Process evaluation of a comprehensive approach to reintegration of disability benefit recipients with multiple problems (CARm) into the labour market.

Purpose: As the effect evaluation of our randomized controlled trial the "Comprehensive Approach of Reintegration for clients with Multiple problems" (CARm) showed no superior effect on re-integration into paid employment of the clients when compared with clients of the care as usual, we conducted this process evaluation to gain insight into whether the intervention was conducted according to protocol.

Methods: Using questionnaires on recruitment, reach, dose delivered, dose received, fidelity, context, and satisfaction we collected data from 40 labour experts of the Public Employment Service of the Dutch Social Security Institute, and from 166 disability benefit recipients dealing with multiple problems.

Results: Only few of the labour experts provided the key elements of the intervention to their clients.

Comprehensive approach to reintegration of disability benefit recipients with multiple problems (CARm) into the labour market: results of a randomized controlled trial.

Purpose: Although most clients on work disability benefits face multiple problems, most traditional interventions for (re)integration focus on a single problem. The aim of this study was to evaluate the "Comprehensive Approach to Reintegrate clients with multiple problems" (CARm), which provides a strategy for labour experts to build a relationship with each client in order to support clients in their needs and mobilize their social networks.

Methods: This study is a stratified, two-armed, non-blinded randomized controlled trial (RCT), with a 12-month follow-up period.

Exploring treatment adherence in long-term sick-listed workers and the impact of coping strategies, illness perceptions and perceived health.

Background: Treatment adherence is important to improve return to work in sick-listed workers. Especially in long-term sick-listed workers who apply for a disability benefit and therefore have not (fully) returned to work, it is of great value to gain insight in the adherence to advice of physicians. Non-adherence could be one of the main reasons why they have not returned to work and are sick-listed for a long-term.

Social Insurance Literacy of Dutch Workers Receiving Disability Benefits and its Associations with Socio-Economic Characteristics.

Purpose This study explores the concept social insurance literacy (SIL) and corresponding questionnaire (SILQ) among workers receiving disability benefits and the comprehensibility of the social security institute (SSI), and examines associations with socio-economic characteristics. Methods 1753 panel members of the Dutch SSI were approached to complete the SILQ-NL37. This measure was based on the original SILQ.

Content Validation of a Practice-Based Work Capacity Assessment Instrument Using ICF Core Sets.

Purpose: A shift from providing long-term disability benefits to promoting work reintegration of people with remaining work capacity in many countries requires new instruments for work capacity assessments. Recently, a practice-based instrument addressing biopsychosocial aspects of functioning, the Social Medical Work Capacity instrument (SMWC), was developed. Our aim was to examine the content validity of the SMWC using ICF core sets.

Extension of human lncRNA transcripts by RACE coupled with long-read high-throughput sequencing (RACE-Seq).

Long non-coding RNAs (lncRNAs) constitute a large, yet mostly uncharacterized fraction of the mammalian transcriptome. Such characterization requires a comprehensive, high-quality annotation of their gene structure and boundaries, which is currently lacking. Here we describe RACE-Seq, an experimental workflow designed to address this based on RACE (rapid amplification of cDNA ends) and long-read RNA sequencing.

Comprehensive comparative homeobox gene annotation in human and mouse.

Homeobox genes are a group of genes coding for transcription factors with a DNA-binding helix-turn-helix structure called a homeodomain and which play a crucial role in pattern formation during embryogenesis. Many homeobox genes are located in clusters and some of these, most notably the HOX genes, are known to have antisense or opposite strand long non-coding RNA (lncRNA) genes that play a regulatory role. Because automated annotation of both gene clusters and non-coding genes is fraught with difficulty (over-prediction, under-prediction, inaccurate transcript structures), we set out to manually annotate all homeobox genes in the mouse and human genomes.

The Vertebrate Genome Annotation browser 10 years on.

The Vertebrate Genome Annotation (VEGA) database (http://vega.sanger.ac.

Structural and functional annotation of the porcine immunome.

Background: The domestic pig is known as an excellent model for human immunology and the two species share many pathogens. Susceptibility to infectious disease is one of the major constraints on swine performance, yet the structure and function of genes comprising the pig immunome are not well-characterized. The completion of the pig genome provides the opportunity to annotate the pig immunome, and compare and contrast pig and human immune systems.

Sequencing and comparative analysis of the gorilla MHC genomic sequence.

Major histocompatibility complex (MHC) genes play a critical role in vertebrate immune response and because the MHC is linked to a significant number of auto-immune and other diseases it is of great medical interest. Here we describe the clone-based sequencing and subsequent annotation of the MHC region of the gorilla genome. Because the MHC is subject to extensive variation, both structural and sequence-wise, it is not readily amenable to study in whole genome shotgun sequence such as the recently published gorilla genome.

Sequencing and characterization of the FVB/NJ mouse genome.

Background: The FVB/NJ mouse strain has its origins in a colony of outbred Swiss mice established in 1935 at the National Institutes of Health. Mice derived from this source were selectively bred for sensitivity to histamine diphosphate and the B strain of Friend leukemia virus. This led to the establishment of the FVB/N inbred strain, which was subsequently imported to the Jackson Laboratory and designated FVB/NJ.

Tracking and coordinating an international curation effort for the CCDS Project.

The Consensus Coding Sequence (CCDS) collaboration involves curators at multiple centers with a goal of producing a conservative set of high quality, protein-coding region annotations for the human and mouse reference genome assemblies. The CCDS data set reflects a 'gold standard' definition of best supported protein annotations, and corresponding genes, which pass a standard series of quality assurance checks and are supported by manual curation. This data set supports use of genome annotation information by human and mouse researchers for effective experimental design, analysis and interpretation.

Meeting report: a workshop on Best Practices in Genome Annotation.

Efforts to annotate the genomes of a wide variety of model organisms are currently carried out by sequencing centers, model organism databases and academic/institutional laboratories around the world. Different annotation methods and tools have been developed over time to meet the needs of biologists faced with the task of annotating biological data. While standardized methods are essential for consistent curation within each annotation group, methods and tools can differ between groups, especially when the groups are curating different organisms.

The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes.

Effective use of the human and mouse genomes requires reliable identification of genes and their products. Although multiple public resources provide annotation, different methods are used that can result in similar but not identical representation of genes, transcripts, and proteins. The collaborative consensus coding sequence (CCDS) project tracks identical protein annotations on the reference mouse and human genomes with a stable identifier (CCDS ID), and ensures that they are consistently represented on the NCBI, Ensembl, and UCSC Genome Browsers.

Dynamic instability of the major urinary protein gene family revealed by genomic and phenotypic comparisons between C57 and 129 strain mice.

Background: The major urinary proteins (MUPs) of Mus musculus domesticus are deposited in urine in large quantities, where they bind and release pheromones and also provide an individual 'recognition signal' via their phenotypic polymorphism. Whilst important information about MUP functionality has been gained in recent years, the gene cluster is poorly studied in terms of structure, genic polymorphism and evolution.

Results: We combine targeted sequencing, manual genome annotation and phylogenetic analysis to compare the Mup clusters of C57BL/6J and 129 strains of mice.

Variation analysis and gene annotation of eight MHC haplotypes: the MHC Haplotype Project.

The human major histocompatibility complex (MHC) is contained within about 4 Mb on the short arm of chromosome 6 and is recognised as the most variable region in the human genome. The primary aim of the MHC Haplotype Project was to provide a comprehensively annotated reference sequence of a single, human leukocyte antigen-homozygous MHC haplotype and to use it as a basis against which variations could be assessed from seven other similarly homozygous cell lines, representative of the most common MHC haplotypes in the European population. Comparison of the haplotype sequences, including four haplotypes not previously analysed, resulted in the identification of >44,000 variations, both substitutions and indels (insertions and deletions), which have been submitted to the dbSNP database.

The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts.

Here we report the new features and improvements in our latest release of the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/), a comprehensive annotation resource for human genes and transcripts.

The vertebrate genome annotation (Vega) database.

The Vertebrate Genome Annotation (Vega) database (http://vega.sanger.ac.

The DNA sequence and biological annotation of human chromosome 1.

The reference sequence for each human chromosome provides the framework for understanding genome function, variation and evolution. Here we report the finished sequence and biological annotation of human chromosome 1. Chromosome 1 is gene-dense, with 3,141 genes and 991 pseudogenes, and many coding sequences overlap.

Pseudo-messenger RNA: phantoms of the transcriptome.

The mammalian transcriptome harbours shadowy entities that resist classification and analysis. In analogy with pseudogenes, we define pseudo-messenger RNA to be RNA molecules that resemble protein-coding mRNA, but cannot encode full-length proteins owing to disruptions of the reading frame. Using a rigorous computational pipeline, which rules out sequencing errors, we identify 10,679 pseudo-messenger RNAs (approximately half of which are transposon-associated) among the 102,801 FANTOM3 mouse cDNAs: just over 10% of the FANTOM3 transcriptome.

DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage.

Chromosome 17 is unusual among the human chromosomes in many respects. It is the largest human autosome with orthology to only a single mouse chromosome, mapping entirely to the distal half of mouse chromosome 11. Chromosome 17 is rich in protein-coding genes, having the second highest gene density in the genome.

Genomic anatomy of the Tyrp1 (brown) deletion complex.

Chromosome deletions in the mouse have proven invaluable in the dissection of gene function. The brown deletion complex comprises >28 independent genome rearrangements, which have been used to identify several functional loci on chromosome 4 required for normal embryonic and postnatal development. We have constructed a 172-bacterial artificial chromosome contig that spans this 22-megabase (Mb) interval and have produced a contiguous, finished, and manually annotated sequence from these clones.