Tel: +1 (713) 798-4011
Application deadline is Monday, November 12, 2018
[httpshttp://statgen.research.bcm.eduus/files/2019/Application_Advanced_Gene_Mapping_Jan_2019Rockefeller_advanced_course_flyer_2019.html pdf Click here for application formcourse flyer]– Please Post and Distribute
[httpshttp://statgen.research.bcm.edu/files/2019/Rockefeller_advanced_course_flyer_2019.pdf Click here for course flyer] – Please Post and Distribute [https://statgen.research.bcm.eduus/files/2019/adv_gene_mapping_schedule_2019.pdf Click here for course schedule]
===Lecture Handouts===
====Gonçalo Abecasis====
* Presentations
** [httpshttp://statgen.research.bcm.eduus/files/2019/01/slides/abecasis/00.%20Warm-up%20to%20Genomewide%20Analyses.pdf Genome-wide Analysis]** [httpshttp://statgen.research.bcm.eduus/files/2019/01/slides/abecasis/01.%20Genotype%20Imputation.pdf Genotype Imputation]** [httpshttp://statgen.research.bcm.eduus/files/2019/01/slides/abecasis/02.%20Meta-Analysis.pdf Meta Analysis]** [httpshttp://statgen.research.bcm.eduus/files/2019/01/slides/abecasis/03.%20Sequencing.pdf Sequencing]
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* Data Sets
** [httpshttp://statgen.research.bcm.eduus/files/2018/01/abecasis/exercises.tar.gz Download]
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====Heather Cordell====
* Presentations
** [httpshttp://statgen.research.bcm.eduus/files/2019/01/slides/cordell/hjc-NY2016-GWAS-nopage.pdf Genome-wide Association Studies - case/control and family-based]** [httpshttp://statgen.research.bcm.eduus/files/2019/01/slides/cordell/hjc-NY2019-MixedModels-nopage.pdf Mixed Models and Family-Based Methods]
* Exercises
** [httpshttp://statgen.research.bcm.eduus/files/2019/01/slides/cordell/Computer%20Practical%20Exercise.pdf Family-based Association Analysis - FaST-LMM, PLINK and R]** [httpshttp://statgen.research.bcm.eduus/files/2019/01/slides/cordell/Computer%20Practical%20Exercise%202.pdf Mixed models Association Analysis Computer - GCTA, PLINK, and R]
====Nancy Cox====
* Presentations
** [httpshttp://statgen.research.bcm.eduus/files/2019/01/slides/cox/DataIntegration_Cox_Lecture2_NJC_2019.pdf Data Integration]
====Suzanne Leal====
* Presentations
** [httpshttp://statgen.research.bcm.eduus/files/2019/01/slides/leal/data_quality_control_1.pdf Data Quality Control]** [httpshttp://statgen.research.bcm.eduus/files/2019/01/slides/leal/NGS_data_qc.pdf NGS Data Quality Control]** [httpshttp://statgen.research.bcm.eduus/files/2019/01/slides/leal/analysis_rare_variants.pdf Complex Trait Association Analysis of Rare Variants]** [httpshttp://statgen.research.bcm.eduus/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]** [httpshttp://statgen.research.bcm.eduus/files/2019/01/slides/leal/power_sample_sizes.pdf Power Analysis for Individual Variants and Rare Variant Aggregate Association Analysis]
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* Exercises
** [https://statgen.research.bcm.edu/files/2018/01/leal/PLINK_data_QC_V2_1.pdf PLINK GWAS Data QC]
** [https://statgen.research.bcm.edu/files/2018/01/leal/GWAS_Data_Controlling_for_Substructure_V2_2.pdf PLINK GWAS Association Analysis Controlling for Population Substructure]
** [https://statgen.research.bcm.edu/files/2018/01/leal/GenABEL_with_PLINK1.9_3.pdf GenABEL]
** [https://statgen.research.bcm.edu/files/2018/01/leal/rvtdt_exercise_v2.pdf RV-TDT]
** [https://statgen.research.bcm.edu/files/2018/01/leal/FunctionalAnnotation_exercise_2018v2.pdf Functional Annotation]
** [https://statgen.research.bcm.edu/files/2018/01/leal/SEQSpark_exercise_Final_v1.pdf SEQSpark]
** [https://statgen.research.bcm.edu/files/2018/01/leal/VAT_exercise_revised_nographs.pdf VAT]
* Commands
** [[AdvGeneMap2018Commands|Exercise Commands]]
* Exercise Datasets
** [https://statgen.research.bcm.edu/files/2018/01/leal/exercises.tar.gz Download]
-->
====Shamil Sunyaev====
* Presentations
** [httpshttp://statgen.research.bcm.eduus/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]** [http://statgen.us/files/2019/01/slides/sunyaev/Rockefeller_function_2019.pdf Annotating gene sequence variation]** [http://statgen.us/files/2019/01/slides/sunyaev/Rockefeller_pop_gen_2019.pdf Intro to population genetics]
===Practical Exercises===
* [httpshttp://statgen.research.bcm.eduus/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]
===Exercise Data Sets===
* [httpshttp://statgen.research.bcm.eduus/files/2019/01/datasets/Plink_DataQC.tar.gz Genome-wide Association Analysis - Quality Control - PLINK]* [httpshttp://statgen.research.bcm.eduus/files/2019/01/datasets/Plink_substructure.tar.gz Genome-wide Association Analysis - MDS and PCA – PLINK]* [httpshttp://statgen.research.bcm.eduus/files/2019/01/datasets/FASTLMMLGCTA.tar.gz Family-based Association Analysis- FaST-LMM, PLINK]* [httpshttp://statgen.research.bcm.eduus/files/2019/01/datasets/FASTLMMLGCTA.tar.gz Mixed models Association Analysis Computer – GCTA, PLINK and R]* [httpshttp://statgen.research.bcm.eduus/files/2019/01/datasets/Plink_DataQC.tar.gz Sequence data quality control and association analysis (VAT)]* [httpshttp://statgen.research.bcm.eduus/files/2019/01/datasets/pseq.tar.gz Association Analysis of Sequence Data using PLINK/SEQ (PSEQ)]* [httpshttp://statgen.research.bcm.eduus/files/2019/01/datasets/rvtdt.tar.gz Rare-Variant Transmission Disequilibrium Test (RV-TDT)]* [httpshttp://statgen.research.bcm.eduus/files/2019/01/datasets/FunctionalAnnotation.tar.gz Functional Annotation]* [httpshttp://statgen.research.bcm.eduus/files/2019/01/datasets/mach.tar.gz MaCH]* [httpshttp://statgen.research.bcm.eduus/files/2019/01/datasets/metal.tar.gz METAL]* [httpshttp://statgen.research.bcm.eduus/files/2019/01/datasets/raremetal.tar.gz RAREMETAL]
===Commands===