Non-invasive prenatal diagnosis of single gene disorders by paternal mutation exclusion: 3 years of clinical experience

Application of Digital Polymerase Chain Reaction (dPCR) in Non-Invasive Prenatal Testing (NIPT)

This article reviews the current applications of the digital polymerase chain reaction (dPCR) in non-invasive prenatal testing (NIPT) and explores its potential to complement or surpass the capabilities of Next-Generation Sequencing (NGS) in prenatal testing. The growing incidence of genetic disorders in maternal-fetal medicine has intensified the demand for precise and accessible NIPT options, which aim to minimize the need for invasive prenatal diagnostic procedures. Cell-free fetal DNA (cffDNA), the core analyte in NIPT, is influenced by numerous factors such as maternal DNA contamination, placental health, and fragment degradation. dPCR, with its inherent precision and ability to detect low-abundance targets, demonstrates robustness against these interferences. Although NGS remains the gold standard due to its comprehensive diagnostic capabilities, its high costs limit widespread use, particularly in resource-limited settings. In contrast, dPCR provides comparable accuracy with lower complexity and expense, making it a promising alternative for prenatal testing.

Foetal achondroplasia: Prenatal diagnosis, outcome and perspectives

BACKGROUND

Achondroplasia, due to a specific pathogenic variant in FGFR3, is the most common viable skeletal dysplasia and the diagnosis is mostly done in the prenatal period. Since 2021, the use of Vosoritide, a specific treatment for achondroplasia, validated in phase 3 placebo-controlled trials, has been recommended to significantly increase the height of children and infants. In the light of these new therapeutic prospects, a complete understanding of the pathophysiology of skeletal damages occurring from foetal life is required.

OBJECTIVES

To describe foetal imaging and the antenatal and postnatal management of pregnancies complicated by a diagnosis of foetal achondroplasia.

METHODS

A retrospective and descriptive study, including all pregnant women with a prenatal diagnosis of achondroplasia, was conducted in the prenatal unit of Necker Hospital (Paris, France) between 2009 and 2022. Maternal and obstetric characteristics and foetal imaging (ultrasound and bone CT) were collected. Pregnancy outcomes, paediatric follow-up in the case of live births, and post-mortem examination (PME) data in the case of termination of pregnancy were reported. In addition, we have prospectively developed a specific research protocol using foetal brain MRI to assess the anatomy of the foramen magnum, following the same approach currently recommended in the postnatal period.

RESULTS

29 cases of achondroplasia were included. Median gestational age at referral was 31+2 weeks', about 1 week after the suspected diagnosis on routine ultrasound. Shortening of the femoral length and of all the other long bones, macrocephaly, facial abnormalities, increased metaphyseal-diaphyseal angle and tapering of the proximal femoral bone were the five most prevalent ultrasound signs. Foetal diagnosis was done by the identification of the foetal FGFR3 mutation and/or by CT scans (n = 15) where specific abnormalities of the long bones, platyspondyly and abnormal profile have been described in 100 % of cases. PME revealed: i) on external examinations (n = 7) that all fetuses had very short long bones, moderate platyspondyly, small iliac wings with internal spines, macrocrania, and narrow thorax, ii) on internal examination (n = 5) all had severe abnormalities in the growth plate and particularities in the temporal cortex and hippocampal region. One foetal MRI was performed at 33 weeks' and revealed tight stenosis of the foramen magnum and compression of the spinal cord. Of the live-born infants for whom follow-up was known (n = 6), 2/6 (including the case who had a foetal MRI) required neurosurgical intervention in the first few months of life for spinal cord compression due to severe stenosis of the foramen magnum.

CONCLUSION

A complete mapping of the skeletal features present in foetuses with achondroplasia is reported here, providing a better understanding of the pathophysiology of this condition. New tools such as foetal MRI, to assess the risk of postnatal severe neurological complications, could help improve the care pathway of the affected neonates.

Noninvasive screening of fetal RHD genotype in Chinese pregnant women with serologic RhD-negative phenotype

BACKGROUND

Noninvasive fetal RHD genotyping has been provided to nonimmunized RhD-negative pregnant women to guide anti-D prophylaxis. Among the Chinese, more than 30% of the RhD-negative phenotype is associated with variant RHD alleles, which would limit the accuracy of fetal RHD status prediction; thus, more targeting and proper programs need to be developed.

STUDY DESIGN AND METHODS

Fluorescence quantitative polymerase chain reaction PCR (qPCR) or Sanger sequencing on all RHD exons was used to detect maternal RHD genotypes. For pregnant women with RHD*01N.01 or RHD*01N.03 alleles, the presence of RHD exons 5 and 10 in cell-free DNA was determined by qPCR. For pregnant women with the RHD(1227G>A) allele, high-throughput sequencing on exon 9 of the RHD gene and RHCE gene was used to predict fetal RhD phenotype.

RESULTS

Among 65 cases of Chinese pregnant women with the serologic RhD-negative phenotype, three major genotypes were identified: RHD*01N.01/RHD*01N.01 (61.5%), RHD*01N.01/RHD(1227G>A) or RHD*01N.03/RHD(1227G>A) (20%), and RHD*01N.01/RHD*01N.03 (13.8%), along with three cases of minor genotypes (4.6%). For 43 pregnant women with the RHD*01N.01 or RHD*01N.03 alleles, qPCR on maternal cell-free DNA yielded a 98.5% (42/43) accuracy rate and 100% successful prediction rate. High-throughput sequencing was successfully used to predict fetal RhD phenotypes for 13 pregnant women with RHD(1227G>A).

CONCLUSION

On the basis of maternal RHD genotyping, fetal genotyping through qPCR or high-throughput sequencing can improve the accuracy and success rate of prenatal fetal RhD phenotype prediction among Chinese pregnant women. It plays a potential role in guiding anti-D prophylaxis and pregnancy management in Chinese pregnant women.

Non-invasive prenatal diagnosis (NIPD): current and emerging technologies

Prenatal testing is important for the early detection and diagnosis of rare genetic conditions with life-changing implications for the patient and their family. Gaining access to the fetal genotype can be achieved using gold-standard invasive sampling methods, such as amniocentesis and chorionic villus sampling, but these carry a small risk of miscarriage. Non-invasive prenatal diagnosis (NIPD) for select rare monogenic conditions has been in clinical service in England since 2012 and has revolutionised the field of prenatal diagnostics by reducing the number of women undergoing invasive sampling procedures. Fetal-derived genomic material is present in a highly fragmented form amongst the maternal cell-free DNA (cfDNA) in circulation, with sequence coverage across the entire fetal genome. Cell-free fetal DNA (cffDNA) is the foundation for NIPD, and several technologies have been clinically implemented for the detection of paternally inherited and de novo pathogenic variants. Conversely, a low abundance of cffDNA within a high background of maternal cfDNA makes assigning maternally inherited variants to the fetal fraction a significantly more challenging task. Research is ongoing to expand available tests for maternal inheritance to include a broader range of monogenic conditions, as well as to uncover novel diagnostic avenues. This review covers the scope of technologies currently clinically available for NIPD of monogenic conditions and those still in the research pipeline towards implementation in the future.

Non-invasive prenatal diagnosis (NIPD): how analysis of cell-free DNA in maternal plasma has changed prenatal diagnosis for monogenic disorders

Cell-free fetal DNA (cffDNA) is released into the maternal circulation from trophoblastic cells during pregnancy, is detectable from 4 weeks and is representative of the entire fetal genome. The presence of this cffDNA in the maternal bloodstream has enabled clinical implementation of non-invasive prenatal diagnosis (NIPD) for monogenic disorders. Detection of paternally inherited and de novo mutations is relatively straightforward, and several methods have been developed for clinical use, including quantitative polymerase chain reaction (qPCR), and PCR followed by restriction enzyme digest (PCR-RED) or next-generation sequencing (NGS). A greater challenge has been in the detection of maternally inherited variants owing to the high background of maternal cell-free DNA (cfDNA). Molecular counting techniques have been developed to measure subtle changes in allele frequency. For instance, relative haplotype dosage analysis (RHDO), which uses single nucleotide polymorphisms (SNPs) for phasing of high- and low-risk alleles, is clinically available for several monogenic disorders. A major drawback is that RHDO requires samples from both parents and an affected or unaffected proband, therefore alternative methods, such as proband-free RHDO and relative mutation dosage (RMD), are being investigated. cffDNA was thought to exist only as short fragments (<500 bp); however, long-read sequencing technologies have recently revealed a range of sizes up to ∼23 kb. cffDNA also carries a specific placental epigenetic mark, and so fragmentomics and epigenetics are of interest for targeted enrichment of cffDNA. Cell-based NIPD approaches are also currently under investigation as a means to obtain a pure source of intact fetal genomic DNA.

Molecular Characterization of a Rare Case of Monozygotic Dichorionic Diamniotic Twin Pregnancy after Single Blastocyst Transfer in Preimplantation Genetic Testing (PGT)

Preimplantation genetic testing (PGT) is widely used to select unaffected embryos, increasing the odds of having a healthy baby. During the last few decades, it was accepted that monozygotic dichorionic diamniotic twin pregnancies occurred from the embryo splitting before Day 3 postfertilization according to Corner's dogma. Hence, the occurrence of a dichorionic diamniotic twin pregnancy after a single blastocyst transfer was considered a dizygotic pregnancy resulting from blastocyst transfer and concurrent natural fertilization. In our study, we have provided for the first time molecular proof that a single blastocyst transfer can result in a monozygotic dichorionic diamniotic twin pregnancy, invalidating Corner's dogma. In this case, we recommend systematically assessing the genetic status of dichorionic twins after single blastocyst transfer using prenatal diagnosis to exclude the risk from a potential concurrent spontaneous pregnancy and to ensure that both fetuses are unaffected. To achieve this goal, we have developed here an innovative noninvasive prenatal diagnosis by exclusion of paternal variants with droplet digital PCR, maximizing the reliability of genetic diagnosis. Further multicentric prospective studies using genetic testing are now required to establish the rate of blastocyst splitting leading to dichorionic pregnancy in PGT and to identify the risk factors.