Difference between revisions of "Advgenemap2022"

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==General Information==
 
==General Information==
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An Advanced Gene Mapping course will be held in New York from Monday through Friday, January 10-14, 2022. 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.).
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An Advanced Gene Mapping course will be held in New York from Monday through Friday, January 10-14, 2022. The cost of the 5-day course is $100 for student, academic, and government researchers and $2,500 for researchers working in industry. This fee covers tuition and course-related expenses (cloud computing, etc.).
  
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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.
+
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; linear mixed models (LMM) and generalized LMM (GLMM); meta-analysis; sample size estimation and power calculations; detecting gene x gene and gene x environmental interactions; heritability estimation; 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. 
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A variety of freely available software will be used to perform the practical exercises, due to differences in their functionality. PSEQ and VAT will be used to analyze sequence data to perform annotation, quality control, rare variant association analysis, and meta-analysis. FaST-LMM, GCTA-MLMA, REGENIE will be implemented to analyze population- and family-based data by applying generalized linear mixed models (qualitative traits) and linear mixed models (quantitative traits). For rare variant association analysis of trio data, RV-TDT will be applied. MultiPhen (multivariate) and PLINK (univariate) will be contrasted in their ability to detect pleiotropy; Mediation analysis will be performed using R to aid in distinguishing between biological, mediated, and spurious pleiotropy. To make inferences on causality, Mendelian randomization will be performed using MR-base. Estimation of polygenic risk scores will be performed using LDpred and non-parametric shrinkage. SuSie will be used for fine mapping to aid in the detection of causal susceptibility variants. Heritability estimates will be performed using GCTA. For analysis of eQTLs, Matrix eQTL will be used. Analysis of imputed expression data will be performed by applying PrediXCan; To perform analytical and empirical power analysis for single and rare variant aggregate tests, a variety of tools will be used that includes the Armitage Power Tool and the SKAT R library will be used. Additionally, variant annotation will be performed with ANNOVAR as well as directly using a variety of functional prediction and conservation tools, e.g. CADD, GERP, MutationTaster, MutPred, Polyphen-2, and SIFT.
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A variety of freely available software will be used to perform the practical exercises, due to differences in their functionality.FaST-LMM, REGENIE will be implemented to analyze population- and family-based data by applying GLMM and LMM. Mediation analysis will be performed using R to aid in distinguishing between biological, mediated, and spurious pleiotropy. To make inferences on causality, Mendelian randomization will be performed using MR-base. Estimation of polygenic risk scores will be performed using LDpred. mvSuSiE and SuSiE will be used for fine mapping to aid in the detection of causal susceptibility variants. Heritability estimates will be performed using LDSC. Imputation and Analysis of imputed RNAseq expression data will be performed by applying FUSION; To perform analytical and empirical power analysis for single and rare variant aggregate tests, a variety of tools will be used that includes the Armitage Power Tool and the SKAT R library will be used. Additionally, variant annotation will be performed with ANNOVAR as well as directly using a variety of functional prediction and conservation tools, e.g. CADD, GERP, MutationTaster, MutPred, Polyphen-2, and SIFT.
  
 
==Course Instructors==
 
==Course Instructors==
−
 
 
The instructors for the course are Heather Cordell (University of Newcastle), 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).
 
The instructors for the course are Heather Cordell (University of Newcastle), 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).
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==Additional Information==
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The maximum number of participants for this course is 32.  
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Only individuals who are fully vaccinated for COVID can attend the course. With your application form include a scan of your COVID vaccination documentation. We will be following COVID protocols and the wearing of masks will be required.
 +
 +
The course is wheelchair accessible. All disabilities will be accommodated. Handicapped individuals are encouraged to apply.
 +
 +
Travel stipends of up to $1,000 each are available. Eligibility requirements are: (1) sufficient background and practical experience in statistical analysis of genetic data, and (2) demonstrated financial need. Preference for stipends will be given to pre-doctoral students and postdoctoral researchers. To apply for such a stipend, please attach a letter of request and enclose a letter of reference and proof of student or postdoctoral status.
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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.
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For additional information contact the course organizer [mailto:suzannemleal@gmail.com?subject=Rockefeller%20Advanced%20Gene%20Mapping%20Course%202022 Suzanne Leal]: <br />email: [mailto:suzannemleal@gmail.com suzannemleal@gmail.com] or [mailto:sml3@cumc.columbia.edu sml3@cumc.columbia.edu]
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The deadline for the course application is November 12, 2021
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[http://statgen.us/files/2022/01/adv_gene_mapping_schedule_2022.pdf Click here for the course schedule]
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[http://statgen.us/files/2022/01/Application%20Advanced%20Gene%20Mapping%20Course%202022–%20New%20York.html Click here for the application form]
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[http://statgen.us/files/2022/01/Rockefeller_advanced_course_flyer_2022.pdf Click here for the course flyer] (please post and distribute)
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==Handouts==
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===Heather Cordell===
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====Lectures====
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*[https://statgen.us/files/2022/01/lectures/Cordell/NY2021-lecture1.pdf Genome-Wide Association Studies]
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*[https://statgen.us/files/2022/01/lectures/Cordell/NY2022-lecture2.pdf  Linear Mixed Models and G×G or G×E interactions]
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===Andy DeWan===
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====Lectures====
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*[https://statgen.us/files/2022/01/lectures/DeWan/DeWan_Adv_Gene_Mapping_Mendelian%20Randomization.pdf Mandelian Randomization: An Introduction]
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*[https://statgen.us/files/2022/01/lectures/DeWan/Rockefeller_Adv_Course_DeWan_pleiotropy_2022.pdf From Cross-Phenotype Associations to Pleiotropy in Human Genetic Studies]
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===Suzanne Leal===
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====Lectures====
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*[https://statgen.us/files/2022/01/lectures/Leal/Data_qc.pdf Data Quality Control]
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*[https://statgen.us/files/2022/01/lectures/Leal/analysis_rare_variants.pdf Analysis of Rare Variants]
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*[https://statgen.us/files/2022/01/lectures/Leal/power_sample_sizes.pdf Power Analysis]
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===Judy Matuk===
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====Lectures====
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*[https://statgen.us/files/2022/01/lectures/Matuk/Rockefeller_HSR%20Ethics%20and%20Regulations%20PPT_%20jm%201.11.2022.pdf The Ethics and Regulation of Human Subjects Research]
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===Jurg Ott===
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====Lectures====
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*[https://statgen.us/files/2022/01/lectures/Ott/GenotypePatterns2022-01.pdf Assocaition Analysis of Genotype Patterns with Digenic Traits]
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===Shamil Sunyaev===
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====Lectures====
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*[https://statgen.us/files/2022/01/lectures/Sunyaev/Rockefeller_complex_traits_2022.pptx Analysis of Complex Traits]
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*[https://statgen.us/files/2022/01/lectures/Sunyaev/Rockefeller_function_2022.pptx Functional Annotation of Coding and Non-coding Variants]
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*[https://statgen.us/files/2022/01/lectures/Sunyaev/Rockefeller_pop_gen_2022.pptx Population Genetics]
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*[https://statgen.us/files/2022/01/lectures/Sunyaev/Rockefeller_polygenic_2021.pptx Polygenic Risk Scores]
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===Gao Wang===
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====Lectures====
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*[https://statgen.us/files/2022/01/lectures/Wang/Lecture_TWAS_methods.pdf PhenotypePrediction and Transcriptome-Wide Association Studies]
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*[https://statgen.us/files/2022/01/lectures/Wang/Lecture_Multivariate_Analysis.pdf Multivariate Analysis in Genetic Association Studies]
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*[https://statgen.us/files/2022/01/lectures/Wang/Lecture_Linkage_Disequilibrium.pdf Linkage Disequilibrium in Genetic Association Studies]
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*[https://statgen.us/files/2022/01/lectures/Wang/Lecture_Functional_Annotation_Integration.pdf Integrating GWAS with Functional Annotations]
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*[https://statgen.us/files/2022/01/lectures/Wang/Lecture_Fine_Mapping_Basic.pdf Statistical Fine-Mapping in Genetic Association Studies]
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*[https://statgen.us/files/2022/01/lectures/Wang/Lecture_Fine_Mapping_Summary_Stats.pdf Fine-Mapping with Summary Statistics: Current Methods and Practical Considerations]
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'''                          This course is supported by funding from the National Human Genome Research Institute.'''

Latest revision as of 19:52, 17 January 2022

Advanced Gene Mapping Course

The Rockefeller University, New York 
Welch - The Great Hall
Monday through Friday, January 10-14, 2022

General Information

An Advanced Gene Mapping course will be held in New York from Monday through Friday, January 10-14, 2022. The cost of the 5-day course is $100 for student, academic, and government researchers and $2,500 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; linear mixed models (LMM) and generalized LMM (GLMM); meta-analysis; sample size estimation and power calculations; detecting gene x gene and gene x environmental interactions; heritability estimation; 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. 

A variety of freely available software will be used to perform the practical exercises, due to differences in their functionality.FaST-LMM, REGENIE will be implemented to analyze population- and family-based data by applying GLMM and LMM. Mediation analysis will be performed using R to aid in distinguishing between biological, mediated, and spurious pleiotropy. To make inferences on causality, Mendelian randomization will be performed using MR-base. Estimation of polygenic risk scores will be performed using LDpred. mvSuSiE and SuSiE will be used for fine mapping to aid in the detection of causal susceptibility variants. Heritability estimates will be performed using LDSC. Imputation and Analysis of imputed RNAseq expression data will be performed by applying FUSION; To perform analytical and empirical power analysis for single and rare variant aggregate tests, a variety of tools will be used that includes the Armitage Power Tool and the SKAT R library will be used. Additionally, variant annotation will be performed with ANNOVAR as well as directly using a variety of functional prediction and conservation tools, e.g. CADD, GERP, MutationTaster, MutPred, Polyphen-2, and SIFT.

Course Instructors

The instructors for the course are Heather Cordell (University of Newcastle), Andrew DeWan (Yale University), Suzanne Leal (The Rockefeller University & Columbia University), 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

The maximum number of participants for this course is 32.  

Only individuals who are fully vaccinated for COVID can attend the course. With your application form include a scan of your COVID vaccination documentation. We will be following COVID protocols and the wearing of masks will be required.

The course is wheelchair accessible. All disabilities will be accommodated. Handicapped individuals are encouraged to apply.

Travel stipends of up to $1,000 each are available. Eligibility requirements are: (1) sufficient background and practical experience in statistical analysis of genetic data, and (2) demonstrated financial need. Preference for stipends will be given to pre-doctoral students and postdoctoral researchers. To apply for such a stipend, please attach a letter of request and enclose a letter of reference and proof of student or postdoctoral status.

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 contact the course organizer Suzanne Leal: 
email: suzannemleal@gmail.com or sml3@cumc.columbia.edu

The deadline for the course application is November 12, 2021

Click here for the course schedule

Click here for the application form

Click here for the course flyer (please post and distribute)

Handouts

Heather Cordell

Lectures

Andy DeWan

Lectures

Suzanne Leal

Lectures

Judy Matuk

Lectures

Jurg Ott

Lectures

Shamil Sunyaev

Lectures

Gao Wang

Lectures


                          This course is supported by funding from the National Human Genome Research Institute.

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