A draft human pangenome reference.

Here the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals. These assemblies cover more than 99% of the expected sequence in each genome and are more than 99% accurate at the structural and base pair levels.

GAB1 as a Marker of Recurrence in Anterior Skull Base Meningioma.

Background: About one-third of anterior skull base meningiomas show Hedgehog pathway activation. We have recently identified GAB1 as a surrogate marker for Hedgehog pathway-activated meningiomas.

Objective: To determine the reproducibility and prognostic value of GAB1 marker in anterior skull base meningiomas.

Roles and outcomes of stereotactic biopsy for adult patients with brainstem lesion.

Purpose: This study aimed to assess the benefit-risk ratio by determining diagnostic yield and safety of brainstem biopsies in adult patients. The secondary objectives were (i) to compare brainstem biopsy safety and postbiopsy patients' outcomes and survival with those of patients biopsied for a brain or cerebellar lesion, and (ii) to assess the impact of brainstem biopsy on final diagnosis and further therapeutic management.

Methods: Among 1784 stereotactic biopsies performed in adult patients at a tertiary center between April 2009 and October 2020, we retrospectively examined 50 consecutive brainstem biopsies.

The K-mer File Format: a standardized and compact disk representation of sets of k-mers.

Summary: Bioinformatics applications increasingly rely on ad hoc disk storage of k-mer sets, e.g. for de Bruijn graphs or alignment indexes.

Cutevariant: a standalone GUI-based desktop application to explore genetic variations from an annotated VCF file.

Summary: Cutevariant is a graphical user interface (GUI)-based desktop application designed to filter variations from annotated VCF file. The application imports data into a local SQLite database where complex filter queries can be built either from GUI controllers or using a domain-specific language called Variant Query Language. Cutevariant provides more features than existing applications and is fully customizable thanks to a complete plugins architecture.

Severity, timeline, and management of complications after stereotactic brain biopsy.

Objective: The literature shows discrepancies in stereotactic brain biopsy complication rates, severities, and outcomes. Little is known about the timeline of postbiopsy complications. This study aimed to analyze 1) complications following brain biopsies, using a graded severity scale, and 2) a timeline of complication occurrence.

Somatic Mutations in Sporadic Cerebral Cavernous Malformations.

Background: Cerebral cavernous malformations (CCMs) are common sporadic and inherited vascular malformations of the central nervous system. Although familial CCMs are linked to loss-of-function mutations in (), , or (), the genetic cause of sporadic CCMs, representing 80% of cases, remains incompletely understood.

Methods: We developed two mouse models harboring mutations identified in human meningiomas with the use of the prostaglandin D2 synthase (PGDS) promoter.

Outpatient stereotactic brain biopsies.

Outpatient neurosurgery is rising popularity leading to patients' satisfaction and cost-savings. Although several North-American teams have shown the safety of outpatient stereotactic brain biopsies, few data from other countries with different health care systems are available. We therefore conducted a feasibility and safety study on the outpatient stereotactic brain biopsies.

GAB1 overexpression identifies hedgehog-activated anterior skull base meningiomas.

Aims: Mutations activating the hedgehog (Hh) signalling pathway have been described in anterior skull base meningiomas, raising hope for the use of targeted therapies. However, identification of Hh-activated tumours is hampered by the lack of a reliable immunohistochemical marker. We report the evaluation of GAB1, an immunohistochemical marker used to detect Hh pathway activation in medulloblastoma, as a potential marker of Hh-activated meningiomas.

Sustained growth of intraosseous hormone-associated meningiomas after cessation of progestin therapy.

Hormone-associated meningiomas tend to stop growing or decrease in size after cessation of certain progestins, mainly cyproterone acetate. We report three observations on the natural history of hormone-associated intraosseous meningiomas, showing in a first patient that those tumors may grow rapidly under nomegestrol. We then demonstrate the sustained growth of intraosseous hormone-associated meningiomas after cessation of promesgestone and nomegestrol, independently of the intracranial portion, which concurrently decreased in size in the second case or was resected at the time of nomegestrol withdrawal in the third case, thus giving new insights into the tumorigenesis mechanisms of hormone-associated intraosseous meningiomas.

Angiographic Anatomy of the Middle Meningeal Artery in Relation to Chronic Subdural Hematoma Embolization.

Purpose: Middle meningeal artery (MMA) embolization is emerging as a potential treatment of chronic subdural hematomas (CSDHs). The purpose of this study is to describe MMA angiographic anatomy in relation to CSDH embolization.

Methods: This retrospective monocentric study was performed on imaging data of MMA embolization procedures for CSDH treatment performed between March 15, 2018 and April 30, 2020.

Custom surgical management of invasive malignant tumors of the scalp.

Background: There is no universal management protocol concerning invasive malignant tumors of the scalp with bone and dura mater invasion. The aims of this study were to report and discuss our experience in the management of these forms of tumors.

Methods: We retrospectively reviewed all consecutive patients of microsurgical scalp reconstruction performed after resection of invasive cutaneous malignancies of the scalp, calvarium, and dura mater from 2017 to 2019, at Pitié-Salpêtrière University Hospital (Paris, France).

yacrd and fpa: upstream tools for long-read genome assembly.

Motivation: Genome assembly is increasingly performed on long, uncorrected reads. Assembly quality may be degraded due to unfiltered chimeric reads; also, the storage of all read overlaps can take up to terabytes of disk space.

Results: We introduce two tools: yacrd for chimera removal and read scrubbing, and fpa for filtering out spurious overlaps.

Graph analysis of fragmented long-read bacterial genome assemblies.

Motivation: Long-read genome assembly tools are expected to reconstruct bacterial genomes nearly perfectly; however, they still produce fragmented assemblies in some cases. It would be beneficial to understand whether these cases are intrinsically impossible to resolve, or if assemblers are at fault, implying that genomes could be refined or even finished with little to no additional experimental cost.

Results: We propose a set of computational techniques to assist inspection of fragmented bacterial genome assemblies, through careful analysis of assembly graphs.

[Coexistence of a disc herniation and psoas hematoma revealed by L3 deficiency].

Radiculopathy is a constellation of symptoms secondary to a pathology affecting the nerve root, the most frequent cause of which is a herniated intervertebral disc. We report a case of a 58-year-old man under anticoagulant admitted to the neurosurgery department of Lariboisière hospital (Paris) for an L3 motor deficit that occurred progressively over a period of 24 hours with an L3-L4 disc herniation on the MRI. However, a psoas hematoma was also noted.