An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge

There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data were donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease-causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance. RESULTS: A total of 30 international groups were engaged. The entries reveal a general convergence of practices on most elements of the analysis and interpretation process. However, even given this commonality of approach, only two groups identified the consensus candidate variants in all disease cases, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization. CONCLUSIONS: The CLARITY Challenge provides a comprehensive assessment of current practices for using genome sequencing to diagnose and report genetic diseases. There is remarkable convergence in bioinformatic techniques, but medical interpretation and reporting are areas that require further development by many groups

Neotype designation for Thymallus aeliani Valenciennes, 1848 from a museum topotype specimen and its affiliation with Adriatic grayling on the basis of mitochondrial DNA

In 1848, the grayling Thymallus aeliani (Valenciennes) was described from Lake Maggiore, Italy, in the north Adriatic basin. Genetic analyses of the mitochondrial control region showed a unique evolutionary history of grayling inhabiting the rivers of northern Adriatic basin, from the upper reaches of the Po River and its left tributaries in the west to the Soča River in the east, which resulted in the designation of this phylogenetic lineage as Adriatic grayling. Consequently, the name T. aeliani was connected to the Adriatic lineage, re-establishing the validity of this taxon. However, the mitochondrial haplotypes belonging to Adriatic grayling were never compared with the type specimens of T. aeliani, as their whereabouts were unknown. In this study, a neotype for T. aeliani was designated using topotypical specimens stored at the Natural History Museum in Vienna. The neotype (NMW 68027:2 labelled as “Lago Maggiore, Bellotti, 1880”) was designated pursuant to the conditions stipulated in Article 75.3 of the International Code of Zoological Nomenclature. Furthermore, the mitochondrial control region of the neotype was compared to haplotypes of the Adriatic lineage and showed high genetic similarity, which therefore connects the species name T. aeliani to the Adriatic grayling. This crucial step in fixing nomenclatural status of this species is very important for its protection and management

Genetic assessment of native trout populations (Salmo trutta complex) in Lombardy (North Italy): implication for future conservation and management

The brown trout is a complex of developing species distributed around the Palearctic region. Glacial and interglacial peaks allowed the divergence of five main mitochondrial lineages. The reconstruction of its recent evolutionary history is essential to set-up concrete management and conservation efforts. Attempts to identify its native distribution is exacerbated by stocking activities with allochthonous strains during last century, which can lead to genetic introgression. An exhaustive genetic investigation has never been conducted in North Italy, especially in Lombardy region, which is posing critical management and conservation issues. In order to investigate the evolutionary status of trout in this area a genetic assessment of remote trout populations (possibly less impacted by introductions) was completed throughout the alpine and subalpine basins in Lombardy. For further strengthening, a few historical samples (back to 1821) collected in museums has been analysed. Genetic analyses covered more than 200 fish from 13 populations plus one population of hatchery-reared fish, used for stocking. Evolutionary history was inferred using the mitochondrial control region marker, whilst the level of introgression using the nuclear gene LDH-C1. Outputs revealed strong signs of introgression with the allochthonous strain. Nevertheless, the mitochondrial lineages linked to the Mediterranean brown trout is present in the current samples as well as in the museum samples, suggesting its historical presence in the ecosystems of alpine and subalpine basins

Corrigendum to «Contrasting morphology with molecular data: an approach to revision of species complexes based on the example of European (Cyprinidae)» by Palandačić et al. 2017

This corrigendum, in the sense of the Glossary of the International Code of Zoological Nomenclature (ICZN 1999, p. 102), is to ensure that the ICZN criteria for the availability of the two new nomenclatural acts, namely the designations of the neotype of Phoxinus csikii Hankó, 1922 and the lectotype of Phoxinus marsilii Heckel, 1836, are satisfied

New data on Garra makiensis (Cyprinidae, Labeoinae) from the Awash River (Ethiopia) with remarks on its relationships to congeners on the Arabian Peninsula

On the African continent, the genus Garra consists of several species often insufficiently separated from each other by diagnostic characters. Herein, a detailed morphological redescription of Garra makiensis from the Awash River drainage is presented, together with additional data on the type specimens of G. makiensis and G. rothschildi. Mitochondrial CO1 sequence data are also provided, including the historic paralectotype of G. makiensis, with a comparison to Garra species from Africa and the Middle East. Based on these sequences, G. makiensis clusters outside the group of African congeners and is a sister lineage to species from the south-east of the Arabian Peninsula. Although morphologically variable, G. makiensis is characterised by having a single unbranched pectoral-fin ray, a short distance between vent and anal-fin origin (7.3–19.7 % of pelvic – anal distance), chest and belly covered with scales, and a prominent axillary scale at base of pelvic fin (18.8–35.5 % of pelvic-fin length)