Search

Comprehensive genome annotation is essential to understand the impact of clinically relevant variants. However, the absence of a standard for clinical reporting and browser display complicates the process of consistent interpretation and reporting. To address these challenges, Ensembl/GENCODE1and RefSeq2launched a joint initiative, the Matched Annotation from NCBI and EMBL-EBI (MANE) collaboration, to converge on human gene and transcript annotation and to jointly define a high-value set of transcripts and corresponding proteins. Here, we describe the MANE transcript sets for use as universal standards for variant reporting and browser display. The MANE Select set identifies a representative transcript for each human protein-coding gene, whereas the MANE Plus Clinical set provides additional transcripts at loci where the Select transcripts alone are not sufficient to report all currently known clinical variants. Each MANE transcript represents an exact match between the exonic sequences of an Ensembl/GENCODE transcript and its counterpart in RefSeq such that the identifiers can be used synonymously. We have now released MANE Select transcripts for 97% of human protein-coding genes, including all American College of Medical Genetics and Genomics Secondary Findings list v3.0 (ref.3) genes. MANE transcripts are accessible from major genome browsers and key resources. Widespread adoption of these transcript sets will increase the consistency of reporting, facilitate the exchange of data regardless of the annotation source and help to streamline clinical interpretation.

SUMMARYClinicians assessing children with autism are sometimes faced with a dilemma, especially if there is a definite or suspected history of abuse or neglect: is this autism or attachment disorder? This is important because the attachment disorders (reactive attachment disorder and disinhibited social engagement disorder) are thought to be caused by abuse or neglect, whereas autism is not. We discuss the Coventry Grid, a clinical tool aiming to aid differentiation between autism and attachment disorders. We examine the small body of empirical studies focusing on this differential diagnosis and find that the Coventry Grid can be regarded as an evidence-based tool. We also discuss preliminary findings regarding a relatively unstructured observational method involving two assessors who engage the child in jokes and playful social dilemmas, which might help clinicians elicit the information required to complete the Coventry Grid.

Ensembl (https://www.ensembl.org) is unique in its flexible infrastructure for access to genomic data and annotation. It has been designed to efficiently deliver annotation at scale for all eukaryotic life, and it also provides deep comprehensive annotation for key species. Genomes representing a greater diversity of species are increasingly being sequenced. In response, we have focussed our recent efforts on expediting the annotation of new assemblies. Here, we report the release of the greatest annual number of newly annotated genomes in the history of Ensembl via our dedicated Ensembl Rapid Release platform (http://rapid.ensembl.org). We have also developed a new method to generate comparative analyses at scale for these assemblies and, for the first time, we have annotated non-vertebrate eukaryotes. Meanwhile, we continually improve, extend and update the annotation for our high-value reference vertebrate genomes and report the details here. We have a range of specific software tools for specific tasks, such as the Ensembl Variant Effect Predictor (VEP) and the newly developed interface for the Variant Recoder. All Ensembl data, software and tools are freely available for download and are accessible programmatically.

Ensembl (https://www.ensembl.org) has produced high-quality genomic resources for vertebrates and model organisms for more than twenty years. During that time, our resources, services and tools have continually evolved in line with both the publicly available genome data and the downstream research and applications that utilise the Ensembl platform. In recent years we have witnessed a dramatic shift in the genomic landscape. There has been a large increase in the number of high-quality reference genomes through global biodiversity initiatives. In parallel, there have been major advances towards pangenome representations of higher species, where many alternative genome assemblies representing different breeds, cultivars, strains and haplotypes are now available. In order to support these efforts and accelerate downstream research, it is our goal at Ensembl to create high-quality annotations, tools and services for species across the tree of life. Here, we report our resources for popular reference genomes, the dramatic growth of our annotations (including haplotypes from the first human pangenome graphs), updates to the Ensembl Variant Effect Predictor (VEP), interactive protein structure predictions from AlphaFold DB, and the beta release of our new website.

Background: Antimicrobial usage and stewardship programmes during COVID-19 have been poorly studied. Prescribing practice varies despite national guidelines, and there is concern that stewardship principles have suffered. Aim: To analyse antibiotic prescriptions during the COVID-19 pandemic at a teaching hospital and to propose improved approaches to stewardship. Methods: We reviewed COVID-19 admissions to medical wards and intensive care units (ICUs) in a London teaching hospital to assess initial antibiotic usage and evidence of bacterial co-infection, and to determine if our current antibiotic guidelines were adhered to. Findings: Data from 130 inpatients (76% medical and 24% ICU) were obtained. On admission, 90% were treated with antibiotics. No microbiological samples taken on admission provided definitive evidence of respiratory co-infection. In 13% of cases, antibiotics were escalated, usually without supporting clinical, radiological or laboratory evidence. In 16% of cases, antibiotics were stopped or de-escalated within 72 h. Blood results and chest radiographs were characteristic of COVID-19 in 20% of ward patients and 42% of ICU patients. Overall mortality was 25% at 14 days – similar to rates described for the UK as a whole. Conclusion: The majority of patients received antibiotics despite limited evidence of co-infection. Most patients received narrower spectrum antibiotics than recommended by NICE. As understanding of the natural history of COVID-19 infections progresses, stewardship programmes will need to evolve; however, at this point, we feel that a more restrictive antibiotic prescribing approach is warranted. We propose strategies for effective stewardship and estimate the effect this may have on antibiotic consumption.

The Ensembl project (https://www.ensembl.org) annotates genomes and disseminates genomic data for vertebrate species. We create detailed and comprehensive annotation of gene structures, regulatory elements and variants, and enable comparative genomics by inferring the evolutionary history of genes and genomes. Our integrated genomic data are made available in a variety of ways, including genome browsers, search interfaces, specialist tools such as the Ensembl Variant Effect Predictor, download files and programmatic interfaces. Here, we present recent Ensembl developments including two new website portals. Ensembl Rapid Release (http://rapid.ensembl.org) is designed to provide core tools and services for genomes as soon as possible and has been deployed to support large biodiversity sequencing projects. Our SARS-CoV-2 genome browser (https://covid-19.ensembl.org) integrates our own annotation with publicly available genomic data from numerous sources to facilitate the use of genomics in the international scientific response to the COVID-19 pandemic. We also report on other updates to our annotation resources, tools and services. All Ensembl data and software are freely available without restriction.

Data availability: No new data were generated or analysed in support of this research. Copyright © The Author(s) 2022. GENCODE produces high quality gene and transcript annotation for the human and mouse genomes. All GENCODE annotation is supported by experimental data and serves as a reference for genome biology and clinical genomics. The GENCODE consortium generates targeted experimental data, develops bioinformatic tools and carries out analyses that, along with externally produced data and methods, support the identification and annotation of transcript structures and the determination of their function. Here, we present an update on the annotation of human and mouse genes, including developments in the tools, data, analyses and major collaborations which underpin this progress. For example, we report the creation of a set of non-canonical ORFs identified in GENCODE transcripts, the LRGASP collaboration to assess the use of long transcriptomic data to build transcript models, the progress in collaborations with RefSeq and UniProt to increase convergence in the annotation of human and mouse protein-coding genes, the propagation of GENCODE across the human pan-genome and the development of new tools to support annotation of regulatory features by GENCODE. Our annotation is accessible via Ensembl, the UCSC Genome Browser and https://www.gencodegenes.org. National Human Genome Research Institute of the National Institutes of Health [U41HG007234, R01HG004037]; Wellcome Trust [WT222155/Z/20/Z]; European Molecular Biology Laboratory. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. Funding for open access charge: National Institutes of Health.

Ensembl (https://www.ensembl.org) has produced high-quality genomic resources for vertebrates and model organisms for more than twenty years. During that time, our resources, services and tools have continually evolved in line with both the publicly available genome data and the downstream research and applications that utilise the Ensembl platform. In recent years we have witnessed a dramatic shift in the genomic landscape. There has been a large increase in the number of high-quality reference genomes through global biodiversity initiatives. In parallel, there have been major advances towards pangenome representations of higher species, where many alternative genome assemblies representing different breeds, cultivars, strains and haplotypes are now available. In order to support these efforts and accelerate downstream research, it is our goal at Ensembl to create high-quality annotations, tools and services for species across the tree of life. Here, we report our resources for popular reference genomes, the dramatic growth of our annotations (including haplotypes from the first human pangenome graphs), updates to the Ensembl Variant Effect Predictor (VEP), interactive protein structure predictions from AlphaFold DB, and the beta release of our new website.

Ensembl (https://www.ensembl.org) is unique in its flexible infrastructure for access to genomic data and annotation. It has been designed to efficiently deliver annotation at scale for all eukaryotic life, and it also provides deep comprehensive annotation for key species. Genomes representing a greater diversity of species are increasingly being sequenced. In response, we have focussed our recent efforts on expediting the annotation of new assemblies. Here, we report the release of the greatest annual number of newly annotated genomes in the history of Ensembl via our dedicated Ensembl Rapid Release platform (http://rapid.ensembl.org). We have also developed a new method to generate comparative analyses at scale for these assemblies and, for the first time, we have annotated non-vertebrate eukaryotes. Meanwhile, we continually improve, extend and update the annotation for our high-value reference vertebrate genomes and report the details here. We have a range of specific software tools for specific tasks, such as the Ensembl Variant Effect Predictor (VEP) and the newly developed interface for the Variant Recoder. All Ensembl data, software and tools are freely available for download and are accessible programmatically.

Global travel is increasingly a fact of modern life, and the rapid spread of severe acute respiratory syndrome coronavirus 2 leading to lockdown across the world has demonstrated the interconnectedness of the world's population. Illness in the returning traveller can range from trivial to life-threatening, and the concept of imported infection can be an intimidating diagnostic and management challenge. An important caveat is that even if your patient has returned from cuddling multimammate rats in Guinea 1 week ago, they could be febrile from a distinctly non-tropical urinary tract infection. That said, antimicrobial resistance is an established concern among returned travellers, which has further infection control implications. Infection control issues regarding isolation, personal protective equipment and notification to public health should always be considered for returning travellers on presentation often before diagnostic confirmation has been made. Always consider the risk of high-consequence infectious diseases.

The Ensembl project (https://www.ensembl.org) annotates genomes and disseminates genomic data for vertebrate species. We create detailed and comprehensive annotation of gene structures, regulatory elements and variants, and enable comparative genomics by inferring the evolutionary history of genes and genomes. Our integrated genomic data are made available in a variety of ways, including genome browsers, search interfaces, specialist tools such as the Ensembl Variant Effect Predictor, download files and programmatic interfaces. Here, we present recent Ensembl developments including two new website portals. Ensembl Rapid Release (http://rapid.ensembl.org) is designed to provide core tools and services for genomes as soon as possible and has been deployed to support large biodiversity sequencing projects. Our SARS-CoV-2 genome browser (https://covid-19.ensembl.org) integrates our own annotation with publicly available genomic data from numerous sources to facilitate the use of genomics in the international scientific response to the COVID-19 pandemic. We also report on other updates to our annotation resources, tools and services. All Ensembl data and software are freely available without restriction.

Background Olfactory receptor (OR) genes are the largest multi-gene family in the mammalian genome, with 874 in human and 1483 loci in mouse (including pseudogenes). The expansion of the OR gene repertoire has occurred through numerous duplication events followed by diversification, resulting in a large number of highly similar paralogous genes. These characteristics have made the annotation of the complete OR gene repertoire a complex task. Most OR genes have been predicted in silico and are typically annotated as intronless coding sequences. Results Here we have developed an expert curation pipeline to analyse and annotate every OR gene in the human and mouse reference genomes. By combining evidence from structural features, evolutionary conservation and experimental data, we have unified the annotation of these gene families, and have systematically determined the protein-coding potential of each locus. We have defined the non-coding regions of many OR genes, enabling us to generate full-length transcript models. We found that 13 human and 41 mouse OR loci have coding sequences that are split across two exons. These split OR genes are conserved across mammals, and are expressed at the same level as protein-coding OR genes with an intronless coding region. Our findings challenge the long-standing and widespread notion that the coding region of a vertebrate OR gene is contained within a single exon. Conclusions This work provides the most comprehensive curation effort of the human and mouse OR gene repertoires to date. The complete annotation has been integrated into the GENCODE reference gene set, for immediate availability to the research community.

The Ensembl project (https://www.ensembl.org) makes key genomic data sets available to the entire scientific community without restrictions. Ensembl seeks to be a fundamental resource driving scientific progress by creating, maintaining and updating reference genome annotation and comparative genomics resources. This year we describe our new and expanded gene, variant and comparative annotation capabilities, which led to a 50% increase in the number of vertebrate genomes we support. We have also doubled the number of available human variants and added regulatory regions for many mouse cell types and developmental stages. Our data sets and tools are available via the Ensembl website as well as a through a RESTful webservice, Perl application programming interface and as data files for download.

The fifth edition of the Diagnostic and Statistical Manual ( DSM) categorizes reactive attachment disorder (RAD) and disinhibited social engagement disorder (DSED) as two separate disorders, and their criteria are revised. For DSED, the core symptoms focus on abnormal social disinhibition, and symptoms regarding lack of selective attachment have been removed. The core symptoms of RAD are the absence of attachment behaviors and emotional dysregulation. In this study, an international team of researchers modified the Child and Adolescent Psychiatric Assessment for RAD to update it from DSM-IV to DSM-5 criteria for RAD and DSED. We renamed the interview the reactive attachment disorder and disinhibited social engagement disorder assessment (RADA). Foster parents of 320 young people aged 11 to 17 years completed the RADA online. Confirmatory factor analysis of RADA items identified good fit for a three-factor model, with one factor comprising DSED items (indiscriminate behaviors with strangers) and two factors comprising RAD items (RAD1: failure to seek/accept comfort, and RAD2: withdrawal/hypervigilance). The three factors showed differential associations with clinical symptoms of emotional and social impairment. Time in foster care was not associated with scores on RAD1, RAD2, or DSED. Higher age was associated with lower scores on DSED, and higher scores on RAD1.

The Consensus Coding Sequence (CCDS) project provides a dataset of protein-coding regions that are identically annotated on the human and mouse reference genome assembly in genome annotations produced independently by NCBI and the Ensembl group at EMBL-EBI. This dataset is the product of an international collaboration that includes NCBI, Ensembl, HUGO Gene Nomenclature Committee, Mouse Genome Informatics and University of California, Santa Cruz. Identically annotated coding regions, which are generated using an automated pipeline and pass multiple quality assurance checks, are assigned a stable and tracked identifier (CCDS ID). Additionally, coordinated manual review by expert curators from the CCDS collaboration helps in maintaining the integrity and high quality of the dataset. The CCDS data are available through an interactive web page (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi) and an FTP site (ftp://ftp.ncbi.nlm.nih.gov/pub/CCDS/). In this paper, we outline the ongoing work, growth and stability of the CCDS dataset and provide updates on new collaboration members and new features added to the CCDS user interface. We also present expert curation scenarios, with specific examples highlighting the importance of an accurate reference genome assembly and the crucial role played by input from the research community.

The most widely appreciated role of DNA is to encode protein, yet the exact portion of the human genome that is translated remains to be ascertained. We previously developed PhyloCSF, a widely used tool to identify evolutionary signatures of protein-coding regions using multispecies genome alignments. Here, we present the first whole-genome PhyloCSF prediction tracks for human, mouse, chicken, fly, worm, and mosquito. We develop a workflow that uses machine learning to predict novel conserved protein-coding regions and efficiently guide their manual curation. We analyze more than 1000 high-scoring human PhyloCSF regions and confidently add 144 conserved protein-coding genes to the GENCODE gene set, as well as additional coding regions within 236 previously annotated protein-coding genes, and 169 pseudogenes, most of them disabled after primates diverged. The majority of these represent new discoveries, including 70 previously undetected protein-coding genes. The novel coding genes are additionally supported by single-nucleotide variant evidence indicative of continued purifying selection in the human lineage, coding-exon splicing evidence from new GENCODE transcripts using next-generation transcriptomic data sets, and mass spectrometry evidence of translation for several new genes. Our discoveries required simultaneous comparative annotation of other vertebrate genomes, which we show is essential to remove spurious ORFs and to distinguish coding from pseudogene regions. Our new coding regions help elucidate disease-associated regions by revealing that 118 GWAS variants previously thought to be noncoding are in fact protein altering. Altogether, our PhyloCSF data sets and algorithms will help researchers seeking to interpret these genomes, while our new annotations present exciting loci for further experimental characterization.

Variants in IQSEC2, escaping X inactivation, cause X-linked intellectual disability with frequent epilepsy in males and females. We aimed to investigate sex-specific differences., SCOPUS: ar.j, info:eu-repo/semantics/published

This Article was originally published under Nature Research’s License to Publish, but has now been made available under a CC BY 4.0 license. The PDF and HTML versions of the Article have been modified accordingly.

A systematic review of reactive attachment disorder (RAD)/disinhibited social engagement disorder (DSED) in adolescence highlighted that young people with the disorder had indiscriminate friendliness with difficulties in establishing and maintaining stable relationships. Most reported experiences of rejection. We were struck by similarities between the above and features of emergence of personality disorders (EPD). This feasibility study aimed to determine best ways of recruiting and retaining vulnerable young people and the proportion of participants with RAD/DSED who might have emerging borderline personality disorder (EBPD). Participants were referred to the study by their treating clinicians from local mental health teams. Results showed strong association between RAD/DSED and EBPD. Participant characteristics showed high levels of out of home placements, early termination of school careers, suicide attempts, quasipsychotic symptoms, and multiagency involvements. They experienced the project as an opportunity to talk about relationships and reported that they would like more of this in usual clinical contacts. They all agreed to be contacted for future studies. Previous studies have shown that early detection and treatment of emergent personality traits can alter trajectory. Future research will continue to explore these trajectories, explore detection of vulnerability factors, and evaluate interventions.

Background Important work has been carried out adapting cognitive behavioural therapy for people with intellectual disabilities. However, there is a lack of alternative psychological therapies available for people with intellectual disabilities and emotional difficulties. Behavioural activation for depression is less reliant on verbal communication and focuses on increasing purposeful activity and reducing avoidance. Method This feasibility study involved the development and piloting of an adapted manual of behavioural activation for people with intellectual disabilities. The intervention consisted of 10–12 sessions and a key adaptation was that the therapist worked with the clients alongside a significant other in their life, either a paid carer or family member. Baseline, post-intervention (3 months after entering the study) and 6-month quantitative follow-up data were obtained. Primary outcome data were gathered, concerning depressive symptoms, participants' levels of activity and general well-being. Results Twenty-three adults with intellectual disabilities with symptoms of depression were recruited from specialist health services. In terms of acceptability, the behavioural activation intervention was well received and only two individuals dropped out, with a further two lost to follow-up. The main measures of depression appeared to be sensitive to change. Pre- to post-intervention data showed a significant reduction in self-report of depressive symptoms with a strong effect size (r = 0.78), that was maintained at follow-up (r = 0.86). Positive change was also obtained for informant reports of depressive symptoms from pre- to post-intervention, with a strong effect size (r = 0.7). Once again, this positive change was maintained at follow-up (r = 0.72). Conclusions The study suggested that behavioural activation may be a feasible and worthwhile approach to tackling depression in people with intellectual disabilities. However, a randomised controlled trial would be required to establish its effectiveness, with more sensitive measurement of change in activity.

In order to be effective, public service occupations like library and information science must reconcile the values held amongst professionals with the perspectives and needs of the community being served. Such reconciliation is difficult because of the evolving and potentially conflicting values of librarians and library users. During the RUSA President's Program "Our Values, Ourselves" four prominent figures in Library Science discussed the past, present, and future of libraries and their role in society. The presenters were: Wayne Bivens-Tatum, Philosophy and Religion Librarian at Princeton University; Wayne Wiegand, E William Summers Professor of Library and Information Studies Emeritus at Florida State University; Lisa Carlucci Thomas, Director and Founder, Design Think Do; and Jeanne Goodrich, former Executive Director, Las Vegas-Clark County Library District (retired September 2014). The pieces presented here are edited versions of the presentations, and are abbreviated from the full remarks.--Editor THE ENLIGHTENMENT VALUES OF LIBRARIES Wayne Bivens-Tatum I'm going to focus on the historical motivations for the founding and development of modern academic and public libraries. These may or may not be the values that libraries still have, but they were the values that founded them. I argue they were founded upon an array of Enlightenment values, including the use of human reason to study the world, to create and disseminate new knowledge, and to educate the citizens of a democratic republic and enrich their lives. The Enlightenment can be roughly divided into the philosophical and the political. By Philosophical Enlightenment, I mean all those principles of Enlightenment that coalesce around scholarship and research, the increase of knowledge, the belief in the benefits of science and education, and the right and even obligation to publish scholarly findings. In contrast, Political Enlightenment could be considered the Philosophical Enlightenment democratized--Enlightenment at least within the reach of everyone, even if not desired by everyone. This rough division plays itself out in the history of libraries. Academic libraries--and the universities they support--to a great extent fulfill the promises of the Philosophical Enlightenment to collect, organize, preserve, and within limitations disseminate scholarly knowledge and the human record. Public libraries fall into the category of the Political Enlightenment, and many have conceived their mission partly as one of making knowledge more available to people. Enlightenment--philosophical and political--involves the creation of knowledge and its democratic dissemination to prepare autonomous citizens of a democratic republic, as well as the improvement of their lives in various ways. Academic libraries, from large research libraries to smaller college libraries, are products of the Enlightenment and its promotion of reason and freedom. The pursuit of knowledge for its own sake wherever it might lead, the examination of every possible topic in the light of reason, and the freedom to publish that research to the world--the underlying principles of modern universities--led to the inevitable creation of the libraries capable of supporting those goals. While scholars investigated, examined, experimented and wrote and wrote and wrote, academic librarians worked to acquire, preserve, organize, and make accessible the materials they needed, and in the process built up a national network of cooperative collections and services in the support of scholarship. Public libraries in the United States began as efforts to educate citizens in a democracy and to Americanize immigrants. The Boston Public Library was pitched as the natural extension of the free public schooling system Boston had already implemented. Early promotion by the American Library Association on behalf of libraries often focused on education and improving citizen's lives. …

Children who have experienced early adversity have been known to be at risk of developing cognitive, attachment, and mental health problems; therefore, it is crucial that children entering foster care can be properly assessed as early as possible. There are known difficulties in assessing children in foster care, for example, in finding a reliable informant. An ongoing randomised controlled trial in Glasgow, Scotland, recruiting infants entering foster care, provides a unique opportunity to explore some of the issues which need to be considered when assessing these children. The assessment data of 70 infants entering care is described while exploring the reliability of foster carers as informants and the importance of infant engagement with tasks. This group of infants was shown to be having more problems than children from the general population. While correlations were found between a carer’s level of concern about a child and the severity of a child’s problem, there were still a number of children displaying worrying problem scores whom foster carers did not report concern. The child’s engagement in the cognitive task showed associations with the child’s attainment on the task. Findings emphasise the importance of a holistic assessment for these children and all should be considered as potential cases with Maltreatment-Associated Psychiatric Problems (MAPP).

Schistosomiasis is one of the most prevalent parasitic diseases, affecting millions of people in developing countries. Amongst the human-infective species, Schistosoma mansoni is also the most commonly used in the laboratory and here we present the systematic improvement of its draft genome. We used Sanger capillary and deep-coverage Illumina sequencing from clonal worms to upgrade the highly fragmented draft 380 Mb genome to one with only 885 scaffolds and more than 81% of the bases organised into chromosomes. We have also used transcriptome sequencing (RNA-seq) from four time points in the parasite's life cycle to refine gene predictions and profile their expression. More than 45% of predicted genes have been extensively modified and the total number has been reduced from 11,807 to 10,852. Using the new version of the genome, we identified trans-splicing events occurring in at least 11% of genes and identified clear cases where it is used to resolve polycistronic transcripts. We have produced a high-resolution map of temporal changes in expression for 9,535 genes, covering an unprecedented dynamic range for this organism. All of these data have been consolidated into a searchable format within the GeneDB (www.genedb.org) and SchistoDB (www.schistodb.net) databases. With further transcriptional profiling and genome sequencing increasingly accessible, the upgraded genome will form a fundamental dataset to underpin further advances in schistosome research., Author Summary Schistosomiasis is a disease caused by parasitic blood flukes of the genus Schistosoma. Human-infective species are prevalent in developing countries, where they represent a major disease burden as well as an impediment to socioeconomic development. In addition to its clinical relevance, Schistosoma mansoni is the species most widely used for laboratory experimentation. In 2009, the first draft of the S. mansoni and S. japonicum genomes were published. Both genome sequences represented a great step forward for schistosome research, but their highly fragmented nature compromised the quality of potential downstream analyses. In this study, we have substantially improved both the genome and the transcriptome resources for S. mansoni. We collated existing data and added deep DNA sequence data from clonal worms and RNA sequence data from four key time points in the life cycle of the parasite. We were able to identify transcribed regions to single-base resolution and have profiled gene expression from the free-living larvae to the early human parasitic stage. We uncovered extensive use of single transcripts from multiple genes, which the organism subsequently resolves by trans-splicing. All data from this study comprise a major new release of the genome, which is publicly and easily accessible.

L’article examine la notion d’autorite a partir de deux mouvements apparemment contradictoires : l’evolution du concept d’autorite parentale allant vers un apparent affaiblissement de cette notion et une certaine immanence de l’autorite dans le cadre judiciaire de l’assistance educative. Les conditions de la manifestation de cette autorite sont explorees a travers les notions de cadre, de rituels et d’offre de pensee.

Postural management is assumed to be a valid and necessary strategy in the care of individuals with neuromuscular disorders who may be at risk of developing musculoskeletal deformity. To date, the evidence base for postural management remains relatively unexplored. This article reviews 150 articles that relate to the evidence for postural management in some common clinical conditions. The work was undertaken by members of the Scottish Seating and Wheelchair Group. The sample of literature was graded according to Sackett’s levels of evidence, which describe on a scale of one to five the scientific rigour of each study. The areas explored were physiological function, neonates and children under 5 years of age, progressive neuromuscular disorders, cerebral palsy, activities of daily living, older people, neuromuscular scoliosis and neurological disorders. The reliability and distribution of this evidence for postural management is discussed.

BackgroundReactive attachment disorder (RAD) is associated with early childhood maltreatment and has unknown population prevalence beyond infancy.AimsTo estimate RAD prevalence in a deprived population of children.MethodAll 1646 children aged 6-8 years old in a deprived sector of an urban UK centre were screened for RAD symptoms. Parents of high and low scorers were interviewed using semi-structured interviews probing for psychopathology and individuals likely to have RAD were offered face-to-face assessment.ResultsQuestionnaire data were available from 92.8% of teachers and 65.8% of parents. Assessments were conducted with 50% of those invited and missing data were imputed - based on the baseline data - for the rest. We calculated that there would be 23 children with definite RAD diagnoses, suggesting that the prevalence of RAD in this population was 1.40% (95% CI 0.94-2.10).ConclusionsIn this deprived general population, RAD was not rare.

Reactive attachment disorder (RAD) is a severe disorder of social functioning. Previous research has shown that children with RAD may have poor cognitive and language abilities; however, findings mainly come from biased, institutionalised samples. This paper describes the characteristics of all children who were given a suspected or likely diagnosis of reactive attachment disorder in an epidemiological study of approximately 1,600 children investigating the prevalence of RAD in the general population. We found that children with RAD are more likely to have multiple comorbidities with other disorders, lower IQs than population norms, more disorganised attachment, more problem behaviours, and poorer social skills than would be found in the general population and therefore have a complex presentation than can be described as ESSENCE. We discuss the clinical and educational implications.

The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. The newly identified elements also show a statistical correspondence to sequence variants linked to human disease, and can thereby guide interpretation of this variation. Overall, the project provides new insights into the organization and regulation of our genes and genome, and is an expansive resource of functional annotations for biomedical research. The Consortium is funded by grants from the NHGRI as follows: production grants: U54HG004570 (B. E. Bernstein); U01HG004695 (E. Birney); U54HG004563 (G. E. Crawford); U54HG004557 (T. R. Gingeras); U54HG004555 (T. J. Hubbard); U41HG004568 /n(W. J. Kent); U54HG004576 (R. M. Myers); U54HG004558 (M. Snyder);/nU54HG004592 (J. A. Stamatoyannopoulos). Pilot grants: R01HG003143 (J. Dekker); RC2HG005591 and R01HG003700 (M. C. Giddings); R01HG004456-03 (Y. Ruan); U01HG004571 (S. A. Tenenbaum); U01HG004561 (Z. Weng); RC2HG005679 (K. P. White). This project was supported in part by American Recovery and/nReinvestment Act (ARRA) funds from the NHGRI through grants U54HG004570, U54HG004563, U41HG004568, U54HG004592, R01HG003143, RC2HG005591,R01HG003541, U01HG004561, RC2HG005679andR01HG003988(L. Pennacchio). In addition, work from NHGRI Groups was supported by the Intramural Research/nProgram of the NHGRI (L. Elnitski, ZIAHG200323; E. H. Margulies, ZIAHG200341). Research in the Pennachio laboratory was performed at Lawrence Berkeley National Laboratory and at the United States Department of Energy Joint Genome Institute, Department of Energy Contract DE-AC02-05CH11231, University of California.

Supergenes are tight clusters of loci that facilitate the co-segregation of adaptive variation, providing integrated control of complex adaptive phenotypes1. Polymorphic supergenes, in which specific combinations of traits are maintained within a single population, were first described for ‘pin’ and ‘thrum’ floral types in Primula1 and Fagopyrum2, but classic examples are also found in insect mimicry3, 4, 5 and snail morphology6. Understanding the evolutionary mechanisms that generate these co-adapted gene sets, as well as the mode of limiting the production of unfit recombinant forms, remains a substantial challenge7, 8, 9, 10. Here we show that individual wing-pattern morphs in the polymorphic mimetic butterfly Heliconius numata are associated with different genomic rearrangements at the supergene locus P. These rearrangements tighten the genetic linkage between at least two colour-pattern loci that are known to recombine in closely related species9, 10, 11, with complete suppression of recombination being observed in experimental crosses across a 400-kilobase interval containing at least 18 genes. In natural populations, notable patterns of linkage disequilibrium (LD) are observed across the entire P region. The resulting divergent haplotype clades and inversion breakpoints are found in complete association with wing-pattern morphs. Our results indicate that allelic combinations at known wing-patterning loci have become locked together in a polymorphic rearrangement at the P locus, forming a supergene that acts as a simple switch between complex adaptive phenotypes found in sympatry. These findings highlight how genomic rearrangements can have a central role in the coexistence of adaptive phenotypes involving several genes acting in concert, by locally limiting recombination and gene flow.

The mimetic wing patterns of Heliconius butterflies are an excellent example of both adaptive radiation and convergent evolution. Alleles at the HmYb and HmSb loci control the presence/absence of hindwing bar and hindwing margin phenotypes respectively between divergent races of Heliconius melpomene, and also between sister species. Here, we used fine-scale linkage mapping to identify and sequence a BAC tilepath across the HmYb/Sb loci. We also generated transcriptome sequence data for two wing pattern forms of H. melpomene that differed in HmYb/Sb alleles using 454 sequencing technology. Custom scripts were used to process the sequence traces and generate transcriptome assemblies. Genomic sequence for the HmYb/Sb candidate region was annotated both using the MAKER pipeline and manually using transcriptome sequence reads. In total, 28 genes were identified in the HmYb/Sb candidate region, six of which have alternative splice forms. None of these are orthologues of genes previously identified as being expressed in butterfly wing pattern development, implying previously undescribed molecular mechanisms of pattern determination on Heliconius wings. The use of next-generation sequencing has therefore facilitated DNA annotation of a poorly characterized genome, and generated hypotheses regarding the identity of wing pattern at the HmYb/Sb loci.

The Human and Vertebrate Analysis and Annotation (HAVANA) group at the Wellcome Trust Sanger Institute produced the manually annotated geneset for the Encyclopedia of DNA Elements (ENCODE) pilot project and, as part of the Gencode subgroup, are reprising this role in the scale up to cover the whole human genome. Our manual annotation is checked computationally and validated experimentally. Loci and transcripts predicted to be absent from the initial annotation are identified by comparison with a number of state-of-the-art algorithms for identifying exons, splice sites, transcripts and pseudogenes. Where novel features are confirmed the annotation is updated. Annotated coding transcripts are analysed to assess their coding potential by investigating patterns of conservation within the coding sequence (CDS) and comparing predicted secondary structures of annotated CDSs to similar proteins with solved structures. Annotated coding transcripts are also checked against the current set of human Consensus CDSs (CCDS) to check agreement with other participating centres (EBI, NCBI, & UCSC).An initial round of annotation and analysis of chromosomes 21 and 22 has shown that while HAVANA annotation is both comprehensive and robust, it has benefitted from computational review. 13 novel non-coding loci, 27 novel splice variants and 6 extensions to existing variants were identified, many of which were found using supporting EST/mRNA sequences that were not present at the time of initial annotation. Fewer than 10 annotated CDSs required reclassification, no CCDS sequences required updating and 26 novel pseudogene were added. The annotation of human chromosome 2 is complete and we are currently annotating chromosomes 3 and 7. Data from all members of Gencode is distributed via DAS and is now visible in our Zmap annotation interface, allowing assessment of computational predictions contemporaneous with first-pass gene annotation.

This article is part of the supplement: Beyond the Genome: The true gene count, human evolution and disease genomics, Boston, MA, USA. 11-13 October 2010., The GENCODE consortium is a sub group of the ENCODE consortium. Its aim is to provide complete annotation of genes in the human genome including protein-coding loci, non-coding loci and pseudogenes, based on experimental evidence. The final aim is for the HAVANA team to manually annotate the complete genome. This is a time-consuming process which will be completed over the course of the ENCODE project. Currently, to provide a set of annotation covering the complete genome, rather than just the regions that have been manually annotated, a merge of manual annotation from HAVANA with automatic annotation from the Ensembl automatically annotated gene set is created. This process also adds unique full-length CDS predictions from the Ensembl protein coding set into manually annotated genes, to provide the most complete up to date annotation of the genome possible. Also included in the set are short and long ncRNA genes predicted by the Ensembl prediction pipelines and a consensus set of pseudogene predictions agreed between Havana, Yale and UCSC. The CCDS set is also fully represented within the GENCODE set. The GENCODE set is the default annotation available in Ensembl and is also available in the UCSC genome browser. All the annotation is tagged as to whether it is produced by manual annotation alone, automatic annotation alone, or by both approaches. We are currently working to provide confidence levels for annotation, based on depth and type of evidence supporting it.