Non PCR-amplified Transcripts and AFLP fragments as reduced representations of the quail genome for 454 Titanium sequencing

<p>Abstract</p> <p>Background</p> <p>SNP (Single Nucleotide Polymorphism) discovery is now routinely performed using high-throughput sequencing of reduced representation libraries. Our objective was to adapt 454 GS FLX based sequencing methodologies in order to obtain the largest possible dataset from two reduced representations libraries, produced by AFLP (Amplified Fragment Length Polymorphism) for genomic DNA, and EST (Expressed Sequence Tag) for the transcribed fraction of the genome.</p> <p>Findings</p> <p>The expressed fraction was obtained by preparing cDNA libraries without PCR amplification from quail embryo and brain. To optimize the information content for SNP analyses, libraries were prepared from individuals selected in three quail lines and each individual in the AFLP library was tagged. Sequencing runs produced 399,189 sequence reads from cDNA and 373,484 from genomic fragments, covering close to 250 Mb of sequence in total.</p> <p>Conclusions</p> <p>Both methods used to obtain reduced representations for high-throughput sequencing were successful after several improvements.</p> <p>The protocols may be used for several sequencing applications, such as <it>de novo </it>sequencing, tagged PCR fragments or long fragment sequencing of cDNA.</p

Simple Shared Motifs (SSM) in conserved region of promoters: a new approach to identify co-regulation patterns

<p>Abstract</p> <p>Background</p> <p>Regulation of gene expression plays a pivotal role in cellular functions. However, understanding the dynamics of transcription remains a challenging task. A host of computational approaches have been developed to identify regulatory motifs, mainly based on the recognition of DNA sequences for transcription factor binding sites. Recent integration of additional data from genomic analyses or phylogenetic footprinting has significantly improved these methods.</p> <p>Results</p> <p>Here, we propose a different approach based on the compilation of Simple Shared Motifs (SSM), groups of sequences defined by their length and similarity and present in conserved sequences of gene promoters. We developed an original algorithm to search and count SSM in pairs of genes. An exceptional number of SSM is considered as a common regulatory pattern. The SSM approach is applied to a sample set of genes and validated using functional gene-set enrichment analyses. We demonstrate that the SSM approach selects genes that are over-represented in specific biological categories (Ontology and Pathways) and are enriched in co-expressed genes. Finally we show that genes co-expressed in the same tissue or involved in the same biological pathway have increased SSM values.</p> <p>Conclusions</p> <p>Using unbiased clustering of genes, Simple Shared Motifs analysis constitutes an original contribution to provide a clearer definition of expression networks.</p

Absence de bénéfice extra-osseux de doses élevées de vitamine D3 chez les transplantés rénaux dans une étude prospective, multicentrique, en double aveugle, randomisée

International audienc

MO023: Flank pain has a major negative impact on health-related quality of life in ADPKD: The CYSTic I Study

Abstract Background and Aims ADPKD is the most common inherited kidney disease in man, a major cause of end-stage renal disease and is a significant medical and economic burden worldwide. However, the impact of this major disease on the quality of life of patients with preserved kidney function has not been systematically explored. Method The CYSTic I study was an observational, prospective study designed to study the natural history of ADPKD in adult patients with preserved kidney function (eGFR ≥30 ml/min/1.73m2). 465 patients were recruited from six expert centres across Europe (Belgium, France, Italy, Netherlands, Spain and UK) with baseline data recorded including HR-QoL (Health-Related Quality of Life) incorporating a Kidney Disease QOL short form questionnaire (KDQoL-SF v1.3), MRI for Total Kidney Volume (TKV) and DNA for genotyping. The cohort was stratified by baseline eGFR, Ht-TKV or genotype and correlated with HR-QOL scores. Bivariate and multivariate analyses were applied to examine the relationship between HRQoL and variables of interest. KDQoL-SF scores were calculated using an online tool provided by the Rand organisation. Results Mean age of the participants was 44 years, 54.6% were female with a mean eGFR of 77ml/min/1.73m2 and Ht-TKV of 849ml/m. 72.3% had PKD1 mutations. 32.5% of participants reported flank pain that was not significantly correlated with eGFR, Ht-TKV or genotype. Of all the variables examined, flank pain showed significant negative associations with the highest number of KDQoL-SF subscale scores assessed (12/20). Conclusion Our results indicate that flank pain is common, likely to be under-reported in routine care but has a major negative impact on patient-reported quality of life