AnFiSA: An open-source computational platform for the analysis of sequencing data for rare genetic disease

Despite genomic sequencing rapidly transforming from being a bench-side tool to a routine procedure in a hospital, there is a noticeable lack of genomic analysis software that supports both clinical and research workflows as well as crowdsourcing. Furthermore, most existing software packages are not forward-compatible in regards to supporting ever-changing diagnostic rules adopted by the genetics community. Regular updates of genomics databases pose challenges for reproducible and traceable automated genetic diagnostics tools. Lastly, most of the software tools score low on explainability amongst clinicians. We have created a fully open-source variant curation tool, AnFiSA, with the intention to invite and accept contributions from clinicians, researchers, and professional software developers. The design of AnFiSA addresses the aforementioned issues via the following architectural principles: using a multidimensional database management system (DBMS) for genomic data to address reproducibility, curated decision trees adaptable to changing clinical rules, and a crowdsourcing-friendly interface to address difficult-to-diagnose cases. We discuss how we have chosen our technology stack and describe the design and implementation of the software. Finally, we show in detail how selected workflows can be implemented using the current version of AnFiSA by a medical geneticist.

[Psychopathological consequences of confinement]

The psychological effects of isolation have already been described in the literature (polar expeditions, submarines, prison). Nevertheless, the scale of confinement implemented during the COVID-19 pandemic is unprecedented. In addition to reviewing the published studies, we need to anticipate the psychological problems that could arise during or at a distance from confinement. We have gone beyond the COVID-19 literature in order to examine the implications of the known consequences of confinement, like boredom, social isolation, stress, or sleep deprivation. Anxiety, post-traumatic stress disorder, depression, suicidal or addictive behaviours, domestic violence are described effects of confinement, but the mechanisms of emergence of these disorders and their interrelationships remain to be studied. For example, what are the mechanisms of emergence of post-traumatic stress disorders in the context of confinement? We also remind the reader of points of vigilance to be kept in mind with regard to eating disorders and hallucinations. Hallucinations are curiously ignored in the literature on confinement, whereas a vast literature links social isolation and hallucinations. Due to the broad psychopathological consequences, we have to look for these various symptoms to manage them. We quickly summarize the diagnostic and therapeutic approaches already in place, such as telemedicine, which is undergoing rapid development during the COVID-19 crisis.

Impaired retinal processing in regular cannabis users: Potential benefit of electroretinogram as a biomark

Cannabis is one of the most prevalent drugs used in industrialized countries. Regular cannabis use is associated with impairments in highly integrative cognitive functions such as memory, attention and executive functions. However, the neural impact of cannabis use remains poorly understood. Elucidating the cerebral mechanisms underlying these deficits represents now a crucial step in addictive disorders. The retina is a part of the central nervous system due to its embryonic origin thereby reflecting the neurochemistry of the brain. Furthermore its measure is well standardized allowing good reproducibility. Considering the anatomical and functional distribution of endocannabinoids in the retina [1], we evaluated the retinal function in regular cannabis users and healthy control subjects. Recordings of flash electroretinogram (fERG) were performed in regular cannabis users and healthy controls using guidelines of international society for clinical electrophysiology of vision (ISCEV) [2]. Both amplitude and implicit time of a-wave and b-wave were assessed in scotopic and photopic conditions. Measurements of fERG showed increased implicit time of a-wave and b-wave in both photopic and scotopic conditions in regular cannabis users compared to healthy controls. These findings suggest that retinal processing may be altered at the level of photoreceptor and bipolar cells in regular cannabis users. These results are consistent with previous reports in animal species, which show the involvement of the cannabinoid system in the regulation of the retinal metabolism thus leading to alterations of fERG measurements. Since alterations in the central neurotransmission may affect the ERG measurements, the retina might constitute a possible biomarker of brain disorders in addictive diseases [3].

Alterations in retinal processing in regular cannabis users

Introduction

Cannabis is one of the most prevalent drugs used worldwide. However, the neural consequences of cannabis remain poorly understood. There is a need for a rapid improvement of the scientific knowledge on the cerebral impact of cannabis use. Since the retina is an easy-to-access part of the central nervous system, it can reflect the neurochemistry of the brain.

Objectives

Considering the anatomical and functional distribution of the cannabinoid system in the retinal ganglion cells, the objective of this study was to assess whether the regular use of cannabis could affect the ganglion cells functioning.

Aims

Assessment of the ganglion cells function in regular cannabis users compared to healthy controls.

Methods

Recordings of pattern electroretinogram (PERG) were performed in regular cannabis users and healthy controls using standard of the International Society for Clinical Electrophysiology of Vision (ISCEV). The amplitude and implicit time of the PERG N95 were assessed.

Results

The N95 implicit time of PERG was significantly decreased in regular cannabis users compared to healthy controls.

Conclusions

We found alterations in the ganglion cells function in regular cannabis users, as showed by the increase in N95 implicit time. The ganglion cells represent the ultimate retinal relay before the visual information is relayed to the brain and, according to these results, we suppose that the signal elicited by these cells and transferred through the visual pathways is altered in cannabis users. A direct action of exogenous cannabinoids in the retinal glutamatergic transmission is discussed.

Disclosure of interest

The authors have not supplied their declaration of competing interest.

Low time resolution in schizophrenia Lengthened windows of simultaneity for visual, auditory and bimodal stimuli

The guarantee of perceptual coherence for events through everyday life situations depends upon the capacity to correctly integrate series of multi-sensory experiences. Patients with schizophrenia have been shown to reveal a deficit in integrating, i.e., "binding", perceptual information together. However, results in the literature have also suggested the reverse effect. Indeed, in certain paradigms patients have revealed more binding phenomenon than healthy controls and reported experiencing two distinct events as occurring "together". This finding suggests that patients may require longer time intervals between two distinct events before being able to perceive them as "one-after-the-other". The question here was to test whether this perceptual binding abnormality in schizophrenia is confined to events within the same modality or whether it is also present across sensory modalities. Thirty patients with schizophrenia were compared with 33 normal controls using a simultaneity judgement paradigm. There were two uni-modal conditions in which stimuli were presented in the same modality (visual or auditory) and one bimodal condition (audio-visual). Participants were presented with stimuli varying across a range of inter-stimulus intervals (ISI). They were required to judge whether they experienced two stimuli as occurring "together" or "one-after-the-other". Compared to controls and in all conditions, patients needed larger ISI to experience two stimuli as "one-after-the-other" (all ISI x Group interactions p<5 x 10(-5)). These abnormalities correlated with the disorganization dimension but not with the dosage of chlorpromazine equivalent. The increase of the time interval needed to perceive two stimuli as "one-after-the-other", reflect an abnormally low time resolution in patients with schizophrenia. We discuss the possible involvement of anatomical disconnectivity in schizophrenia which would specifically affect the time integration properties of neural assemblies.

Lorazepam, sedation, and conscious recollection: a dose-response study with healthy volunteers

The role of sedation in the benzodiazepine-induced impairment of conscious recollection is still subject to debate. The aim of this study was to investigate further the role of sedation using the Remember-Know procedure and a physiological measure of sedation based on pupillography in addition to standard measures of sedation and attention (digit-symbol substitution task, symbol cancellation task, self-rated sedation). Twelve subjects were tested after the intake of placebo, lorazepam 0.026 mg/kg and lorazepam 0.038 mg/kg, administered in a randomized order, with a minimum interval of 8 days between each administration. On a recognition memory task, they were asked to give 'Remember', 'Know' or 'Guess' responses to items that were recognized on the basis of conscious recollection, familiarity, or guessing, respectively. Lorazepam selectively impaired recognition based on 'Remember' responses. This impairment was greater in the lorazepam 0.038 mg/kg than in the lorazepam 0.026 mg/kg groups. Measures of sedation were not correlated with the proportion of 'Remember' responses. These results suggest that sedation alone cannot account for the impairment of conscious recollection induced by lorazepam.

Different effects of lorazepam and diazepam on perceptual integration

Recent research has established the detrimental effect of lorazepam, a benzodiazepine, on both implicit and explicit memory. Furthermore, lorazepam is known to affect perceptual integration. Diazepam, on the other hand, though being a benzodiazepine too, only impairs explicit memory, leaving implicit memory fairly intact. Little is known about the effect of diazepam on perceptual integration. The present study aimed at filling in this gap, by comparing the effects of lorazepam and diazepam on the detection of discontinuities in random-shaped outlines. In line with previous findings, the results in a lorazepam-treated group were quite different from the results in a placebo-treated group. The results in a diazepam-treated group were analogous to the results in the placebo-treated group and different from the results in the lorazepam-treated group. This shows that lorazepam and diazepam differ, not only with respect to their effect on implicit memory, but also with respect to their effect on perceptual integration. It is argued that this bears important consequences for memory research that makes use of a pharmacological dissociation rationale.

Effects of lorazepam on vision and oculomotor balance

BACKGROUND

Previous studies have shown an effect of the tranquilizer lorazepam on visual perception. We explored the effects of the drug on binocular vision, visual acuity and accommodation.

SUBJECTS AND METHODS

Twenty-four paid healthy volunteers (13 women, 11 men) were recruited from the University of Strasbourg (mean age: 23.6 years, mean weight: 66.8 Kg). They were randomly assigned to one of two parallel groups of 12 subjects each (a placebo group and a lorazepam 0.038 mg/kg group). Visual acuity was measured for each eye separately (Snellen chart and Parinaud scale). Binocular vision was studied using the cover tests, measurement of the fusional amplitudes (with Berens prisms), and the Duane Scale Test (near point rule) measuring convergence and/or accommodation in centimeters or diopters as a function of age.

RESULTS

Regarding vision, there was no lorazepam effect, at either 33 cm or 5 m. An esophoria was observed after the intake of lorazepam (0Delta before intake and 2.8Delta after intake, p=0.001). Both fusional convergence and fusional divergence amplitudes decreased by lorazepam, (p=0.008, and p=0.002). Lorazepam also impaired the near point of convergence but did not affect accommodation.

CONCLUSION

A single dose of lorazepam induces an esophoric oculomotor imbalance and impaired fusional convergence and divergence amplitudes without impairing visual acuity or accommodation.

Effects of a benzodiazepine, lorazepam, on motion integration and segmentation: an effect on the processing of line-ends?

Previous studies have shown that the perceptual integration of component motions distributed across space is inhibited whenever segmentation cues, such as line-ends, are salient. Herein, we investigate to what extent enhanced inhibition induced by lorazepam, a benzodiazepine facilitating the fixation of GABA on GABAA receptors, modifies the balance between motion integration and motion segmentation at the behavioural level. Motion integration was tested in 16 healthy volunteers taking a single and oral dose of either placebo or lorazepam (0.038 mg kg-1). The stimulus consisted of an outlined diamond presented behind four, otherwise invisible, apertures and translating along a circular trajectory (Lorenceau & Shiffrar (1992). Vision Research, 32, 263-273). Under these conditions, recovering the global diamond direction requires the integration of the component motions available within each aperture. The observers were asked to discriminate the global, clockwise or counter-clockwise, diamond direction under difficult--at high luminance contrasts--or easy--at low luminance contrasts--conditions. Overall, reaction times and error rates increased in the lorazepam group as compared to the placebo group, suggesting strong non-specific effects. However, the changes in performance in the lorazepam group are not homogeneous across conditions, suggesting that lorazepam also induces specific effects that modulate the integration/segmentation balance. Additional experiments performed with visible apertures or visible diamond vertices indicate that the effects of lorazepam are unlikely to reflect a deficit of motion processing or motion integration mechanisms since performance is only slightly impaired in the lorazepam as compared to the placebo group under these conditions. These results suggest that lorazepam might specifically modulate the saliency of line-ends, presumably because processing these features involves inhibitory mechanisms using GABA as a neuromediator, and in turn modify the balance between motion integration and segmentation.

Lorazepam: A New Tool to Study the Processing of Discontinuities

The involvement of GABAA in the computation of visual information has been suggested in numerous electrophysiological studies. It might play a role, in particular, in the generation of the responses of hypercomplex cells involved in the processing of discontinuities. Benzodiazepines like lorazepam enhance the fixation of GABA on the GABAA receptor. We tested the hypothesis that lorazepam enhances the detection of discontinuities, with static stimuli composed of horizontal line-segments. There were four types of stimuli, with (1) collinear and discontinuous, (2) collinear and continuous, (3) parallel and discontinuous, and (4) parallel and continuous elements. A stimulus was presented on each trial in the centre of a computer screen for 160 ms. The task was to decide whether the stimulus was continuous or discontinuous. Response was given on two response keys. The results showed that lorazepam-treated subjects were faster at detecting a discontinuity when the stimulus included two aligned line-segments (− −) as compared to two parallel line-segments (=). Placebo-treated subjects displayed equivalent performance in the two conditions. These results support the hypothesis that lorazepam enhances responses to line-ends. They are consistent with previous results, obtained with static drawings, letters, fragmented squares, and dynamic stimuli. Lorazepam might be a useful tool to investigate visuo-perceptual integration processes and to link experimental psychology and electrophysiology.

Lorazepam impairs perceptual integration of visual forms: a central effect

Previous studies have shown a lorazepam effect on visual perception. We tested whether this impairment resulted from a peripheral effect induced by benzodiazepines. A first experiment showed that a single dose of lorazepam induces an oculomotor imbalance without impairing visual acuity or accommodation. In a second experiment, we tested whether the impairment induced by lorazepam on visual perception still occurred in monocular vision. Subjects matched incomplete forms controlled on the spacing and alignment of their local contour elements. A reference object was first displayed and followed by two laterally displayed objects, a target and a distractor. The distractor was the mirror-reversed version of the target. Performance was impaired in the lorazepam group when the reference was an incomplete form with a spacing of 10.8' or 22.2' of arc. These results were not correlated with sedation. They confirm that lorazepam has a central deleterious effect on visual perception. A post-hoc analysis also suggested that lorazepam-treated subjects used asymmetry in the stimuli as a compensatory strategy. This result is discussed in relation to previous hypotheses about the physiological mechanisms that determine the effects of lorazepam on visual perception.

Effects of lorazepam on perceptual integration of visual forms in healthy volunteers

We tested whether lorazepam (a benzodiazepine) affects perceptual processes involved in the computation of contour information. Subjects matched incomplete forms whose contour was composed of line segments varying in their spacing and in their alignment. An initial centrally displayed object (a reference) was followed by two laterally displayed pictures, a target and a distractor. The distractor was the mirror-reversed version of the target. In one condition, the reference was always an outline drawing of an object. In another condition, the reference was either an outline drawing or an incomplete form. All subjects were run in both conditions. Lorazepam 0.038 mg/kg induced a larger increase in RTs than the placebo and lorazepam 0.026 mg/kg when the spacing between local contour elements was larger than 10.8' arc and when the line segments were not aligned. Performance was improved in the 0.038 mg/kg lorazepam group when subjects started with the condition in which the reference was always an outline drawing. Performance was not correlated with sedation. These results show that lorazepam impairs visual perception. They are interpreted in terms of impaired binding processes, which can be compensated for by the use of stored object representations. This effect is consistent with electrophysiological studies showing that the neuromediator GABA is involved in perceptual processes.

Time course of the effects of diazepam and lorazepam on perceptual priming and explicit memory

The effects of diazepam and lorazepam on explicit memory and perceptual priming were studied 50, 130 and 300 min after drug administration. Sixty healthy volunteers were randomly assigned to one of five parallel groups (placebo, diazepam 0.2 or 0.3 mg/kg, lorazepam 0.026 or 0.038 mg/kg). The corresponding doses of benzodiazepines exerted a similar negative effect on explicit performance. Lorazepam markedly impaired priming performance, whereas the effect of diazepam was intermediate between that of placebo and that of lorazepam 0.038 mg/kg. The impairment was maximal at the theoretical peak plasma concentration. Contamination by explicit memory could account for the decrease in priming performance observed in the diazepam groups.

Lorazepam and diazepam effects on memory acquisition in priming tasks

Unlike diazepam, lorazepam has repeatedly been shown to impair perceptual priming as well as explicit memory. To determine whether this deleterious effect was due to an impairment in acquisition of information, 60 healthy volunteers were randomly assigned to five treatment groups (placebo, lorazepam 0.026 or 0.038 mg/kg, diazepam 0.2 or 0.3 mg/kg) and successively performed perceptual priming tasks and a free-recall task. Priming performance on information learned before or 2 h after drug administration, i.e. at the peak concentration of lorazepam, was assessed under the influence of the drugs, using a picture-fragment and a word-stem completion task. Free-recall performance was altered by both drugs. Lorazepam decreased priming performance when information was acquired after, but not before, drug administration, indicating that the drug alters the acquisition of information. Lorazepam also impaired the ability to identify fragmented pictures, but there was no evidence that this perceptual effect accounts for the priming impairment. Surprisingly, diazepam also decreased priming when information was acquired after drug administration, suggesting that, at least in certain circumstances, the two benzodiazepines may exert similar effects on priming measures.

The computation of contour information in complex objects

Perceptual organisation, and especially the computation of contour information, has been the object of considerable interest in the last few years. In the first part of the paper we review recent accounts on the mechanisms involved in the processing of contour. In the second part we report an experiment designed to examine (1) how physical parameters such as spatial proximity and collinearity of elements affect the integration of global contour in objects and (2) whether the activation of stored representations of objects facilitates the computation of contour. Incomplete forms varying in the spacing and the alignment of line segments on their contour were used as stimuli in a matching task. Subjects were asked to decide which of two laterally displayed figures matched a reference form presented previously. The matching target and the distractor were physically identical but differed in their orientation. In one condition the reference object was always an outline drawing of an object. In a second condition the reference object was either a complete object or a more or less identifiable incomplete form. Little variation in performance was found for forms having continuous and discontinuous contour up to a spacing of 5 pixels (10.8 min) between elements. Response times and errors increased abruptly beyond this limit. This effect occurred in the two conditions of reference stimulus, suggesting that the computation of contour information is more affected by physical constraints at early processes than by high-level processes involving activation of stored structural representations of objects.