==General Information==
An Advanced Gene Mapping course will be held in online from Monday through Friday, January 2725-3129, 20202021. The cost of the 5-day course is $100 for student, academic, and government researchers and $1,500 for researchers working in industry. This fee covers tuition and course-related expenses (cloud computing, etc.).
The course emphasis is on analyzing sequence and other omics data to elucidate the genetic etiology of complex human disease traits. Topics will include: data quality control of sequence and other types of data; single variant and aggregate rare variant association analysis of whole-genome data (genotype, sequence, and imputed) for qualitative and quantitative traits (population and family-based data); controlling for population admixture and substructure; generalized linear mix models and linear mixed models; meta-analysis; sample size estimation and power calculations; detecting gene x gene and gene x environmental interactions; analysis of epigenomic data, e.g methylation, and chromatin; heritability estimation using variant and RNA-Seq data; analysis of RNA-Seq data; eQTL mapping; elucidating pleiotropy; functional prediction and variant annotation; estimation of polygenic risk scores; Mendelian randomization; mediation analysis; and fine mapping.''' '''As mandated by the NIH there will also be a special session on responsible conduct of research that will include sessions on conflict of interest, research ethics, data management (security), and ethical use of human research subjects.
==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).
==More Additional Information==The maximum number of participants for this online course is 2534.
Knowledge genetic association analysis, genetic epidemiology and/or statistical genetics are screening criteria for the selection of participants. Please describe your experience in detail in your application. It is helpful if you also enclose a copy of your CV. We may contact you personally to discuss your application. Although 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 [mailto:montagk@rockefeller.edu?subject=Rockefeller Advanced Gene Mapping Course 2021 Katherine Montague]: <br />email: [mailto:montagk@rockefeller.edu montagk@rockefeller.edu] <br /><br />
For additional information on the scientific program contact the course organizer [mailto:suzannemleal@gmail.com?subject=Rockefeller Advanced Gene Mapping Course 2021 Suzanne Leal]: <br />email: [mailto:suzannemleal@gmail.com suzannemleal@gmail.com] or [mailto:sml3@cumc.columbia.edu sml3@cumc.columbia.edu]
==Course Photo - 2020==
[[File:142FBA93-B26F-45A4-A0C5-264B812AB558.JPG|thumb|none|300px]]
Applications are no longer being accepted.
[http://statgen.us/files/2021/02/adv_gene_mapping_schedule_2021.pdf Click here for course schedule]
[http://statgen.us/files/2021/02/Application_Advanced_Gene_Mapping_Course_2021_New_York.html Click here for the application form]
[http://statgen.us/files/2021/02/Rockefeller_advanced_course_flyer_2021.pdf Click here for course flyer] (please post and distribute)
===[https://github.com/statgenetics/statgen-courses/wiki/How-to-launch-course-tutorials How to run the exercises]===
==Handouts==
====[//www.statgen.us/files/2020/01/docs/lectures/Lecture_booklet.pdf All Lectures]====
====[//www.statgen.us/files/2020/01/docs/exercises/Booklet_exercises.pdf All Exercises]====
===Heather Cordell===
[http://www.statgen.us/files/2021/02/bios/about_HJC.pdf About Heather Cordell]
====Lectures====
* [http://www.statgen.us/files/20202021/01/docs02/lectures/NY2020NY2021-lecture1-nopause_4nopause.pdf Genome-wide association studies (GWAS) - Part 1]* [http://www.statgen.us/files/2020/012021/docs02/lectures/NY2020NY2021-lecture2-nopause_4nopause.pdf Genome-wide association studies (GWAS) - Part 2]
====Exercises====
* [[Tutorials#FastLMM | http://statgen.us/files/2021/02/exercises/FASTLMM-NY2020.pdf Family-based Association using FaST-LMM, PLINK and R]] | * [httpshttp://githubstatgen.comus/statgeneticsfiles/statgen-courses2021/blob02/masterexercises/docker/fastlmmGCTA-gctaNY2021.dockerfile dockefile] and [https://hub.docker.com/r/statisticalgenetics/fastlmm-gcta/tags docker imagepdf GCTA]* [[Tutorials#GCTA|GCTA]] | [httpshttp://github.com/statgenetics/statgen-courses/blob/master/docker/fastlmm-gcta.dockerfile dockefile] and [https:us/files/hub.docker.com2021/r02/statisticalgeneticsexercises/fastlmmEpistasis-gcta/tags docker image]* [[Tutorials#Epistasis_NY2020.28PLINK_and_CASSI.29 | pdf Interaction analysis using PLINK and CASSI]] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/epistasis.dockerfile dockerfile] and [https://hub.docker.com/r/statisticalgenetics/epistasis/tags docker image]
===Nancy Cox===
[http://statgen.us/files/2021/02/bios/about_njc.pdf about Nancy Cox]
====Lectures====
* [http://www.statgen.us/files/2020/012021/docs02/lectures/LealCourse_Cox_Jan2020LealCourse_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] ====LecturesLecture====* [http://www.statgen.us/files/20202021/02/lectures/DeWan_Adv_Gene_Mapping_Mendelian%20Randomization.pdf Mendelian randomization]* [http://statgen.us/files/012021/docs02/lectures/Rockefeller_Adv_Course_DeWan_pleiotropy_4Rockefeller_Adv_Course_DeWan_pleiotropy.pdf From cross-phenotype associations to pleiotropy in human genetic studiesPleiotropy]
====Exercises====
* [[Tutorials#Pleiotropy|http://statgen.us/files/2021/02/exercises/pleio_exercise.pdf Pleiotropy]] | * [httpshttp://githubstatgen.comus/files/2021/02/exercises/pleio_exercise_answers.pdf Answers to Pleitropy Exercise]* [http:/statgenetics/statgen-courses.us/blobfiles/master2021/docker02/pleiotropyexercises/MR_exercise.dockerfile dockefilepdf Mendelian Randomization] and * [httpshttp://hubwww.dockerstatgen.comus/rfiles/statisticalgenetics2021/pleiotropy02/tags docker imageexercises/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://www.statgen.us/files/2020/012021/docs02/lectures/data_quality_control_1.pdf Data Quality Control]* [http://www.statgen.us/files/20202021/01/docs02/lectures/NGS_data_qc.pdf NGS Data Quality Control]* [http://www.statgen.us/files/20202021/01/docs02/lectures/analysis_rare_variants_part_1.pdf Complex Trait Association Analysis of Rare VariantsObtained from Sequence Data: Population-Based Data]* [http://www.statgen.us/files/2020/012021/docs02/lectures/power_sample_sizes.pdf Power Analysis for Single and Rare Variant Aggregate Association Analyses]* [//www.statgen.us/files/2020/01/docs/lectures/Analysis_rare_variants_part_2.pdf National Heart Lung and Blood Institute Exome Sequencing Project]
====Exercises====
* [[Tutorials#PSEQ|PLINK/SEQ (PSEQ)]] | [httpshttp://githubstatgen.comus/statgeneticsfiles/statgen-courses2021/blob02/masterexercises/docker/pseqPSEQ_exercise.dockerfile dockefilepdf PLINK/SEQ (PSEQ)] and * [httpshttp://hub.dockerstatgen.comus/rfiles/statisticalgenetics2021/pseq02/tags docker image]* [[Tutorials#Variant_Association_Tools|exercises/VAT_2021.pdf Association Analysis of Sequence Data using Variant Association Tools for Complex Traits]] | * [httpshttp://githubstatgen.comus/statgeneticsfiles/statgen-courses2021/blob02/masterexercises/docker/vatArmitage_sample_size.dockerfile dockerfilepdf Cochran Armitage Trend Test for GWAS power analysis] and * [httpshttp://hub.dockerstatgen.comus/rfiles/statisticalgenetics2021/vat02/tags docker imageexercises/FunctionalAnnotation.2021.pdf ANNOVAR Annotation]* [[Tutorials#Cochran_Armitage_Trend_Test|Cochran Armitage Trend Test http://statgen.us/files/2021/02/exercises/GWAS_Data_Controlling_for_Substructure_V2.pdf Genome-Wide Association - Association Analysis Controlling for GWAS power analysis]Population Substructure]* [[Tutorials#Annotation|ANNOVAR Annotation]] | [httpshttp://githubstatgen.comus/statgeneticsfiles/statgen-courses2021/blob02/masterexercises/docker/annovarPLINK_data_QC_V2.dockerfile dockefilepdf Genome-Wide Association Analysis - Data Quality Control] and ===Judy Matuk===[httpshttp://hubwww.dockerstatgen.comus/rfiles/statisticalgenetics2021/annovar02/tags docker imagebios/about_jm.pdf About Judy Matuk]
===Bogdan Pasanuic===
====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/20202021/0102/docsbios/lectures/finemapping_pasaniucabout_jo.pdf Statistical fine-mapping of GWAS signalsAbout Jurg Ott]<!--====ExercisesLectures====* finemap[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://www.statgen.us/files/2020/012021/docs02/lectures/Rockefeller_pop_gen_2020Rockefeller_complex_traits_2021.pdf Population GeneticsComplex Traits]* [http://www.statgen.us/files/20202021/01/docs02/lectures/Rockefeller_complex_traits_2020Rockefeller_functional_annotation_2021.pdf Evolution, maintenance and allelic architecture of complex traitsFunctional Annotation]* [http://www.statgen.us/files/20202021/01/docs02/lectures/Rockefeller_polygenic_2020Rockefeller_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/20202021/0102/docsbios/about_gw.pdf About Gao Wang] ====Lectures====* [http://statgen.us/files/2021/02/lectures/Rockefeller_function_2019Lecture_Univariate_Fine_Mapping.pdf Functional AnnotationStatistical fine-mapping]* [http://statgen.us/files/2021/02/lectures/Lecture_Multivariate_Analysis.pdf Multivariate analysis]
====Exercises====
* [[Tutorials#Polygenic_risk_prediction_https://github.28NPS_methodcom/statgenetics/statgen-courses/raw/master/handout/finemapping.29|Polygenic risk prediction using nondocx Statistical fine-parametric shrinkage]mapping in association studies] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/npsfinemap.dockerfile dockefiledockerfile] and [https://hub.docker.com/r/statisticalgenetics/npsfinemap/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]