Difference between revisions of "2015AdvancedGeneMapping"

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(Shamil Sunyaev)
 
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====Ben Neale====
 
====Ben Neale====
 
* Presentations
 
* Presentations
* [http://statgen.us/files/2015/02/neale/handouts/Neale_Rockefeller_course_2015.pdf Neale lectures combined]
+
** [http://statgen.us/files/2015/02/neale/handouts/Neale_Rockefeller_course_2015.pdf Neale lectures combined]
 
* Exercises
 
* Exercises
 
** [http://statgen.us/files/2015/02/neale/exercises/neale.tar.bz2 Download Data Sets] (decompress using "tar jxvf neale.tar.bz2")
 
** [http://statgen.us/files/2015/02/neale/exercises/neale.tar.bz2 Download Data Sets] (decompress using "tar jxvf neale.tar.bz2")
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====Shamil Sunyaev====
 
====Shamil Sunyaev====
 
* Presentations
 
* Presentations
** [http://statgen.us/files/201501/sunyaev/handouts/Rockefeller_pop_gen_2014.pdf Population genetics]
+
** [http://statgen.us/files/2015/02/sunyaev/handouts/Rockefeller_pop_gen_2014.pdf Population genetics]
** [http://statgen.us/files/201501/sunyaev/handouts/Rockefeller_mutation_2015.pdf Mutation]
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** [http://statgen.us/files/2015/02/sunyaev/handouts/Rockefeller_mutation_2015.pdf Mutation]
** [http://statgen.us/files/201501/sunyaev/handouts/Rockefeller_complex_traits_2015.pdf Complex traits]
+
** [http://statgen.us/files/2015/02/sunyaev/handouts/Rockefeller_complex_traits_2015.pdf Complex traits]
 
* Exercises
 
* Exercises
** [http://statgen.us/files/201501/sunyaev/handouts/Rockefeller_tutorial.pdf Annotation tutorial]
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** [http://statgen.us/files/2015/02/sunyaev/handouts/Rockefeller_tutorial.pdf Annotation tutorial]
  
 
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===Data-sets Used During the Course===
 
===Data-sets Used During the Course===
* [http://statgen.us/files/201501/exercises/cordell.tar.bz2 Heather Cordell's Data Sets]
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* [http://statgen.us/files/2015/02/cordell/exercises/cordell.tar.bz2 Heather Cordell's Data Sets]
* [http://statgen.us/files/201501/exercises/francioli.tar.bz2 Laurent Francioli's Data Sets]
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* [http://statgen.us/files/2015/02/francioli/exercises/francioli.tar.bz2 Laurent Francioli's Data Sets]
* [http://statgen.us/files/201501/exercises/leal.tar.bz2 Suzanne Leal's Data Sets]
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* [http://statgen.us/files/2015/02/leal/exercises/leal.tar.bz2 Suzanne Leal's Data Sets]
* [http://statgen.us/files/201501/exercises/neale.tar.bz2 Ben Neale's Data Sets]
+
* [http://statgen.us/files/2015/02/neale/exercises/neale.tar.bz2 Ben Neale's Data Sets]
  
 
In order to obtain a particular data set, please follow the following steps:
 
In order to obtain a particular data set, please follow the following steps:
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# Change to this subdirectory (''cd'' command) and proceed with the exercise.
 
# Change to this subdirectory (''cd'' command) and proceed with the exercise.
 
-->
 
-->
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===Software===
 
===Software===
 
* [http://annovar.openbioinformatics.org/en/latest/ ANNOVAR]
 
* [http://annovar.openbioinformatics.org/en/latest/ ANNOVAR]

Latest revision as of 15:09, 7 June 2016

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

Laurent Francioli

Suzanne Leal

Ben Neale

Shamil Sunyaev


Software

Links


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