnancy can provide circulating trophoblasts and offers a DNA source for genetic analysis of both the mother and the fetus. This study aimed to develop a cell-based noninvasive prenatal test (NIPT) to screen for the 50 most common CF variants.

Methods

Blood samples were collected from 30 pregnancies undergoing invasive diagnostics and circulating trophoblasts were harvested in 27. Cystic fibrosis testing was conducted using two different methods: by fragment length analysis and by our newly developed NGS-based CF analysis.

Results

In all 27 cases, cell-based NIPT provided a result using both methods in agreement with the invasive test result.

Conclusion

This study shows that cell-based NIPT for CF screening provides a reliable result without the need for partner- and proband samples.     

Prenatal diagnosis in a female carrying a deletion close to the duchenne locus

Family studies including the proband are usually needed before a prenatal diagnosis may be performed for Duchenne muscular dystrophy. We report here on prenatal diagnosis in a family where the solitary index case was dead, and where the consultand and her mother were assumed to be carriers by independent evidence. DNA anaylsis revealed that both the consultand and her mother had an X chromosome deleted for DNA material in the Xp21 region. The female fetus also carried the deleted X chromosome.     

Female pseudohermaphroditism in a fetus with a deletion 9(q22.2q31.1)

Interstitial deletions of chromosomal region 9q are rarely seen. We report the first prenatal diagnosis of a de novo interstitial deletion 9q. The fetus was karyotyped for intrauterine growth retardation (IUGR). Conventional and molecular cytogenetics showed female karyotype with a de novo deletion of the chromosomal region 9(q22.2q31.1) leading to a partial monosomy 9q. At autopsy, the fetus showed growth retardation, dysmorphy, and a female pseudohermaphroditism. These results suggest that a gene(s) for genital development reside in chromosomal region 9q22.2q31.1. Copyright © 2002 John Wiley & Sons, Ltd.     

Prenatal diagnosis of monosomy 4p14→pter and trisomy 11q25→qter: clinical presentations and outcomes

We present the case of a pregnant woman with low free β-HCG in maternal serum Down syndrome screening that led to prenatal diagnosis of a fetus with 46,XY,der(4)t(4;11)(p14; q25). This chromosomal aneuploidy resulted from unbalanced segregation of a paternal balanced translocation, t(4;11)(p14;q25). Prenatal ultrasound revealed intrauterine growth restriction, cleft lip and palate, a thick nuchal fold, a single umbilical artery, and pyelectasis. Array-based comparative genomic hybridization and short tandem repeat markers further located the exact breakpoint of translocation. The woman had her pregnancy terminated at 23 weeks of gestational age. The proband had general appearance of Wolf–Hirschhorn syndrome and some unique findings, including single umbilical artery, severe immunoglobulin deficiency, scalp defect, and underlying bony defect. Our case underscores the importance of fetal karyotyping when low maternal serum free β-HCG is found. It also adds information on the fetal presentations of monosomy 4p14→pter and trisomy 11q25→qter. Copyright © 2005 John Wiley & Sons, Ltd.     

Prenatal diagnosis of Pelizaeus-Merzbacher disease: detection of proteolipid protein gene duplication by quantitative fluorescent multiplex PCR

A prenatal diagnosis of Pelizaeus-Merzbacher disease (PMD) resulting from proteolipid protein gene (PLP) duplication was performed by a quantitative fluorescent multiplex PCR method. PLP gene copy number was determined in the proband, the pregnant mother, the male fetus and two aunts. Small amounts of genomic DNA extracted from peripheral blood and from chorionic villi were used. The fetus, in common with the proband, was identified as PMD-affected being a carrier of the PLP gene duplication, inherited from the mother, while the two aunts were non-carriers. The data obtained were confirmed by segregation analysis of a PLP-associated dinucleotide-repeat polymorphism amplified by the same multiplex PCR. Copyright © 2001 John Wiley & Sons, Ltd.     

Double-outlet right ventricle with absent left ventricle and mitral atresia in a fetus with a deletion 22q12

Interstitial deletions of chromosomal region 22q12 are rare. We report the prenatal diagnosis of a de novo interstitial deletion 22q12. The fetus was karyotyped because of a complex cardiac anomaly. Conventional and molecular cytogenetics showed a female karyotype with a de novo pericentric inversion of one chromosome 22 associated with a deletion of the chromosomal region 22q12 leading to a partial monosomy 22q12. At autopsy, the fetus showed double-outlet right ventricle (DORV) with absent left ventricle and mitral atresia. This observation suggests that one or several genes for the early looping step of heart development may reside in chromosomal region 22q12. Further studies are needed to identify these genes, and to search microdeletions of 22q12 region in patients with DORV. Copyright © 2004 John Wiley & Sons, Ltd.     

Prenatal diagnostic testing for familial dysautonomia using linked genetic markers

Familial dysautonomia (FD), a recessively inherited disease, has been mapped to chromosome 9q31. Highly polymorphic dinucleotide repeat markers flanking the genetic locus and at the same genetic location have been identified. We describe the prenatal diagnosis of FD using linkage and linkage disequilibrium analyses with these markers. Twelve families were analysed for informativeness and of these, seven went on to have prenatal testing (a total of eight fetuses tested). All of these fetuses were predicted to be heterozygous unaffected (FD carriers). Seven fetuses have come to term and are normal. In the absence of a recombinant proband, a panel of three proximal and three distal markers is sufficient to provide informative flanking markers and an 87–96 per cent likelihood of a highly predictive test. In an additional family at 1:4 risk for FD, no DNA was available from the propositus. This family was analysed using linkage disequilibrium to the #18 allele of the tightly linked marker D9S58 in conjunction with linkage analysis using data from two unaffected children. Prenatal diagnosis in this family indicated an affected fetus.     

DNA-based prenatal carrier detection for group a xeroderma pigmentosum in a chorionic villus sample

DNA-based prenatal carrier detection of group A xeroderma pigmentosum (XP-A) is reported. Chorionic villus sampling was done at the tenth gestational week in a pregnant woman whose first child suffers from XP-A. Genomic DNAs from the villi, proband, and parents were PCR (polymerase chain reaction)-amplified using three sets of primers, because the PCR and a subsequent enzyme digestion with HphI, AlwNI, or MseI may detect the three most frequent mutations of the XP-A complementing gene (XPAC) in Japanese XP-A patients. The results showed that the proband is a homozygote and that the parents and fetus are heterozygotes for a base substitution at the 3′ acceptor site of intron 3 of XPAC, indicating that the fetus is a healthy carrier of XP-A. This is the first case of prenatal carrier detection of the disorder.     

Prenatal molecular diagnosis of gaucher disease

Prenatal diagnosis of Gaucher disease, the most prevalent glycolipid storage disease, is based on a reliable enzyme assay of cells from amniocentesis or chorionic villous samples. However, this method cannot differentiate among the various forms of the disease. This report details four cases of prenatal diagnosis of Gaucher disease, three of which predate the use of molecular diagnosis. DNA mutation analysis to determine the genotype was predictive of the phenotypic status of the fetus and conformed to the genotype of an affected proband where available.     

Prenatal diagnosis of primary anophthalmia with a 3q27 interstitial deletion involving SOX2

We report an interstitial deletion of chromosome 3q26-q28 in a fetus in which anophthalmia had been detected prenatally. FISH analysis, using BAC clones encompassing the SOX2 locus, showed that SOX2 gene was involved in the chromosomal breakpoint of the deletion. This case confirms that haploinsufficiency for SOX2 plays a crucial role in human eye development and emphasizes the necessity of careful chromosomal analysis, including FISH analysis of the 3q region, in case of prenatal discovery of anophthalmia. Copyright © 2004 John Wiley & Sons, Ltd.     

Resolution of DNA linkage discrepancies through analysis of a VNTR locus in a family study of cystic fibrosis

First-trimester prenatal diagnosis of a fetus at 25 per cent risk for cystic fibrosis (CF) was performed by indirect linkage analysis of polymorphic markers using Southern blotting and polymerase chain reaction (PCR) amplification. The results revealed discrepancies in the allelic patterns between the father and the affected child, thereby complicating the prediction of fetal outcome. Analysis of a highly polymorphic VNTR locus within the human retinoblas-toma (RB) gene on chromosome 13 showed that the affected child and the fetus did not have the same biological father, and therefore the affected child could not be used to determine linkage of markers in the father of the fetus. The analysis of VNTR loci can be an effective method of resolving conflicting data during prenatal diagnosis of monogenic diseases.     

Prenatal diagnosis of jumping translocation involving chromosome 22 with ultrasonographic findings

We report on the prenatal diagnosis and ultrasonographic findings of a second-trimester fetus with jumping translocation involving chromosome 22. A 28-year-old gravida 2, partus 1, Turkish woman was referred for genetic counselling and ultrasonographic examination at 18 weeks' gestation because of a high risk of trisomy 21 in triple test. Prenatal ultrasonography showed tetralogy of Fallot with a diverticular dilatation of the pulmonary artery, flattened brow, complete absence of the right upper limb, hypospadias, oligodactyly (three digits) in left hand and in both feet, and hyperechogenic abdominal foci. Amniocentesis revealed a karyotype of 46,XY[4]/46,XY,−8,+ der(8),t(8;22)(q24.3;q11.21)[2]/45, XY,−22,−8,+ der(8)t(8;22)(q24.3;q11.21)[22]/45,XY,−22,−5,+ der(5)t(5;22)(q35.3;q11.21)[44]. A C-banding and FISH study with a specific centromeric probe (D14Z1/D22Z1) for chromosome 22 was made. In our case, partial monosomy for the regions 22q11.21→22pter, 8q24.3→8qter and 5q35.3→5qter may partially explain the fetal malformations. Copyright © 2005 John Wiley & Sons, Ltd.     

Fetal translocation between chromosomes 2, 18, and 21 resolved by fish

An apparently balanced t(2q;21q) translocation was discovered in fetal blood and amniocytes of a 22-week fetus, monitored because of ultrasonographic evidence of a heart disease. FISH (fluorescence in situ hybridization) analysis disclosed a complex translocation between chromosomes 2q, 18q, and 21q, which was inherited from the healthy mother. This observation corroborates the usefulness of molecular cytogenetic techniques in raising the quality of prenatal diagnosis and detecting subtle rearrangements not resolved by standard cytogenetics.     

Trisomy 15 mosaicism owing to familial reciprocal translocation t(1;15): implication for prenatal diagnosis

We describe a 4-year-old female child with severe global mental retardation, myoclonic epilepsy, proximal hypotonia and dysmorphisms, whose prenatal diagnosis following amniocentesis revealed a constitutional female karyotype carrying a t(1;15)(q10;p11) familial reciprocal translocation. Post-natal high-resolution karyotype, Fluorescence in situ hybridization (FISH) screening for subtelomeric rearrangements, VNTR search for UPD15 in the blood and fibroblast, and WCP1 and 15 in the mother, failed to provide an explanation for the complex clinical phenotype of the proband. Since the pachytene configuration of the translocated chromosomes defines a high probability of 3:1 segregation, an extensive workup was undertaken to look for a possibly cryptic mosaicism. Four percent of the cells with trisomy 15 was found in the peripheral blood lymphocytes examined by classical cytogenetic technique and interphase FISH analysis. The clinical features associated with cryptic trisomy 15 mosaicism and the problems concerning prenatal diagnosis and genetic counselling for carriers of translocations at high risk of 3:1 segregation are discussed. Copyright © 2006 John Wiley & Sons, Ltd.     

Prenatal diagnosis of de novo distal 11q deletion associated with sonographic findings of unilateral duplex renal system,pyelectasis and orofacial clefts

In utero diagnosis of de novo distal 11q deletion associated with renal and orofacial malformations has not been previously described. We present a 35-year-old pregnant woman with prenatal sonographic findings of a unilateral duplex renal system, pyelectasis and orofacial clefts at 20 weeks' gestation. Both genetic amniocentesis and postnatal cytogenetic analysis revealed de novo 46,XX,del(11)(q23). After birth, the fetus manifested a dysmorphic phenotype correlated with del(11q) syndrome. Genetic marker analysis showed a paternally derived distal deletion of chromosome 11q and a breakpoint centromeric to D11S1341. The present case represents the earliest prenatal diagnosis of a duplex renal system, pyelectasis and an additional feature of orofacial clefts associated with distal 11q deletion. Prenatal sonographic detection of a duplex renal system, pyelectasis and orofacial clefts should warrant a careful assessment of fetal anatomy and prompt cytogenetic analysis looking for chromosomal aberrations. Copyright © 2001 John Wiley & Sons, Ltd.     

Neuropsychiatric aspects of 22q11.2 deletion syndrome: considerations in the prenatal setting

Most major neuropsychiatric outcomes of concern to families are not detectable by prenatal ultrasound. The introduction of genome-wide chromosomal microarray analysis to prenatal clinical diagnostic testing has increased the detection of pathogenic 22q11.2 deletions, which cause the most common genomic disorder. The recent addition of this and other microdeletions to non-invasive prenatal screening methods using cell-free fetal DNA has further propelled interest in outcomes. Conditions associated with 22q11.2 deletions include intellect ranging from intellectual disability to average, schizophrenia and other treatable psychiatric conditions, epilepsy, and early-onset Parkinson's disease. However, there is currently no way to predict how severe the lifetime expression will be. Available evidence suggests no major role in these neuropsychiatric outcomes for the congenital cardiac or most other structural anomalies that may be detectable on ultrasound. This article provides an outline of the lifetime neuropsychiatric phenotype of 22q11.2 deletion syndrome that will be useful to clinicians involved in prenatal diagnosis and related genetic counselling. The focus is on information that will be most relevant to two common situations: detection of a 22q11.2 deletion in a fetus or newborn, and new diagnosis of 22q11.2 deletion syndrome in a parent without a previous molecular diagnosis. © 2016 John Wiley & Sons, Ltd.     

Short-term outcome after the prenatal diagnosis of right aortic arch

Objectives

To determine the proportion of children that require surgery in the first year of life and thereafter in order to improve the counseling of parents with a fetus with a right aortic arch (RAA).

Methods

Fetuses diagnosed with isolated RAA, defined as the absence of intra- or extracardiac anomalies, between 2007 and 2021 were extracted from the prospective registry PRECOR.

Results

In total, 110 fetuses were included, 92 with a prenatal diagnosis of RAA and 18 with double aortic arch (DAA). The prevalence of 22q11 deletion syndrome was 5.5%. Six pregnancies were terminated and five cases were false-positive; therefore, the follow-up consisted of 99 neonates. Surgery was performed in 10 infants (10%) in the first year of life. In total, 25 (25%) children had surgery at a mean age of 17 months. Eight of these 25 (32%) had a DAA. Only one child, with a DAA, required surgery in the first week of life due to obstructive stridor.

Conclusions

Children with a prenatally diagnosed RAA are at a low risk of acute respiratory postnatal problems. Delivery in a hospital with neonatal intensive care and pediatric cardiothoracic facilities seems only indicated in cases with suspected DAA. Expectant parents should be informed that presently 25% of the children need elective surgery and only incidentally due to acute respiratory distress.     

Non-invasive fetal genotyping for maternal alleles with droplet digital PCR: A comparative study of analytical approaches

Objectives

To develop a flexible droplet digital PCR (ddPCR) workflow to perform non-invasive prenatal diagnosis via relative mutation dosage (RMD) for maternal pathogenic variants with a range of inheritance patterns, and to compare the accuracy of multiple analytical approaches.

Methods

Cell free DNA (cfDNA) was tested from 124 archived maternal plasma samples: 88 cases for sickle cell disease and 36 for rare Mendelian conditions. Three analytical methods were compared: sequential probability ratio testing (SPRT), Bayesian and z-score analyses.

Results

The SPRT, Bayesian and z-score analyses performed similarly well with correct prediction rates of 96%, 97% and 98%, respectively. However, there were high rates of inconclusive results for each cohort, particularly for z-score analysis which was 31% overall. Two samples were incorrectly classified by all three analytical methods; a false negative result predicted for a fetus affected with sickle cell disease and a false positive result predicting the presence of an X-linked IDS variant in an unaffected fetus.

Conclusions

ddPCR can be applied to RMD for diverse conditions and inheritance patterns, but all methods carry a small risk of erroneous results. Further evaluation is required both to reduce the rate of inconclusive results and explore discordant results in more detail.