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==Advanced Gene Mapping Course==
The Rockefeller University, New York<br />Welch – The Great Hall<br />Monday through Friday, January 25-29, 2016
===General Information===
An advanced gene mapping course will be held in New York from Monday through Friday January 25-29, 2016. The cost of the 5-day course is $100 for student, academic and government researchers and $2,500 for researchers working in industry. This fee covers tuition and course related expenses (handouts, etc.) but not room and board.
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. The exercises will be carried out using a variety of computer programs including ANNOVAR, BEAM3, CADD, GERP, GotCloud, GenAbel, PLINK, Polyphen-2, R, SEQPower, Variant Association Tools (VAT), etc. Topics include: Analysis of whole genome association studies; analysis of rare variants using next generation sequence data; analysis of qualitative and quantitative traits (population and family-based data); Linear mixed models; eQTL mapping; prediction models using RNAseq and array data; inferences for heritability estimation and prediction; functional predication of variant sites, variant annotation; variant calling, controlling for population substructure\admixture (principal components analysis\multidimensionality scaling); data quality control of genotype and sequence data; meta-analysis; gene x gene interaction; sample size estimation and evaluating power for common and rare variants.
===Course Instructors===
The instructors for the course are: [http://csg.sph.umich.edu/abecasis/ Gonçalo Abecasis] (University of Michigan), [http://www.staff.ncl.ac.uk/heather.cordell/ Heather Cordell] (University of Newcastle), [https://medschool.vanderbilt.edu/brain-institute/person/nancy-j-cox-phd Nancy Cox] (Vanderbilt University), [https://www.bcm.edu/research/labs/center-for-statistical-genetics Suzanne Leal] (The Rockefeller University & Baylor College of Medicine), and [http://www.fas.harvard.edu/~biophys/Shamil_Sunyaev.htm Shamil Sunyaev] (Harvard University).
===More Information===
The maximum number of participants is 30. The course will take place in the Great Hall in Welch at The Rockefeller University, which is equipped with PCs running under LINUX. The course is wheel chair accessible. All disabilities will be accommodated. Handicapped individuals are encouraged to apply.
Four travel stipends of up to $1,000 each are available. Eligibility requirements are: (1) sufficient background and practical experience in statistical analysis of genetic data, and (2) demonstrated financial need. Preference for stipends will be given to pre-doctoral students and postdoctoral researchers. To apply for such a stipend, please attach a letter of request and enclose a letter of reference and proof of student or postdoctoral status.
Knowledge genetic association analysis, genetic epidemiology and/or statistical genetics are screening criteria for selection of participants. Please describe your experience in detail in your application. We may contact you personally to discuss your application. Although experience of using LINUX is not necessary it is highly beneficial to have basic knowledge of this operating system before the start of the course.
For additional information, please contact [mailto:montagk@rockefeller.edu Katherine Montague]:<br />email: [mailto:montagk@rockefeller.edu montagk@rockefeller.edu]<br />Tel: +1 (212) 327-7979
For additional information on scientific program contact the course organizer Suzanne Leal:<br />email: [mailto:sleal@bcm.edu sleal@bcm.edu] or [mailto:suzannemleal@gmail.com suzannemleal@gmail.com]<br />Tel: +1 (713) 798-4011
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===Lecture Handouts & Practical Exercises===
====Gonçalo Abecasis====
* Presentations
** [https://statgen.research.bcm.edu/files/201601/abecasis/presentations/Genome-wide_Analysis.pdf Genome-wide Analysis]
** [https://statgen.research.bcm.edu/files/201601/abecasis/presentations/Genotype_Imputation.pdf Genotype Imputation.pdf]
** [https://statgen.research.bcm.edu/files/201601/abecasis/presentations/Meta_Analysis.pdf Meta Analysis]
** [https://statgen.research.bcm.edu/files/201601/abecasis/presentations/Sequence_Data.pdf Sequence Data]
* Exercises
** Data Sets
*** [http://csg.sph.umich.edu/mktrost/seqshopExampleMay2015.tar.gz GotCloud]
*** [http://csg.sph.umich.edu/abecasis/MACH/download/ Mach] (example included with mach program)
*** [http://csg.sph.umich.edu//abecasis/Metal/download/GlucoseExample.tar.gz Metal]
====Heather Cordell====
* Videos
** [https://statgen.research.bcm.edu/files/2016/01/cordell/videos/StatisticalMethods.mp4 Statistical Methods]
** [https://statgen.research.bcm.edu/files/2016/01/cordell/videos/Interactions.mp4 Interactions]
* Presentations
** [https://statgen.research.bcm.edu/files/2016/01/cordell/presentations/hjc-NY2016-GWAS-3persheet.pdf Statistical Methods]
** [https://statgen.research.bcm.edu/files/2016/01/cordell/presentations/hjc-interactions2016-3persheet.pdf Interactions]
* Exercises
** [https://statgen.research.bcm.edu/files/2016/01/cordell/exercises/hjc-epistasis2015.html Interaction analysis using PLINK, CASSI, ORMDR and BEAM3]
** [https://statgen.research.bcm.edu/files/2016/01/cordell/data/cordell.tgz Download Data Sets] (decompress using "tar zxvf cordell.tgz")
====Nancy Cox/Eric Gamazon====
* Presentations
** [https://statgen.research.bcm.edu/files/2016/01/cox/presentations/Gene_Regulation_and_the_Genomics_of_Complex_Traits.pdf Gene Regulation and the Genomics of Complex Traits]
* Exercises
** [https://statgen.research.bcm.edu/files/2016/01/cox/data/cox.tgz Download Data Sets] (decompress using "tar zxvf cox.tgz")
====Suzanne Leal====
* Presentations
** [https://statgen.research.bcm.edu/files/2016/01/leal/presentations/data_quality_control_1_16_16_M2.pdf QC of Genotype Data]
** [https://statgen.research.bcm.edu/files/2016/01/leal/presentations/NGS_Data_Quality_Control_1_16_15_edited.pdf QC of NGS Data]
** [https://statgen.research.bcm.edu/files/2016/01/leal/presentations/analysis_rare_variants_1_18_16_edited.pdf Analysis of Rare Variant Data]
** [https://statgen.research.bcm.edu/files/2016/01/leal/presentations/power_analysis_rare_variants_1_18_16_T2.pdf Power Analysis]
* Exercises
** [https://statgen.research.bcm.edu/files/2016/01/leal/exercises/PLINK_data_QC_NYC_2016_M1pdf.pdf GWAS QC]
** [https://statgen.research.bcm.edu/files/2016/01/leal/exercises/GWAS_Data_SubstructureNYC_M2.pdf GWAS ASSOC MDS]
** [https://statgen.research.bcm.edu/files/2016/01/leal/exercises/GenABEL-Rockefeller_M3.pdf GenABEL]
** [https://statgen.research.bcm.edu/files/2016/01/leal/exercises/VAT-JAN2016NYC_T1.pdf VAT]
** [https://statgen.research.bcm.edu/files/2016/01/leal/exercises/Armitage_sample_size_NYC_2016_T_2.doc Armitage Power]
** [https://statgen.research.bcm.edu/files/2016/01/leal/exercises/SEQPower-JAN2016NYC_T3.pdf SEQPower]
** [https://statgen.research.bcm.edu/files/2016/01/leal/data/leal.tgz Download Data Sets] (decompress using "tar zxvf leal.tgz")
** [https://statgen.research.bcm.edu/files/2016/01/leal/data/ExAC.DB.gz Download ExAC Database] (decompress using "gzip -d ExAC.DB.gz")
* Commands
** [https://statgen.research.bcm.edu/files/2016/01/leal/commands/VAT_commands_JAN2016NYC.docx Variant Association Tools]
** [[AdvGeneMap2016Commands |GenABEL and GWAS Commands]]
====Shamil Sunyaev====
* Presentations
** [https://statgen.research.bcm.edu/files/2016/01/sunyaev/presentations/Population_Genetics.pdf Population Genetics]
** [https://statgen.research.bcm.edu/files/2016/01/sunyaev/presentations/Analysis_of_Complex_Traits.pdf Analysis of Complex Traits]
** [https://statgen.research.bcm.edu/files/2016/01/sunyaev/presentations/Mutation.pdf Mutation]
** [https://statgen.research.bcm.edu/files/2016/01/sunyaev/presentations/Functionally_Significant_Variants.pdf Functionally Significant Variants]
* Exercises
** [https://statgen.research.bcm.edu/files/2016/01/sunyaev/exercises/Bioinformatic_Tools_EX.pdf Bioinformatic Tools]
===Software===
* [http://sites.stat.psu.edu/~yuzhang/ BEAM3]
* [http://cassi.cas.org/ CASSI]
* [http://cnsgenomics.com/software/gcta/mlmassoc.html GCTA-MLMA]
* [http://www.genabel.org/ GenABEL]
* [http://genome.sph.umich.edu/wiki/GotCloud GotCloud]
* [https://cran.r-project.org/web/packages/ORMDR/index.html ORMDR]
* [http://csg.sph.umich.edu/abecasis/MACH/ MACH]
* [http://www.bios.unc.edu/research/genomic_software/Matrix_eQTL/ Matrix eQTL]
* [http://csg.sph.umich.edu/abecasis/metal/ METAL]
* [http://genome.sph.umich.edu/wiki/Minimac3 Minimac]
* [http://pngu.mgh.harvard.edu/~purcell/plink/ PLINK]
* [https://github.com/hakyimlab/PrediXcan PrediXCan]
* [https://www.r-project.org/ R]
* [http://genome.sph.umich.edu/wiki/RAREMETAL RareMetal]
* [http://genome.sph.umich.edu/wiki/RAREMETALWORKER RareMetalWorker]
* [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).