2015AdvancedGeneMapping

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

• Presentations
  • Gene-Gene and Gene-Environment interactions
  • Genome-wide association studies
• Exercises
  • Interaction analysis
  • Download Data Sets (decompress using "tar jxvf cordell.tar.bz2")

Laurent Francioli

• Presentations
  • Next-generation sequencing
  • Alignment
  • SNP and Indel Calling
  • Variant filtering
  • Genotyping NGS data
  • NGS variants output and visualizaion: VCF and IGV
• Exercises
  • Variant calling exercises
  • Download Data Sets (decompress using "tar jxvf francioli.tar.bz2")

Suzanne Leal

• Presentations
  • Complex Trait Associaton Analysis of Rare Variants Obtained from Sequence Data
  • Data Quality Control
  • Sample Size and Power Analysis For Associaton Studies Analysis of Individual Variants
  • Power Analysis for Rare Variants - Aggregate Analysis
• Exercises
  • Sample Size Calculation
  • GWAS_Data_Data_cleaning_linux_updated_2_5_15.pdf
  • GWAS_Data_Controlling_for_Admixture_linux_2_5_15.pdf
  • Genome Wide Association using GenABEL
  • SEQPower
  • Variant Association Tools
  • Download Data Sets (decompress using "tar jxvf leal.tar.bz2")

Ben Neale

• Presentations
• Neale lectures combined
• Exercises
  • Download Data Sets (decompress using "tar jxvf neale.tar.bz2")

Shamil Sunyaev

• Presentations
  • Population genetics
  • Mutation
  • Complex traits
• Exercises
  • Annotation tutorial

Software

• ANNOVAR
• BEAM3
• CASSI
• GATK
• GenABEL
• IGV
• ORMDR
• PLINK
• R
• SEQPower
• VAT

Links

• Armitrage Test for Trends
• AlignGVGD
• GERP
• GenMAPP
• MAPP
• MIPS .
• MutationTaster
• MutPred
• PDB
• Pfam
• Polyphen-2
• SIFT
• SMART
• SNAP
• SNPs3D
• STRING
• UniProt

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