Difference between revisions of "Advgenemap2019"

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===More Information===
 
===More Information===
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The maximum number of participants is 30. The course will take place in the Great Hall in Welch at The Rockefeller University, Students will perform exercises by connecting to the cloud using their own laptops. Laptops are also available for students to use for the duration of the course. The course is wheelchair accessible. All disabilities will be accommodated. Handicapped individuals are encouraged to apply.
+
The maximum number of participants is 30. The course will take place in the Great Hall in Welch at The Rockefeller University, Students will perform exercises by connecting to the cloud using their own laptops. Laptops are also available for students to use for the duration of the course. The course is wheelchair 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.
 
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.
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Tel: +1 (713) 798-4011
 
Tel: +1 (713) 798-4011
  
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Application deadline is Monday, November 12, 2018
 
  
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[https://statgen.research.bcm.edu/files/2019/Application_Advanced_Gene_Mapping_Jan_2019.html Click here for application form]
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[http://statgen.us/files/2019/Rockefeller_advanced_course_flyer_2019.pdf Click here for course flyer] – Please Post and Distribute
  
−
[https://statgen.research.bcm.edu/files/2019/Rockefeller_advanced_course_flyer_2019.pdf Click here for course flyer] – Please Post and Distribute
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[http://statgen.us/files/2019/adv_gene_mapping_schedule_2019.pdf Click here for course schedule]
  
−
[https://statgen.research.bcm.edu/files/2019/adv_gene_mapping_schedule_2019.pdf Click here for course schedule]
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===Lecture Handouts===
 +
====Gonçalo Abecasis====
 +
* Presentations
 +
** [http://statgen.us/files/2019/01/slides/abecasis/00.%20Warm-up%20to%20Genomewide%20Analyses.pdf Genome-wide Analysis]
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** [http://statgen.us/files/2019/01/slides/abecasis/01.%20Genotype%20Imputation.pdf Genotype Imputation]
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** [http://statgen.us/files/2019/01/slides/abecasis/02.%20Meta-Analysis.pdf Meta Analysis]
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** [http://statgen.us/files/2019/01/slides/abecasis/03.%20Sequencing.pdf Sequencing]
 +
<!--
 +
* Data Sets
 +
** [http://statgen.us/files/2018/01/abecasis/exercises.tar.gz Download]
 +
-->
 +
 
 +
====Heather Cordell====
 +
* Presentations
 +
** [http://statgen.us/files/2019/01/slides/cordell/hjc-NY2016-GWAS-nopage.pdf Genome-wide Association Studies - case/control and family-based]
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** [http://statgen.us/files/2019/01/slides/cordell/hjc-NY2019-MixedModels-nopage.pdf Mixed Models and Family-Based Methods]
 +
* Exercises
 +
** [http://statgen.us/files/2019/01/slides/cordell/Computer%20Practical%20Exercise.pdf Family-based Association Analysis - FaST-LMM, PLINK and R]
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** [http://statgen.us/files/2019/01/slides/cordell/Computer%20Practical%20Exercise%202.pdf Mixed models Association Analysis Computer - GCTA, PLINK, and R]
 +
 
 +
====Nancy Cox====
 +
* Presentations
 +
** [http://statgen.us/files/2019/01/slides/cox/DataIntegration_Cox_Lecture2_NJC_2019.pdf Data Integration]
 +
 
 +
====Suzanne Leal====
 +
* Presentations
 +
** [http://statgen.us/files/2019/01/slides/leal/data_quality_control_1.pdf Data Quality Control]
 +
** [http://statgen.us/files/2019/01/slides/leal/NGS_data_qc.pdf NGS Data Quality Control]
 +
** [http://statgen.us/files/2019/01/slides/leal/analysis_rare_variants.pdf Complex Trait Association Analysis of Rare Variants]
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** [http://statgen.us/files/2019/01/slides/leal/Trio_and_Family_Based_Association_analysis_3_new_format.pdf Family Based Rare Variant Association Analysis: Trios, Sibpairs and Extended Families]
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** [http://statgen.us/files/2019/01/slides/leal/power_sample_sizes.pdf Power Analysis for Individual Variants and Rare Variant Aggregate Association Analysis]
 +
 
 +
====Shamil Sunyaev====
 +
* Presentations
 +
** [http://statgen.us/files/2019/01/slides/sunyaev/Rockefeller_polygenic_2019.pdf Genetic Risk Prediction]
 +
** [http://statgen.us/files/2019/01/slides/sunyaev/Rockefeller_complex_traits_2019.pdf Evolution, maintenance and allelic architecture of complex traits]
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** [http://statgen.us/files/2019/01/slides/sunyaev/Rockefeller_function_2019.pdf Annotating gene sequence variation]
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** [http://statgen.us/files/2019/01/slides/sunyaev/Rockefeller_pop_gen_2019.pdf Intro to population genetics]
 +
 
 +
===Practical Exercises===
 +
* [http://statgen.us/files/2019/01/exercise_booklet_1_24_19.pdf Exercise Booklet]
 +
 
 +
* [http://statgen.us/files/tutorials/gwas-qc/PLINK_data_QC_V2.pdf Genome-wide Association Analysis - Quality Control - PLINK]
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* [http://statgen.us/files/tutorials/gwas-substructure/GWAS_Data_Controlling_for_Substructure_V2.pdf Genome-wide Association Analysis - MDS and PCA – PLINK]
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* [http://statgen.us/files/tutorials/vat/VAT_exercise_2019_1_nographs.pdf Sequence data quality control and association analysis (VAT)]
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* [http://statgen.us/files/tutorials/pseq/PSEQ_exercise_2019.pdf Association Analysis of Sequence Data using PLINK/SEQ (PSEQ)]
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* [http://statgen.us/files/tutorials/rvtdt/rvtdt_exercise_v3.pdf Rare-Variant Transmission Disequilibrium Test (RV-TDT)]
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* [http://statgen.us/files/tutorials/Armitage_sample_size_revised.pdf Power and Sample Size Calculations – Cochran Armitage Test for Trend ]
 +
* [http://statgen.us/files/tutorials/functional-annotation/FunctionalAnnotation_exercise_2019.pdf Functional Annotation]
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* [http://csg.sph.umich.edu/abecasis/MaCH/tour/ MaCH]
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* [https://genome.sph.umich.edu/wiki/METAL_Quick_Start METAL]
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* [https://genome.sph.umich.edu/wiki/Tutorial:_RAREMETAL RAREMETAL]
 +
 
 +
===Exercise Data Sets===
 +
* [http://statgen.us/files/2019/01/datasets/Plink_DataQC.tar.gz Genome-wide Association Analysis - Quality Control - PLINK]
 +
* [http://statgen.us/files/2019/01/datasets/Plink_substructure.tar.gz Genome-wide Association Analysis - MDS and PCA – PLINK]
 +
* [http://statgen.us/files/2019/01/datasets/FASTLMMLGCTA.tar.gz Family-based Association Analysis- FaST-LMM, PLINK]
 +
* [http://statgen.us/files/2019/01/datasets/FASTLMMLGCTA.tar.gz Mixed models Association Analysis Computer – GCTA, PLINK and R]
 +
* [http://statgen.us/files/2019/01/datasets/Plink_DataQC.tar.gz Sequence data quality control and association analysis (VAT)]
 +
* [http://statgen.us/files/2019/01/datasets/pseq.tar.gz Association Analysis of Sequence Data using PLINK/SEQ (PSEQ)]
 +
* [http://statgen.us/files/2019/01/datasets/rvtdt.tar.gz Rare-Variant Transmission Disequilibrium Test (RV-TDT)]
 +
* [http://statgen.us/files/2019/01/datasets/FunctionalAnnotation.tar.gz Functional Annotation]
 +
* [http://statgen.us/files/2019/01/datasets/mach.tar.gz MaCH]
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* [http://statgen.us/files/2019/01/datasets/metal.tar.gz METAL]
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* [http://statgen.us/files/2019/01/datasets/raremetal.tar.gz RAREMETAL]
  
 
===Commands===
 
===Commands===
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:::* [[Family-based Association Exercise|Family-based Association Analysis- FaST-LMM, PLINK and R]]
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* [[Genome-wide Association-Quality Control Exercise|Genome-wide Association Analysis-Quality Control-PLINK]]
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:::* [[Mixed models Association Analysis_Exercise|Mixed models Association Analysis Computer – GCTA, PLINK and R]]
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* [[Genome-wide Association-MDS and PCA Exercise|Genome-wide Association Analysis-MDS and PCA-PLINK]]
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:::* [[Popgen_Exercise|Popgen]]
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* [[Family-based Association Exercise|Family-based Association Analysis- FaST-LMM, PLINK and R]]
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:::* [[PSEQ_Exercise|PSEQ]]
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* [[Mixed models Association Analysis_Exercise|Mixed models Association Analysis Computer – GCTA, PLINK and R]]
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:::* [[Regression_Exercise|Regression]]
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* [[VAT_Exercise|Sequence data quality control and association analysis (VAT)]]
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:::* [[RV-TDT_Exercise|RV-TDT]]
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* [[PSEQ_Exercise|Association Analysis of Sequence Data using PLINK/SEQ (PSEQ)]]
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:::* [[SEQPower_Exercise|SEQPower]]
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* [[RV-TDT_Exercise|Rare-Variant Transmission Disequilibrium Test (RV-TDT)]]
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:::* [[VAT_Exercise|VAT]]
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* [[Functional Annotation_Exercise|Functional Annotation]]
 +
 
 +
===Software===
 +
* [http://www.openbioinformatics.org/annovar/ ANNOVAR]
 +
* [https://github.com/MicrosoftGenomics/FaST-LMM FasT-LLM]
 +
* [https://cnsgenomics.com/software/gcta/ GCTA]
 +
* [https://genome.sph.umich.edu/wiki/MaCH MaCH]
 +
* [https://genome.sph.umich.edu/wiki/METAL METAL]
 +
* [https://genome.sph.umich.edu/wiki/Minimac Minimac]
 +
* [http://zzz.bwh.harvard.edu/plink/ PLINK]
 +
* [https://atgu.mgh.harvard.edu/plinkseq/ PLINK/SEQ]
 +
* [https://genome.sph.umich.edu/wiki/RAREMETAL RAREMETAL]
 +
* [[RV-TDT|RV-TDT]]
 +
* [http://bioinformatics.org/spower/ SEQPower]
 +
* [http://varianttools.sourceforge.net/ Variant Association Tools]
  
 
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 19:01, 20 May 2019

Advanced Gene Mapping Course

The Rockefeller University, New York
Welch – The Great Hall
Monday through Friday, January 28-February 1, 2019

General Information

An advanced gene mapping course will be held in New York from Monday through Friday, January 28-February 1 2019. The cost of the 5-day course is $100 for student, academic and government researchers and $2,800 for researchers working in industry. This fee covers tuition and course-related expenses (handouts, etc.) but not room and board.

The course emphasis is on the 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 prediction 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 Goncalo 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, Students will perform exercises by connecting to the cloud using their own laptops. Laptops are also available for students to use for the duration of the course. The course is wheelchair 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 the 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 flyer – Please Post and Distribute

Click here for course schedule

Lecture Handouts

Gonçalo Abecasis

Heather Cordell

Nancy Cox

Suzanne Leal

Shamil Sunyaev

Practical Exercises

Exercise Data Sets

Commands

Software

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

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