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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.
[http://statgen.us/files/2015/02/Advanced_Gene_Mapping_Course_Schedule_2015.pdf Course Schedule]
===Course Instructors===
The instructors for the course are: [http://www.staff.ncl.ac.uk/heather.cordell/ Heather Cordell] (University of Newcastle), Laurent Francioli (University Medical Center Utrecht), [https://www.bcm.edu/research/labs/center-for-statistical-genetics Suzanne Leal] (The Rockefeller University & Baylor College of Medicine), [https://www.broadinstitute.org/scientific-community/science/programs/psychiatric-disease/stanley-center-psychiatric-research/benjam Ben Neale] (Broad Institute and Harvard University) and [http://www.brighamandwomens.org/research/depts/medicine/genetics/pis/Sunyaev/default.aspx Shamil Sunyaev] (Harvard University).
===Lecture Handouts & Practical Exercises===
====Heather Cordell====
* Presentations
** [http://statgen.us/files/201501/cordell/handouts/hjc-interactions2015-3persheet.pdf Gene-Gene and Gene-Environment interactions]
** [http://statgen.us/files/201501/cordell/handouts/NY2015-GWAS-3persheet.pdf Genome-wide association studies]
* Exercises
** [http://statgen.us/files/201501/cordell/handouts/Practical-epistasis2014-pdf.pdf Interaction analysis]
** [http://statgen.us/files/201501/exercises/cordell.tar.bz2 Download Data Sets] (decompress using "tar jxvf cordell.tar.bz2")
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====Laurent Francioli====
* Presentations
** [http://statgen.us/files/2015/02/francioli/handouts/01-NGS.pdf Next-generation sequencing]
** [http://statgen.us/files/2015/02/francioli/handouts/02-Alignment.pdf Alignment]
** [http://statgen.us/files/2015/02/francioli/handouts/03-SNP_and_Indel_Calling.pdf SNP and Indel Calling]
** [http://statgen.us/files/2015/02/francioli/handouts/04-Variant_Filtering.pdf Variant filtering]
** [http://statgen.us/files/2015/02/francioli/handouts/05-Genotyping_NGS.pdf Genotyping NGS data]
** [http://statgen.us/files/2015/02/francioli/handouts/06-VCF_and_IGV.pdf NGS variants output and visualizaion: VCF and IGV]
* Exercises
** [http://statgen.us/files/201501/francioli/handouts/01_variant_calling_exercices.pdf Variant calling exercises]
** [http://statgen.us/files/201501/exercises/francioli.tar.bz2 Download Data Sets] (decompress using "tar jxvf francioli.tar.bz2")
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* [http://statgen.us/files/201501/francioli/handouts.tar.bz2 tarball download]
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====Suzanne Leal====
* Presentations
** [http://statgen.us/files/201501/leal/lectures/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]
** [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]
** [http://statgen.us/files/201501/leal/lectures/power_analysis_rare_variants_2_5_15.pdf Power Analysis for Rare Variants - Aggregate Analysis]
* 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/GWAS_Data_Data_cleaning_linux_updated_2_5_15.pdf GWAS_Data_Data_cleaning_linux_updated_2_5_15.pdf]
** [http://statgen.us/files/2015/02/leal/exercises/GWAS_Data_Controlling_for_Admixture_linux_2_5_15.pdf GWAS_Data_Controlling_for_Admixture_linux_2_5_15.pdf]
** [http://statgen.us/files/2015/02/leal/exercises/GenABEL-Rockefeller_2_5_15.pdf Genome Wide Association using GenABEL]
** [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/exercises/leal.tar.bz2 Download Data Sets] (decompress using "tar jxvf leal.tar.bz2")
====Ben Neale====
* Presentations
* [http://statgen.us/files/201501/neale/Neale_Rockefeller_course_2015.pdf Neale lectures combined]
* Exercises
** [http://statgen.us/files/201501/exercises/neale.tar.bz2 Download Data Sets] (decompress using "tar jxvf neale.tar.bz2")
====Shamil Sunyaev====
* Presentations
** [http://statgen.us/files/201501/sunyaev/handouts/Rockefeller_pop_gen_2014.pdf Population genetics]
** [http://statgen.us/files/201501/sunyaev/handouts/Rockefeller_mutation_2015.pdf Mutation]
** [http://statgen.us/files/201501/sunyaev/handouts/Rockefeller_complex_traits_2015.pdf Complex traits]
* Exercises
** [http://statgen.us/files/201501/sunyaev/handouts/Rockefeller_tutorial.pdf Annotation tutorial]
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===Data-sets Used During the Course===
* [http://statgen.us/files/201501/exercises/cordell.tar.bz2 Heather Cordell's Data Sets]
* [http://statgen.us/files/201501/exercises/francioli.tar.bz2 Laurent Francioli's Data Sets]
* [http://statgen.us/files/201501/exercises/leal.tar.bz2 Suzanne Leal's Data Sets]
* [http://statgen.us/files/201501/exercises/neale.tar.bz2 Ben Neale's Data Sets]
In order to obtain a particular data set, please follow the following steps:
# Download the respective data archive file (''*.tar.bz2'') and place it into an appropriate directory.
# At the command prompt (aka shell or terminal), make this directory the working directory by using the ''cd'' command.
# Extract the data files by typing ''tar xjvf'' and adding the name of the archive file. The data files will then be in a corresponding subdirectory.
# Change to this subdirectory (''cd'' command) and proceed with the exercise.
-->
===Software===
* [http://annovar.openbioinformatics.org/en/latest/ ANNOVAR]
* [http://sites.stat.psu.edu/~yuzhang/ BEAM3]
* [http://cassi.cas.org/ CASSI]
* [http://annovar.openbioinformatics.org/en/latest/ GATK]
* [http://www.genabel.org/ GenABEL]
* [https://www.broadinstitute.org/igv/ IGV]
* [https://cran.r-project.org/web/packages/ORMDR/index.html ORMDR]
* [http://pngu.mgh.harvard.edu/~purcell/plink/ PLINK]
* [https://www.r-project.org/ R]
* [http://www.bioinformatics.org/spower/ SEQPower]
* [http://varianttools.sourceforge.net/Association/HomePage VAT]
===Links===
* [http://ihg.helmholtz-muenchen.de/cgi-bin/hw/power2.pl Armitrage Test for Trends]
* [http://agvgd.iarc.fr/ AlignGVGD]
* [http://mendel.stanford.edu/SidowLab/downloads/gerp/index.html GERP]
* [http://www.genmapp.org/ GenMAPP]
* [http://mendel.stanford.edu/SidowLab/downloads/mapp/index.html MAPP]
* [http://mips.helmholtz-muenchen.de/proj/ppi/ MIPS] .
* [http://www.mutationtaster.org/ MutationTaster]
* [http://mutpred.mutdb.org/ MutPred]
* [http://www.rcsb.org/ PDB]
* [http://pfam.sanger.ac.uk/ Pfam]
* [http://genetics.bwh.harvard.edu/pph2 Polyphen-2]
* [http://sift.jcvi.org/ SIFT]
* [http://smart.embl.de/ SMART]
* [http://www.rostlab.org/services/snap/ SNAP]
* [http://snps3d.org/ SNPs3D]
* [http://string.embl.de/ STRING]
* [http://www.uniprot.org/ UniProt]
This course is supported by a grant from the National Institute of Health (NIH) - National Human Genome Research Institute (NHGRI).