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=Genetic Association Course=
==With Application to the Analysis of Sequence and Genotype Data==
===September 5-9, 2016<br />Max Delbrück Center (MDC) for Molecular Medicine<br />Berlin, Germany===
The seventh Annual Berlin Genetic Association Course will be held at the [http://www.mdc-berlin.de/ MDC] in Berlin from September 5-9, 2016. The goal of the course is to teach the course participants both theory and application of methods for population based association analysis, with a concentration on the analysis of exome and whole genome sequence and genotype data.
The cost of the 5 day course is 975 EUR for researchers from an academic institution, and 1,950 EUR for individuals from private (for profit) companies. This fee covers tuition, Monday evening wine and cheese party and course related expenses (handouts, etc.) but not room, board or meals. Inexpensive housing is available for course participants at the MDC and nearby hotels.
Emphasis in this course is on strategies for genetic mapping of complex human traits. It will include theory as well as practical exercises. The exercises will be carried out using a variety of computer programs (PLINK, GenABEL, MACH, UNPHASED, EIGENSTRAT, Variant Association Tools (VAT), SEQPower and R, etc.) and with pencil and paper. The emphasis of this course is analysis of population based whole genome and exome data including genotype and sequence data. TOPICS include: Association analysis of qualitative and quantitative traits; single marker and haplotype analysis; analysis of whole genome association study data; complex trait rare variant association analysis of next generation sequence data; data quality control for genotype and next generation sequence data; haplotype reconstruction; tagSNP selection; controlling population admixture (genomic control, principal components analysis, etc); imputing genotype data from sequence and genotype data; detecting gene x gene and gene x environmental interactions; power and sample size estimation for both genotype and rare variant data; permutation (estimating empirical p-values); and false discovery rate (FDR). The organizers and instructors for the course are [https://www.bcm.edu/research/labs/center-for-statistical-genetics/ Suzanne Leal] (Baylor College of Medicine) and [http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/ Michael Nothnagel] (University of Cologne).
For additional information on the Genetic Association Course please contact [mailto:sleal@bcm.edu?subject=Genetic%20Association%20Course%2C%20Berlin%202015 Suzanne Leal]:
* email: [mailto:sleal@bcm.edu;suzannemleal@gmail.com?subject=Genetic%20Association%20Course%20Berlin%202016 sleal@bcm.edu]
* Tel: +1 (713) 798-4011
* Fax: +1 (713) 798-4012
=====[http://statgen.us/files/2015/09/BerlinHotelTaxExemptionForm.pdf Link to Berlin hotel tax exemption form]=====
=====[https://www.mdc-berlin.de/directions Direction to the MDC Campus]=====
=====0Direction to the classroom=====
Location:
:: MDC - communication center (Building C83 on the [http://www.campus-berlin-buch.de/en/location/ Campus Map])
:: Room Axion 2
The building is red and stands across the street from the campus bus stop and the blue bear.
[[File:MDC_C.jpg|none|300x300px]]
===Course Instructors===
The organizers and instructors for the course are Suzanne Leal (Baylor College of Medicine) and Michael Nothnagel (University of Cologne).
[[File:2016-09_instructors.jpg|none|224x300px]]
===Course Participants===
[[File:2016-09_participants1.jpg|none|400x299px]]
[[File:2016-09_participants2.jpg|none|480x203px]]
===Lecture Slides===
::* [http://statgen.us/files/2016/09/auth/Berlin-lectures_2016-09.pdf Download slides here]
===Commands for Computer Exercises===
::* [[2016-genetic-association-commands|View here]]
===Software Links===
::* [https://faculty.washington.edu/browning/beagle/b3.html Beagle]
::* EIGENSTRAT
::* [http://www.genabel.org/ GenABEL]
::* [http://csg.sph.umich.edu/abecasis/MACH/index.html MACH]
::* [http://pngu.mgh.harvard.edu/~purcell/plink/ PLINK]
::* [https://atgu.mgh.harvard.edu/plinkseq/ PSEQ]
::* [http://www.r-project.org/ R]
::* [http://bioinformatics.org/rv-tdt/ RV-TDT]
::* [http://www.bioinformatics.org/spower/start SEQPower]
::* [https://sites.google.com/site/fdudbridge/software/unphased-3-1 UNPHASED]
::* [http://varianttools.sf.net/VAT Variant Association Tools]
[https://statgen.research.bcm.edu/files/2016/09/schedule_berlin_genetic_association_course_2016.pdf Click here for course schedule]
[https://statgen.research.bcm.edu/files/2016/09/Berlin_Genetic_Association_Course_Application_2016.html Click here for the application form]
[https://statgen.research.bcm.edu/files/2016/09/Berlin_genetic_association_flyer_2016.pdf Click here for course flyer] (please post and distribute)
[https://www.mdc-berlin.de/directions Click here for maps and directions to the MDC]<br />
[http://www.bbb-berlin.de/en/gaestehaeuser.html Click here for the information on MDC Housing]<br />
[http://www.visitberlin.de/en Click here for Berlin tourist information]<br />
[https://statgen.research.bcm.edu/2015SeptMDC/view Click here for photos and datasets from the Analysis of Next Generation Sequence Data Mendelian Traits - Berlin: September 2015]<br />
[https://statgen.research.bcm.edu/2015JuneMDC/view Click here for photos and datasets from the Genetic Association Course - Berlin: June 2015]<br />
[https://statgen.research.bcm.edu/2015MarchMDC/view Click here for photos and datasets from the Analysis of Next Generation Sequence Data Complex Traits - Berlin: March 2015]<br />
[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/ngsdac2014.html Click here for photos and datasets from the Next Generation Sequence Data Analysis Course - Berlin: June 2014]<br />
[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gac2014.html Click here for photos and datasets from the Genetic Association Course - Berlin: March 2014]<br />
[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gac2013.html Click here for photos and datasets from the Genetic Association Course - Berlin: June 2013]<br />
[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gmc2012.html Click here for photos and datasets from the Basic Gene Mapping Course - Berlin: November 2012]<br />
[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gac2012.html Click here for photos from the Genetic Association Course - Berlin: July 2012]<br />
[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gmc2011.html Click here for photos from the Basic Gene Mapping Course - Berlin: November 2011]<br />
[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gac2011.html Click here for photos from the Genetic Association Course - Berlin: July 2011]<br />
[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gmc2010.html Click here for photos from the Basic Gene Mapping Course - Berlin: October 2010]<br />
[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gac2010.html Click here for photos from the Genetic Association Course - Berlin: May 2010]<br />
[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gmc2009.html Click here for photos from the Basic Gene Mapping Course - Berlin: November 2009]<br />
[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gmc2008.html Click here for photos from the Basic Gene Mapping Course - Berlin: July 2008]<br />
[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gmc2007.html Click here for photos from the Basic Gene Mapping Course - Berlin: July 2007]<br />
[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gmc2006.html Click here for photos from the Basic Gene Mapping Course - Berlin: July 2006]<br />
[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gmc2005.html Click here for photos from the Basic Gene Mapping Course - Berlin: July 2005]<br />
[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gmc2004.html Click here for photos from the Basic Gene Mapping Course - Berlin: July 2004]<br />
[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gmc2003.html Click here for photos from the Basic Gene Mapping Course - Berlin: July 2003]