Difference between revisions of "2015AdvancedGeneMapping"

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(Laurent Francioli)
(Suzanne Leal)
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====Suzanne Leal====
 
====Suzanne Leal====
 
* Presentations
 
* Presentations
** [http://statgen.us/files/201501/leal/lectures/analysis_rare_variants.pdf Complex Trait Associaton Analysis of Rare Variants Obtained from Sequence Data]
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** [http://statgen.us/files/2015/02/leal/handouts/analysis_rare_variants.pdf Complex Trait Associaton Analysis of Rare Variants Obtained from Sequence Data]
** [http://statgen.us/files/201501/leal/lectures/data_quality_control_2_5_15.pptx Data Quality Control]
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** [http://statgen.us/files/2015/02/leal/handouts/data_quality_control_2_5_15.pptx Data Quality Control]
** [http://statgen.us/files/201501/leal/lectures/power_analysis_2_5_15.pdf Sample Size and Power Analysis For Associaton Studies Analysis of Individual Variants]
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** [http://statgen.us/files/2015/02/leal/handouts/power_analysis_2_5_15.pdf Sample Size and Power Analysis For Associaton Studies Analysis of Individual Variants]
** [http://statgen.us/files/201501/leal/lectures/power_analysis_rare_variants_2_5_15.pdf Power Analysis for Rare Variants - Aggregate Analysis]
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** [http://statgen.us/files/2015/02/leal/handouts/power_analysis_rare_variants_2_5_15.pdf Power Analysis for Rare Variants - Aggregate Analysis]
 
* Exercises
 
* Exercises
 
** [http://statgen.us/files/2015/02/leal/exercises/Armitage_sample_size_Rockefeller_1_5_15.pdf Sample Size Calculation]
 
** [http://statgen.us/files/2015/02/leal/exercises/Armitage_sample_size_Rockefeller_1_5_15.pdf Sample Size Calculation]
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** [http://statgen.us/files/2015/02/leal/exercises/SEQPower-2015NYC.pdf SEQPower]
 
** [http://statgen.us/files/2015/02/leal/exercises/SEQPower-2015NYC.pdf SEQPower]
 
** [http://statgen.us/files/2015/02/leal/exercises/VAT-2015NYC.pdf Variant Association Tools]
 
** [http://statgen.us/files/2015/02/leal/exercises/VAT-2015NYC.pdf Variant Association Tools]
** [http://statgen.us/files/2015/02/exercises/leal.tar.bz2 Download Data Sets] (decompress using "tar jxvf leal.tar.bz2")
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** [http://statgen.us/files/2015/02/leal/exercises/leal.tar.bz2 Download Data Sets] (decompress using "tar jxvf leal.tar.bz2")
  
 
====Ben Neale====
 
====Ben Neale====

Revision as of 15:05, 7 June 2016

Advanced Gene Mapping Course

The Rockefeller University, New York, Monday through Friday, Feb. 9-13, 2015

General Information

The course emphasis is analysis of complex human disease traits; concentrating on methods to detect rare and common variant associations. The course includes theory as well as practical exercises.

Topics include: Analysis of whole genome association studies; analysis of rare variants using next generation sequence and exome chip data; rare variant association tests; analysis of qualitative and quantitative traits (population and family-based data); detection of de novo variants and significance testing; Mendelian randomization; determining whether inflated test statistics observed with large scale GWAS meta-analysis is driven by confounding or by polygenic inheritance using the LD score approached; functional predication of variant sites; variant annotation, sequence read alignment and variant calling, controlling for population substructure/admixture (principal components analysis/multidimensionality scaling); data quality control of genotype and sequence data; detection of gene x gene interaction; sample size estimation and evaluating power for common and rare variants.

The exercises will be carried out using a variety of computer programs including ANNOVAR, GATK,GenAbel, GERP, PLINK, R, SIFT, SEQPower, Variant Association Tools (VAT), Polyphen-2, etc.

Course Schedule

Course Instructors

The instructors for the course are: Heather Cordell (University of Newcastle), Laurent Francioli (University Medical Center Utrecht), Suzanne Leal (The Rockefeller University & Baylor College of Medicine),  Ben Neale (Broad Institute and Harvard University) and Shamil Sunyaev (Harvard University).

Lecture Handouts & Practical Exercises

Heather Cordell

Laurent Francioli

Suzanne Leal

Ben Neale

Shamil Sunyaev

Software

Links


This course is supported by a grant from the National Institute of Health (NIH) - National Human Genome Research Institute (NHGRI).