Quality assurance for next-generation sequencing diagnostics of rare neurological diseases in the European Reference Network.

In the past decade, next-generation sequencing (NGS) has revolutionised genetic diagnostics for rare neurological disorders (RND). However, the lack of standardised technical, interpretative, and reporting standards poses a challenge for ensuring consistent and high-quality diagnostics globally. To address this, the European Reference Network for Rare Neurological Diseases (ERN-RND) collaborated with the European Molecular Genetics Quality Network (EMQN) to establish an external quality assessment scheme for NGS-based diagnostics in RNDs. The scheme, initiated in 2021 with a pilot involving 29 labs and followed by a second round in 2022 with 42 labs, aimed to evaluate the performance of laboratories in genetic testing for RNDs. Each participating lab analysed genetic data from three hypothetical cases, assessing genotyping, interpretation, and clerical accuracy. Despite a majority of labs using exome or genome sequencing, there was considerable variability in gene content, sequencing quality, adherence to standards, and clinical guidance provision. Results showed that while most labs provided correct molecular diagnoses, there was significant variability in reporting technical quality, adherence to interpretation standards, reporting strategies, and clinical commentary. Notably, some labs returned results with the potential for adverse medical outcomes. This underscores the need for further harmonisation, guideline development, and external quality assessment in the evolving landscape of genomic diagnostics for RNDs. Overall, the experience with the scheme highlighted the generally good quality of participating labs but emphasised the imperative for ongoing improvement in data analysis, interpretation, and reporting to enhance patient safety.

The maternal transcriptome of the crustacean Parhyale hawaiensis is inherited asymmetrically to invariant cell lineages of the ectoderm and mesoderm.

BACKGROUND: The embryo of the crustacean Parhyale hawaiensis has a total, unequal and invariant early cleavage pattern. It specifies cell fates earlier than other arthropods, including Drosophila, as individual blastomeres of the 8-cell stage are allocated to the germ layers and the germline. Furthermore, the 8-cell stage is amenable to embryological manipulations. These unique features make Parhyale a suitable system for elucidating germ layer specification in arthropods. Since asymmetric localization of maternally provided RNA is a widespread mechanism to specify early cell fates, we asked whether this is also true for Parhyale. A candidate gene approach did not find RNAs that are asymmetrically distributed at the 8-cell stage. Therefore, we designed a high-density microarray from 9400 recently sequenced ESTs (1) to identify maternally provided RNAs and (2) to find RNAs that are differentially distributed among cells of the 8-cell stage. RESULTS: Maternal-zygotic transition takes place around the 32-cell stage, i.e. after the specification of germ layers. By comparing a pool of RNAs from early embryos without zygotic transcription to zygotic RNAs of the germband, we found that more than 10% of the targets on the array were enriched in the maternal transcript pool. A screen for asymmetrically distributed RNAs at the 8-cell stage revealed 129 transcripts, from which 50% are predominantly expressed in the early embryonic stages. Finally, we performed knockdown experiments for two of these genes and observed cell-fate-related defects of embryonic development. CONCLUSIONS: In contrast to Drosophila, the four primary germ layer cell lineages in Parhyale are specified during the maternal control phase of the embryo. A key step in this process is the asymmetric distribution of a large number of maternal RNAs to the germ layer progenitor cells.

Turning snails into slugs: induced body plan changes and formation of an internal shell.

The archetypal body plan of conchiferan molluscs is characterized by an external calcareous shell, though internalization of shells has evolved independently in a number of molluscan clades, including gastropod families. In gastropods, the developmental process of torsion is regarded as a hallmark that is associated with a new anatomical configuration. This configuration is present in extant prosobranch gastropod species, which predominantly bear external shells. Here, we show that short-term exposure to platinum during development uncouples at least two of the processes associated with torsion of the freshwater snail Marisa cornuarietis. That is, the anus of the treated snails is located anteriorly, but the gill and the designated mantle tissue remains in a posterior location, thus preventing the formation of an external shell. In contrast to the prosobranchian archetype, platinum treatment results in the formation of a posterior gill and a cone-shaped internal shell, which persists across the lifetime. This first finding of artificially induced snail-slug conversion was also seen in the pulmonate snail Planorbarius corneus and demonstrates that selective alteration of embryonic key processes can result in fundamental changes of an existing body plan and-if altered regulation is inherited-may give rise to a new one.

Germ cells in the crustacean Parhyale hawaiensis depend on Vasa protein for their maintenance but not for their formation.

Germ cells are a population of cells that do not differentiate to form somatic tissue but form the egg and sperm that ensure the reproduction of the organism. To understand how germ cells form, holds a key for identifying what sets them apart from all other cells of the organism. There are large differences between embryos regarding where and when germ cells form but the expression of Vasa protein is a common trait of germ cells. We studied the role of vasa during germ cell formation in the crustacean Parhyale hawaiensis. In a striking difference to the posterior specification of the group of germ cells in the arthropod model Drosophila, all germ cells in Parhyale originate from a single germ line progenitor cell of the 8-cell stage. We found vasa RNA ubiquitously distributed from 1-cell to 16-cell stage in Parhyale and localized to the germ cells from 32-cell stage onwards. Localization of vasa RNA to the germ cells is controlled by its 3'UTR and this could be mimicked by fluorescently labeled 3'UTR RNA. Vasa protein was first detectable at the 100-cell stage. MO-mediated inhibition of vasa translation caused germ cells to die after gastrulation. This means that in Parhyale Vasa protein is not required for the initial generation of the clone of germ cells but is required for their subsequent proliferation and maintenance. It also means that the role of vasa changed substantially during an evolutionary switch in the crustaceans by Parhyale from the specification of a group of germ cells to that of a single germ line progenitor. This is the first functional study of vasa in an arthropod beyond Drosophila.

Cuticle differentiation in the embryo of the amphipod crustacean Parhyale hawaiensis.

The arthropod cuticle is a multilayered extracellular matrix produced by the epidermis during embryogenesis and moulting. Molecularly and histologically, cuticle differentiation has been extensively investigated in the embryo of the insect Drosophila melanogaster. To learn about the evolution of cuticle differentiation, we have studied the histology of cuticle differentiation during embryogenesis of the amphipod crustacean Parhyale hawaiensis, which had a common ancestor with Drosophila about 510 million years ago. The establishment of the layers of the Parhyale juvenile cuticle is largely governed by mechanisms observed in Drosophila, e.g. as in Drosophila, the synthesis and arrangement of chitin in the inner procuticle are separate processes. A major difference between the cuticle of Parhyale and Drosophila concerns the restructuring of the Parhyale dorsal epicuticle after deposition. In contrast to the uniform cuticle of the Drosophila larva, the Parhyale cuticle is subdivided into two regions, the ventral and the dorsal cuticles. Remarkably, the boundary between the ventral and dorsal cuticles is sharp suggesting active extracellular regionalisation. The present analysis of Parhyale cuticle differentiation should allow the characterisation of the cuticle-producing and -organising factors of Parhyale (by comparison with the branchiopod crustacean Daphnia pulex) in order to contribute to the elucidation of fundamental questions relevant to extracellular matrix organisation and differentiation.

Stages of embryonic development in the amphipod crustacean, Parhyale hawaiensis.

Studying the relationship between development and evolution and its role in the generation of biological diversity has been reinvigorated by new techniques in genetics and molecular biology. However, exploiting these techniques to examine the evolution of development requires that a great deal of detail be known regarding the embryonic development of multiple species studied in a phylogenetic context. Crustaceans are an enormously successful group of arthropods and extant species demonstrate a wide diversity of morphologies and life histories. One of the most speciose orders within the Crustacea is the Amphipoda. The embryonic development of a new crustacean model system, the amphipod Parhyale hawaiensis, is described in a series of discrete stages easily identified by examination of living animals and the use of commonly available molecular markers on fixed specimens. Complete embryogenesis occurs in 250 h at 26 degrees C and has been divided into 30 stages. This staging data will facilitate comparative analyses of embryonic development among crustaceans in particular, as well as between different arthropod groups. In addition, several aspects of Parhyale embryonic development make this species particularly suitable for a broad range of experimental manipulations.

Cell lineage analysis of the amphipod crustacean Parhyale hawaiensis reveals an early restriction of cell fates.

In the amphipod crustacean, Parhyale hawaiensis, the first few embryonic cleavages are total and generate a stereotypical arrangement of cells. In particular, at the eight-cell stage there are four macromeres and four micromeres, and each of these cells is uniquely identifiable. We describe our studies of the cell fate pattern of these eight blastomeres, and find that the eight clones resulting from these cells set up distinct cell lineages that differ in terms of proliferation, migration and cell fate. Remarkably, the cell fate of each blastomere is restricted to a single germ layer. The ectoderm originates from three of the macromeres, while the remaining macromere generates the visceral mesoderm. Two of the micromeres generate the somatic mesoderm, a third micromere generates the endoderm and the fourth micromere generates the germline. These findings demonstrate for the first time a total cleavage pattern in an arthropod which results in an invariant cell fate of the blastomeres, but notably, the cell lineage pattern of Parhyale reported shows no clear resemblance to those found in spiralians, nematodes or deuterostomes. Finally, the techniques we have developed for the analysis of Parhyale development suggest that this arthropod may be particularly useful for future functional analyses of crustacean development.

Developmental biologists cast a net over sequenced genomes.

A report on the annual meeting of the Society of Developmental Biology, Madison, Wisconsin, USA, 21-24 July 2002.