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==With Application to the Analysis of Sequence and Genotype Data== | ==With Application to the Analysis of Sequence and Genotype Data== | ||
===June 26-30, 2017<br />Max Delbrück Center (MDC) for Molecular Medicine<br />Berlin, Germany=== | ===June 26-30, 2017<br />Max Delbrück Center (MDC) for Molecular Medicine<br />Berlin, Germany=== | ||
| − | The eigth Annual Berlin Genetic Association Course will be held at the [http://www.mdc-berlin.de/ MDC] in Berlin from | + | The eigth Annual Berlin Genetic Association Course will be held at the [http://www.mdc-berlin.de/ MDC] in Berlin from June 26-30, 2017. 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. | 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. | + | 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]: | For additional information on the Genetic Association Course please contact [mailto:sleal@bcm.edu?subject=Genetic%20Association%20Course%2C%20Berlin%202015 Suzanne Leal]: | ||
| − | + | <!-- | |
Application Deadline May 1, 2017 | Application Deadline May 1, 2017 | ||
| + | --> | ||
| + | |||
* email: [mailto:sleal@bcm.edu;suzannemleal@gmail.com?subject=Genetic%20Association%20Course%20Berlin%202016 sleal@bcm.edu] | * email: [mailto:sleal@bcm.edu;suzannemleal@gmail.com?subject=Genetic%20Association%20Course%20Berlin%202016 sleal@bcm.edu] | ||
* Tel: +1 (713) 798-4011 | * Tel: +1 (713) 798-4011 | ||
* Fax: +1 (713) 798-4012 | * 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]===== | ||
| + | =====Direction 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:2017-06-Instructors.jpg|none|224x300px]] | ||
| + | |||
| + | ===Course Participants=== | ||
| + | [[File:2017-06-Participants.jpg|none|400x299px]] | ||
| + | |||
| + | ===Lecture Slides=== | ||
| + | ::* [https://statgen.research.bcm.edu/files/2017/06/auth/coursebook_lectures.pdf Download slides here] | ||
| + | |||
| + | ===Commands for Computer Exercises=== | ||
| + | ::* [[2016-genetic-association-commands|View here]] | ||
| + | |||
| + | ===Exercise Files=== | ||
| + | ::* [https://statgen.research.bcm.edu/files/2016/09/exercises/exercises.tar.gz All Exercises] | ||
| + | ::* [https://statgen.research.bcm.edu/files/2016/09/exercises/genabel.tar.gz GenABEL] | ||
| + | ::* [https://statgen.research.bcm.edu/files/2016/09/exercises/GWAS_part1.tar.gz GWAS Part 1] | ||
| + | ::* [https://statgen.research.bcm.edu/files/2016/09/exercises/GWAS_part2.tar.gz GWAS Part 2] | ||
| + | ::* [https://statgen.research.bcm.edu/files/2016/09/exercises/haplo.tar.gz haplo] | ||
| + | ::* [https://statgen.research.bcm.edu/files/2016/09/exercises/imputation.tar.gz Imputation] | ||
| + | ::* [https://statgen.research.bcm.edu/files/2016/09/exercises/intro.plink.R.tar.gz Intro to plink and R] | ||
| + | ::* [https://statgen.research.bcm.edu/files/2016/09/exercises/multifactorial.tar.gz multifactorial] | ||
| + | ::* [https://statgen.research.bcm.edu/files/2016/09/exercises/multtest.tar.gz multtest] | ||
| + | ::* [https://statgen.research.bcm.edu/files/2016/09/exercises/pseq.tar.gz plinkSEQ] | ||
| + | ::* [https://statgen.research.bcm.edu/files/2016/09/exercises/rvtdt.tar.gz RV-TDT] | ||
| + | ::* [https://statgen.research.bcm.edu/files/2016/09/exercises/seqpower.tar.gz SeqPower] | ||
| + | ::* [https://statgen.research.bcm.edu/files/2016/09/exercises/vat.tar.gz Variant Association Tools] | ||
| + | |||
| + | ===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/2017/06/schedule_berlin_genetic_association_course_2017.pdf Click here for course schedule] | [https://statgen.research.bcm.edu/files/2017/06/schedule_berlin_genetic_association_course_2017.pdf Click here for course schedule] | ||
| Line 30: | Line 82: | ||
[https://statgen.research.bcm.edu/index.php/Genassoc2016 Click here for photos and data from Genetic Association Course – Berlin: September 2016]<br /> | [https://statgen.research.bcm.edu/index.php/Genassoc2016 Click here for photos and data from Genetic Association Course – Berlin: September 2016]<br /> | ||
[https://statgen.research.bcm.edu/index.php/ComplexNGS2016 Click here for photos and datasets from Analysis of Next Generation Sequence Data for Complex Traits Course – Berlin: July 2016]<br /> | [https://statgen.research.bcm.edu/index.php/ComplexNGS2016 Click here for photos and datasets from Analysis of Next Generation Sequence Data for Complex Traits Course – Berlin: July 2016]<br /> | ||
| − | + | [https://statgen.research.bcm.edu/index.php/2015SeptMDC 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/ | + | [https://statgen.research.bcm.edu/index.php/2015JuneMDC Click here for photos and datasets from the Genetic Association Course - Berlin: June 2015]<br /> |
| − | [https://statgen.research.bcm.edu/ | + | [https://statgen.research.bcm.edu/index.php/2015MarchMDC Click here for photos and datasets from the Analysis of Next Generation Sequence Data Complex Traits - Berlin: March 2015]<br /> |
| − | [https://statgen.research.bcm.edu/ | + | [http://portal.ccg.uni-koeln.de/ccg/index.php?id=89 Click here for photos and datasets from the Genetic Association Course - Berlin: June 2015]<br /> |
| − | [http://portal.ccg.uni-koeln.de/ccg/ | + | [http://portal.ccg.uni-koeln.de/ccg/index.php?id=88 Click here for photos and datasets from the Complex Trait Analysis of NGS Data Course - Berlin: March 2015]<br /> |
| − | [http://portal.ccg.uni-koeln.de/ccg/ | + | [http://portal.ccg.uni-koeln.de/ccg/index.php?id=87 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/ | + | [http://portal.ccg.uni-koeln.de/ccg/index.php?id=86 Click here for photos and datasets from the Genetic Association Course - Berlin: March 2014]<br /> |
| − | [http://portal.ccg.uni-koeln.de/ccg/ | + | [http://portal.ccg.uni-koeln.de/ccg/index.php?id=85 Click here for photos and datasets from the Genetic Association Course - Berlin: June 2013]<br /> |
| − | [http://portal.ccg.uni-koeln.de/ccg/ | + | [http://portal.ccg.uni-koeln.de/ccg/index.php?id=84 Click here for photos and datasets from the Basic Gene Mapping Course - Berlin: November 2012]<br /> |
| − | [http://portal.ccg.uni-koeln.de/ccg/ | + | [http://portal.ccg.uni-koeln.de/ccg/index.php?id=83 Click here for photos from the Genetic Association Course - Berlin: July 2012]<br /> |
| − | [http://portal.ccg.uni-koeln.de/ccg/ | + | [http://portal.ccg.uni-koeln.de/ccg/index.php?id=81 Click here for photos from the Basic Gene Mapping Course - Berlin: November 2011]<br /> |
| − | [http://portal.ccg.uni-koeln.de/ccg/ | + | [http://portal.ccg.uni-koeln.de/ccg/index.php?id=80 Click here for photos from the Genetic Association Course - Berlin: July 2011]<br /> |
| − | [http://portal.ccg.uni-koeln.de/ccg/ | + | [http://portal.ccg.uni-koeln.de/ccg/index.php?id=63 Click here for photos from the Basic Gene Mapping Course - Berlin: October 2010]<br /> |
| − | [http://portal.ccg.uni-koeln.de/ccg/ | + | [http://portal.ccg.uni-koeln.de/ccg/index.php?id=62 Click here for photos from the Genetic Association Course - Berlin: May 2010]<br /> |
| − | [http://portal.ccg.uni-koeln.de/ccg/ | + | [http://portal.ccg.uni-koeln.de/ccg/index.php?id=90 Click here for photos from the Basic Gene Mapping Course - Berlin: November 2009]<br /> |
| − | [http://portal.ccg.uni-koeln.de/ccg/ | + | [http://portal.ccg.uni-koeln.de/ccg/index.php?id=91 Click here for photos from the Basic Gene Mapping Course - Berlin: July 2008]<br /> |
| − | [http://portal.ccg.uni-koeln.de/ccg/ | + | [http://portal.ccg.uni-koeln.de/ccg/index.php?id=92 Click here for photos from the Basic Gene Mapping Course - Berlin: July 2007]<br /> |
| − | [http://portal.ccg.uni-koeln.de/ccg/ | + | [http://portal.ccg.uni-koeln.de/ccg/index.php?id=93 Click here for photos from the Basic Gene Mapping Course - Berlin: July 2006]<br /> |
| − | [http://portal.ccg.uni-koeln.de/ccg/ | + | [http://portal.ccg.uni-koeln.de/ccg/index.php?id=94 Click here for photos from the Basic Gene Mapping Course - Berlin: July 2005]<br /> |
| − | [http://portal.ccg.uni-koeln.de/ccg/ | + | [http://portal.ccg.uni-koeln.de/ccg/index.php?id=95 Click here for photos from the Basic Gene Mapping Course - Berlin: July 2004]<br /> |
| + | [http://portal.ccg.uni-koeln.de/ccg/index.php?id=96 Click here for photos from the Basic Gene Mapping Course - Berlin: July 2003] | ||
Latest revision as of 21:39, 14 July 2017
Contents
- 1 Genetic Association Course
- 1.1 With Application to the Analysis of Sequence and Genotype Data
Genetic Association Course
With Application to the Analysis of Sequence and Genotype Data
June 26-30, 2017
Max Delbrück Center (MDC) for Molecular Medicine
Berlin, Germany
The eigth Annual Berlin Genetic Association Course will be held at the MDC in Berlin from June 26-30, 2017. 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 Suzanne Leal (Baylor College of Medicine) and Michael Nothnagel (University of Cologne).
For additional information on the Genetic Association Course please contact Suzanne Leal:
- email: sleal@bcm.edu
- Tel: +1 (713) 798-4011
- Fax: +1 (713) 798-4012
Link to Berlin hotel tax exemption form
Direction to the MDC Campus
Direction to the classroom
Location:
- MDC - communication center (Building C83 on the Campus Map)
- Room Axion 2
The building is red and stands across the street from the campus bus stop and the blue bear.
Course Instructors
The organizers and instructors for the course are Suzanne Leal (Baylor College of Medicine) and Michael Nothnagel (University of Cologne).
Course Participants
Lecture Slides
Commands for Computer Exercises
Exercise Files
Software Links
Click here for course schedule
Click here for the application form
Click here for course flyer (please post and distribute)
Click here for maps and directions to the MDC
Click here for the information on MDC Housing
Click here for Berlin tourist information
Click here and like us on Facebook
Click here for photos and data from Genetic Association Course – Berlin: September 2016
Click here for photos and datasets from Analysis of Next Generation Sequence Data for Complex Traits Course – Berlin: July 2016
Click here for photos and datasets from the Analysis of Next Generation Sequence Data Mendelian Traits - Berlin: September 2015
Click here for photos and datasets from the Genetic Association Course - Berlin: June 2015
Click here for photos and datasets from the Analysis of Next Generation Sequence Data Complex Traits - Berlin: March 2015
Click here for photos and datasets from the Genetic Association Course - Berlin: June 2015
Click here for photos and datasets from the Complex Trait Analysis of NGS Data Course - Berlin: March 2015
Click here for photos and datasets from the Next Generation Sequence Data Analysis Course - Berlin: June 2014
Click here for photos and datasets from the Genetic Association Course - Berlin: March 2014
Click here for photos and datasets from the Genetic Association Course - Berlin: June 2013
Click here for photos and datasets from the Basic Gene Mapping Course - Berlin: November 2012
Click here for photos from the Genetic Association Course - Berlin: July 2012
Click here for photos from the Basic Gene Mapping Course - Berlin: November 2011
Click here for photos from the Genetic Association Course - Berlin: July 2011
Click here for photos from the Basic Gene Mapping Course - Berlin: October 2010
Click here for photos from the Genetic Association Course - Berlin: May 2010
Click here for photos from the Basic Gene Mapping Course - Berlin: November 2009
Click here for photos from the Basic Gene Mapping Course - Berlin: July 2008
Click here for photos from the Basic Gene Mapping Course - Berlin: July 2007
Click here for photos from the Basic Gene Mapping Course - Berlin: July 2006
Click here for photos from the Basic Gene Mapping Course - Berlin: July 2005
Click here for photos from the Basic Gene Mapping Course - Berlin: July 2004
Click here for photos from the Basic Gene Mapping Course - Berlin: July 2003
