===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).
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 6, 2017===Course Photo===[[File:Rock_Course_Photo_2018.jpg|none|750x999px]]
[https://statgen.research.bcm.edu/files/2018/01/info/Application_Advanced_Gene_Mapping_Jan_2018.htm Click here for application form]
[https://statgen.research.bcm.edu/files/2018/01/info/Rockefeller_advanced_course_flyer_2018.pdf Click here for course flyer] – Please Post and Distribute
[https://statgen.research.bcm.edu/files/2018/01/info/adv_gene_mapping_schedule_2018.pdf Click here for course schedule]
===Lecture Handouts & Practical Exercises===
====Gonçalo 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]
* Data Sets
** [https://statgen.research.bcm.edu/files/2018/01/abecasis/exercises.tar.gz Download]
====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/2018/01/cordell/GxG_INTERACTION.tar.gz Download Dataset]
====Nancy Cox====
* Presentations
** [https://statgen.research.bcm.edu/files/2018/01/cox/GeneticArchitecture_Transcriptomics_Cox_2018.pdf Integrative Approaches for Genetic Studies of Common Human Disease - Genetic Architecture andTranscriptomics]
** [https://statgen.research.bcm.edu/files/2018/01/cox/DataIntegration_Cox_2018.pdf Integrative Approaches for Genetic Studies of Common Human Disease - Data Integration: Genome x Transcriptome x EHR]
====Suzanne Leal====
* Presentations
** [https://statgen.research.bcm.edu/files/2018/01/leal/Analysis_rare_variants_3.pdf Complex Trait Association Analysis of Rare Variants Obtained from Sequence Data: Population-Based Data]
** [https://statgen.research.bcm.edu/files/2018/01/leal/data_quality_control_1.pdf Data Quality Control]
** [https://statgen.research.bcm.edu/files/2018/01/leal/Trio_and_Family_Based_Association_analysis_4.pdf Family Base Association Analysis]
** [https://statgen.research.bcm.edu/files/2018/01/leal/NGS_variant_calling_QC_2.pdf NGS Quality Control]
** [https://statgen.research.bcm.edu/files/2018/01/leal/SEQSpark_5.pdf SEQSpark]
* 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
** [https://statgen.research.bcm.edu/files/2018/01/sunyaev/Rockefeller_pop_gen_2018_1_color.pdf Intro to population genetics]
** [https://statgen.research.bcm.edu/files/2018/01/sunyaev/Rockefeller_complex_traits_2018_2_color.pdf Evolution, maintenance and allelic architecture of complex traits]
** [https://statgen.research.bcm.edu/files/2018/01/sunyaev/Rockefeller_function_2018_3_color.pdf Annotating gene sequence variation]
** [https://statgen.research.bcm.edu/files/2018/01/sunyaev/Rockefeller_mutation_2018_4_color.pdf Understanding human mutation]
===Course Image===
[https://statgen.research.bcm.edu/files/2018/01/AdvancedGeneMapping.ova Download here]
This course is supported by a grant from the National Institute of Health (NIH) - National Human Genome Research Institute (NHGRI).