Fragmentomic cfDNA Patterns in Noninvasive Prenatal Testing and Beyond

The release of fetoplacental cell-free DNA (cfDNA) into the maternal bloodstream opened up new avenues towards noninvasive prenatal testing (NIPT) for aneuploidies, hereditary DNA mutations and other pregnancy-related developmental disorders. Increasingly, cfDNA catches interest for its noninvasive screening value in other areas as well, including oncology. Although there are indications that cfDNA fragmentation is a non-random process, the etiology and different structural aspects of cfDNA are still not well known. The emerging field of cfDNA fragmentomics investigates the existence of tissue and disease specific cfDNA signatures and the chemistry and biology underlying the fragmentation process. This review sheds light on recent developments in cfDNA fragmentomics and illustrates their significance in NIPT improvement and beyond.We discuss aspects of fragment size distributions, epigenetic correlations and putatively enriched cfDNA fragment-end compositions. Combinatorial fragmentomic efforts have provided more insights into the roles of different enzymes that contribute to the fragmentation process in the tissue of origin and in the bloodstream. Altogether, these studies revealed multiple fragmentomic-related biomarkers that can be used to make noninvasive screening and other types of clinical use of cfDNA more robust, by raising its distinctive capacities. This includes multiple complementary approaches to determine the fetal fraction, a key determinant in NIPT. Furthermore, these developments translate to a better understanding of the encountered cfDNA patterns and will catalyze the expansion of screening possibilities in NIPT and beyon

Implementing non-invasive prenatal testing in a national screening program:Lessons learned from the TRIDENT studies

The Dutch NIPT Consortium, a multidisciplinary collaboration of stakeholders in prenatal care initiated and launched the TRIDENT studies. The goal of the TRIDENT studies was to implement non-invasive prenatal testing (NIPT), first as a contingent (second-tier) and later as a first-tier test, and to evaluate this implementation. This paper describes how NIPT can be successfully implemented in a country or state. Important factors include the significance of forming a consortium and encouraging cooperation among relevant stakeholders, appropriate training for obstetric care professionals, and taking into account the perspectives of pregnant women when implementing prenatal tests. We describe the advantages of high sensitivity and specificity when comparing contingent NIPT with first-tier NIPT. This paper emphasizes the value of pre- and post-test counselling and the requirement for a standardized method of information delivery and value clarification, to assist couples in decision making for prenatal screening.</p

Feasibility of preconception screening for thalassaemia in Indonesia: exploring the opinion of Javanese mothers

Background. Thalassaemia has become a major public health issue in Indonesia. It has been estimated that up to 10% of the population carries a gene associated with beta-thalassaemia. Currently, there is no formal recommendation for thalassaemia screening. This study aimed to explore awareness of thalassaemia, and to explore attitudes regarding carrier testing among Javanese mothers. Methods. A quantitative questionnaire, designed using constructs of the Theory of Planned Behaviour, was applied cross-sectionally. Results. Out of 191 mothers who were invited, 180 agreed to participate (RR 94%), of whom 74 had a child affected with thalassaemia. Both attitudes towards receiving information about thalassaemia, and attitudes towards carrier testing were very positive. Awareness of thalassaemia was poor. Mothers, both those with and without an affected child, had barely heard of thalassaemia, nor of carrier testing. However, all mothers, including those with an affected child expressed high levels of interest in carrier testing. Respondents did not perceive that they had any control over carrier testing, and feared stigmatization and being discriminated against if their carrier status was identified. Attitudes towards carrier testing explained 23% of future reproductive intentions, in addition to perceived stigmatization, education level and ‘mother’s age’ (R2 0.44; p 0.001). Conclusion. Responding mothers expressed high levels of interest in receiving information on both thalassaemia and carrier testing. The less educated and the more deprived they were, the keener they were to receive this information. Overall, awareness of thalassaemia was low. Even mothers with affected children seemed unaware of the inheritance pattern and the recurrent risk of having an affected child in a subsequent pregnancy, showing the need for genetic counselling in Indonesia. It is therefore recommended not only to raise awareness about thalassaemia, but to improve the education of healthcare professionals as well. Keywords: thalassaemia; carrier screening; Javanese mothers; genetic awareness; Theory of Planned Behaviour (TpB); awareness; Indonesi

Additional value of advanced ultrasonography in pregnancies with two inconclusive cell-free DNA draws

Objective: We aimed to evaluate the additional value of advanced fetal anatomical assessment by ultrasound in pregnancies with twice inconclusive noninvasive testing (NIPT) due to low fetal fraction (FF). Methods: We performed a multicenter-retrospective study between 2017 and 2020 including 311 pregnancies with twice inconclusive NIPT due to low FF ≤ 1%. Women were offered invasive testing and advanced fetal anatomical assessment at ≤18 weeks' gestation. Ultrasound findings, genetic testing, and pregnancy/postnatal outcomes were evaluated. Results: Ninety-two/311 (29.6%) women underwent invasive testing. Structural anomalies were diagnosed in 13/311 (4.2%) pregnancies (nine at the first scan and four at follow-up). In 6/13 (46.2%) cases, genetic aberrations were confirmed (one case of Trisomy 13 (detectable by NIPT), two of Triploidy, one of 16q12-deletion, HCN4-mutation and UPD(16) (nondetectable by NIPT). Genetic aberrations were found in 4/298 (1.3%) structurallynormal pregnancies (one 47XYY, two microscopic aberrations, one monogenic disorder found postpartum). Structural anomalies in genetically normal fetuses (2.0%) were not more prevalent compared to the general pregnant population (OR 1.0 [0.4–2.2]). Conclusion: In pregnancies with twice inconclusive NIPT due to low FF, fetal structural anomalies are not more prevalent than in the general obstetric population. The detailed anatomical assessment has the added value to detect phenotypical features suggestive of chromosomal/genetic aberrations and identify pregnancies where advanced genetic testing may be indicated

Diagnosis of Fanconi Anemia: Mutation Analysis by Next-Generation Sequencing

Fanconi anemia (FA) is a rare genetic instability syndrome characterized by developmental defects, bone marrow failure, and a high cancer risk. Fifteen genetic subtypes have been distinguished. The majority of patients (≈85%) belong to the subtypes A (≈60%), C (≈15%) or G (≈10%), while a minority (≈15%) is distributed over the remaining 12 subtypes. All subtypes seem to fit within the “classical” FA phenotype, except for D1 and N patients, who have more severe clinical symptoms. Since FA patients need special clinical management, the diagnosis should be firmly established, to exclude conditions with overlapping phenotypes. A valid FA diagnosis requires the detection of pathogenic mutations in a FA gene and/or a positive result from a chromosomal breakage test. Identification of the pathogenic mutations is also important for adequate genetic counselling and to facilitate prenatal or preimplantation genetic diagnosis. Here we describe and validate a comprehensive protocol for the molecular diagnosis of FA, based on massively parallel sequencing. We used this approach to identify BRCA2, FANCD2, FANCI and FANCL mutations in novel unclassified FA patients

Early detection of active Human CytomegaloVirus (hCMV) infection in pregnant women using data generated for noninvasive fetal aneuploidy testing

Background: Prenatal hCMV infections can lead to severe embryopathy and neurological sequelae in neonates. Screening during pregnancy is not recommended by global societies, as there is no effective therapy. Recently, several groups showed that maternal–fetal hCMV transmission can be strongly reduced by administering anti-viral agents early in pregnancy. This calls for a screening method to identify at risk pregnancies at an appropriate gestational age, with the possibility for large-scale enrolment. Non-Invasive Prenatal Testing (NIPT) for fetal aneuploidy screening early in pregnancy is already implemented in many countries and performed on a large-scale basis. We investigated the use of whole genome cell-free DNA (cfDNA) sequencing data, generated for the purpose of NIPT, as (pre-)screening tool to identify women with active hCMV-infections, eligible for therapy. Methods: Coded raw sequencing NIPT data from 204,818 pregnant women from three testing laboratories were analyzed for the presence of hCMV-cfDNA. Samples were stratified by cfDNA-hCMV load. For validation and interpretation, diagnostic hCMV-qPCR and serology testing were performed on a subset of cfDNA-hCMV-positive (n = 112) and -negative (n = 127) samples. Findings: In 1930 samples (0.94%) hCMV fragments were detected. Validation by hCMV-qPCR showed that samples with high cfDNA-hCMV load tested positive and cfDNA-hCMV-negative samples tested negative. In 32/112 cfDNA-hCMV-positive samples (28.6%) the serological profile suggested a recent primary infection: this was more likely in samples with high cfDNA-hCMV load (78.6%) than in samples with low cfDNA-hCMV load (11.0%). In none of the cfDNA-hCMV-negative samples serology was indicative of a recent primary infection.Interpretation: Our study shows that large-scale (pre-)screening for both genetic fetal aberrations and active maternal hCMV infections during pregnancy can be combined in one cfDNA sequencing test, performed on a single blood sample, drawn in the first trimester of pregnancy. Funding: This work was partly funded by the Prenatal Screening Foundation Nijmegen, the Netherlands.</p

A novel CCM2 variant in a family with non-progressive cognitive complaints and cerebral microbleeds

Lobar cerebral microbleeds are most often sporadic and associated with Alzheimer's disease. The aim of our study was to identify the underlying genetic defect in a family with cognitive complaints and multiple lobar microbleeds and a positive family history for early onset Alzheimer's disease. We performed exome sequencing followed by Sanger sequencing for validation purposes on genomic DNA of three siblings with cognitive complaints, reduced amyloid-beta-42 in CSF and multiple cerebral lobar microbleeds. We checked for the occurrence of the variant in a cohort of 363 patients with early onset dementia and/or microbleeds. A novel frameshift variant (c.236_237delAC) generating a premature stop codon in the CCM2 gene shared by all three siblings was identified. Pathogenicity of the variant was supported by the presence of cerebral cavernous malformations in two of the siblings and by the absence of the variant exome variant databases. Two siblings were homozygous for APOE-ε4; one heterozygous. The cognitive complaints, reduced amyloid-beta-42 in CSF and microbleeds suggest preclinical Alzheimer's disease, but the stability of the cognitive complaints does not. We hypothesize that the phenotype in this family may be due to a combination of the CCM2 variant and the APOE status

Early detection of active Human CytomegaloVirus (hCMV) infection in pregnant women using data generated for noninvasive fetal aneuploidy testing

Background: Prenatal hCMV infections can lead to severe embryopathy and neurological sequelae in neonates. Screening during pregnancy is not recommended by global societies, as there is no effective therapy. Recently, several groups showed that maternal–fetal hCMV transmission can be strongly reduced by administering anti-viral agents early in pregnancy. This calls for a screening method to identify at risk pregnancies at an appropriate gestational age, with the possibility for large-scale enrolment. Non-Invasive Prenatal Testing (NIPT) for fetal aneuploidy screening early in pregnancy is already implemented in many countries and performed on a large-scale basis. We investigated the use of whole genome cell-free DNA (cfDNA) sequencing data, generated for the purpose of NIPT, as (pre-)screening tool to identify women with active hCMV-infections, eligible for therapy. Methods: Coded raw sequencing NIPT data from 204,818 pregnant women from three testing laboratories were analyzed for the presence of hCMV-cfDNA. Samples were stratified by cfDNA-hCMV load. For validation and interpretation, diagnostic hCMV-qPCR and serology testing were performed on a subset of cfDNA-hCMV-positive (n = 112) and -negative (n = 127) samples. Findings: In 1930 samples (0.94%) hCMV fragments were detected. Validation by hCMV-qPCR showed that samples with high cfDNA-hCMV load tested positive and cfDNA-hCMV-negative samples tested negative. In 32/112 cfDNA-hCMV-positive samples (28.6%) the serological profile suggested a recent primary infection: this was more likely in samples with high cfDNA-hCMV load (78.6%) than in samples with low cfDNA-hCMV load (11.0%). In none of the cfDNA-hCMV-negative samples serology was indicative of a recent primary infection.Interpretation: Our study shows that large-scale (pre-)screening for both genetic fetal aberrations and active maternal hCMV infections during pregnancy can be combined in one cfDNA sequencing test, performed on a single blood sample, drawn in the first trimester of pregnancy. Funding: This work was partly funded by the Prenatal Screening Foundation Nijmegen, the Netherlands.</p