==Course Instructors==
The instructors for the course are Heather Cordell (University of Newcastle), Nancy Cox (Vanderbilt University), Andrew DeWan (Yale University), Suzanne Leal (The Rockefeller University & Columbia University), [http://www.fas.harvard.edu/~biophys/Shamil_Sunyaev.htm Shamil Sunyaev] (Harvard University) & Gao Wang (Columbia University). Judy Matuk (HRP Consulting Group) will lecture on ethics and the regulation of human subject research. A special guest lecture will be given by Jurg Ott (Rockefeller University).
==Additional Information==
[http://statgen.us/files/2021/02/Rockefeller_advanced_course_flyer_2021.pdf Click here for course flyer] (please post and distribute)
==Course Photo - 2020==[[Filehttps:142FBA93//github.com/statgenetics/statgen-B26Fcourses/wiki/How-45A4to-A0C5launch-264B812AB558.JPG|thumb|none|300px]course-tutorials How to run the exercises]=====Handouts==
===Heather Cordell===
[http://www.statgen.us/files/2021/02/bios/about_HJC.pdf About Heather Cordell]
====Lectures====
* [http://statgen.us/files/2021/02/lectures/NY2021-lecture1-nopause.pdf Genome-wide association studies - Part 1]
* [http://statgen.us/files/2021/02/lectures/NY2021-lecture2-nopause.pdf Genome-wide association studies - Part 2]
====Exercises====
* [http://statgen.us/files/2021/02/exercises/FASTLMM-NY2020.pdf Family-based Association using FaST-LMM, PLINK and R]
* [http://statgen.us/files/2021/02/exercises/GCTA-NY2021.pdf GCTA]
* [http://statgen.us/files/2021/02/exercises/Epistasis-NY2020.pdf Interaction analysis using PLINK and CASSI]
===Nancy Cox===
[http://statgen.us/files/2021/02/bios/about_njc.pdf about Nancy Cox]
====Lectures====
[http://statgen.us/files/2021/02/lectures/LealCourse_Cox_Jan2021.pdf Integrative Approaches in Biobanks: Getting to Biological Mechanisms of Disease]
===Andrew DeWan===
[http://www.statgen.us/files/2021/02/bios/about_atd.pdf About Andy DeWan]
====Lecture====
* [http://statgen.us/files/2021/02/lectures/DeWan_Adv_Gene_Mapping_Mendelian%20Randomization.pdf Mendelian randomization]
* [http://statgen.us/files/2021/02/lectures/Rockefeller_Adv_Course_DeWan_pleiotropy.pdf Pleiotropy]
====Exercises====
* [http://statgen.us/files/2021/02/exercises/pleio_exercise.pdf Pleiotropy]
* [http://statgen.us/files/2021/02/exercises/pleio_exercise_answers.pdf Answers to Pleitropy Exercise]
* [http://statgen.us/files/2021/02/exercises/MR_exercise.pdf Mendelian Randomization]
* [http://www.statgen.us/files/2021/02/exercises/MR_exercise_answers.pdf Mendelian Randomization Answers]
===Suzanne Leal===
[http://www.statgen.us/files/2021/02/bios/about_sml.pdf About Suzanne Leal]
====Lectures====
* [http://statgen.us/files/2021/02/lectures/data_quality_control_1.pdf Data Quality Control]
* [http://statgen.us/files/2021/02/lectures/NGS_data_qc.pdf NGS Data Quality Control]
* [http://statgen.us/files/2021/02/lectures/analysis_rare_variants_part_1.pdf Complex Trait Association Analysis of Rare Variants Obtained from Sequence Data: Population-Based Data]
* [http://statgen.us/files/2021/02/lectures/power_sample_sizes.pdf Power Analysis for Single and Rare Variant Aggregate Association Analyses]
====Exercises====
* [http://statgen.us/files/2021/02/exercises/PSEQ_exercise.pdf PLINK/SEQ (PSEQ)]
* [http://statgen.us/files/2021/02/exercises/VAT_2021.pdf Association Analysis of Sequence Data using Variant Association Tools for Complex Traits]
* [http://statgen.us/files/2021/02/exercises/Armitage_sample_size.pdf Cochran Armitage Trend Test for GWAS power analysis]
* [http://statgen.us/files/2021/02/exercises/FunctionalAnnotation.2021.pdf ANNOVAR Annotation]
* [http://statgen.us/files/2021/02/exercises/GWAS_Data_Controlling_for_Substructure_V2.pdf Genome-Wide Association - Association Analysis Controlling for Population Substructure]
* [http://statgen.us/files/2021/02/exercises/PLINK_data_QC_V2.pdf Genome-Wide Association Analysis - Data Quality Control]
===Judy Matuk===
[http://www.statgen.us/files/2021/02/bios/about_jm.pdf About Judy Matuk]
====Lectures====
* [http://statgen.us/files/2021/02/lectures/Rockefeller_draft_HSR%20Ethics%20and%20Regulations%20PPT_%20jm%201.18.2021.pdf Human Subject Training]
===Jurg Ott===
[http://www.statgen.us/files/2021/02/bios/about_jo.pdf About Jurg Ott]
====Lectures====
[http://www.statgen.us/files/2021/02/lectures/FPMforInteractions2021-01.pptx Frequent Pattern Mining Methods for Finding SNP-SNP Interactions]
===Shamil Sunyaev===
[http://www.statgen.us/files/2021/02/bios/about_ss.pdf About Shamil Sunyaev]
====Exercises====
* [http://statgen.us/files/2021/02/exercises/NPS.pdf Polygenic risk prediction using non-parametric shrinkage] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/nps.dockerfile dockerfile] and [https://hub.docker.com/r/statisticalgenetics/nps/tags docker image]
====Lectures====
* [http://statgen.us/files/2021/02/lectures/Rockefeller_complex_traits_2021.pdf Complex Traits]
* [http://statgen.us/files/2021/02/lectures/Rockefeller_functional_annotation_2021.pdf Functional Annotation]
* [http://statgen.us/files/2021/02/lectures/Rockefeller_polygenic_risk_score_2021.pdf Polygenic Risk Score]
* [http://statgen.us/files/2021/02/lectures/Rockefeller_population_genetics_2021.pdf Population Genetics]
===Gao Wang===
[http://www.statgen.us/files/2021/02/bios/about_gw.pdf About Gao Wang]
====Lectures====
* [http://statgen.us/files/2021/02/lectures/Lecture_Univariate_Fine_Mapping.pdf Statistical fine-mapping]
* [http://statgen.us/files/2021/02/lectures/Lecture_Multivariate_Analysis.pdf Multivariate analysis]
====Exercises====
* [https://github.com/statgenetics/statgen-courses/raw/master/handout/finemapping.docx Statistical fine-mapping in association studies] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/finemap.dockerfile dockerfile] and [https://hub.docker.com/r/statisticalgenetics/finemap/tags docker image]
* [https://github.com/statgenetics/statgen-courses/raw/master/handout/finemapping_answers.docx Answers to fine-mapping exercise questions]
This course is supported by a grant from the National Institute of Health (NIH) - National Human Genome Research Institute (NHGRI).
===Dan Zhou===
[http://www.statgen.us/files/2021/02/bios/about_dz.pdf About Dan Zhou]
====Computer Demonstration====
* [http://statgen.us/files/2021/02/lectures/MR-JTI.pdf MR-JTI: a framework for Joint Tissue Imputation-based TWAS and Mendelian Randomization]