Purpose:
Patients with rare or ultra-rare genetic diseases, which affect 350 million people worldwide, may experience a diagnostic odyssey. High-throughput sequencing leads to an etiological ...diagnosis in up to 50% of individuals with heterogeneous neurodevelopmental or malformation disorders. There is a growing interest in additional omics technologies in translational research settings to examine the remaining unsolved cases.
Methods:
We gathered 30 individuals with malformation syndromes and/or severe neurodevelopmental disorders with negative trio exome sequencing and array comparative genomic hybridization results through a multicenter project. We applied short-read genome sequencing, total RNA sequencing, and DNA methylation analysis, in that order, as complementary translational research tools for a molecular diagnosis.
Results:
The cohort was mainly composed of pediatric individuals with a median age of 13.7 years (4 years and 6 months to 35 years and 1 month). Genome sequencing alone identified at least one variant with a high level of evidence of pathogenicity in 8/30 individuals (26.7%) and at least a candidate disease-causing variant in 7/30 other individuals (23.3%). RNA-seq data in 23 individuals allowed two additional individuals (8.7%) to be diagnosed, confirming the implication of two pathogenic variants (8.7%), and excluding one candidate variant (4.3%). Finally, DNA methylation analysis confirmed one diagnosis identified by genome sequencing (Kabuki syndrome) and identified an episignature compatible with a BAFopathy in a patient with a clinical diagnosis of Coffin-Siris with negative genome and RNA-seq results in blood.
Conclusion:
Overall, our integrated genome, transcriptome, and DNA methylation analysis solved 10/30 (33.3%) cases and identified a strong candidate gene in 4/30 (13.3%) of the patients with rare neurodevelopmental disorders and negative exome sequencing results.
Background
Exome sequencing (ES) has become the most powerful and cost‐effective molecular tool for deciphering rare diseases with a diagnostic yield approaching 30%–40% in solo‐ES and 50% in ...trio‐ES. We applied an innovative parental DNA pooling method to reduce the parental sequencing cost while maintaining the diagnostic yield of trio‐ES.
Methods
We pooled six (Agilent‐CRE‐v2–100X) or five parental DNA (TWIST‐HCE–70X) aiming to detect allelic balance around 8–10% for heterozygous status. The strategies were applied as second‐tier (74 individuals after negative solo‐ES) and first‐tier approaches (324 individuals without previous ES).
Results
The allelic balance of parental‐pool variants was around 8.97%. Sanger sequencing uncovered false positives in 1.5% of sporadic variants. In the second‐tier approach, we evaluated than two thirds of the Sanger validations performed after solo‐ES (41/59–69%) would have been saved if the parental‐pool segregations had been available from the start. The parental‐pool strategy identified a causative diagnosis in 18/74 individuals (24%) in the second‐tier and in 116/324 individuals (36%) in the first‐tier approaches, including 19 genes newly associated with human disorders.
Conclusions
Parental‐pooling is an efficient alternative to trio‐ES. It provides rapid segregation and extension to translational research while reducing the cost of parental and Sanger sequencing.
We applied an innovative parental DNA pooling method to reduce the parental sequencing cost while maintaining the diagnostic yield of trio‐ES. Parental‐pooling is an efficient alternative to trio‐ES. It provides rapid segregation and extension to translational research while reducing the cost of parental and Sanger sequencing.
Obtaining a rapid etiological diagnosis for infants with early-onset rare diseases remains a major challenge. These diseases often have a severe presentation and unknown prognosis, and the genetic ...causes are very heterogeneous. In a French hospital network, we assessed the feasibility of performing accelerated trio-genome sequencing (GS) with limited additional costs by integrating urgent requests into the routine workflow. In addition to evaluating our capacity for such an approach, this prospective multicentre pilot study was designed to identify pitfalls encountered during its implementation. Over 14 months, we included newborns and infants hospitalized in neonatal or paediatric intensive care units with probable genetic disease and in urgent need for etiological diagnosis to guide medical care. The duration of each step and the pitfalls were recorded. We analysed any deviation from the planned schedule and identified obstacles. Trio-GS was performed for 37 individuals, leading to a molecular diagnosis in 18/37 (49%), and 21/37 (57%) after reanalysis. Corrective measures and protocol adaptations resulted in a median duration of 42 days from blood sampling to report. Accelerated trio-GS is undeniably valuable for individuals in an urgent care context. Such a circuit should coexist with a rapid or ultra-rapid circuit, which, although more expensive, can be used in particularly urgent cases. The drop in GS costs should result in its generalized use for diagnostic purposes and lead to a reduction of the costs of rapid GS.
Corramycin 1 is a novel zwitterionic antibacterial peptide isolated from a culture of the myxobacterium Corallococcus coralloides. Though Corramycin displayed a narrow spectrum and modest MICs ...against sensitive bacteria, its ADMET and physchem profile as well as its high tolerability in mice along with an outstanding in vivo efficacy in an Escherichia coli septicemia mouse model were promising and prompted us to embark on an optimization program aiming at enlarging the spectrum and at increasing the antibacterial activities by modulating membrane permeability. Scanning the peptidic moiety by the Ala-scan strategy followed by key stabilization and introduction of groups such as a primary amine or siderophore allowed us to enlarge the spectrum and increase the overall developability profile. The optimized Corramycin 28 showed an improved mouse IV PK and a broader spectrum with high potency against key Gram-negative bacteria that translated into excellent efficacy in several in vivo mouse infection models.
We carry out experiments of 104 m/s velocity oblique impacts into a granular medium (sand). Impact craters have nearly round rims even at a grazing angle of about 10°, however, the strength of ...seismic pulses excited by the impact is dependent upon impact angle, and the ratio between uprange and downrange velocity peaks can be as large as 5, particularly at shallow depths. Crater slope, an offset between crater center and impact site, crater volume, azimuthal variation in ejection angle, seismic pulse shapes and subsurface flow direction are also sensitive to impact angle, but to a much lower degree than subsurface pulse strength. Uprange and downrange pulse peak amplitudes can be estimated from the horizontal and vertical components of the momentum imparted to the medium from the projectile.
•We carry out laboratory experiments of oblique impacts into sand.•The strength of pulses excited by an oblique impact depends upon impact angle.•Downrange subsurface seismic pulses can be up to 5 times stronger than uprange ones.•Pulse peak amplitudes can be estimated from the projectile momentum direction.
Global climate has changed over the past century. Precipitation amounts and intensities are increasing. In this study we investigated the response of seven soil erosion models to a few basic ...precipitation and vegetation related parameters using common data from one humid and one semi-arid watershed. Perturbations were made to inputs for rainfall intensities and amounts, and to ground surface cover and canopy cover. Principal results were that: soil erosion is likely to be more affected than runoff by changes in rainfall and cover, though both are likely to be significantly impacted; percent erosion and runoff will likely change more for each percent change in rainfall intensity and amount than to each percent change in either canopy or ground cover; changes in rainfall amount associated with changes in storm rainfall intensity will likely have a greater impact on runoff and erosion than simply changes in rainfall amount alone; changes in ground cover have a much greater impact on both runoff and erosion than changes in canopy cover alone. The results do not imply that future changes in rainfall will dominate over changes in land use, since land use changes can often be drastic. Given the types of precipitation changes that have occurred over the last century, and the expectations regarding changes over the next century, the results of this study suggest that there is a significant potential for climate change to increase global soil erosion rates unless offsetting conservation measures are taken.
Determining the geographic range of widely dispersed or migratory marine organisms is notoriously difficult, often requiring considerable costs and typically extensive tagging or exploration ...programs. While these approaches are accurate and can reveal important information on the species, they are usually conducted on only a small number of individuals and can take years to produce relevant results, so alternative approaches may be preferable. The presence of latitudinal gradients in stable carbon isotope compositions of marine phytoplankton offers a means to quickly determine likely geographic population ranges of species that rely on productivity from these resources. Across sufficiently large spatial and temporal scales, the stable carbon isotopes of large coastal or pelagic marine species should reflect broad geographic patterns of resource use, and could be used to infer geographic ranges of marine populations. Using two methods, one based on a global mechanistic model and the other on targeted low-cost latitudinal sampling of fishes, we demonstrate and compare these stable isotope approaches to determine the core population geography of an apex predator, the great hammerhead (
Sphyrna mokarran
). Both methods indicated similar geographic ranges and suggested that
S. mokarran
recorded in south-eastern Australia are likely to be from more northern Australian waters. These approaches could be replicated in other areas where coastlines span predictable geographic gradients in isotope values and be used to determine the core population geography of highly mobile species to inform management decisions.
The reappraisal of genetically defined subsets of renal tumors can help to highlight the key pathologic features of specific neoplastic entities. We report the morphologic, immunophenotypic, ...ultrastructural, and molecular features of 11 renal carcinomas bearing a t(X;1)(p11.2;q21) and/or the resulting PRCC-TFE3 gene fusion. The male/female ratio was 4:7. Ten patients were in the age range of 9-29 years and one was 64 years old (mean 21.3 years, median 15 years). The predominant histologic pattern was nested, with islands of tumor cells compartmentalized by thin-walled capillary vasculature. Minor variations on this pattern yielded solid, acinar, alveolar, and tubular architecture. Papillary architecture was seen in nine cases, usually as a minor component. Neoplastic cells were typically characterized by irregularly shaped nuclei with vesicular chromatin and small nucleoli not visible with a 10x objective, and cytoplasm that ranged from clear to densely granular and eosinophilic. Mitoses were extremely rare; 5 were found in 900 high power fields examined from the 11 neoplasms. The most distinctive immunohistochemical feature of these neoplasms was moderate to intense nuclear labeling for TFE3 protein. These tumors were also consistently immunoreactive for the RCC antigen (10 of 11) and CD10 (9 of 9), whereas cytokeratin and epithelial membrane antigen were negative in four cases and were positive focally in the others. Ultrastructurally, all of the six neoplasms examined showed features consistent with conventional-type (clear cell) renal carcinoma, although two demonstrated distinctive intracisternal microtubules. Both tumors tested contained PRCC-TFE3 fusion transcripts. The differential diagnosis includes conventional-type papillary renal cell carcinoma, conventional-type (clear cell) renal carcinoma, and the ASPL-TFE3 renal carcinomas associated with the t(X;17)(p11.2;q25), with the latter two being morphologically the most similar to the t(X;1) renal carcinomas. Aside from their distinctive clinicopathologic features described here, there is experimental evidence suggesting that these tumors may show differential sensitivity to certain chemotherapeutic agents.
Facing the organizational and technological complexity of nuclear infrastructures (NI), the public reluctance in nuclear technology and the increasing restrictive regulatory environment, improving ...the conceptualization and evaluation of NI architecture is crucial for the successful completion of NI projects. Indeed, many technical engineering difficulties or delays in delivery can be avoided by deepening the design and evaluation of NI architectures. In a context where model‐based systems engineering (MBSE) is becoming more and more relevant, it is interesting to integrate evaluation into this process. Although the architecture evaluation (AE) process is rather well defined in the literature and linked to system analysis practices, it is quite difficult to deploy and pilot within complex NI projects. This article proposes a model‐based method, EVAluation for Critical Infrastructure Model Based System Engineering (EVA‐CIME), to facilitate the deployment of AE processes on a project. The components of this method are described and illustrated in a study of a NI design. The benefits and limitations of EVA‐CIME in its state of development are discussed and lead to the conclusion that the method should be extended to foster an AE culture within the company itself.