Difference between revisions of "2015JuneMDC"
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| + | ==Genetic Association Course with Application to Sequence and Genotype Data== | ||
June 22-26, 2015, Max Delbrück Center (MDC) for Molecular Medicine, Berlin, Germany | June 22-26, 2015, Max Delbrück Center (MDC) for Molecular Medicine, Berlin, Germany | ||
| − | General Information | + | |
| + | ===General Information=== | ||
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 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. | ||
| − | 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. | + | |
| − | Link | + | 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; tagSNPselection; 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). |
| − | Direction to the MDC Campus | + | |
| − | 0Direction to the classroom | + | =====[[Media:BerlinHotelExemption.pdf|Link to Berlin hotel tax exemption form]]===== |
| + | =====[https://www.mdc-berlin.de/directions Direction to the MDC Campus]===== | ||
| + | =====0Direction to the classroom===== | ||
Location: | Location: | ||
| − | MDC - communication center (Building C83 on the Campus Map) | + | |
| − | Room Axion 2 | + | :: MDC - communication center (Building C83 on the [http://www.campus-berlin-buch.de/en/location/ Campus Map]) |
| − | Course Instructors | + | :: 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). | The organizers and instructors for the course are Suzanne Leal (Baylor College of Medicine) and Michael Nothnagel (University of Cologne). | ||
| + | [[File:2015JuneInstructors.jpg|none|226x301px]] | ||
| + | |||
| + | [[File:2015JuneMDC_Class.jpeg|none|500x373px]] | ||
| + | |||
| + | ===Commands for Computer Exercises=== | ||
| + | ::* [[2015-june-berlin-commands|View here]] | ||
| + | |||
| + | ===Course Slides=== | ||
| + | ::* [http://statgen.us/uploads/berlin_course_June_2015.pdf Download here] | ||
| + | |||
| + | ===Data Sets Used During the Course=== | ||
| + | ::* [http://statgen.us/files/2016/06/june2015berlin.tar.bz2 Download here] | ||
| − | + | ===Software Links=== | |
| − | + | ::* EIGENSTRAT | |
| − | + | ::* [http://www.genabel.org/ GenABEL] | |
| − | + | ::* [http://pngu.mgh.harvard.edu/~purcell/plink/ PLINK] | |
| − | + | ::* [http://www.r-project.org/ R] | |
| − | + | ::* [http://www.bioinformatics.org/spower/start SEQPower] | |
| − | Software Links | + | ::* [https://sites.google.com/site/fdudbridge/software/unphased-3-1 UNPHASED] |
| − | EIGENSTRAT | + | ::* [http://varianttools.sf.net/VAT Variant Association Tools] |
| − | GenABEL | + | |
| − | PLINK | + | |
| − | R | + | |
| − | SEQPower | + | |
| − | UNPHASED | + | |
| − | Variant Association Tools | + | |
Revision as of 17:58, 5 May 2016
Genetic Association Course with Application to Sequence and Genotype Data
June 22-26, 2015, Max Delbrück Center (MDC) for Molecular Medicine, Berlin, Germany
General Information
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.
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; tagSNPselection; 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).
Link to Berlin hotel tax exemption form
Direction to the MDC Campus
0Direction 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).
