Data analysis methods for copy number discovery and interpretation

Copy number variation (CNV) is an important type of genetic variation that can give rise to a wide variety of phenotypic traits. Differences in copy number are thought to play major roles in processes that involve dosage sensitive genes, providing beneficial, deleterious or neutral modifications to individual phenotypes. Copy number analysis has long been a standard in clinical cytogenetic laboratories. Gene deletions and duplications can often be linked with genetic Syndromes such as: the 7q11.23 deletion of Williams-­‐Bueren Syndrome, the 22q11 deletion of DiGeorge syndrome and the 17q11.2 duplication of Potocki-­‐Lupski syndrome. Interestingly, copy number based genomic disorders often display reciprocal deletion / duplication syndromes, with the latter frequently exhibiting milder symptoms. Moreover, the study of chromosomal imbalances plays a key role in cancer research. The datasets used for the development of analysis methods during this project are generated as part of the cutting-­‐edge translational project, Deciphering Developmental Disorders (DDD). This project, the DDD, is the first of its kind and will directly apply state of the art technologies, in the form of ultra-­‐high resolution microarray and next generation sequencing (NGS), to real-­‐time genetic clinical practice. It is collaboration between the Wellcome Trust Sanger Institute (WTSI) and the National Health Service (NHS) involving the 24 regional genetic services across the UK and Ireland. Although the application of DNA microarrays for the detection of CNVs is well established, individual change point detection algorithms often display variable performances. The definition of an optimal set of parameters for achieving a certain level of performance is rarely straightforward, especially where data qualities vary ... [cont.]

A cultural challenge for the Western Australian legal profession: a lack of diversity at the WA Bar?

At the request of the Western Australian Bar Association, the authors undertook a study into issues of diversity at the Western Australian Bar. Members of the Association had noticed, but not specifically studied, various demographic imbalances in the Bar’s constitution. A review of the literature revealed that there was a paucity of statistical analysis of the makeup of Australian barrister associations generally, let alone into any specific reasons as to how and why a demographic imbalance might exist. Recognising that a clearer picture of the breakdown of the demographics of the Western Australian legal profession and of the specific cultures that might exist at the Bar was needed, the authors undertook a study that examined whether there was an existing legal monoculture at the Bar, and if so what some of the reasons for this might be

A Real Time Motion Capture System, Using USB Based Tri-Axis Magnetic and Inertial Sensors for Movement Based Relaxation

scalable motion capture system based on multiple orientation sensors, each consisting of tri-axis magnetic and gravitational field transducers, for use in kinematic studies; is presented. Outlined is a novel system capable of accessing real time data from multiple sensors, via one universal serial bus host, using a dynamic link library. In addition, design considerations; implementation and performance of the system are analysed and discussed

Reducing Sensor Density Requirements For Kinematic Controllers In A Full Posture Yoga Gaming Application

Integration of whole body movements with virtual reality environments and computer games has many benefits for exercise training and rehabilitation. Such applications can serve as a virtual personal trainer for different exercise therapies. Current examples of this are based on provision of visual feedback to the user via a webcam yet these allow the player to deviate from the desired exercise sequence without direct warning or feedback. This can be solved by tracking body movements using orientation sensors. However, tracking and providing real time feedback for whole body movements for exercise therapies such as Yoga can prove very complex and require the use of a large number of sensors on body segments. In this paper we describe a methodological approach that can facilitate the development of a body movement driven Yoga exercise computer game that can discriminate player performance level with the use of minimum instrumentation

The E-Motion System: Motion Capture and Movement-based Biofeedback Game

This paper describes the development of a movement based training game aimed at teaching users an exercise program. This is achieved through analysing body posture as the player performs the exercise routine while concurrently receiving real-time feedback from the game. An in-depth post game feedback system also features, giving the player a detailed account of their performance after completing the exercise routine. Analysis of the player’s posture is achieved by placing orientation sensors on appropriate parts of the players’ body. The game can then read and interpret data from these sensors reconstructing a live 3D model of the players’ posture. The game has the kinematic data of an expert performing the current exercise routine stored in memory, which is compared to the kinematic data of the current player and appropriate feedback is given to aid the player in performing the exercise. The theme of the prototype game currently developed is that of a yoga training game (E-Yoga)

Reducing Sensor Density Requirements For Kinematic Controllers In A Full Posture Yoga Gaming Application

Integration of whole body movements with virtual reality environments and computer games has many benefits for exercise training and rehabilitation. Such applications can serve as a virtual personal trainer for different exercise therapies. Current examples of this are based on provision of visual feedback to the user via a webcam yet these allow the player to deviate from the desired exercise sequence without direct warning or feedback. This can be solved by tracking body movements using orientation sensors. However, tracking and providing real time feedback for whole body movements for exercise therapies such as Yoga can prove very complex and require the use of a large number of sensors on body segments. In this paper we describe a methodological approach that can facilitate the development of a body movement driven Yoga exercise computer game that can discriminate player performance level with the use of minimum instrumentation

A Prototype Sourceless Kinematic-Feedback Based Video Game for Movement Based Exercise

This paper presents a prototype kinematic and audio feedback based video game, availing of a scalable motion capture acquisition system, based around a number of orientation sensors. The orientation sensors used are USB based tri-axis magnetic and gravitational field transducers. The novel video-game is capable of incorporating the real time data from these sensors to control an on screen avatar, which in turn can be programmed to give appropriate instructions to the user i.e. play a sound file, once the user obtains a certain posture. The video game is designed to promote physical exercise and movement based relaxation, in particular; Yoga. In addition, design considerations; implementation and performance of the system are analyzed, discussed and the accuracy qualitatively analyzed by comparing movement data obtained from it to that of a validated motion analysis technique, the CODA motion analysis system

Large scale variation in DNA copy number in chicken breeds

Background Detecting genetic variation is a critical step in elucidating the molecular mechanisms underlying phenotypic diversity. Until recently, such detection has mostly focused on single nucleotide polymorphisms (SNPs) because of the ease in screening complete genomes. Another type of variant, copy number variation (CNV), is emerging as a significant contributor to phenotypic variation in many species. Here we describe a genome-wide CNV study using array comparative genomic hybridization (aCGH) in a wide variety of chicken breeds. Results We identified 3,154 CNVs, grouped into 1,556 CNV regions (CNVRs). Thirty percent of the CNVs were detected in at least 2 individuals. The average size of the CNVs detected was 46.3 kb with the largest CNV, located on GGAZ, being 4.3 Mb. Approximately 75% of the CNVs are copy number losses relatively to the Red Jungle Fowl reference genome. The genome coverage of CNVRs in this study is 60 Mb, which represents almost 5.4% of the chicken genome. In particular large gene families such as the keratin gene family and the MHC show extensive CNV. Conclusions A relative large group of the CNVs are line-specific, several of which were previously shown to be related to the causative mutation for a number of phenotypic variants. The chance that inter-specific CNVs fall into CNVRs detected in chicken is related to the evolutionary distance between the species. Our results provide a valuable resource for the study of genetic and phenotypic variation in this phenotypically diverse species

Usability Evaluation of E-Motion: A Virtual Rehabilitation System Designed to Demonstrate, Instruct and Monitor a Therapeutic Exercise Programme

The importance of systematic usability evaluation of virtual rehabilitation systems cannot be underestimated. We have developed a virtual rehabilitation system with the functionality to guide a user through a therapeutic exercise programme. Progression is determined by users’ ability to replicate movements as demonstrated by an on-screen character. Visual and auditory corrective feedback is provided during exercise in order to improve the user’s postural control and biomechanical alignment. The objective of this study was to evaluate the usability of our system and subsequently implement modifications aimed at improving fidelity and ease of use. The first stage of our evaluation involved conducting an expert walkthrough with six experts currently researching in areas related to the system design. Following system refinement and modification we conducted a user evaluation study with twelve novice users using VRUSE, a computerised questionnaire-based usability evaluation tool for assessment of virtual environments. Results have provided a systematic evaluation of the system, provided information for guidance on system alterations and will allow comparison of usability levels with similar virtual rehabilitation systems tested with the same protocol

Usability Evaluation of E-Motion: A Virtual Rehabilitation System Designed to Demonstrate, Instruct and Monitor a Therapeutic Exercise Programme

The importance of systematic usability evaluation of virtual rehabilitation systems cannot be underestimated. We have developed a virtual rehabilitation system with the functionality to guide a user through a therapeutic exercise programme. Progression is determined by users’ ability to replicate movements as demonstrated by an on-screen character. Visual and auditory corrective feedback is provided during exercise in order to improve the user’s postural control and biomechanical alignment. The objective of this study was to evaluate the usability of our system and subsequently implement modifications aimed at improving fidelity and ease of use. The first stage of our evaluation involved conducting an expert walkthrough with six experts currently researching in areas related to the system design. Following system refinement and modification we conducted a user evaluation study with twelve novice users using VRUSE, a computerised questionnaire-based usability evaluation tool for assessment of virtual environments. Results have provided a systematic evaluation of the system, provided information for guidance on system alterations and will allow comparison of usability levels with similar virtual rehabilitation systems tested with the same protocol