13 th Course SNP s and Human Diseases November 2016 Final vs

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1 13 th Course SNP s and Human Diseases November 2016 Final vs The analysis of DNA variations, including Single Nucleotide Polymorphisms (SNPs), is a standard research approach to understand causes of disease, in particular the so-called complex diseases such as diabetes, osteoporosis, cancer, Alzheimer disease, etc. The field is changing fast with large scale projects (Human genome, dbsnp, HapMap, 1000genomes, ENCODE) and novel technology being continuously introduced, including Next Generation Sequencing. The aim of this course is to give a broad introduction in SNP techniques and applications. The course is primarily organized for PhD students and postdocs of the Erasmus Postgraduate School Molecular Medicine, Nihes, MGC and other research schools. Other participants, e.g., scientists, students, and technicians from other universities in- and outside Netherlands are also welcome. The total number of participants is limited to 75. The attendance fee of the 5-day course is 750, but some participants can get a discount. See below for all details. This is an advanced course on complex genetics. While there is some overlap in content, the SNP course offers more than the NIHES-ESP 57 course in the Erasmus Summer Program. It is recommended for the participants of the SNP course to have basic knowledge of the central molecular biological dogma's (such as DNA and gene structure, DNA encodes RNA encodes protein, etc.) and of basic genetic principles. So you should have attended last years course Genetics for Dummies, organised also by MolMed, or this years NIHES Summer program Genetic Epidemiology. Basic background knowledge can also be found in any decent textbook of human molecular biology and genetics, such as "Molecular Biology of the Cell" (5th ed.; editors: Alberts et al.; published by Garland Sciences) and "Human Molecular Genetics" (4 th ed.; editors Strachan & Read; published by Garland Sciences; 40,-). To this aim, also a series of basic papers is published on our website: on the course page. At the start of the course a comprehensive reader will be issued. All participants will be requested to send a short presentation or description of their own research and field of interest in advance to the course organisation ( to: molmed@erasmusmc.nl). In this way we get to know your research topics, to better prepare the topics of the course. All participants are expected to prepare some overhead sheets. A selection of the candidates will be asked to present their own research topics on the 1 st course day, Monday. On the first 4 days learning-by-doing sessions ( practicals ) on the bio-informatic and statistical analysis in this field are organised. On the last 2 days, our special guests as key note speakers are scheduled (except Manfred Kayser who speaks on day 2). Subscription is open on: 1

2 If you have any questions, please to: or call, also in emergencies: Sharesma Ghiraw (+31(0) ) or Frank van Vliet (+31(0) ). The organizing committee, Dr. Joyce van Meurs Dr. Fernando Rivadeneira Prof.dr. André Uitterlinden Dr. Frank van Vliet First Day, Monday 14 November, Room Ae-4.06 & OWR-22 Introductory lectures & GWAS Moderator: André Uitterlinden Registration and coffee; room Ae André Uitterlinden, General introduction on the course; overview of the research on SNP s Cornelia van Duijn, General introduction on genetic epidemiology Coffee Break Fernando Rivadeneira, GWAS & Linkage disequilibrium mapping using HapMap Lunch (room Ae 4.06; occupied from 13.00!) Go to computer room OWR Fernando Rivadeneira, Principles of imputing techniques and Coaches: Fernando Rivadeneira, Carolina Medina-Gomez, Linda Broer, Cindy Boer, ; computer room OWR 22 Go to Room Ae Coffee Participants & André Uitterlinden/ Fernando Rivadeneira analysis of imputed data Practical A PLINK (beginners) or CGTA (advanced) All participants must prepare overhead sheets; see introduction Welcome drinks (in Ae 3.27) (Ae-4.06 occupied > 17.00) 2

3 Second Day, Tuesday 15 November, Room Ae-4.06 & C00-3 OMICS Technologies, lectures & practical database usage Moderator: Joyce van Meurs Johan den Dunnen, LGTC/ LUMC, Technologies in genomics Leiden Joyce van Meurs, High throughput Genotyping technologies Coffee break Bas Heijmans, Molecular Epidemiology Dept., LUMC, Leiden DNA Methylation (Illumina 450k methylation array) Lunch (in Ee building, 3 rd floor opposite to the coffee bar; room Ae-4.06 is occupied) Joyce van Meurs, Cindy Boer Dedicated bio informatic tools for SNP analysis, databases, UCSC, ENCODE/ROADMAP Coffee break Manfred Kayser, Forensic Molecular Biology Dept., Genetic basis and prediction of human appearance (go to computer room COO-3) Coaches: Joyce van Meurs, Carolina Medina-Gomez, Cindy Boer, Linda Broer, ; computer room COO-3 Practical B Bio Informatic tools Bio informatics for SNP research: Using NCBI and other web-based tools for SNP search and functionality assessment. Self study on applications & work on given tasks Third Day, Wednesday 16 November, Room OWR-22 & Ae-4.06 NGS - Lectures & Family based studies practical Moderator: Fernando Rivadeneira Robert Kraaij, Next Generation Sequencing (NGS) technologies Joyce van Meurs, RNA sequencing Coffee break Jeroen van Rooij, Characterisation of exome sequencing data in population studies Victor Guryev, UMC Groningen Analysis of structural variations in exome and full genome sequence data Lunch (in room Ae-4.06) Annemieke Verkerk, Family based studies and Next Generation Sequencing Go to computer room OWR Coaches: Jeroen van Rooij, Linda Broer, Annemieke Verkerk, After Coffee break: outside room OWR 22 Practical C Next Generation Sequencing; monogenetic, 1 family; variant calling in sequencing data 3

4 Fourth Day, Thursday 17 November, Room Ae-4.06 & COO-3 SNP research Concepts and applications Moderator: Fernando Rivadeneira Coaches: Joyce van Meurs, more.. in COO-3 Practical D eqtl analysis Coffee break Fernando Rivadeneira, Erasmus MC; go to room Ae Genomes Project: Basic Concepts and its Use in Complex Genetics Lunch (in room Ae 4.06) Lude Franke, UMCG Groningen Interpreting GWAS through expression QTLs, epigenetic QTLs and gene networks Oscar Lao, Population Genomics, CNAG - Centro Nacional de Análisis Genómico, Barcelona Coffee break Oscar Lao, Population Genomics, CNAG & Fernando Rivadeneira, Alexander Hoischen, UMCN Nijmegen Genetic Geography and Population Structure Evolutionary selection underlying the genetic architecture of complex traits Rare and common variants - targeted resequencing of large cohorts by molecular inversion probes (MIPs) John Martens, Genomics of tumors Dinner for all speakers and participants at: Chinese Cantonese Specialities Restaurant TAI WU, Mauritsweg 24-25, Fifth Day, Friday 18 November, Room: Ae-4.06 Complex traits and diseases - Models and clinical applications Moderator: André Uitterlinden Ron van Schaik, Pharmacogenomics Jeroen Raes, VIB, Leuven, Belgium Microbiome Coffee break Douglas Easton, University of Breast cancer Cambridge, Strangeways Research Lab Guido Jenster, Transcriptomics and genomics in Prostate Cancer Lunch Omar Albagha, School of Molecular and Clinical Medicine, Western General Hospital, Edinburgh, UK John Perry, Epidemiology Unit, University of Cambridge, School of Clinical Medicine Coffee break Andy Wood, Genetics of Complex Traits, Peninsula Med.S, Exeter, UK Felix Day, Epidemiology Unit, University of Cambridge, School of Clinical Medicine Paget's disease: from genetics to treatment Reproductive aging Genetics of Anthropometry Collider Bias en LD-Score regression Farewell drinks & informal discussion with all speakers & participants 4

5 History and affiliation This course is already the 13 th issue after the very successful courses from November 2004 until The course is also organised in close cooperation with and under the auspices of the Research School Nihes. We are grateful to all our colleagues from Leiden, Nijmegen and other Universities for the fruitful cooperation. Attendance fees The subscription fee of non-commercial participants for the full course including the final Symposium is 750. Discounts are handled as followed: All PhD and research master students docs get a discount of 50% and pay 375. All participants from the postgraduate school MolMed get a discount of 100% and pay 0. Master students who pay the fee themselves get a discount of 75% and pay 187,75. If these financial requirements pose a problem but you wish to attend the Course, please contact Frank van Vliet, managing director of the Erasmus Postgraduate School Mol Med, at: f.vanvliet@erasmusmc.nl. ECTS Full attendance of this course, including the practical s, will be awarded with 2 ECTS. Invoices Fees can be paid upon an INVOICE. Shortly after your registration you will receive the INVOICE per mail. Payment per bank can be done on account: /, (IBAN code bank: NL86ANBA ; SWIFT code bank: ABNANL2A), together with the number on your INVOICE. Late participants can also pay in cash upon signing in for the Course. Cancellations The fees are for all the days of the Course. There is no discount for partaking only in part of the Course. Cancellation is possible, but only up to one week before the start of the Course. Later cancellation will not be accepted, but you are allowed to send a substitute. Commercial participants & sponsors Companies are invited to inquire for participation and sponsoring. 5