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Introduction Inflammatory Bowel Disease (IBD) is a complex genetic disease characterised by chronic inflammation of the gastro-intestinal tract. Genome-wide association study (GWAS) meta-analysis and replication has identified over 200 genomic regions involved in IBD susceptibility although only a few of the associated single nucleotide polymorphisms (SNPs) directly alter the coding sequence of a gene. In addition, >92 of the IBD-susceptibility loci are known to co-localise with active regulatory elements, suggesting the majority of IBD associated SNPs alter gene expression in some way. Here we employ whole transcriptome sequencing to investigate the role of altered gene expression in intestinal tissue. Methods Patients and non-IBD control individuals were recruited after informed consent through endoscopy clinics at Guy’s and St Thomas’ Hospital, London. Whole RNA was extracted from 2–4 colonic biopsies from 104 IBD patients (76 CD, 28 UC) and 24 non-IBD controls and ribo-depleted (Ribo-zero, Illumina). We performed whole RNA sequencing using Illumina TruSeq and HiSeq2500 on pools of 4 indexed RNA libraries across 1–2 lanes. Quality control of sequence reads was performed via FastQC. Subsequent alignment and assembly, quantification and differential expression (DE) analysis of each transcript was performed using Tophat2, Cufflinks, Cuffmerge and EdgeR. Results So far a detailed bioinformatics analysis has been carried out on the first 32 whole RNA-seq libraries. We have observed expression above background (FPKM > 1) for approximately 46% of all known transcripts located within known IBD susceptibility loci. DE analysis identified 249 transcripts with significant difference in expression (q Conclusion We have generated high coverage whole RNAseq data on intestinal biopsy samples from 128 individuals. We have shown Disclosure of Interest None Declared

Primary Ciliary Dyskinesia (PCD) is a genetically heterogeneous condition. characterised by impaired mucociliary clearance and chronic sino-pulmonary disease. Over 30 causative gene mutations resulting in dysfunctional ciliary motility and structure have been identified. Ciliary ultrastructure examined by Transmission Electron Microscopy (TEM) is currently the diagnostic gold standard. Patients with mutations in the gene DNAH11 have a hyperfrequent ciliary beat and clinical symptoms of PCD. Diagnosis of a DNAH11 defect by TEM is difficult due to apparently normal ciliary ultrastructure. The electron tomography technique, an extension of TEM, produces 3D models of cilia with superior resolution. The aim of this study was to determine if electron tomography can detect ultrastructural abnormalities in patients with DNAH11 defects. Immunofluorescence by specific antibodies for DNAH11 showed localisation to the proximal portion of cilia. Proximal cilia cross sections from araldite embedded nasal brush biopsies were examined. Dual axis tomograms were collected on a Philips CM200 electron microscope. The data were analysed using IMOD software and averaged using PEET. Electron tomography and averaging of cilia cross sections indicated a deficiency in the outer dynein arm, consistent across all patients with a DNAH11 defect (n = 5) compared to healthy controls (n = 3) and patients with PCD due to a defect of the central pair or nexin link (n = 3) (Figure 1). A reduction in outer dynein arm volume of 30% was identified compared to healthy and PCD controls. In conclusion, a mutation in DNAH11 results in a subtle abnormality in ultrastructure. The defects are specific to the ‘forearm’ of the outer dynein arm and only detectable at the base of the cilium where DNAH11 is located. Electron tomography is highly effective in visualising this defect.