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Functional Genomics Workshop Functional Guy’s and St Thomas’ NHS Foundation Trust and King’s College London’s comprehensive Genomics Biomedical Research Centre Workshop 10-12 February 2016 Introduction Functional Genomics Workshop 10-12 th February 2016 St Thomas’ Hospital Governors’ Hall King’s College London London, UK Aims of the workshop • To highlight new advances in understanding the functional impact of genetic variation in immune mediated inflammatory and related diseases. • To provide delegates with an experimental framework for investigating the functional basis of genetic variation. • To provide opportunities for investigators and their collaborators to network in this field of research. Organising Committee Tim Vyse (KCL) Lars Klareskog (Karolinska Institute) Tom Huizinga (Leiden University Medical Centre) Jane Worthington (Manchester University) Frank Nestlé (KCL) Richard Trembath (KCL) Andrew Cope (KCL) Workshop Sponsors BTCURE EU IMI Programme NIHR/Biomedical Research Centre at Guy’s and St Thomas’ NHS Foundation Trust and King’s College London Workshop programme Keynote Lectures: 45mins Plenary Talks: 25mins + 5min discussion Abstract presentations: 10mins Day 1 : Wednesday 10 th February (including discussion) 12:30 Registration opens in Governor’s Hall, St Thomas’ Hospital 13:50 Welcome and Opening Remarks 14:00 - 15:30: Session 1 – Rheumatoid Arthritis (Chair: Jane Worthington) Plenary 1 Soumya Raychaudhuri (Harvard Medical School, Boston, US): Using human genetics to define molecular mechanisms of rheumatoid arthritis Plenary 2 Fina Kurreeman (Leiden University Medical Centre, The Netherlands): Novel ncRNA in the TRAF1-C5 region associated with Rheumatoid arthritis Plenary 3 Andrew Cope (Kings College London, UK): PTPN22 links integrin-mediated adhesion with autoimmunity 15:30 - 16:00 Tea break with poster viewing 16:00 - 17:30: Session 2 – Genetics of the immune response (Chair: Kerrin Small) Plenary 4 Frank Nestlé (Kings College London, UK) : Genetic Architecture of the Human Immune System Selected abstract presentations (10 min each, including discussion) A1. Sylvie Grandemange (INSERM, Paris, France): NLRP1 mutations cause autoinflammatory diseases in human: implication of the NLRP1 inflammasome? A2. Elena Lopez-Isac (CSIC, Madrid, Spain): Interrogating the common genetic background for systemic sclerosis and rheumatoid arthritis through a cross-disease meta-analysis of Genome-wide Association Studies. Plenary 5 Julian Knight (University of Oxford, UK) : eQTL mapping of induced innate immune response 17:30 - 18:15: Session 3 – Keynote Lecture (Chair: Tim Vyse) Speaker: Manolis Dermitzakis (University of Geneva, Switzerland) : Population and personal genomics to reveal disease biology End of Day 1 Scientific sessions 18:30 – 21:00 Welcome Reception in Central Hall, St Thomas’ Hospital 1 Workshop programme Day 2: Thursday 11 th February MORNING SESSION 08:30 – 10:30: Session 4 – Functional genomics of mucosal and epithelial immunity (Chair: Graham Lord) Plenary 6 Daniel Graham (Broad Institute, Boston, USA): Coping with stress in mucosal tissues Plenary 7 Holm Uhlig (University of Oxford, UK): The genetic landscape of monogenic forms of inflammatory bowel disease Plenary 8 Anne Bowcock (Imperial College, London, UK): Role of CARD14 in psoriasis pathogenesis Plenary 9 Linde Meyaard (University Medical Centre, Utrecht, The Netherlands): A functional SNP associated with atopic dermatitis controls cell type-specific methylation of the immune checkpoint gene SIRL-1 10:30 - 11:00 Coffee break with poster viewing 11:00 - 13:00: Session 5 – Novel approaches, technologies and tools – I (Chair: Richard Trembath) Plenary 10 Richard Trembath (Kings College London, UK) : Sequencing in a specific population for recessive variants Plenary 11 Trevor Lawley (Sanger Institute, Cambridge, UK) : Levels of genomic and functional diversity in the human intestinal microbiota Plenary 12 Alka Saxena (NIHR-BRC at Guy’s and St Thomas’ NHS Foundation Trust, London, UK) : Single cell technologies Selected abstract presentations (10 min each, including discussion) A3. Eric Schordan (FIRALIS SAS, Huningue, France): miRNA profiling using HTG-Edgeseq platform predicts response to anti-TNF therapy in rheumatoid arthritis α A4. Chris Odhams (King’s College London, UK): Discovering SLE candidate genes and mechanisms by eQTL analysis using RNA-Seq. A5. Angela Hodges (King’s College London, UK): AD-associated TREM2 variants lead to fewer microglia expressing HLA-DP, DQ, DR in the hippocampus of post-mortem human brains 13:00 - 14:00 Lunch with posters 2 Day 2: Thursday 11 th February AFTERNOON SESSION 14:00 – 16:00: Session 6 – Whole organism models to dissect gene function – I (Chair: Lars Klareskog) Plenary 13 David Rawlings (Seattle Children’s Hospital, Washington, US): Altered B cell signaling orchestrates loss of tolerance and systemic autoimmunity Plenary 14 Stephen McMahon (King’s College London, UK): Pain – why does it hurt so much? Plenary 15 George Kollias (Alexander Fleming Institute, Athens, Greece): Mesenchymal causalities in chronic inflammation Selected abstract presentations (10 min each, including discussion) A6. Miranda Houtman (Karolinska Institute, Solna, Sweden): Investigation of the associated PTPN2 locus in rheumatoid arthritis: importance of long non-coding RNA A7. Olfa Khalifa (INSERM, Paris, France): New genes in the X chromosome associated with Rheumatoid Arthritis A8. Klementy Shchetynsky (Karolinska Institute, Solna, Sweden): Discovery of new candidate genes for rheumatoid arthritis by integration of genetic association data with expression pathway analysis 16:00 - 16:30 Tea break 16:30 - 18:00: Session 7 – Novel approaches, technologies and tools – II (Chair: Frank Nestlé) Plenary 16 Nicholas Luscombe (Francis Crick Institute, London, UK) : Using hiCLIP to identify long-range loops in RNAs Plenary 17 Aviv Madar (Cornell University, New York, USA) : Computational biology as applied to hypersensitivity DNase analysis Plenary 18 Phil de Jager (Harvard Medical School, Boston, USA) : eQTL analyses and systems biology in MS and dementia End of Day 2 Scientific session s Speakers Dinner (Meeting in the Park Plaza Westminster Bridge hotel lobby at 7:45pm) Free evening for all other delegates 3 Workshop programme Day 3: Friday 12 th February MORNING SESSION 09:00 – 11:00: Session 8 – Autoimmunity - I (Chair: Deborah Cunninghame-Graham) Plenary 19 David Morris (Kings College London, UK): Genes, ancestry and prevalence in SLE Plenary 20 Kim Simpfendorfer (Feinstein Institute, New York, USA): Investigating immune endophenotypes in healthy human carriers of autoimmune disease-associated risk haplotypes in BLK and TNIP1 Plenary 21 Ward Wakeland (University of Texas Southwestern, Dallas, US): A genomic analysis of susceptibility to systemic autoimmunity Plenary 22 Gil McVean University of Oxford, UK): Dissecting the structure and phenotypic consequences of HLA genomic variation 11:00 - 11:30 Coffee break 11:30 - 13:00: Session 9 - Whole organism models to dissect gene function – II (Chair: Andrew Cope) Plenary 23 Marc Dionne (Imperial College London, UK) : Infections and immune responses in Drosophila Plenary 24 Chrissy Hammond (Bristol University, UK) : Using zebrafish to unpick the interactions between biomechanics and genes in making, shaping and maintaining a joint Plenary 25 Rikard Holmdahl (Karolinksa Institute, Sweden) : Positioning and analysis of the major genes controlling arthritis in rats 13:00 - 14:00 Lunch with posters AFTERNOON SESSION 14:00 – 15:00: Session 10 – Autoimmunity – II (Chair: Tim Vyse) Plenary 26 Stephen Sawcer (University of Cambridge, UK): Making progress in MS Selected abstract presentations (10 min each, including discussion) A9. Michelle Krishnan (King’s College London, UK): Investigation of biological pathways involved in brain development in preterm neonates using a multivariate phenotype and sparse regression A10. Gisela Orozco (University of Manchester, UK): Capture Hi-C reveals a novel causal gene, IL20RA, in the pan-autoimmune genetic susceptibility region 6q23 15:00 - 15:45: Session 11 - Keynote Lecture (Tim Vyse) Speaker: John Todd (University of Cambridge, UK) : Type I Diabetes Closing remarks and Depart 4 Soumya Raychaudhuri Session 1 Divisions of Genetics & Rheumatology Day 1: Wednesday Brigham & Women's Hospital 10 th February Harvard Medical School Boston USA Using human genetics to define molecular mechanisms of rheumatoid arthritis Dr. Raychaudhuri is an Associate Professor at Harvard Medical School and at Brigham and Women’s Hospital. He is also appointed as an Associate Member at the Broad Institute and a Professor in Genetics at the University of Manchester. He matriculated into the Stanford University NIH funded MST program in 1997 after completing degrees in mathematics and biophysics at the University at Buffalo. In 2004, he completed both his medical training and his doctoral training in biomedical informatics under Russ Altman. After completing his clinical training in Internal Medicine, he joined the rheumatology fellowship training program in 2006, and concurrently completed his postdoctoral fellowship training under Mark Daly at the Broad Institute. Since starting his own group in 2010 at Harvard Medical School and Brigham and Women’s Hospital, his lab has focused on finding and fine-mapping disease alleles in rheumatoid arthritis (with a particular interest in the HLA region), age related macular degeneration and other diseases. He has also been devising integrative statistical genetics strategies
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