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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



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