Difference between revisions of "Advgenemap2017"

From Statistical Genetics Courses

Jump to: navigation, search
(Created page with "__NOTITLE__ ==Advanced Gene Mapping Course== The Rockefeller University, New York<br />Welch – The Great Hall<br />Monday through Friday, January 23-27, 2017 ===General In...")
 
(→‎Heather Cordell)
 
(29 intermediate revisions by the same user not shown)
Line 26: Line 26:
 
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
 
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
  
−
Application deadline is Monday, November 11, 2016
+
<!--Application deadline is Friday, November 18, 2016-->
 +
<!--[https://statgen.research.bcm.edu/files/2017/01/Application_Advanced_Gene_Mapping_Jan_2017.htm Click here for application form]-->
 +
<!--[https://statgen.research.bcm.edu/files/2017/01/Rockefeller_advanced_course_flyer_2017.pdf Click here for course flyer] – Please Post and Distribute-->
 +
[https://statgen.research.bcm.edu/files/2017/01/adv_gene_mapping_schedule_2017.pdf Click here for course schedule]
 +
===Course Participants===
 +
[[File:2017-01_Participants.jpg|none|427x200px]]
  
−
[https://statgen.research.bcm.edu/files/2017/01/Application_Advanced_Gene_Mapping_Jan_2017.htm Click here for application form]
+
===Lecture Handouts & Practical Exercises===
 +
====Gon&ccedil;alo Abecasis====
 +
* Presentations
 +
** [https://statgen.research.bcm.edu/files/2017/01/abecasis/presentation/Genome-wide_Analysis.pdf Genome-wide Analysis]
 +
** [https://statgen.research.bcm.edu/files/2017/01/abecasis/presentation/Genotype_Imputation.pdf Genotype Imputation]
 +
** [https://statgen.research.bcm.edu/files/2017/01/abecasis/presentation/Meta_Analysis.pdf Meta Analysis]
 +
** [https://statgen.research.bcm.edu/files/2017/01/abecasis/presentation/Sequence_Data.pdf Sequence Data]
  
−
[https://statgen.research.bcm.edu/files/2017/01/Rockefeller_advanced_course_flyer_2017.pdf Click here for course flyer] – Please Post and Distribute
+
====Heather Cordell====
 +
* Presentations
 +
** [https://statgen.research.bcm.edu/files/2017/01/cordell/hjc-NY2016-GWAS-nopage.pdf Statistical Methods]
 +
** [https://statgen.research.bcm.edu/files/2017/01/cordell/HJC-interactions2017-nopage.pdf Interactions]
 +
* Exercises
 +
** [https://statgen.research.bcm.edu/files/2017/01/cordell/hjc-epistasis2015-ComputerPractical.pdf Interaction analysis using PLINK, CASSI, ORMDR and BEAM3]
 +
** [https://statgen.research.bcm.edu/files/2017/01/cordell/cordell.tar.bz2 Download Data Sets] (decompress using "tar jxvf cordell.tar.bz2")
 +
 
 +
====Nancy Cox====
 +
* [http://statgen.us/files/2017/01/cox/Cox_NewYork_talks.pdf Presentation]
 +
* [http://statgen.us/files/2017/01/cox/ClassTutorial.docx Exercise]
 +
 
 +
====Suzanne Leal====
 +
* Presentations
 +
** [https://statgen.research.bcm.edu/files/2017/01/leal/presentation/data_quality_control_M2.pdf QC of Genotype Data]
 +
** [https://statgen.research.bcm.edu/files/2017/01/leal/presentation/NGS%20Data%20Quality%20Control_M3.pdf QC of NGS Data]
 +
** [https://statgen.research.bcm.edu/files/2017/01/leal/presentation/analysis_rare_variants_part_1.pdf Analysis of Rare Variant Data - Part 1]
 +
** [https://statgen.research.bcm.edu/files/2017/01/leal/presentation/analysis_of_rare_variants_part_2.pdf Analysis of Rare Variant Data - Part 2]
 +
** [https://statgen.research.bcm.edu/files/2017/01/leal/presentation/power_analysis_rare_variants_T2.pdf Power Analysis]
 +
* Exercises
 +
** [https://statgen.research.bcm.edu/files/2017/01/leal/docs/PLINK_data_QC_M1.pdf GWAS QC]
 +
** [https://statgen.research.bcm.edu/files/2017/01/leal/docs/GWAS_Data_Controlling_for_Substructure_M2.pdf GWAS ASSOC MDS]
 +
** [https://statgen.research.bcm.edu/files/2017/01/leal/docs/GenABEL-Rockefeller_M_3.pdf GenABEL]
 +
** [https://statgen.research.bcm.edu/files/2017/01/leal/docs/22-1-VAT-JAN2016NYC_T1.pdf VAT]
 +
** [https://statgen.research.bcm.edu/files/2017/01/leal/docs/Armitage_sample_size_NYC_2017_T_2.pdf Armitage Power]
 +
** [https://statgen.research.bcm.edu/files/2017/01/leal/docs/22-3-SEQPower-JAN2016NYC_T3.pdf SEQPower]
 +
** [https://statgen.research.bcm.edu/files/2017/01/leal/data/leal.tar.bz2 Download Data Sets] (decompress using "tar jxvf leal.tar.bz2")
 +
** [https://statgen.research.bcm.edu/files/2017/01/leal/data/ExAC.DB.bz2 Download ExAC Database] (decompress using "bzip2 -d ExAC.DB.bz2")
 +
* Commands
 +
** [[AdvGeneMap2017Commands |GenABEL, GWAS and VAT Commands]]
 +
 
 +
====Shamil Sunyaev====
 +
* Presentations
 +
** [http://statgen.us/files/2017/01/sunyaev/Rockefeller_complex_traits_2017_six_per_page.pdf Evolution, maintenance and allelic architecture of complex traits]
 +
** [http://statgen.us/files/2017/01/sunyaev/Rockefeller_function_2017_six_per_page.pdf Annotating Gene Sequence Variation]
 +
** [http://statgen.us/files/2017/01/sunyaev/Rockefeller_pop_gen_2017_six_per_page.pdf Population Genetics]
 +
* Exercises
 +
** [http://statgen.us/files/2017/01/sunyaev/Rockefeller_tutorial.pdf hypertriglyceridemia example]
 +
** [http://genetics.bwh.harvard.edu/wiki/sunyaevlab/jlim Joint Likelihood Mapping]
 +
** [http://genetics.bwh.harvard.edu/pines PINES]
 +
 
 +
===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]
  
−
[https://statgen.research.bcm.edu/files/2017/01/adv_gene_mapping_schedule_2017.pdf Click here for course schedule]
 
  
 
This course is supported by a grant from the National Institute of Health (NIH) - National Human Genome Research Institute (NHGRI).
 
This course is supported by a grant from the National Institute of Health (NIH) - National Human Genome Research Institute (NHGRI).

Latest revision as of 03:30, 12 January 2018

Advanced Gene Mapping Course

The Rockefeller University, New York
Welch – The Great Hall
Monday through Friday, January 23-27, 2017

General Information

An advanced gene mapping course will be held in New York from Monday through Friday January 23-27, 2017. 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 BEAM3, GERP, GotCloud, GenAbel, Matrix-eQTL, PLINK, PrediXCan, 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: Gonçalo Abecasis (University of Michigan), Heather Cordell (University of Newcastle), Nancy Cox (Vanderbilt University), Suzanne Leal (The Rockefeller University & Baylor College of Medicine), and 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 Katherine Montague:
email: montagk@rockefeller.edu
Tel: +1 (212) 327-7979


For additional information on scientific program contact the course organizer Suzanne Leal:
email: sleal@bcm.edu or suzannemleal@gmail.com
Tel: +1 (713) 798-4011

Click here for course schedule

Course Participants

2017-01 Participants.jpg

Lecture Handouts & Practical Exercises

Gonçalo Abecasis

Heather Cordell

Nancy Cox

Suzanne Leal

Shamil Sunyaev

Software

Links


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

Retrieved from "http://statgen.us/index.php?title=Advgenemap2017&oldid=405"