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1.
Article in English | MEDLINE | ID: mdl-38879662

ABSTRACT

Recently, the use of polygenic risk scores in embryo screening (PGT-P) has been introduced on the premise of reducing polygenic disease risk through embryo selection. However, it has been met with extensive critique: considered "technology-driven" rather than "evidence-based", concerns exist about its validity, utility, ethics, and societal effects. Its scientific foundations and criticisms thus need to be carefully considered. However, seeing as PGT-P is already offered in some settings, further questions need to be addressed, in order to give due diligence to various aspects of PGT-P. By examining the complexities of clinical introduction of PGT-P, we discuss whether PGT-P could be responsibly implemented in the first place, what elements need to be addressed if PGT-P is clinically implemented, and subsequently how counselling and decision-making of its users could be envisaged. By dissecting these elements, we provide an overview of important practical questions of PGT-P and emphasize elements of PGT-P that we think have yet to be given sufficient attention. These questions and elements are for example related to the potential target group, scope, and decision-making possibilities of PGT-P. The aspects we raise are crucial to consider by the scientific community and policy makers for the development of guidelines and/or an ethical framework for PGT-P.

2.
JCO Oncol Pract ; : OP2300594, 2024 Apr 12.
Article in English | MEDLINE | ID: mdl-38608208

ABSTRACT

In this article, we defined comprehensive recommendations for the clinical follow-up of pregnant women with a malignancy-suspicious NIPT result, on the basis of the vast experience with population-based NIPT screening programs in two European countries complemented with published large data sets. These recommendations provide a tool for classifying NIPT results as malignancy-suspicious, and guide health care professionals in structured clinical decision making for the diagnostic process of pregnant women who receive such a malignancy-suspicious NIPT result.

3.
bioRxiv ; 2024 Mar 18.
Article in English | MEDLINE | ID: mdl-38562770

ABSTRACT

The 22q11.2 deletion syndrome (22q11.2DS) is the most common microdeletion disorder. Why the incidence of 22q11.2DS is much greater than that of other genomic disorders remains unknown. Short read sequencing cannot resolve the complex segmental duplicon structure to provide direct confirmation of the hypothesis that the rearrangements are caused by non-allelic homologous recombination between the low copy repeats on chromosome 22 (LCR22s). To enable haplotype-specific assembly and rearrangement mapping in LCR22 regions, we combined fiber-FISH optical mapping with whole genome (ultra-)long read sequencing or rearrangement-specific long-range PCR on 24 duos (22q11.2DS patient and parent-of-origin) comprising several different LCR22-mediated rearrangements. Unexpectedly, we demonstrate that not only different paralogous segmental duplicon but also palindromic AT-rich repeats (PATRR) are driving 22q11.2 rearrangements. In addition, we show the existence of two different inversion polymorphisms preceding rearrangement, and somatic mosaicism. The existence of different recombination sites and mechanisms in paralogues and PATRRs which are copy number expanding in the human population are a likely explanation for the high 22q11.2DS incidence.

4.
PLoS One ; 19(3): e0297739, 2024.
Article in English | MEDLINE | ID: mdl-38457477

ABSTRACT

In recent years, the importance of isolating single cells from blood circulation for several applications, such as non-invasive tumour diagnosis, the monitoring of minimal residual disease, and the analysis of circulating fetal cells for prenatal diagnosis, urged the need to set up innovative methods. For such applications, different methods were developed. All show some weaknesses, especially a limited sensitivity, and specificity. Here we present a new method for isolating a single or a limited number of cells adhered to SBS slides (Tethis S.p.a.) (a glass slide coated with Nanostructured Titanium Dioxide) by Laser Capture Microdissection (LCM) and subsequent Whole Genome Amplification. SBS slides have been shown to have an optimal performance in immobilizing circulating tumour cells (CTCs) from early breast cancer patients. In this work, we spiked cancer cells in blood samples to mimic CTCs. By defining laser parameters to cut intact samples, we were able to isolate genetically intact single cells. We demonstrate that SBS slides are optimally suited for isolating cells using LCM and that this method provides high-quality DNA, ideal for gene-specific assays such as PCR and Sanger sequencing for mutation analysis.


Subject(s)
Neoplastic Cells, Circulating , Pregnancy , Female , Humans , Laser Capture Microdissection/methods , Neoplastic Cells, Circulating/pathology , DNA
5.
Nat Commun ; 15(1): 2220, 2024 Mar 12.
Article in English | MEDLINE | ID: mdl-38472221

ABSTRACT

Circulating cell-free DNA (cfDNA) fragments have characteristics that are specific to the cell types that release them. Current methods for cfDNA deconvolution typically use disease tailored marker selection in a limited number of bulk tissues or cell lines. Here, we utilize single cell transcriptome data as a comprehensive cellular reference set for disease-agnostic cfDNA cell-of-origin analysis. We correlate cfDNA-inferred nucleosome spacing with gene expression to rank the relative contribution of over 490 cell types to plasma cfDNA. In 744 healthy individuals and patients, we uncover cell type signatures in support of emerging disease paradigms in oncology and prenatal care. We train predictive models that can differentiate patients with colorectal cancer (84.7%), early-stage breast cancer (90.1%), multiple myeloma (AUC 95.0%), and preeclampsia (88.3%) from matched controls. Importantly, our approach performs well in ultra-low coverage cfDNA datasets and can be readily transferred to diverse clinical settings for the expansion of liquid biopsy.


Subject(s)
Cell-Free Nucleic Acids , Humans , DNA Fragmentation , Transcriptome , Biology , Biomarkers, Tumor/genetics
6.
Genes (Basel) ; 15(1)2024 01 20.
Article in English | MEDLINE | ID: mdl-38275609

ABSTRACT

Gollop-Wolfgang complex (GWC) is a rare congenital limb anomaly characterized by tibial aplasia with femur bifurcation, ipsilateral bifurcation of the thigh bone, and split hand and monodactyly of the feet, resulting in severe and complex limb deformities. The genetic basis of GWC, however, has remained elusive. We studied a three-generation family with four GWC-affected family members. An analysis of whole-genome sequencing results using a custom pipeline identified the WNT11 c.1015G>A missense variant associated with the phenotype. In silico modelling and an in vitro reporter assay further supported the link between the variant and GWC. This finding further contributes to mapping the genetic heterogeneity underlying split hand/foot malformations in general and in GWC specifically.


Subject(s)
Abnormalities, Multiple , Hand Deformities, Congenital , Humans , Abnormalities, Multiple/genetics , Femur , Tibia
7.
Soc Sci Med ; 343: 116599, 2024 Feb.
Article in English | MEDLINE | ID: mdl-38244362

ABSTRACT

The recent introduction of polygenic risk scores within preimplantation genetic testing (PGT-P) has been met with many concerns. To get more insights into the perspectives of relevant stakeholders on the socio-ethical aspects of PGT-P, an interview study with 31 healthcare professionals involved in reproductive medicine and genetics in Europe and North-America was performed. Healthcare professionals in our study were concerned that PGT-P was going too far in terms of selection, with regards to both medical conditions and non-medical traits. Healthcare professionals were worried about the ethical 'slippery slope' of PGT-P, the increasing medicalization of reproductive health, the commercial context of PGT-P, and potential stigmatization and discrimination. There were also concerns that the availability and the 'technological imperative' of PGT-P could lead to pressure and a sense of responsibility for parents to use PGT-P. Additionally, it could cause new anxieties about the child's health before the child has even been born. Since PGT-P provides polygenic risk scores before birth, the autonomy of the child has to be considered. These socio-ethical concerns heighten existing debates regarding reproductive genetic technologies and show that the specifics of PGT-P make this screening option especially ethically controversial.


Subject(s)
Preimplantation Diagnosis , Pregnancy , Female , Child , Humans , Genetic Risk Score , Genetic Testing , Health Personnel , Delivery of Health Care
8.
Eur J Hum Genet ; 32(3): 309-316, 2024 Mar.
Article in English | MEDLINE | ID: mdl-38278868

ABSTRACT

Non-invasive prenatal testing (NIPT) can not only accurately detect early in pregnancy the presence of chromosomal abnormalities but also fetal sex. However, whether fetal sex should be reported after performing NIPT is ethically contentious. In Belgium, NIPT is practically fully reimbursed and offered to all pregnant women as a first-tier screening. In practice, fetal sex is reported upon request of the expectant parents; however, this is not stipulated in guidelines. As more countries are offering NIPT and looking to implement it in public healthcare, challenges and insights of healthcare professionals working in Belgium can be of value for others. We assessed healthcare professionals' experiences with and perspectives on sex determination and reporting following NIPT in Belgium by conducting a semi-structured interview study. We interviewed 30 professionals involved in prenatal screening. While overall healthcare professionals did not consider reporting fetal sex to be an issue if the expectant parents want to know, some consider the reporting of a non-medical trait like fetal sex problematic when it is reimbursed or if it could lead to sex-selective termination of pregnancy. Moreover, the strong desire of expectant parents to know fetal sex risks compromising informed decision-making about NIPT. In this way, fetal sex may distract from the primary aim of NIPT as a test for medical conditions. Improving pre-test counseling both in terms of quality and availability may help overcome some of these issues.


Subject(s)
Pregnant Women , Prenatal Diagnosis , Pregnancy , Humans , Female , Prenatal Diagnosis/psychology , Counseling , Aneuploidy , Delivery of Health Care
9.
Am J Obstet Gynecol ; 230(3): 368.e1-368.e12, 2024 Mar.
Article in English | MEDLINE | ID: mdl-37717890

ABSTRACT

BACKGROUND: The 22q11.2 deletion syndrome is the most common microdeletion syndrome and is frequently associated with congenital heart disease. Prenatal diagnosis of 22q11.2 deletion syndrome is increasingly offered. It is unknown whether there is a clinical benefit to prenatal detection as compared with postnatal diagnosis. OBJECTIVE: This study aimed to determine differences in perinatal and infant outcomes between patients with prenatal and postnatal diagnosis of 22q11.2 deletion syndrome. STUDY DESIGN: This was a retrospective cohort study across multiple international centers (30 sites, 4 continents) from 2006 to 2019. Participants were fetuses, neonates, or infants with a genetic diagnosis of 22q11.2 deletion syndrome by 1 year of age with or without congenital heart disease; those with prenatal diagnosis or suspicion (suggestive ultrasound findings and/or high-risk cell-free fetal DNA screen for 22q11.2 deletion syndrome with postnatal confirmation) were compared with those with postnatal diagnosis. Perinatal management, cardiac and noncardiac morbidity, and mortality by 1 year were assessed. Outcomes were adjusted for presence of critical congenital heart disease, gestational age at birth, and site. RESULTS: A total of 625 fetuses, neonates, or infants with 22q11.2 deletion syndrome (53.4% male) were included: 259 fetuses were prenatally diagnosed (156 [60.2%] were live-born) and 122 neonates were prenatally suspected with postnatal confirmation, whereas 244 infants were postnatally diagnosed. In the live-born cohort (n=522), 1-year mortality was 5.9%, which did not differ between groups but differed by the presence of critical congenital heart disease (hazard ratio, 4.18; 95% confidence interval, 1.56-11.18; P<.001) and gestational age at birth (hazard ratio, 0.78 per week; 95% confidence interval, 0.69-0.89; P<.001). Adjusting for critical congenital heart disease and gestational age at birth, the prenatal cohort was less likely to deliver at a local community hospital (5.1% vs 38.2%; odds ratio, 0.11; 95% confidence interval, 0.06-0.23; P<.001), experience neonatal cardiac decompensation (1.3% vs 5.0%; odds ratio, 0.11; 95% confidence interval, 0.03-0.49; P=.004), or have failure to thrive by 1 year (43.4% vs 50.3%; odds ratio, 0.58; 95% confidence interval, 0.36-0.91; P=.019). CONCLUSION: Prenatal detection of 22q11.2 deletion syndrome was associated with improved delivery management and less cardiac and noncardiac morbidity, but not mortality, compared with postnatal detection.


Subject(s)
DiGeorge Syndrome , Heart Defects, Congenital , Infant , Infant, Newborn , Pregnancy , Female , Humans , Male , DiGeorge Syndrome/diagnosis , DiGeorge Syndrome/genetics , Retrospective Studies , Prenatal Diagnosis , Heart Defects, Congenital/diagnosis , Heart Defects, Congenital/epidemiology , Heart Defects, Congenital/genetics , Prenatal Care
10.
Eur J Hum Genet ; 32(1): 31-36, 2024 Jan.
Article in English | MEDLINE | ID: mdl-37029316

ABSTRACT

Maternally inherited 15q11-q13 duplications are generally found to cause more severe neurodevelopmental anomalies compared to paternally inherited duplications. However, this assessment is mainly inferred from the study of patient populations, causing an ascertainment bias towards patients at the more severe end of the phenotypic spectrum. Here, we analyze the low coverage genome-wide cell-free DNA sequencing data obtained from pregnant women during non-invasive prenatal screening (NIPS). We detect 23 15q11-q13 duplications in 333,187 pregnant women (0.0069%), with an approximately equal distribution between maternal and paternal duplications. Maternally inherited duplications are always associated with a clinical phenotype (ranging from learning difficulties to intellectual impairment, epilepsy and psychiatric disorders), while paternal duplications are normal or associated with milder phenotypes (mild learning difficulties and dyslexia). This data corroborates the difference in impact between paternally and maternally inherited 15q11-q13 duplications, contributing to the improvement of genetic counselling. We recommend reporting 15q11-q13 duplications identified during genome-wide NIPS with appropriate genetic counselling for these pregnant women in the interest of both mothers and future children.


Subject(s)
Mothers , Paternal Inheritance , Pregnancy , Child , Humans , Female , Alleles , Phenotype , Chromosomes, Human, Pair 15/genetics
11.
Nat Med ; 29(9): 2206-2215, 2023 09.
Article in English | MEDLINE | ID: mdl-37640858

ABSTRACT

Preeclampsia (PE) is a leading cause for peripartal morbidity, especially if developing early in gestation. To enable prophylaxis in the prevention of PE, pregnancies at risk of PE must be identified early-in the first trimester. To identify at-risk pregnancies we profiled methylomes of plasma-derived, cell-free DNA from 498 pregnant women, of whom about one-third developed early-onset PE. We detected DNA methylation differences between control and PE pregnancies that enabled risk stratification at PE diagnosis but also presymptomatically, at around 12 weeks of gestation (range 9-14 weeks). The first-trimester risk prediction model was validated in an external cohort collected from two centers (area under the curve (AUC) = 0.75) and integrated with routinely available maternal risk factors (AUC = 0.85). The combined risk score correctly predicted 72% of patients with early-onset PE at 80% specificity. These preliminary results suggest that cell-free DNA methylation profiling is a promising tool for presymptomatic PE risk assessment, and has the potential to improve treatment and follow-up in the obstetric clinic.


Subject(s)
Cell-Free Nucleic Acids , Pre-Eclampsia , Pregnancy , Humans , Female , Epigenome , Pre-Eclampsia/diagnosis , Pre-Eclampsia/genetics , Area Under Curve , Cell-Free Nucleic Acids/genetics , DNA Methylation/genetics
12.
Prenat Diagn ; 43(10): 1333-1343, 2023 09.
Article in English | MEDLINE | ID: mdl-37592442

ABSTRACT

OBJECTIVES: To assess maternal characteristics and comorbidities in patients with persistent uninterpretable non-invasive prenatal testing (NIPT) and to evaluate the association with adverse pregnancy outcome in a general risk population. METHODS: A retrospective cohort study (July 2017-December 2020) was conducted of patients with persistent uninterpretable NIPT samples. Maternal characteristics and pregnancy outcomes were compared with the general Belgian obstetric population. RESULTS: Of the 148 patients with persistent uninterpretable NIPT, 37 cases were due to a low fetal fraction (LFF) and 111 due to a low quality score (LQS). Both groups (LFF, LQS) showed more obesity (60.6%, 42.4%), multiple pregnancies (18.9%, 4.5%) and more obstetrical complications. In the LQS group, a high rate of maternal auto-immune disorders (30.6%) was seen and hypertensive complications (17.6%), preterm birth (17.6%) and neonatal intensive care unit (NICU) admission (22%) were significantly increased. In the LFF group hypertensive complications (21.6%), gestational diabetes (20.6%), preterm birth (27%), SGA (25.6%), major congenital malformations (11.4%), c-section rate (51.4%) and NICU admission (34.9%) were significantly increased. Chromosomal abnormalities were not increased in both groups. CONCLUSIONS: Patients with persistent uninterpretable NIPT have significantly more maternal obesity, comorbidities and adverse pregnancy outcome than the general population and should receive high-risk pregnancy care. Distinguishing between LFF and LQS optimizes counseling because maternal characteristics and pregnancy outcome differ between these groups.


Subject(s)
Premature Birth , Infant, Newborn , Humans , Female , Pregnancy , Premature Birth/diagnosis , Premature Birth/epidemiology , Retrospective Studies , Prenatal Care , Fetus , Family
13.
NPJ Genom Med ; 8(1): 17, 2023 Jul 18.
Article in English | MEDLINE | ID: mdl-37463940

ABSTRACT

Congenital heart disease (CHD) affecting the conotruncal region of the heart, occurs in 40-50% of patients with 22q11.2 deletion syndrome (22q11.2DS). This syndrome is a rare disorder with relative genetic homogeneity that can facilitate identification of genetic modifiers. Haploinsufficiency of TBX1, encoding a T-box transcription factor, is one of the main genes responsible for the etiology of the syndrome. We suggest that genetic modifiers of conotruncal defects in patients with 22q11.2DS may be in the TBX1 gene network. To identify genetic modifiers, we analyzed rare, predicted damaging variants in whole genome sequence of 456 cases with conotruncal defects and 537 controls, with 22q11.2DS. We then performed gene set approaches and identified chromatin regulatory genes as modifiers. Chromatin genes with recurrent damaging variants include EP400, KAT6A, KMT2C, KMT2D, NSD1, CHD7 and PHF21A. In total, we identified 37 chromatin regulatory genes, that may increase risk for conotruncal heart defects in 8.5% of 22q11.2DS cases. Many of these genes were identified as risk factors for sporadic CHD in the general population. These genes are co-expressed in cardiac progenitor cells with TBX1, suggesting that they may be in the same genetic network. The genes KAT6A, KMT2C, CHD7 and EZH2, have been previously shown to genetically interact with TBX1 in mouse models. Our findings indicate that disturbance of chromatin regulatory genes impact the TBX1 gene network serving as genetic modifiers of 22q11.2DS and sporadic CHD, suggesting that there are some shared mechanisms involving the TBX1 gene network in the etiology of CHD.

15.
Abdom Radiol (NY) ; 48(5): 1590-1598, 2023 05.
Article in English | MEDLINE | ID: mdl-37095202

ABSTRACT

Noninvasive prenatal screening (NIPS) tests for fetal chromosomal anomalies through maternal blood sampling. It is becoming widely available and standard of care for pregnant women in many countries. It is performed in the first trimester of pregnancy, usually between 9 and 12 weeks. Fragments of fetal cell-free deoxyribonucleic acid (DNA) floating in maternal plasma are detected and analyzed by this test to assess for chromosomal aberrations. Similarly, maternal tumor-derived cell-free DNA (ctDNA) released from the tumor cells also circulates in the plasma. Hence, the presence of genomic anomalies originating from maternal tumor-derived DNA may be detected on the NIPS-based fetal risk assessment in pregnant patients. Presence of multiple aneuploidies or autosomal monosomies are the most commonly reported NIPS abnormalities detected with occult maternal malignancies. When such results are received, the search for an occult maternal malignancy begins, in which imaging plays a crucial role. The most commonly detected malignancies via NIPS are leukemia, lymphoma, breast and colon cancers. Ultrasound is a reasonable radiation-free modality for imaging during pregnancy, specially when there are localizing symptoms or findings, such as palpable lumps. While there are no consensus guidelines on the imaging evaluation for these patients, when there are no localizing symptoms or clinically palpable findings, whole body MRI is recommended as the radiation-free modality of choice to search for an occult malignancy. Based on clinical symptoms, practice patterns, and available resources, breast ultrasound, chest radiographs, and targeted ultrasound evaluations can also be performed initially or as a follow-up for MRI findings. CT is reserved for exceptional circumstances due to its higher radiation dose. This article intends to increase awareness of this rare but stressful clinical scenario and guide imaging evaluation for occult malignancy detected via NIPS during pregnancy.


Subject(s)
Neoplasms , Noninvasive Prenatal Testing , Pregnancy , Humans , Female , Prenatal Diagnosis/methods , Aneuploidy , DNA
17.
Eur J Hum Genet ; 31(10): 1133-1138, 2023 10.
Article in English | MEDLINE | ID: mdl-36935419

ABSTRACT

Preimplantation genetic testing using polygenic risk scores (PGT-P) has recently been introduced. However, PGT-P has been met with many ethical concerns. It is therefore important to get insights into the perspectives of stakeholders regarding PGT-P. We performed a qualitative interview study on the views of healthcare professionals toward PGT-P. We conducted in-depth semi-structured interviews with 31 healthcare professionals working in the field of preimplantation genetic testing. The interviews explored the attitudes of healthcare professionals toward the technology of PGT-P, e.g., the validity, utility, limitations and potential benefits of PGT-P. We found that most healthcare professionals were concerned about the prematurity of introducing PGT-P into clinical practice. They had various ethical considerations, such as concerns related to validity and utility of PGT-P, limited embryos and options, and difficulties for prospective parents regarding comprehension and informed decision-making. Positive aspects were also identified, e.g., regarding reproductive autonomy and potential health benefits. Overall, most healthcare professionals considered that clinical implementation of PGT-P is premature. More comprehensive, longitudinal and inclusive studies are needed first, though these might not improve PGT-P enough to responsibly implement it. Healthcare professionals were also concerned that PGT-P could cause anxiety and create difficult choices for prospective parents. These perspectives and ethical considerations are crucial to consider for future guidelines and recommendations regarding PGT-P.


Subject(s)
Preimplantation Diagnosis , Pregnancy , Female , Humans , Prospective Studies , Genetic Testing , Attitude , Delivery of Health Care , Aneuploidy
18.
Mol Psychiatry ; 28(5): 2071-2080, 2023 May.
Article in English | MEDLINE | ID: mdl-36869225

ABSTRACT

22q11.2 deletion is one of the strongest known genetic risk factors for schizophrenia. Recent whole-genome sequencing of schizophrenia cases and controls with this deletion provided an unprecedented opportunity to identify risk modifying genetic variants and investigate their contribution to the pathogenesis of schizophrenia in 22q11.2 deletion syndrome. Here, we apply a novel analytic framework that integrates gene network and phenotype data to investigate the aggregate effects of rare coding variants and identified modifier genes in this etiologically homogenous cohort (223 schizophrenia cases and 233 controls of European descent). Our analyses revealed significant additive genetic components of rare nonsynonymous variants in 110 modifier genes (adjusted P = 9.4E-04) that overall accounted for 4.6% of the variance in schizophrenia status in this cohort, of which 4.0% was independent of the common polygenic risk for schizophrenia. The modifier genes affected by rare coding variants were enriched with genes involved in synaptic function and developmental disorders. Spatiotemporal transcriptomic analyses identified an enrichment of coexpression between modifier and 22q11.2 genes in cortical brain regions from late infancy to young adulthood. Corresponding gene coexpression modules are enriched with brain-specific protein-protein interactions of SLC25A1, COMT, and PI4KA in the 22q11.2 deletion region. Overall, our study highlights the contribution of rare coding variants to the SCZ risk. They not only complement common variants in disease genetics but also pinpoint brain regions and developmental stages critical to the etiology of syndromic schizophrenia.


Subject(s)
DiGeorge Syndrome , Schizophrenia , Humans , Young Adult , Adult , Schizophrenia/genetics , DiGeorge Syndrome/genetics , Brain , Gene Expression Profiling , Whole Genome Sequencing
19.
Hum Reprod ; 38(3): 511-519, 2023 03 01.
Article in English | MEDLINE | ID: mdl-36625546

ABSTRACT

STUDY QUESTION: Can long-read amplicon sequencing be beneficial for preclinical preimplantation genetic testing (PGT) workup in couples with a de novo pathogenic variant in one of the prospective parents? SUMMARY ANSWER: Long-read amplicon sequencing represents a simple, rapid and cost-effective preclinical PGT workup strategy that provides couples with de novo pathogenic variants access to universal genome-wide haplotyping-based PGT programs. WHAT IS KNOWN ALREADY: Universal PGT combines genome-wide haplotyping and copy number profiling to select embryos devoid of both familial pathogenic variants and aneuploidies. However, it cannot be directly applied in couples with a de novo pathogenic variant in one of the partners due to the absence of affected family members required for phasing the disease-associated haplotype. STUDY DESIGN, SIZE, DURATION: This is a prospective study, which includes 32 families that were enrolled in the universal PGT program at the University Hospital of Leuven between 2018 and 2022. We implemented long-read amplicon sequencing during the preclinical PGT workup to deduce the parental origin of the disease-associated allele in the affected partner, which can then be traced in embryos during clinical universal PGT cycles. PARTICIPANTS/MATERIALS, SETTING, METHODS: To identify the parental origin of the disease-associated allele, genomic DNA from the carrier of the de novo pathogenic variant and his/her parent(s) was used for preclinical PGT workup. Primers flanking the de novo variant upstream and downstream were designed for each family. Following long-range PCR, amplicons that ranged 5-10 kb in size, were sequenced using Pacific Bioscience and/or Oxford Nanopore platforms. Next, targeted variant calling and haplotyping were performed to identify parental informative single-nucleotide variants (iSNVs) linked to the de novo mutation. Following the preclinical PGT workup, universal PGT via genome-wide haplotyping was performed for couples who proceeded with clinical PGT cycle. In parallel, 13 trophectoderm (TE) biopsies from three families that were analyzed by universal PGT, were also used for long-read amplicon sequencing to explore this approach for embryo direct mutation detection coupled with targeted long-read haplotyping. MAIN RESULTS AND THE ROLE OF CHANCE: The parental origin of the mutant allele was identified in 24/32 affected individuals during the preclinical PGT workup stage, resulting in a 75% success rate. On average, 5.95 iSNVs (SD = 4.5) were detected per locus of interest, and the average distance of closest iSNV to the de novo variant was ∼1750 bp. In 75% of those cases (18/24), the de novo mutation occurred on the paternal allele. In the remaining eight families, the risk haplotype could not be established due to the absence of iSNVs linked to the mutation or inability to successfully target the region of interest. During the time of the study, 12/24 successfully analyzed couples entered the universal PGT program, and three disease-free children have been born. In parallel to universal PGT analysis, long-read amplicon sequencing of 13 TE biopsies was also performed, confirming the segregation of parental alleles in the embryo and the results of the universal PGT. LIMITATIONS, REASONS FOR CAUTION: The main limitation of this approach is that it remains targeted with the need to design locus-specific primers. Because of the restricted size of target amplicons, the region of interest may also remain non-informative in the absence of iSNVs. WIDER IMPLICATIONS OF THE FINDINGS: Targeted haplotyping via long-read amplicon sequencing, particularly using Oxford Nanopore Technologies, provides a valuable alternative for couples with de novo pathogenic variants that allows access to universal PGT. Moreover, the same approach can be used for direct mutation analysis in embryos, as a second line confirmation of the preclinical PGT result or as a potential alternative PGT procedure in couples, where additional family members are not available. STUDY FUNDING/COMPETING INTEREST(S): This work was supported by KU Leuven funding (no. C1/018 to J.R.V.) and Fonds Wetenschappelijk Onderzoek (1241121N to O.T.). J.R.V. is co-inventor of a patent ZL910050-PCT/EP2011/060211-WO/2011/157846 'Methods for haplotyping single-cells' and ZL913096-PCT/EP2014/068315-WO/2015/028576 'Haplotyping and copy number typing using polymorphic variant allelic frequencies' licensed to Agilent Technologies. All other authors have no conflict of interest to declare. TRIAL REGISTRATION NUMBER: N/A.


Subject(s)
Preimplantation Diagnosis , Humans , Pregnancy , Child , Female , Male , Prospective Studies , Preimplantation Diagnosis/methods , Genetic Testing/methods , Aneuploidy , Mutation
20.
J Bioeth Inq ; 20(1): 41-49, 2023 03.
Article in English | MEDLINE | ID: mdl-36630060

ABSTRACT

Expanded non-invasive prenatal testing (NIPT) has provoked ethical concerns about its justifiable scope. In this paper, we evaluate the role of the child's right to an open future in setting the scope of NIPT. This 'open future principle' has been cited in arguments both limiting and expanding parental freedoms. This moral right holds that adult autonomy rights which children cannot yet exercise should nonetheless be protected until they can. Its purpose is to protect the future autonomy of the child as a future adult. Several authors have extended this rationale from child to fetus. However, the right was not anticipated to apply to the fetus, a non-legal entity in many jurisdictions. The aim of this paper is to reconsider whether this principle is useful to help deliberate the scope of NIPT. We find that extending the open future principle to delineate the scope of NIPT is theoretically flawed. We contend that in the prenatal context its value primarily lies with counselling for prenatal screening where it can be used to encourage parents' reflection on the implications of knowing for the sake of knowing on their future children and their relationship with them.


Subject(s)
Genetic Testing , Prenatal Diagnosis , Pregnancy , Female , Adult , Humans , Child , Fetus , Morals , Dissent and Disputes
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