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Abstract A growing number of druggable targets and national initiatives for precision oncology necessitate broad genomic profiling for many cancer patients. Whole exome sequencing (WES) offers unbiased analysis of the entire coding sequence, segmentation-based detection of copy number alterations (CNAs), and accurate determination of complex biomarkers including tumor mutational burden (TMB), homologous recombination repair deficiency (HRD), and microsatellite instability (MSI). To assess the inter-institution variability of clinical WES, we performed a comparative pilot study between German Centers of Personalized Medicine (ZPMs) from five participating institutions. Tumor and matched normal DNA from 30 patients were analyzed using custom sequencing protocols and bioinformatic pipelines. Calling of somatic variants was highly concordant with a positive percentage agreement (PPA) between 91 and 95% and a positive predictive value (PPV) between 82 and 95% compared with a three-institution consensus and full agreement for 16 of 17 druggable targets. Explanations for deviations included low VAF or coverage, differing annotations, and different filter protocols. CNAs showed overall agreement in 76% for the genomic sequence with high wet-lab variability. Complex biomarkers correlated strongly between institutions (HRD: 0.79–1, TMB: 0.97–0.99) and all institutions agreed on microsatellite instability. This study will contribute to the development of quality control frameworks for comprehensive genomic profiling and sheds light onto parameters that require stringent standardization.

Abstract Background Congenital hydrocephalus is characterized by ventriculomegaly, defined as a dilatation of cerebral ventricles, and thought to be due to impaired cerebrospinal fluid (CSF) homeostasis. Primary congenital hydrocephalus is a subset of cases with prenatal onset and absence of another primary cause, e.g., brain hemorrhage. Published series report a Mendelian cause in only a minority of cases. In this study, we analyzed exome data of PCH patients in search of novel causal genes and addressed the possibility of an underlying oligogenic mode of inheritance for PCH. Materials and methods We sequenced the exome in 28 unrelated probands with PCH, 12 of whom from families with at least two affected siblings and 9 of whom consanguineous, thereby increasing the contribution of genetic causes. Patient exome data were first analyzed for rare (MAF

Tetrasomy 9p is a chromosomal disorder characterized by the presence of a supernumerary chromosome. This rare abnormality exhibits a broad phenotypic variability and is not clearly distinguishable from other more frequent aneuploidies in the prenatal setting. We present two prenatal cases with dissimilar phenotypes, one with solely increased fetal nuchal translucency and one with multiple congenital anomalies, and discuss prior studies. These cases illustrate the difficulty of prenatally diagnosing this condition based on phenotypic information alone. We conclude that invasive prenatal diagnosis with (molecular) karyotyping is the best choice for the prenatal detection of tetrasomy 9p.

We present a case of a fetus with cranial abnormalities typical of open spina bifida but with an intact spine shown on both ultrasound and fetal MRI. Expert ultrasound examination revealed a very small tract between the spine and the skin, and a postmortem examination confirmed the diagnosis of a dorsal dermal sinus. Genetic analysis found a mosaic 3q23q27 duplication in the form of a marker chromosome. This case emphasizes that meticulous prenatal ultrasound examination has the potential to diagnose even closed subtypes of neural tube defects. Furthermore, with cerebral anomalies suggesting a spina bifida, other imaging techniques together with genetic tests and measurement of alpha-fetoprotein in the amniotic fluid should be performed.

Whole exome sequencing (WES) has become part of the postnatal diagnostic work-up of both pediatric and adult patients with a range of disorders. In the last years, WES is slowly being implemented in the prenatal setting as well, although some hurdles remain, such as quantity and quality of input material, minimizing turn-around times, and ensuring consistent interpretation and reporting of variants. We present the results of 1 year of prenatal WES in a single genetic center. Twenty-eight fetus-parent trios were analyzed, of which seven (25%) showed a pathogenic or likely pathogenic variant that explained the fetal phenotype. Autosomal recessive (4), de novo (2) and dominantly inherited (1) mutations were detected. Prenatal rapid WES allows for a timely decision-making in the current pregnancy, adequate counseling with the possibility of preimplantation or prenatal genetic testing in future pregnancies and screening of the extended family. With a diagnostic yield in selected cases of 25% and a turn-around time under 4 weeks, rapid WES shows promise for becoming part of pregnancy care in fetuses with ultrasound anomalies in whom chromosomal microarray did not uncover the cause.

Abstract In the age of noninvasive prenatal testing, there is still an important role for invasive prenatal diagnosis, even for chromosomes 13, 18, and 21.

Abstract Background Primary microcephaly (PM) is defined as a significant reduction in occipitofrontal circumference (OFC) of prenatal onset. Clinical and genetic heterogeneity of PM represents a diagnostic challenge. Methods We performed detailed phenotypic and genomic analyses in a large cohort (n = 169) of patients referred for PM and could establish a molecular diagnosis in 38 patients. Results Pathogenic variants in ASPM and WDR62 were the most frequent causes in non‐consanguineous patients in our cohort. In consanguineous patients, microarray and targeted gene panel analyses reached a diagnostic yield of 67%, which contrasts with a much lower rate in non‐consanguineous patients (9%). Our series includes 11 novel pathogenic variants and we identify novel candidate genes including IGF2BP3 and DNAH2. We confirm the progression of microcephaly over time in affected children. Epilepsy was an important associated feature in our PM cohort, affecting 34% of patients with a molecular confirmation of the PM diagnosis, with various degrees of severity and seizure types. Conclusion Our findings will help to prioritize genomic investigations, accelerate molecular diagnoses, and improve the management of PM patients.

Introduction: Organotypic Hippocampal Brain Slices (OHBS) provide a better alternative to in vivo models to scrutinize Traumatic Brain Injury (TBI). We followed a well-established TBI protocol but noticed that several factors might influence the results in such a set-up. Here, we describe a structured approach to generate more comparable results and discuss why specific eligibility criteria should be applied. Methods: We defined necessary checkpoints and developed inclusion and exclusion criteria that took into consideration the observed variation in such a model. Objective measures include the identification and exclusion of pre-damaged slices and outliers. In this study, six steps were outlined. Results: A six-step approach to enhance comparability is proposed and summarized in a flowchart. We applied the suggested measures to data derived from our TBI-experiments, examining the impact of three different interventions in 1459 OHBS. Our exemplary results show that more precise findings are ensured through equal requirements set for all slices. Conclusion: Results in a TBI experiment on OHBS should be critically analyzed as inhomogeneity may occur. In other words, a structured approach to comparing the results should be followed to ensure achieving more precise findings. Further research is recommended to confirm and further develop this framework.

Early amniocentesis (EA)—before 15 gestational weeks—is not recommended because of a high rate of miscarriages. Most studies performed amniocentesis at very early stages of pregnancy (11–13 weeks of gestational age). However, amniocentesis performed at 14 gestational weeks could be an important alternative to mid-trimester amniocentesis (MA) because it shortens the time period between the screening (non-invasive prenatal test (NIPT)) and the diagnostic test (amniocentesis). This study aimed to compare the procedure-related risk of miscarriage between MA (15 + 0 to 17 + 6 weeks of gestational age) and EA (14 + 0–6 weeks of gestational age). This is a multicentric, retrospective cohort study from 1 January 2007 to 21 November 2018, comparing the MA to the EA cohort. Procedure-related fetal loss is defined as spontaneous abortion occurring within 4 weeks of the procedure. Multiple gestations, amniocenteses performed after 17 or before 14 weeks, indications other than prenatal genetic diagnoses and procedures performed by less experienced gynaecologists were excluded. Complete outcome data were available for 1107 out of 1515 women (73.1%): 809 (69.9%) in the MA and 298 (83.2%) in the EA cohort. No significant difference was found (EA 0.82% vs. MA 0.36%; p = 0.646). The difference was 0.46% (odds ratio = 0.673; 95% confidence interval = 0.123–3.699). This study found no significant difference in the procedure-related risk of miscarriage when EA was compared to MA. EA might be considered a safe alternative, though further research is necessary.

Effective pharmacological neuroprotection is one of the most desired aims in modern medicine. We postulated that a combination of two clinically used drugs—nimodipine (L-Type voltage-gated calcium channel blocker) and amiloride (acid-sensing ion channel inhibitor)—might act synergistically in an experimental model of ischaemia, targeting the intracellular rise in calcium as a pathway in neuronal cell death. We used organotypic hippocampal slices of mice pups and a well-established regimen of oxygen-glucose deprivation (OGD) to assess a possible neuroprotective effect. Neither nimodipine (at 10 or 20 µM) alone or in combination with amiloride (at 100 µM) showed any amelioration. Dissolved at 2.0 Vol.% dimethyl-sulfoxide (DMSO), the combination of both components even increased cell damage (p = 0.0001), an effect not observed with amiloride alone. We conclude that neither amiloride nor nimodipine do offer neuroprotection in an in vitro ischaemia model. On a technical note, the use of DMSO should be carefully evaluated in neuroprotective experiments, since it possibly alters cell damage.

Solid catalysts with ionic liquid layers (SCILLs) are heterogeneous catalysts which benefit significantly in terms of selectivity from a thin coating of an ionic liquid (IL). In the present work, we study the interaction of CO with a Pd model SCILL consisting of a 1-butyl-1-methylpyrrolidinium bis(trifluoromethylsulfonyl)-imide ([C4C1Pyr][NTf2]) film deposited on Pd(111). We investigate the CO permeability and stability of the IL film via pressure modulation experiments by infrared reflection absorption spectroscopy (IRAS) in ultrahigh vacuum (UHV) and at ambient pressure conditions by time-resolved, temperature-programmed, and polarization-modulated (PM) IRAS experiments. In addition, we performed molecular dynamics (MD) simulations to identify adsorption motifs, their abundance, and the influence of CO. We find a strongly bound IL wetting monolayer (ML) and a potentially dewetting multilayer. Molecular reorientation of the IL at the interface and multilayer dewetting allow for the accumulation of CO at the metal/IL interface. Our results confirm that co-adsorption of CO changes the molecular structure of the IL wetting layer which confirms the importance to study model SCILL systems under in situ conditions. [ABSTRACT FROM AUTHOR]