Soft windowing application to improve analysis of high-throughput phenotyping data.

MOTIVATION: High-throughput phenomic projects generate complex data from small treatment and large control groups that increase the power of the analyses but introduce variation over time. A method is needed to utlize a set of temporally local controls that maximizes analytic power while minimizing noise from unspecified environmental factors. RESULTS: Here we introduce 'soft windowing', a methodological approach that selects a window of time that includes the most appropriate controls for analysis. Using phenotype data from the International Mouse Phenotyping Consortium (IMPC), adaptive windows were applied such that control data collected proximally to mutants were assigned the maximal weight, while data collected earlier or later had less weight. We applied this method to IMPC data and compared the results with those obtained from a standard non-windowed approach. Validation was performed using a resampling approach in which we demonstrate a 10% reduction of false positives from 2.5 million analyses. We applied the method to our production analysis pipeline that establishes genotype-phenotype associations by comparing mutant versus control data. We report an increase of 30% in significant P-values, as well as linkage to 106 versus 99 disease models via phenotype overlap with the soft-windowed and non-windowed approaches, respectively, from a set of 2082 mutant mouse lines. Our method is generalizable and can benefit large-scale human phenomic projects such as the UK Biobank and the All of Us resources. AVAILABILITY AND IMPLEMENTATION: The method is freely available in the R package SmoothWin, available on CRAN http://CRAN.R-project.org/package=SmoothWin. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Principles and application of LIMS in mouse clinics.

Large-scale systemic mouse phenotyping, as performed by mouse clinics for more than a decade, requires thousands of mice from a multitude of different mutant lines to be bred, individually tracked and subjected to phenotyping procedures according to a standardised schedule. All these efforts are typically organised in overlapping projects, running in parallel. In terms of logistics, data capture, data analysis, result visualisation and reporting, new challenges have emerged from such projects. These challenges could hardly be met with traditional methods such as pen & paper colony management, spreadsheet-based data management and manual data analysis. Hence, different Laboratory Information Management Systems (LIMS) have been developed in mouse clinics to facilitate or even enable mouse and data management in the described order of magnitude. This review shows that general principles of LIMS can be empirically deduced from LIMS used by different mouse clinics, although these have evolved differently. Supported by LIMS descriptions and lessons learned from seven mouse clinics, this review also shows that the unique LIMS environment in a particular facility strongly influences strategic LIMS decisions and LIMS development. As a major conclusion, this review states that there is no universal LIMS for the mouse research domain that fits all requirements. Still, empirically deduced general LIMS principles can serve as a master decision support template, which is provided as a hands-on tool for mouse research facilities looking for a LIMS.

A mu-delta opioid receptor brain atlas reveals neuronal co-occurrence in subcortical networks.

Opioid receptors are G protein-coupled receptors (GPCRs) that modulate brain function at all levels of neural integration, including autonomic, sensory, emotional and cognitive processing. Mu (MOR) and delta (DOR) opioid receptors functionally interact in vivo, but whether interactions occur at circuitry, cellular or molecular levels remains unsolved. To challenge the hypothesis of MOR/DOR heteromerization in the brain, we generated redMOR/greenDOR double knock-in mice and report dual receptor mapping throughout the nervous system. Data are organized as an interactive database offering an opioid receptor atlas with concomitant MOR/DOR visualization at subcellular resolution, accessible online. We also provide co-immunoprecipitation-based evidence for receptor heteromerization in these mice. In the forebrain, MOR and DOR are mainly detected in separate neurons, suggesting system-level interactions in high-order processing. In contrast, neuronal co-localization is detected in subcortical networks essential for survival involved in eating and sexual behaviors or perception and response to aversive stimuli. In addition, potential MOR/DOR intracellular interactions within the nociceptive pathway offer novel therapeutic perspectives.

Correlation between groin pain and cup design of hip-resurfacing implants: a prospective study.

PURPOSE: Cup design has been incriminated as the source of groin pain after hip resurfacing but has not been well described; thus, it was assessed in a prospective study looking at three implant types. METHODS: A group-match was done between three groups of hip resurfacing devices according to age, sex, body mass index, activity level, osteoarthritis aetiology and pre-operative scores. RESULTS: The global groin pain rate was 5.7 % at six months and 2.7 % at last follow-up. Groin pain rate was significantly different between the three groups (p = 0.004) and had a strong influence on the subjective results (p = 0.04). No groin pain emerged between six months and last follow-up. No clinical differences were noted in Harris hip score and Merle d'Aubigné-Postel score at last follow-up. However, the Oxford hip score and Devane activity score were significantly lower for cups with macrostructures. CONCLUSION: The low groin pain rate in this prospective cohort was probably secondary to the specific surgical technique used and seems to be correlated with cup design. Macrostructures on the external part of the cup could be significantly harmful.

Mouse large-scale phenotyping initiatives: overview of the European Mouse Disease Clinic (EUMODIC) and of the Wellcome Trust Sanger Institute Mouse Genetics Project.

Two large-scale phenotyping efforts, the European Mouse Disease Clinic (EUMODIC) and the Wellcome Trust Sanger Institute Mouse Genetics Project (SANGER-MGP), started during the late 2000s with the aim to deliver a comprehensive assessment of phenotypes or to screen for robust indicators of diseases in mouse mutants. They both took advantage of available mouse mutant lines but predominantly of the embryonic stem (ES) cells resources derived from the European Conditional Mouse Mutagenesis programme (EUCOMM) and the Knockout Mouse Project (KOMP) to produce and study 799 mouse models that were systematically analysed with a comprehensive set of physiological and behavioural paradigms. They captured more than 400 variables and an additional panel of metadata describing the conditions of the tests. All the data are now available through EuroPhenome database (www.europhenome.org) and the WTSI mouse portal (http://www.sanger.ac.uk/mouseportal/), and the corresponding mouse lines are available through the European Mouse Mutant Archive (EMMA), the International Knockout Mouse Consortium (IKMC), or the Knockout Mouse Project (KOMP) Repository. Overall conclusions from both studies converged, with at least one phenotype scored in at least 80% of the mutant lines. In addition, 57% of the lines were viable, 13% subviable, 30% embryonic lethal, and 7% displayed fertility impairments. These efforts provide an important underpinning for a future global programme that will undertake the complete functional annotation of the mammalian genome in the mouse model.

Metal-on-Metal Bearing: Is This the End of the Line? We Do Not Think So.

BACKGROUND: Recent studies have recommended the discontinuation of metal-on-metal (MoM) components in total hip arthroplasty (THA) because of adverse effects reported with large-diameter MoM THA. This is despite favorable long-term results observed with 28 and 32 mm MoM bearings. QUESTIONS/PURPOSES: The aim of this study was to assess the value of calls for an end to MoM bearings as THA components. Specifically, we wish to address the risks associated with MoM bearings including adverse soft tissue reactions, metal ion release, and carcinogenic risk. METHODS: The study evaluates the arguments in the literature reporting on MoM (adverse soft tissue reactions, metal ion release, and carcinogenic risk) and the experience of the current authors who re-introduced these bearings in 1995. They are balanced by a benefit-risk review of the literature and the authors' experience with MoM use. RESULTS: Adverse reactions to metallic debris as well as metal ion release are predictable and can be prevented by adequate design (arc of coverage, clearance), metallurgy (forged instead of cast alloy, high-carbide content), and appropriate component orientation. There is no scientific evidence that carcinogenicity is increased in subjects with MoM hip prostheses. MoM articulations appear to be attractive allowing safe hip resurfacing, decreasing the risk of THA revision in active patients, and providing secure THA fixation with cement in cages in severely deformed hips. MoM bearings in women of child-bearing age are controversial, but long-term data on metallic devices in adolescents undergoing spinal surgery seem reassuring. DISCUSSION: Adequate selection of MoM articulations ensures their safe use. These articulations are sensitive to orientation. Fifteen years of safe experience with 28- and 32-mm bearings of forged alloy and high-carbide content is the main reason for retaining them in primary and revision THA.

Cementless metal-on-metal versus ceramic-on-polyethylene hip arthroplasty in patients less than fifty years of age: a comparative study with twelve to fourteen-year follow-up.

BACKGROUND: We previously reported the outcomes of a case-control study, at a minimum of five years of follow-up, comparing metal-on-metal and ceramic-on-polyethylene bearings for cementless primary hip arthroplasty in active patients below the age of fifty years. This report is an update on these groups after a minimum duration of follow-up of twelve years. METHODS: Thirty-nine metal-on-metal cementless hip replacements with a 28-mm-diameter Metasul articulation were compared with a control group that included thirty-nine cementless ceramic-on-polyethylene hip replacements performed with a 28-mm-diameter head. The Metasul group included thirty patients with a mean age of forty years (range, twenty-three to forty-nine years), and the control group included thirty-two patients with a mean age of forty-one years (range, fifteen to forty-nine years). The groups were matched for age, activity level, preoperative Harris hip score, acetabular cup diameter, and indication for hip arthroplasty. All patients had a high level of activity, with 82% rated as grade IV or V according to the Devane scale. RESULTS: After a mean duration of follow-up of thirteen years (twelve to fourteen years), only one hip (3%) had asymptomatic acetabular osteolysis and no hip (0%) had been revised in the metal-on-metal group, whereas eighteen hips (46%) had osteolysis and eleven hips (28%) had been revised because of wear or osteolysis in the ceramic-on-polyethylene group (p < 0.003). In the metal-on-metal group, the median Co concentration in the whole blood was 0.95 µg/L (0.4 to 4.8 µg/L) and the median Cr concentration was 1.2 µg/L (0.1 to 5.6 µg/L). The twelve-year survival rate (with reoperation for any reason as the end point) was 100% in the metal-on-metal group and 70% (95% confidence interval, 63% to 77%) in the ceramic-on-polyethylene group (p = 0.003). CONCLUSIONS: After twelve to fourteen years of follow-up, metal-on-metal implants demonstrated better radiographic and survival results than ceramic-on-polyethylene implants in young, very active patients. Current wrought metal-on-metal implants with a 28-mm-diameter head and high carbide concentration did not produce the high rates of osteolysis and allergic reactions that may be observed with cast low-carbide metal-on-metal bearings after a shorter duration of follow-up.

Systematic gene expression mapping clusters nuclear receptors according to their function in the brain.

Nuclear receptors (NRs) compose a large family of transcription factors that operate at the interface between genes and environment, acting as sensors and effectors that translate endocrine and metabolic cues into well-defined gene expression programs. We report here on a systematic quantitative and anatomical expression atlas of the 49 NR genes in 104 regions of the adult mouse brain, organized in the interactive MousePat database. MousePat defines NR expression patterns to cellular resolution, a requirement for functional genomic strategies to understand the function of a highly heterogeneous and complex organ such as the brain. Using MousePat data, NR expression patterns can be clustered into anatomical and regulatory networks that delineate the role of NRs in brain functions, like the control of feeding and learning/memory. Mining the MousePat resource will improve the understanding of NR function in the brain and elucidate hierarchical networks that control behavior and whole body homeostasis.

Mouse Phenotype Database Integration Consortium: integration [corrected] of mouse phenome data resources.

Understanding the functions encoded in the mouse genome will be central to an understanding of the genetic basis of human disease. To achieve this it will be essential to be able to characterize the phenotypic consequences of variation and alterations in individual genes. Data on the phenotypes of mouse strains are currently held in a number of different forms (detailed descriptions of mouse lines, first-line phenotyping data on novel mutations, data on the normal features of inbred lines) at many sites worldwide. For the most efficient use of these data sets, we have initiated a process to develop standards for the description of phenotypes (using ontologies) and file formats for the description of phenotyping protocols and phenotype data sets. This process is ongoing and needs to be supported by the wider mouse genetics and phenotyping communities to succeed. We invite interested parties to contact us as we develop this process further.