The International Gene Trap Consortium Website: a portal to all publicly available gene trap cell lines in mouse.

Gene trapping is a method of generating murine embryonic stem (ES) cell lines containing insertional mutations in known and novel genes. A number of international groups have used this approach to create sizeable public cell line repositories available to the scientific community for the generation of mutant mouse strains. The major gene trapping groups worldwide have recently joined together to centralize access to all publicly available gene trap lines by developing a user-oriented Website for the International Gene Trap Consortium (IGTC). This collaboration provides an impressive public informatics resource comprising approximately 45 000 well-characterized ES cell lines which currently represent approximately 40% of known mouse genes, all freely available for the creation of knockout mice on a non-collaborative basis. To standardize annotation and provide high confidence data for gene trap lines, a rigorous identification and annotation pipeline has been developed combining genomic localization and transcript alignment of gene trap sequence tags to identify trapped loci. This information is stored in a new bioinformatics database accessible through the IGTC Website interface. The IGTC Website (www.genetrap.org) allows users to browse and search the database for trapped genes, BLAST sequences against gene trap sequence tags, and view trapped genes within biological pathways. In addition, IGTC data have been integrated into major genome browsers and bioinformatics sites to provide users with outside portals for viewing this data. The development of the IGTC Website marks a major advance by providing the research community with the data and tools necessary to effectively use public gene trap resources for the large-scale characterization of mammalian gene function.

DNA methylation profiling of the human major histocompatibility complex: a pilot study for the human epigenome project.

The Human Epigenome Project aims to identify, catalogue, and interpret genome-wide DNA methylation phenomena. Occurring naturally on cytosine bases at cytosine-guanine dinucleotides, DNA methylation is intimately involved in diverse biological processes and the aetiology of many diseases. Differentially methylated cytosines give rise to distinct profiles, thought to be specific for gene activity, tissue type, and disease state. The identification of such methylation variable positions will significantly improve our understanding of genome biology and our ability to diagnose disease. Here, we report the results of the pilot study for the Human Epigenome Project entailing the methylation analysis of the human major histocompatibility complex. This study involved the development of an integrated pipeline for high-throughput methylation analysis using bisulphite DNA sequencing, discovery of methylation variable positions, epigenotyping by matrix-assisted laser desorption/ionisation mass spectrometry, and development of an integrated public database available at http://www.epigenome.org. Our analysis of DNA methylation levels within the major histocompatibility complex, including regulatory exonic and intronic regions associated with 90 genes in multiple tissues and individuals, reveals a bimodal distribution of methylation profiles (i.e., the vast majority of the analysed regions were either hypo- or hypermethylated), tissue specificity, inter-individual variation, and correlation with independent gene expression data.

Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing.

Human cancers often carry many somatically acquired genomic rearrangements, some of which may be implicated in cancer development. However, conventional strategies for characterizing rearrangements are laborious and low-throughput and have low sensitivity or poor resolution. We used massively parallel sequencing to generate sequence reads from both ends of short DNA fragments derived from the genomes of two individuals with lung cancer. By investigating read pairs that did not align correctly with respect to each other on the reference human genome, we characterized 306 germline structural variants and 103 somatic rearrangements to the base-pair level of resolution. The patterns of germline and somatic rearrangement were markedly different. Many somatic rearrangements were from amplicons, although rearrangements outside these regions, notably including tandem duplications, were also observed. Some somatic rearrangements led to abnormal transcripts, including two from internal tandem duplications and two fusion transcripts created by interchromosomal rearrangements. Germline variants were predominantly mediated by retrotransposition, often involving AluY and LINE elements. The results demonstrate the feasibility of systematic, genome-wide characterization of rearrangements in complex human cancer genomes, raising the prospect of a new harvest of genes associated with cancer using this strategy.

Islands of euchromatin-like sequence and expressed polymorphic sequences within the short arm of human chromosome 21.

The goals of the human genome project did not include sequencing of the heterochromatic regions. We describe here an initial sequence of 1.1 Mb of the short arm of human chromosome 21 (HSA21p), estimated to be 10% of 21p. This region contains extensive euchromatic-like sequence and includes on average one transcript every 100 kb. These transcripts show multiple inter- and intrachromosomal copies, and extensive copy number and sequence variability. The sequencing of the "heterochromatic" regions of the human genome is likely to reveal many additional functional elements and provide important evolutionary information.

Neuropathic bladder and intermittent catheterization: social and psychological impact on families.

Clean intermittent catheterization (CIC) is the mainstay of management in neuropathic vesicourethral dysfunction, both to improve continence and, more importantly, to preserve renal function. We looked at the effects of this procedure on children, adolescents, and their families. In particular, we wished to see if there were any differences between those who successfully catheterized and those who did not. Forty families were enrolled into the study. Ages of children and adolescents (23 females, 17 males) ranged from 1 to 20 years. Most participants (n=31) had spina bifida. Other causes of bladder dysfunction included transverse myelitis, spinal cord injury, and spinal neuroblastoma. Parents were assessed using the Effects of Handicap on Parents semi-structured interview, the Socioemotional Functioning Interview, and a semi-structured interview, specifically designed for the study, which looked at family characteristics and experience related to diagnosis and catheterization. In addition, the Rutter Parental 'A' Scale Questionnaire was used to screen for emotional and behavioural disorders in the child. Results showed that CIC by carer or self-catheterization itself did not cause major emotional and behavioural problems but the bladder problem may act as a focus that puts considerable strain family relationships. Although most parents disliked CIC they complied with the suggested management. It is important that all those involved understand the aims of management and success can be achieved by combined input from medical, psychological, and specialist nursing staff. The problem is lifelong and continued support from a multidisciplinary team is essential.

Neuropathic bladder and intermittent catheterization: social and psychological impact on children and adolescents.

This paper describes part of larger study involving 40 families of children and adolescents with neuropathic bladder looking at the psychosocial impact of catheterization on them and their families. This study focuses on their experiences of clean intermittent catheterization (CIC) and self-catheterization (SC). Twenty-eight children and adolescents (11 males, 17 females; mean age 9 years, SD 2 years 7 months, range 5 to 20 years) with neuropathic bladder (mostly with spina bifida) participated in a semi-structured interview to explore their understanding of micturition and catheterization, and their views about the introduction and practical use of this technique. Participants were invited to draw self-portraits and figure diagrams to depict their understanding of CIC and SC. Age-appropriate self-esteem measures (Harter Pictorial Scale of Perceived Competence, the Self-Perception Profile, and the Culture-Free Self-Esteem Inventory) were administered to see if catheterization status affected emotional well-being. In an extension of this study, children's experiences of SC were explored by a postal questionnaire to all children successfully using SC who were attending the Paediatric Neuropathic Bladder Clinic. Children aged <5 years, those with learning difficulties, and those using indwelling catheters were excluded. From a total sample of 66 (31 females, 35 males), 52 parents and 42 children and adolescents (28 females and 14 males) responded. No significant difference was observed in self-esteem for those successfully catheterizing. Specific challenges involved learning SC and practical use of the technique. Concerns were leakage and being wet, and peers finding out about their continence management. Implications for the education, problem solving, and support of families and young people to promote cooperation and optimal benefits from catheterization are discussed.

Predicting language outcome in infants with autism and pervasive developmental disorder.

BACKGROUND: To examine longitudinal associations between diagnosis, joint attention, play and imitation abilities and language outcome in infants with autism and pervasive developmental disorder. METHODS AND PROCEDURES: Experimental measures of joint attention, play and imitation were conducted with a sample of infants with autism spectrum disorder at age 20 months. Language outcome was assessed at age 42 months. A within-group longitudinal correlational design was adopted. OUTCOMES AND RESULTS: Language at 42 months was higher for children with a diagnosis of pervasive developmental disorder than for children with a diagnosis of autism. Language at follow-up was also positively associated with performance on experimental measures of joint attention and imitation, but not with performance on experimental measures of play and 'goal detection' at 20 months, nor with a non-verbal intelligence quotient, although these associations were not examined independent of diagnosis. However, floor effects on the measure of play at 20 months and the small sample size limit the conclusions that can be drawn. CONCLUSIONS: Individual differences in infant social-communication abilities as well as diagnosis may predict language outcome in preschoolers with autism spectrum disorders. Attention should be directed at assessing these skills in 2- and 3-year-old children referred for a diagnosis of autism spectrum disorder. Imitation and joint attention abilities may be important targets for early intervention.

The Ensembl Web site: mechanics of a genome browser.

The Ensembl Web site (http://www.ensembl.org/) is the principal user interface to the data of the Ensembl project, and currently serves >500,000 pages (approximately 2.5 million hits) per week, providing access to >80 GB (gigabyte) of data to users in more than 80 countries. Built atop an open-source platform comprising Apache/mod_perl and the MySQL relational database management system, it is modular, extensible, and freely available. It is being actively reused and extended in several different projects, and has been downloaded and installed in companies and academic institutions worldwide. Here, we describe some of the technical features of the site, with particular reference to its dynamic configuration that enables it to handle disparate data from multiple species.

Molecular systematics, GISH and the origin of hybrid taxa in Nicotiana (Solanaceae).

Phylogenetic relationships in the genus Nicotiana were investigated using parsimony analyses of the internal transcribed spacer (ITS) regions of nuclear ribosomal DNA (nrDNA). In addition, origins of some amphidiploid taxa in Nicotiana were investigated using the techniques of genomic in situ hybridization (GISH), and the results of both sets of analyses were used to evaluate previous hypotheses about the origins of these taxa. Phylogenetic analyses of the ITS nrDNA data were performed on the entire genus (66 of 77 naturally occurring species, plus three artificial hybrids), comprising both diploid and polyploid taxa, and on the diploid taxa only (35 species) to examine the effects of amphidiploids on estimates of relationships. All taxa, regardless of ploidy, produced clean, single copies of the ITS region, even though some taxa are hybrids. Results are compared with a published plastid (matK) phylogeny using fewer, but many of the same, taxa. The patterns of relationships in Nicotiana, as seen in both analyses, are largely congruent with each other and previous evolutionary ideas based on morphology and cytology, but some important differences are apparent. None of the currently recognized subgenera of Nicotiana is monophyletic and, although most of the currently recognized sections are coherent, others are clearly polyphyletic. Relying solely upon ITS nrDNA analysis to reveal phylogenetic patterns in a complex genus such as Nicotiana is insufficient, and it is clear that conventional analysis of single data sets, such as ITS, is likely to be misleading in at least some respects about evolutionary history. ITS sequences of natural and well-documented amphidiploids are similar or identical to one of their two parents-usually, but not always, the maternal parent-and are not in any sense themselves 'hybrid'. Knowing how ITS evolves in artificial amphidiploids gives insight into what ITS analysis might reveal about naturally occurring amphidiploids of unknown origin, and it is in this perspective that analysis of ITS sequences is highly informative.

A pilot randomised control trial of a parent training intervention for pre-school children with autism. Preliminary findings and methodological challenges.

Few attempts have been made to conduct randomised control trials (RCTs) of interventions for pre-school children with autism. We report findings of a pilot RCT for a parent training intervention with a focus on the development of joint attention skills and joint action routines. Twenty-four children meeting ICD-10 criteria for childhood autism (mean age = 23 months) were identified using the CHAT screen and randomised to the parent training group or to local services only. A follow-up was conducted 12 months later (mean age = 35 months). There was some evidence that the parent training group made more progress in language development than the local services group. However, the present pilot study was compromised by several factors: a reliance on parental report to measure language, non-matching of the groups on initial IQ, and a lack of systematic checking regarding the implementation of the parent training intervention. Furthermore, three parents in the local services group commenced intensive, home-based behavioural intervention during the course of the study. The difficulties encountered in the conduct of RCTs for pre-school children with autism are discussed. Methodological challenges and strategies for future well-designed RCTs for autism interventions are highlighted.