Objective Evaluation of Multiple Sclerosis Lesion Segmentation using a Data Management and Processing Infrastructure

We present a study of multiple sclerosis segmentation algorithms conducted at the international MICCAI 2016 challenge. This challenge was operated using a new open-science computing infrastructure. This allowed for the automatic and independent evaluation of a large range of algorithms in a fair and completely automatic manner. This computing infrastructure was used to evaluate thirteen methods of MS lesions segmentation, exploring a broad range of state-of-theart algorithms, against a high-quality database of 53 MS cases coming from four centers following a common definition of the acquisition protocol. Each case was annotated manually by an unprecedented number of seven different experts. Results of the challenge highlighted that automatic algorithms, including the recent machine learning methods (random forests, deep learning, …), are still trailing human expertise on both detection and delineation criteria. In addition, we demonstrate that computing a statistically robust consensus of the algorithms performs closer to human expertise on one score (segmentation) although still trailing on detection scores

Annotated mitochondrial genome with Nanopore R9 signal for <i>Nippostrongylus brasiliensis</i>

Nippostrongylus brasiliensis, a nematode parasite of rodents, has a parasitic life cycle that is an extremely useful model for the study of human hookworm infection, particularly in regards to the induced immune response. The current reference genome for this parasite is highly fragmented with minimal annotation, but new advances in long-read sequencing suggest that a more complete and annotated assembly should be an achievable goal. We de-novo assembled a single contig mitochondrial genome from N. brasiliensis using MinION R9 nanopore data. The assembly was error-corrected using existing Illumina HiSeq reads, and annotated in full (i.e. gene boundary definitions without substantial gaps) by comparing with annotated genomes from similar parasite relatives. The mitochondrial genome has also been annotated with a preliminary electrical consensus sequence, using raw signal data generated from a Nanopore R9 flow cell

The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics.

ABSTRACT: A global genome database of all of Earth’s species diversity could be a treasure trove of scientific discoveries. However, regardless of the major advances in genome sequencing technologies, only a tiny fraction of species have genomic information available. To contribute to a more complete planetary genomic database, scientists and institutions across the world have united under the Earth BioGenome Project (EBP), which plans to sequence and assemble high-quality reference genomes for all ∼1.5 million recognized eukaryotic species through a stepwise phased approach. As the initiative transitions into Phase II, where 150,000 species are to be sequenced in just four years, worldwide participation in the project will be fundamental to success. As the European node of the EBP, the European Reference Genome Atlas (ERGA) seeks to implement a new decentralised, accessible, equitable and inclusive model for producing high-quality reference genomes, which will inform EBP as it scales. To embark on this mission, ERGA launched a Pilot Project to establish a network across Europe to develop and test the first infrastructure of its kind for the coordinated and distributed reference genome production on 98 European eukaryotic species from sample providers across 33 European countries. Here we outline the process and challenges faced during the development of a pilot infrastructure for the production of reference genome resources, and explore the effectiveness of this approach in terms of high-quality reference genome production, considering also equity and inclusion. The outcomes and lessons learned during this pilot provide a solid foundation for ERGA while offering key learnings to other transnational and national genomic resource projects.info:eu-repo/semantics/publishedVersio

Nanopore sequencing and assembly of a human genome with ultra-long reads

We report the sequencing and assembly of a reference genome for the human GM12878 Utah/Ceph cell line using the MinION (Oxford Nanopore Technologies) nanopore sequencer. 91.2 Gb of sequence data, representing ~30× theoretical coverage, were produced. Reference-based alignment enabled detection of large structural variants and epigenetic modifications. De novo assembly of nanopore reads alone yielded a contiguous assembly (NG50 ~3 Mb). Next, we developed a protocol to generate ultra-long reads (N50 > 100kb, up to 882 kb). Incorporating an additional 5×-coverage of these data more than doubled the assembly contiguity (NG50 ~6.4 Mb). The final assembled genome was 2,867 million bases in size, covering 85.8% of the reference. Assembly accuracy, after incorporating complementary short-read sequencing data, exceeded 99.8%. Ultra-long reads enabled assembly and phasing of the 4 Mb major histocompatibility complex (MHC) locus in its entirety, measurement of telomere repeat length and closure of gaps in the reference human genome assembly GRCh38

Venous thrombosis of the left ovarian and extension to the renal vein

peer reviewedLa thrombose veineuse ovarienne est une complication rare, mais sérieuse du post-partum. La veine ovarienne droite est impliquée dans 80 % des cas et la veine ovarienne gauche dans moins de 6 % des cas, la thrombose est bilatérale dans 14 % des cas. Le tableau clinique peut être typique avec une douleur abdominale, de la fièvre et une hyperleucocytose, mais peut également se présenter sous forme d’une symptomatologie moins évocatrice, rendant le diagnostic plus difficile. Les complications principales sont l’extension du thrombus à la veine rénale ou la veine cave inférieure, le sepsis et l’embolie pulmonaire. Son diagnostic repose essentiellement sur les techniques d’imagerie, en particulier le scanner et la résonance magnétique dont la sensibilité et la spécificité sont élevées. Le traitement des formes non compliquées comprend une antibiothérapie et des anticoagulants. Les cas de thromboses veineuses ovariennes compliquées nécessitent parfois une prise en charge chirurgicale. Le taux de morbidité et de mortalité peut être réduit par un diagnostic précoce et un traitement adapté. A l’heure actuelle, grâce à l’instauration rapide du traitement approprié, les complications létales sont devenues exceptionnelles.Ovarian vein thrombosis is a rare, but potentially serious postpartum complication. In 80 % of the cases, it occurs on the right side and in less than 6 % on the left side; it is bilateral in 14 % of cases. The usual clinical features include abdominal pain, fever and leucocytosis. However, the diagnosis is often complicated by other non specific signs and symptoms. Ovarian vein thrombosis may cause sepsis, pulmonary thromboembolism, and thrombosis of the inferior vena cava and the renal vein. The diagnosis can be established by CT scan or nuclear magnetic resonance imaging, which has a high sensitivity and specificity. Treatment for the ovarian vein thrombosis includes antibiotics and anticoagulation. The complications can sometimes be surgically managed. Prompt diagnosis and treatment can decrease the morbidity and the mortality. Nowadays, the fatal issue is rare as the appropriate treatment is quickly instaured

Two large reciprocal translocations characterized in the disease resistance-rich burmannica genetic group of Musa acuminata.

Banana cultivars are derived from hybridizations involving Musa acuminata subspecies. The latter diverged following geographical isolation in distinct South-east Asian continental regions and islands. Observation of chromosome pairing irregularities in meiosis of hybrids between these subspecies suggested the presence of large chromosomal structural variations. The aim of this study was to characterize such rearrangements