Medical Genetics & Functional Genomics

ABSTRACTMiller syndrome (MIM#263750) is a rare autosomal recessive acrofacial dysostosis associated with biallelic DHODH variants. Since the identification of the gene in 2010, five case reports have described a variable phenotype in only nine individuals from eight families. We present a cohort of 10 individuals from seven families affected by Miller syndrome, spanning the prenatal stage to 46 years of age. We report on the largest cohort of Miller syndrome to date, which highlights novel findings, including optic atrophy in multiple members of one consanguineous family. The typical postaxial limb defects, including the absence of the 5th digit, were consistent with prior descriptions, but we highlighted the frequent involvement of preaxial structures (thumb and tibial hypoplasia). A higher incidence of camptodactyly and the presence of facial nevus in two patients were notable findings. Congenital heart defects, primarily atrial septal defects, were common, and all living individuals had normal neurodevelopment. This cohort expands the phenotypic spectrum of Miller syndrome associated with variation in DHODH, presenting new findings such as preaxial involvement and facial nevus simplex. Optic atrophy in one family could prompt screening of other cases. Early prenatal diagnosis, particularly in the presence of cardinal limb and cardiac malformations, is crucial for management and genetic counseling.

What is the optimal stage (immature vs mature) and most efficient vitrification technique (semi-automated vs manual) to ensure the safety of the rescue-IVM (r-IVM) procedure for oocyte cryopreservation? Human oocytes should be cryopreserved after r-IVM at the mature stage (r-MII oocytes) by semi-automated or manual vitrification. r-IVM of immature oocytes may increase the number of oocytes cryopreserved for fertility preservation. However, the best stage and vitrification system (semi-automated or manual) for cryopreserving oocytes with the least possible impact on nuclear quality is unclear. From January 2020 to June 2024, a prospective study was conducted on patients undergoing ICSI, including cases with at least one immature germinal vesicle (GV) stage oocyte on the day of oocyte collection, resulting in a total of 414 oocytes. The study included 175 patients under 37 years old with no ovulatory disorder and undergoing ICSI. A total of 414 immature oocytes were collected and divided into five groups. The control group included fresh in vitro-matured oocytes (IVM, n = 81). After r-IVM, oocytes were vitrified by a semi-automated technique (IVM+VITg group, n = 63) or a closed manual procedure (IVM+VITm group, n = 66). Before r-IVM, oocytes were vitrified using both techniques (VITg+IVM group, n = 113 and VITm+IVM group, n = 91). The fresh IVM group combined IVM, IVM+VITg, and IVM+VITm groups.Survival rates of oocytes were evaluated 2-h post-warming. r-IVM was performed in a time-lapse incubator , allowing the assessment of r-IVM rates and maturation kinetics, including GV breakdown (GVBD) and first polar body extrusion timings. We assessed the quality of oocyte nuclear maturation through the evaluation of meiotic spindle polarity and chromosomes alignment by 3D analysis of confocal microscopy images and aneuploidy rate by array-CGH (a-CGH). The oocyte post-warming survival rate was lower when semi-automated vitrification was performed before r-IVM (50% for VITg+IVM group) compared with the three other groups (88% for IVM+VITg, 93% for IVM+VITm, and 80% for VITm+IVM, adjusted P-value < 0.001). IVM rates were not different between the three groups (fresh IVM: 80%, VITg+IVM: 80% and VITm+IVM: 69%, Pa = 0.131). Longer GVBD timings were observed when semi-automated vitrification was performed before r-IVM (VITg+IVM: 10.4 h) compared with Fresh IVM (7.9 h, Pa = 0.003). The percentages of oocytes with bipolar spindles or/and aligned chromosomes were not different between the five groups. Similarly, there was no difference in aneuploidy rates (monosomy or trisomy) between the five study groups (Pa = 0.847). Shorter GVBD timings were observed for oocytes with a bipolar spindle or aligned chromosomes (7.8 h) than for oocytes with a non-bipolar spindle or misaligned chromosomes (10.1 h, Pa = 0.011). The results are limited to the type of biological samples (GV-stage immature oocytes from stimulated ovaries) and the defined study population (patients < 37 years old without ovulatory disorders) used in this study. Furthermore, additional research is required to evaluate the ability of oocytes to undergo successful fertilization and embryo development, as well as their capacity to result in a live birth. Our findings provide reassurance regarding the use of semi-automated technique after r-IVM in clinics to optimize and standardize oocyte vitrification. The emerging field of r-IVM combined with cryopreservation by vitrification represents a promising option for fertility preservation, particularly for patients with a poor response to ovarian stimulation. Moreover, our study has revealed a previously unidentified correlation between extended GVBD timing and aberrant spindle morphology and chromosome misalignment. This provides a promising new non-invasive marker of nuclear oocyte quality for use in clinical practice. This study was funded by the French Biomedicine Agency (grant number: ABM 20AMP004) and the University Hospital of Clermont-Ferrand (France, Bourse Innovation). There are no conflicts of interest to be declared for any of the authors. There are no patents, products in development, or marketed products to declare. ClinicalTrials.gov ID NCT03680937.

Abstract In 30-40% of fetuses with structural defects, the causal variant remains undiagnosed after karyotype, chromosomal microarray and exome sequencing. This study presents the results of a reanalysis of unsolved prenatal ES (pES) and investigates how postnatal/postmortem phenotyping contributes to identify relevant variants. Prospective reanalysis of pES data was performed in undiagnosed fetuses enrolled in the AnDDI-Prénatome cohort study. Postnatal/postmortem data up to 3 years were merged with prenatal features using HPO terms. The reanalysis involved updating the bioinformatic processing of raw data and periodic querying of the raw pES data using a GREP query. The reanalysis was performed in 58/94 (62%) unsolved pES, including 8 variants of unknown significance. Clinical examination at birth was available for all live newborns, and postmortem examination was available in 12 terminated fetuses. Additional features were identified in 27/58 fetuses (44%). The contribution of updated postnatal/postmortem phenotyping to the identification of relevant variants was limited. Only one new diagnosis was made, but thanks to the new implication of the SNAPC4 gene in the human disease rather than the additional clinical data provided by the postnatal update of the phenotype. Only one of the three additional VUS identified by reanalysis was also considered thanks to additional features provided by postmortem examination. In conclusion, in cases of unsolved pES, the benefit of prospective reanalysis of unsolved pES appears to be limited, even over time. It may be more appropriate to offer postnatal genome sequencing rather than pES reanalysis with postnatal/postmortem phenotyping update to establish a causal diagnosis.

Dilated cardiomyopathy (DCM) is a clinical disorder characterised by reduced contractility of the heart muscle that is not explained by coronary artery disease or abnormal haemodynamic loading. Although Mendelian disease is well described, clinical testing yields a genetic cause in a minority of patients. The role of complex inheritance is emerging, however the common genetic architecture is relatively unexplored. To improve our understanding of the genetic basis of DCM, we perform a genome-wide association study (GWAS) meta-analysis comprising 14,255 DCM cases and 1,199,156 controls, and a multi-trait GWAS incorporating correlated cardiac magnetic resonance imaging traits of 36,203 participants. We identify 80 genetic susceptibility loci and prioritize 61 putative effector genes for DCM by synthesizing evidence from 8 gene prioritization strategies. Rare variant association testing identifies genes associated with DCM, includingMAP3K7, NEDD4L, andSSPN. Through integration with single-nuclei transcriptomics from 52 end-stage DCM patients and 18 controls, we identify cellular states, biological pathways, and intercellular communications driving DCM pathogenesis. Finally, we demonstrate that a polygenic score predicts DCM in the general population and modulates the penetrance of rare pathogenic and likely pathogenic variants in DCM-causing genes. Our findings may inform the design of novel clinical genetic testing strategies incorporating polygenic background and the genes and pathways identified may inform the development of targeted therapeutics.

Le phéochromocytome est très rare pendant la grossesse et peut avoir une évolution fatale s’il n’est pas détecté. Les défis diagnostiques et thérapeutiques sont décrits à l’aide de quatre vignettes de cas, et l’épidémiologie est discutée.

BackgroundArray-CGH is the first-tier genetic test both in pre- and postnatal developmental disorders worldwide. Variants of uncertain significance (VUS) represent around 10~15% of reported copy number variants (CNVs). Even though VUS reanalysis has become usual in practice, no long-term study regarding CNV reinterpretation has been reported.MethodsThis retrospective study examined 1641 CGH arrays performed over 8 years (2010–2017) to demonstrate the contribution of periodically re-analyzing CNVs of uncertain significance. CNVs were classified using AnnotSV on the one hand and manually curated on the other hand. The classification was based on the 2020 American College of Medical Genetics (ACMG) criteria.ResultsOf the 1641 array-CGH analyzed, 259 (15.7%) showed at least one CNV initially reported as of uncertain significance. After reinterpretation, 106 of the 259 patients (40.9%) changed categories, and 12 of 259 (4.6%) had a VUS reclassified to likely pathogenic or pathogenic. Six were predisposing factors for neurodevelopmental disorder/autism spectrum disorder (ASD). CNV type (gain or loss) does not seem to impact the reclassification rate, unlike the length of the CNV: 75% of CNVs downgraded to benign or likely benign are less than 500 kb in size.ConclusionsThis study’s high rate of reinterpretation suggests that CNV interpretation has rapidly evolved since 2010, thanks to the continuous enrichment of available databases. The reinterpreted CNV explained the phenotype for ten patients, leading to optimal genetic counseling. These findings suggest that CNVs should be reinterpreted at least every 2 years.

Embryonic development is dictated by tight regulation of DNA replication, cell division and differentiation. Mutations in DNA repair and replication genes disrupt this equilibrium, giving rise to neurodevelopmental disease characterized by microcephaly, short stature and chromosomal breakage. Here, we identify biallelic variants in two components of the RAD18-SLF1/2-SMC5/6 genome stability pathway, SLF2 and SMC5, in 11 patients with microcephaly, short stature, cardiac abnormalities and anemia. Patient-derived cells exhibit a unique chromosomal instability phenotype consisting of segmented and dicentric chromosomes with mosaic variegated hyperploidy. To signify the importance of these segmented chromosomes, we have named this disorder Atelís (meaning - incomplete) Syndrome. Analysis of Atelís Syndrome cells reveals elevated levels of replication stress, partly due to a reduced ability to replicate through G-quadruplex DNA structures, and also loss of sister chromatid cohesion. Together, these data strengthen the functional link between SLF2 and the SMC5/6 complex, highlighting a distinct role for this pathway in maintaining genome stability.