Pregnancy complications contribute substantially to maternal and fetal morbidity and mortality. If complications are suspected early in pregnancy, individuals could be triaged to escalate care and ideally reduce adverse outcomes. However, clinical risk factors are poor predictors early in gestation. Cell-free DNA (cfDNA) fragmentomics has emerged as a promising biomarker in multiple disease states but has yet to be implemented in the prenatal setting. Here, we analyzed 1910 first-trimester blood cfDNA samples from pregnant individuals at high risk of an adverse pregnancy outcome (APO) because of twinning, a preexisting immune-mediated disease (IMD), or cytomegalovirus infection and from low-risk individuals. We extracted multimodal cfDNA fragmentome features, including transcriptome-aware cell-type composition estimates, end-motif frequencies and fragment length profiles, and trained models that could discriminate each high-risk group from controls, except diabetes. In IMDs, we further identified a cfDNA fragmentome profile associated with APOs in patients with clinically quiescent and serologically inactive disease. At a fixed false-positive rate of 10%, we could correctly discriminate 54, 38, 73, and 90% of patients with systemic IMD, thyroid-related IMD, Crohn’s disease, and psoriasis, respectively, who went on to have an APO from those who did not. These results were validated in an independent cohort of pregnant patients with IMD from an external center. The fragmentome was additive to and independent of clinical risk factors and fetal fraction estimates in stratifying APO risk in IMD. Overall, these findings support the further investigation of fragmentomics for triage of high-risk pregnant patients to improve prenatal care.

Cohesin orchestrates gene expression via three-dimensional chromosome folding. Genes encoding cohesin and cohesin loaders have been associated with Mendelian disorders, whereas genes encoding cohesin release factors, including WAPL and its binding partners PDS5A and PDS5B, have not. We explored the relevance of cohesin release factors in Mendelian disease by phenotyping individuals with heterozygous predicted damaging variants in WAPL (n = 27), PDS5A (n = 8), and PDS5B (n = 8), by modeling WAPL deficiency in human cells and mice, and by aggregating disease association statistics from consortia studies. We identified a WAPL-related disorder featuring developmental delay, intellectual disability, and risk of other developmental anomalies. Similarities between individuals with damaging WAPL variants and those with large, recurrent 10q22.3q23.2 (10q) deletions encompassing WAPL nominate WAPL as a driver gene within this genomic disorder region. While individuals with PDS5A or PDS5B variants exhibited features of developmental disorders, neither cohort-based statistics nor subject phenotyping associated these genes with specific phenotypes. We used CRISPR to generate truncating variants in WAPL and 10q deletion or duplication in human induced pluripotent stem cells (iPSCs) and induced neurons. Transcriptomics identified significant overlap between WAPL haploinsufficiency and 10q deletion differentially expressed genes. Mice with 50% Wapl expression exhibited mild deficits of growth and learning/memory, whereas those with 25% residual Wapl displayed birth defects and postnatal lethality, revealing a dosage liability threshold below the level of heterozygosity. In summary, we delineated a genetic condition caused by cohesin release factor deficiency, nominated WAPL as a driver gene within a genomic disorder region, and further illuminated dosage sensitivity of human cohesin.

Purpose: A substantial fraction of structural variants (SVs) and complex genomic regions escapes detection by short-read sequencing, while clinical epigenetic analyses remain restricted to a small number of targeted assays. Long-read sequencing (LRS) technologies represent a promising approach to reduce the diagnostic gap in genetic testing for developmental disorders (DD). Methods: We developed a comprehensive nanopore LRS analytical pipeline enabling detection of genetic and epigenetic variation and applied it to 28 patient-parents trios with unsolved DD following short read exome or genome sequencing. Results: LRS resolved nine (32.1%) of previously undiagnosed individuals and identified potential diagnoses in an additional six (21.4%). LRS was essential for the detection of three SVs of interest and one single nucleotide variant (SNV) and allowed detection of three (likely) pathogenic SNVs missed by exome sequencing. Systematic methylation analysis revealed skewed X-inactivation, an isolated imprinting defect as well as disease-associated episignatures. Conclusion: The added diagnostic yield attributable to LRS was 7.1%, rising to 14.3% when potential diagnoses were included, highlighting the value of LRS in reducing the diagnostic gap while streamlining the diagnostic workflow. Concurrent methylation profiling provides functional context that may help prioritize and interpret SVs, addressing one of the major remaining challenges associated with their increased detection.

Cohesin is a fundamental genome-organizing complex that orchestrates three-dimensional chromosome folding and gene expression via DNA loop extrusion. Alterations to genes encoding cohesin subunits and cohesin loaders cause Mendelian disorders, including Cornelia de Lange syndrome (CdLS). By contrast, disruption of factors that remove cohesin from DNA, including WAPL and its binding partners PDS5A and PDS5B, have not yet been associated with human disease. Here, we explored the relevance of these cohesin release factors in Mendelian disease by establishing a rare disease cohort of deeply phenotyped individuals with heterozygous, predicted damaging variants in WAPL (n=27), PDS5A (n=8), and PDS5B (n=8), by modeling WAPL deficiency in human cell lines and mice, and by aggregating rare disease association statistics from consortia studies. We identified a WAPL-related disorder characterized by developmental delay, intellectual disability, and risk of other developmental anomalies including clubfoot. Similarities between individuals with damaging WAPL variants and those with large, recurrent 10q22.3q23.2 (10q) deletions (which encompass WAPL) nominate WAPL as a driver gene within this genomic disorder region. While carriers of PDS5A or PDS5B variants exhibited features of developmental disorders, neither cohort-based statistics nor case phenotyping associated these genes with specific phenotypes. We used CRISPR engineering to generate truncating variants in WAPL, as well the 7.8 Mb 10q deletion or duplication in human iPSCs and induced neurons. Transcriptomic analyses identified differentially expressed genes in both models, with highly significant overlap between WAPL haploinsufficiency and 10q deletion signatures. Mice with 50% residual Wapl expression exhibited mild deficits of growth and learning/memory, whereas those with 25% residual Wapl expression displayed birth defects and postnatal lethality, revealing a dosage liability threshold below the level of heterozygosity. In summary, we delineated a novel genetic condition caused by cohesin release factor deficiency, nominated WAPL as a driver gene within a genomic disorder region, and further illuminated dosage sensitivity of human cohesin.

ABSTRACT Background Sickle cell anemia (SCA) is highly prevalent in Central Africa. This disease causes severe manifestations in children, requiring treatment. Hydroxyurea (HU) is currently the most effective treatment for SCA. We evaluated the use of HU in children living in rural Central Africa. Methods We conducted a clinical trial using HU in the Kisantu Saint Luc Hospital (KSLH) in the DR Congo (DRC) from November 2017 to February 2020. SCA patients aged 6 months to 18 years, with a moderate to severe form of SCA (Adegoke score), were treated with an entry HU dose of 15 mg/kg per day, followed with gradual dose escalation of 5 mg/kg per day increments every 6 months, up to a maximally tolerated dose of 30 mg/Kg/day. To determine the clinical and biological response to the treatment (efficacy of HU), we compared the clinical and biological data collected during the first and second year of treatment to the baseline values. Results Sixty‐nine patients (37 boys and 32 girls; sex‐ratio M/F 1.15) were eligible for the clinical trial using HU. Only 39 patients remained at the end of the clinical trial (56.5%). On average, the HbF increased to 3‐fold at 12 months and 3.3‐fold at 24 months, which was significantly different to the baseline. Thirty‐seven (80.4%) patients presented a good clinical response, whereas 9 (19.6%) did not. Conclusion This clinical demonstrated the clinical and biological effectiveness of HU treatment in a cohort of young Congolese patients. In addition to tremendous logistical challenges, low adherence is the major threat to HU treatment in a rural area. There is a need to implement appropriate strategies to increase the adherence to the HU treatment in these rural settings. Trial Registration: ClinicalTrials.gov identifier: NCT05681598

OBJECTIVE:Prenatal cell-free DNA screening is widely used to assess the risk of fetal trisomy 21, 18, and 13. Although commercial and laboratory-developed tests (LDTs) show high accuracy in validation studies, real-world longitudinal performance data are lacking. METHOD:In Belgium, prenatal cell-free DNA screening is a population screening offered to all pregnant people, regardless of their a priori risk. Over 3 years, all confirmatory diagnostic tests after a positive prenatal cell-free DNA screening result were recorded along with the technologies used and their outcomes. Positive predictive values (PPVs) for the three common fetal trisomies were calculated per technology. RESULTS:A total of 1158 diagnostic tests were performed after a positive prenatal cell-free DNA screening. Of these, 58.5% came from an LDT, 15.7% from VeriSeq (Illumina), 6.6% from Harmony (Roche), 5% from Vanadis (Perkin-Elmer); for 14.2% the technology could not be traced. PPVs ranged from 92.2% to 65.7% for trisomy 21, from 82.8% to 44.4% for trisomy 18, and from 40% to 18.2% for trisomy 13. Overall, the LDT performed better than the commercial tests. CONCLUSION:This study confirms the reported accuracy of commercial tests and LDT, while showing that LDT generally outperforms commercial tests. Despite high specificities across tests, differences in PPVs significantly impact pregnant people and the national health care system.

The rare X-linked female-restricted Hardikar syndrome (HDKR, OMIM # 301068) is characterized by multiple congenital anomalies including orofacial clefts, gastrointestinal, genitourinary, and cardiac anomalies, but cognitive and neurobehavioral development is rarely impaired. HDKR is caused by heterozygous frameshift, splice or nonsense variants in the MED12 gene. Besides HDKR, MED12 pathogenic variants cause a broad spectrum of developmental disorders, collectively referred to as MED12-related disorders, including Opitz-Kaveggia syndrome or FG syndrome type 1 (OKS, OMIM #305450), Lujan-Fryns syndrome (MRXSLF, OMIM #309520), X-linked Ohdo syndrome (OHDOX, OMIM #300895) and isolated intellectual disability. Here we report four individuals with HDKR, including the first of maternally inherited HDKR, and we review molecular and clinical data from 33 individuals with HDKR and 215 individuals with other MED12-related disorders retrieved through a literature and public database search. We highlight sella turcica cysts as a new Hardikar syndrome-related feature, and we introduce clinical guidelines for the diagnosis and management of individuals with HDKR.

Developmental disorders (DD), including intellectual disability (ID) and birth defects, affect approximately 7% of individuals worldwide, contributing to high mortality and lifelong morbidity. These disorders impose significant financial and psychological burdens on affected families. Genetic causes are identified in over 40% of DD cases, but diagnostic challenges, lack of appropriate management and curative treatments, and limited knowledge of natural history complicate management. Genetic testing, such as exome sequencing, is the standard diagnostic approach in developed countries. However, access to genetics services in low- and middle-income countries remains limited. Key barriers include poor access to specialist services in general, limited infrastructure, insufficient expertise in medical genetics, and outdated medical training curricula. The Deciphering Developmental Disorders in Africa (DDD-Africa) international training program initiative aims to address some of these disparities by establishing a network of trained professionals across African countries. This network will drive genomic research by identifying patients with DD, assessing them appropriately to direct genomic testing, and providing support to affected families. The training program consists of three phases: (1) an online course covering training in current core medical genetics concepts, (2) a 2-week on-site practical training in Johannesburg in identification, clinical assessment, and variant interpretation of DD patients, and (3) a hands-on implementation of the complete diagnostic process with four families recruited at each team's home institute. The program trains healthcare professionals consisting of a clinician and laboratory scientist together, emphasizing the need for collaboration and a comprehensive understanding of integrated genetic clinical assessment and laboratory diagnostics. Ultimately, the initiative seeks to enhance diagnostic capabilities and family support, fostering a strong pan-African network in the field of DD.

INTRODUCTION:Dysmorphism is an important characteristic, but its evaluation is largely subjective. A good clinical assessment (dysmorphism) can facilitate a more accurate and efficient diagnosis. We therefore evaluated an automated artificial intelligence tool for facial dysmorphism, D-score, available in Face2Gene. METHODOLOGY:We evaluated 2D frontal facial photographs of pediatric individuals with a developmental delay/intellectual disability from the Democratic Republic of Congo (144) and Belgium (137) as being dysmorphic or not, first clinically, and second by D-score analysis. We determined the performance of D-score by calculating sensitivity, specificity, positive predictive value, negative predictive value, F1-score and Cohen's Kappa (κ). We also evaluated the effects of sex, age, and ethnicity on D-Score. RESULTS:Of the 144 Congolese children, 69 (47.9%) were dysmorphic, compared to 40.9% in the Belgian cohort. D-score in the Congolese cohort showed a sensitivity of 85.5%, a specificity of 68%, a PPV of 71.1%, and an NPV of 83.6%. The F1-score was 0.78. The k was 0.531 (0.395-0.666) with a standard error of 0.069, p = 0.000. In the Belgian cohort, sensitivity was 71.4%, specificity 71.6%, PPV 63.5%, and NPV 78.4%. The F1-score was 0.672. The k was 0.422 (0.270-0.574) with a standard error of 0.078, p = 0.000. There was no statistically significant difference depending on age and sex. CONCLUSION:D-score is not replacing the gestalt facial evaluation, but it is promising to be used in clinical practice as a supplementary tool for precision in the dysmorphism evaluation, especially when dealing with rare or less common genetic conditions.

Purpose: ARID1A/ARID1B haploinsufficiency leads to Coffin-Siris syndrome, duplications of ARID1A lead to a distinct clinical syndrome, whilst ARID1B duplications have not yet been linked to a phenotype. Methods: We collected patients with duplications encompassing ARID1A and ARID1B duplications. Results: 16 ARID1A and 13 ARID1B duplication cases were included with duplication sizes ranging from 0.1 to 1.2 Mb (1-44 genes) for ARID1A and 0.9 to 10.3 Mb (2-101 genes) for ARID1B. Both groups shared features, with ARID1A patients having more severe intellectual disability, growth delay, and congenital anomalies. DNA methylation analysis showed that ARID1A patients had a specific methylation pattern in blood, which differed from controls and from patients with ARID1A or ARID1B loss-of-function variants. ARID1B patients appeared to have a distinct methylation pattern, similar to ARID1A duplication patients, but further research is needed to validate these results. Five cases with duplications including ARID1A or ARID1B initially annotated as duplications of uncertain significance were evaluated using PhenoScore and DNA methylation reanalysis, resulting in the reclassification of 2 ARID1A and 2 ARID1B duplications as pathogenic. Conclusion: Our fi ndings reveal that ARID1B duplications manifest a clinical phenotype, and ARID1A duplications have a distinct episignature that overlaps with that of ARID1B duplications, providing further evidence for a distinct and emerging BAFopathy caused by whole-gene duplication rather than haploinsufficiency. (c) 2024 The Authors. Published by Elsevier Inc. on behalf of American College of Medical Genetics and Genomics. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

A subset of developmental disorders (DD) is characterized by disease-specific genome-wide methylation changes. These episignatures inform on the underlying pathogenic mechanisms and can be used to assess the pathogenicity of genomic variants as well as confirm clinical diagnoses. Currently, the detection of these episignature requires the use of indirect methylation profiling methodologies. We hypothesized that long-read whole genome sequencing would not only enable the detection of single nucleotide variants and structural variants but also episignatures. Genome-wide nanopore sequencing was performed in 40 controls and 20 patients with confirmed or suspected episignature-associated DD, representing 13 distinct diseases. Following genomic variant and methylome calling, hierarchical clustering and dimensional reduction were used to determine the compatibility with microarray-based episignatures. Subsequently, we developed a support vector machine (SVM) for the detection of each DD. Nanopore sequencing-based methylome patterns were concordant with microarray-based episignatures. Our SVM-based classifier identified the episignatures in 17/19 patients with a (likely) pathogenic variant and none of the controls. The remaining patients in which no episignature was identified were also classified as controls by a commercial microarray assay. In addition, we identified all underlying pathogenic single nucleotide and structural variants and showed haplotype-aware skewed X-inactivation evaluation directs clinical interpretation. This proof-of-concept study demonstrates nanopore sequencing enables episignature detection. In addition, concurrent haplotyped genomic and epigenomic analyses leverage simultaneous detection of single nucleotide/structural variants, X-inactivation, and imprinting, consolidating a multi-step sequential process into a single diagnostic assay.

Exome (ES) or genome (GS) sequencing are recommended as first- or second-tier molecular tests for patients with developmental disorders (DD), but the clinical utility of GS continues to be debated. This prospective randomized trial involving all Belgian Human Genetics centers compared the standard of care (SoC) - combining ES and chromosomal microarray analysis or shallow GS - with GS for 567 individuals with unexplained DD. The diagnostic yield of GS was 39.8% (113/284) vs 30% for SoC (85/283) (p=0.015), mainly due to an increased detection of single nucleotide variants and indels (+8.7%). GS also enabled the detection of three non-coding (potential) pathogenic variants. Diagnostic yield was higher for females (45.5%, 97/213) compared to males (28.5%, 101/354) (p<0.001). De novo variants were found for 23.6% of patients. Analysis of inherited variants in genes associated with autosomal dominant phenotypes contributed more to the diagnostic yield (3.9%) than X-linked variants (1.9%), and to a similar extent as autosomal recessive variants (4.1%). This nationwide study indicates GS outperforms SoC for the diagnosis of patients with DD in a decentralized hospital setting and well-characterized cohort. The results also highlight the importance of evaluating autosomal dominant inherited variants in genomics analyses for DD. ### Competing Interest Statement Illumina Inc. (San Diego, CA, USA) provided the consumables for WGS of the samples used for the ring trial and the 284 probands and their parent(s) sequenced in the WGS arm, as well as access to the Emedgene platform. ### Clinical Trial NCT07051213 ### Funding Statement Illumina Inc. (San Diego, CA, USA) provided the consumables for WGS of the samples used for the ring trial and the 284 probands and their parent(s) sequenced in the WGS arm, as well as access to the Emedgene platform. This work was additionally supported by grants from the KU Leuven, C1-C14/22/125 and by FWO-TBM grant T-003819N, FWO grant G0A2622N to VJR. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The Ethical Commission of the University Hospitals of Leuven (UZ Leuven) gave ethical approval for this work (S64603). I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes Information regarding the phenotype and molecular diagnosis of study participants are shared in the supplementary files. The raw sequencing data generated during this study will be shared on EGA (EGAC00001003120).

PURPOSE/INTRODUCTION:Inherited retinal disorders (IRD) are a highly heterogeneous group of retinal diseases often characterized by progressive bilateral degeneration of rod and cone photoreceptors. Very little information is available on the genotype and phenotype of IRD in Central Africa. We investigated genetic causes of IRD in a well-characterized group of patients from the Democratic Republic of Congo (DRC). MATERIALS AND METHODS:Ten patients, from eight families, with a clinical diagnosis of IRD in Kinshasa (DRC) were investigated. Each patient underwent general, dysmorphological and ophthalmic examination. DNA was extracted in the Centre for Human Genetics of the University of Kinshasa and clinical Whole Genome Sequencing (cWGS) was performed at Illumina Clinical Service Laboratory through the Illumina iHope program. RESULTS:The eight probands comprised 4 males and 4 females aged between 17.5 and 76 years. Nyctalopia and reduced visual acuity were the main complaints. All patients had normal hearing and were nondysmorphic. Fundus examination revealed bone-spicule pigment in all patients. Twelve plausible causal variants were identified in six genes: ADAM9, RP1, MERTK, CYP4V2, USH2A, and IFT140. One SNV and one intragenic CNV were novel. The SNV was assumed to be in trans with an intragenic SNV in three families, consistent with the well-known autosomal recessive inheritance for IRD in those genes. CONCLUSION:We report on the first cohort of African IRD patients investigated by cWGS. Our results indicate that also in Congolese patients, the spectrum of causal genes is broad and we expand the spectrum of causal variants in known IRD genes. This report demonstrates the power of cWGS, especially for genetically heterogeneous diseases.

Genotype imputation from low-pass sequencing data presents unique opportunities for genomic analyses but comes with specific challenges. In this study, we explore the impact of quality filters on genetic ancestry and Polygenic Score (PGS) estimation after imputing 32,769 low-pass genome-wide sequences (LPS) from noninvasive prenatal screening (NIPS) with an average autosomal sequence depth of ∼0.15×. In studies involving ultra-low coverage sequences, conventional approaches to secure genotype accuracy may fail, especially when multiple samples are pooled. To enhance the proportion of high-quality genotypes in large data sets, we introduce a filtering approach called GDI that combines genotype probability (GP), alternate allele dosage (DS), and INFO score filters. We demonstrate that the imputation tools QUILT and GLIMPSE2 achieve similar accuracy, which is high enough for broad-scale ancestry mapping but insufficient for high resolution principal component analysis (PCA), when applied without filters. With the GDI approach, we can achieve quality that is adequate for such purposes. Furthermore, we explored the impact of imputation errors, choice of variants, and filtering methods on PGS prediction for height in 1911 subjects with height data. We show that polygenic scores predict 23.7% of variance in height in our imputed data and that, contrary to the effect on PCA, the GDI filter does not improve the performance of PGS in height prediction. These results highlight that imputed LPS data can be leveraged for further biomedical and population genetic use, but there is a need to consider each downstream analysis tool individually for its imputation quality thresholds and filtering requirements.

ABSTRACTBackgroundA subset of developmental disorders (DD) is characterized by disease-specific genome-wide methylation changes. These episignatures inform about underlying pathogenic mechanisms and can be used to assess the pathogenicity of genomic variants as well as confirm clinical diagnoses. Currently, episignature detection requires the use of indirect methylation profiling microarrays. We hypothesized that long-read whole genome sequencing would not only enable the detection of single nucleotide variants and structural variants but also episignatures.MethodsGenome-wide nanopore sequencing was performed in forty controls and twenty patients with confirmed or suspected episignature-associated DD, representing thirteen distinct diseases. Following variant and methylome calling, hierarchical clustering and dimensional reduction were used to determine the compatibility with microarray-based episignatures. Subsequently, we developed a support vector machine for each DD.ResultsNanopore sequencing based methylome patterns were concordant with microarray-based episignatures. Our classifier identified episignatures in 17/20 disease samples and none of the controls. The remaining three patient samples were classified as controls by both our classifier and a commercial microarray assay. In addition, we identified all underlying pathogenic single nucleotide and structural variants and showed haplotype-aware skewed X-inactivation evaluation directs clinical interpretation.ConclusionThis proof-of-concept study demonstrates nanopore sequencing enables concurrent haplotyped genomic and epigenomic analyses.

Recognizing Mendelian causes is crucial in molecular diagnostics and counseling for patients with autism spectrum disorder (ASD). We explored facial dysmorphism and facial asymmetry in relation to genetic causes in ASD patients and studied the potential of objective facial phenotyping in discriminating between Mendelian and multifactorial ASD. In a cohort of 152 ASD patients, 3D facial images were used to calculate three metrics: a computational dysmorphism score, a computational asymmetry score, and an expert dysmorphism score. High scores for each of the three metrics were associated with Mendelian causes of ASD. The computational dysmorphism score showed a significant correlation with the average expert dysmorphism score. However, in some patients, different dysmorphism aspects were captured making the metrics potentially complementary. The computational dysmorphism and asymmetry scores both enhanced the individual expert dysmorphism scores in differentiating Mendelian from non-Mendelian cases. Furthermore, the computational asymmetry score enhanced the average expert opinion in predicting a Mendelian cause. By design, our study does not allow to draw conclusions on the actual point-of-care use of 3D facial analysis. Nevertheless, 3D morphometric analysis is promising for developing clinical dysmorphology applications in diagnostics and training.

IntroductionAround 1 in 1000–2000 pregnancies are affected by a cancer diagnosis. Previous studies have shown that chemotherapy during pregnancy has reassuring cognitive and cardiac neonatal outcomes, and hence has been proposed as standard of care. However, although these children perform within normal ranges for their age, subtle differences have been identified. Given that chemotherapeutic compounds can cross the placenta, the possibility that prenatal chemotherapy exposure mutates the offspring’s genome and/or epigenome, with potential deleterious effects later in life, urges to be investigated.Methods and analysesThis multicentric observational study aims to collect cord blood, meconium and neonatal buccal cells at birth, as well as peripheral blood, buccal cells and urine from infants when 6, 18 and/or 36 months of age. Using bulk and single-cell approaches, we will compare samples from chemotherapy-treated pregnant patients with cancer, pregnant patients with cancer not treated with chemotherapy and healthy pregnant women. Potential chemotherapy-related newborn genomic and/or epigenomic alterations, such as single nucleotide variants, copy number variants and DNA-methylation alterations, will be identified in mononuclear and epithelial cells, isolated from blood, buccal swabs and urine. DNA from maternal peripheral blood and paternal buccal cells will be used to determine de novo somatic mutations in the neonatal blood and epithelial cells. Additionally, the accumulated exposure of the fetus, and biological effective dose of alkylating agents, will be assessed in meconium and cord blood via mass spectrometry approaches.Ethics and disseminationThe Ethics Committee Research of UZ/KU Leuven (EC Research) and the Medical Ethical Review Committee of University Medical Center Amsterdam have approved the study. Results of this study will be disseminated via presentations at (inter)national conferences, through peer-reviewed, open-access publications, via social media platforms aimed to inform patients and healthcare workers, and through the website of the International Network on Cancer, Infertility and Pregnancy (www.cancerinpregnancy.org).

Here we report the case of a young boy with developmental delay, thin sparse hair, early closure of the anterior fontanel, bilateral choanal atresia, brachyturicephaly; and dysmorphic features closely resembling those seen in trichorhinophalangeal syndrome (TRPS). These features include sparse hair, sparse lateral eyebrows, a bulbous pear shaped nose, a long philtrum, thin lips, small/hypoplastic nails, pes planovalgus; bilateral cone-shaped epiphyses at the proximal 5th phalanx, slender long bones, coxa valga, mild scoliosis, and delayed bone age.Given that TRPS had been excluded by a thorough genetic analysis, whole exome sequencing was performed and a heterozygous likely pathogenic variant was identified in the FBXO11 gene (NM_001190274.2: c.1781A>G; p.His594Arg), confirming the diagnosis of the newly individualized IDDFBA syndrome: Intellectual Developmental Disorder, dysmorphic Facies, and Behavioral Abnormalities (OMIM# 618089)Our findings further delineate the clinical spectrum linked to FBXO11 and highlight the importance of investigating further cases with mutations in this gene to establish a potential genotype-phenotype correlation.