Advgenemap2023 - Revision history

Serveradmin: Undo revision 1462 by Serveradmin (talk)

2023-06-04T14:43:27Z

Undo revision 1462 by Serveradmin (talk)

Serveradmin at 14:41, 4 June 2023

2023-06-04T14:41:14Z

Serveradmin: /* Additional Information */

2023-01-30T13:23:55Z

‎Additional Information

Serveradmin: /* Advanced Gene Mapping Course */

2023-01-30T13:04:17Z

‎Advanced Gene Mapping Course

Serveradmin: /* Additional Information */

2023-01-13T18:41:23Z

‎Additional Information

Serveradmin: /* Additional Information */

2023-01-13T15:57:25Z

‎Additional Information

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2023-01-13T15:54:42Z

‎Additional Information

Serveradmin at 17:44, 6 December 2022

2022-12-06T17:44:15Z

Serveradmin at 17:43, 6 December 2022

2022-12-06T17:43:51Z

Serveradmin: Created page with " NOTITLE Advanced Gene Mapping Course The Rockefeller University, New York ¶ Welch - The Great Hall ¶ Monday through Friday, May 22-26, 2003 General Information A..."

2022-12-06T17:42:39Z

Created page with "__ NOTITLE __ Advanced Gene Mapping Course The Rockefeller University, New York ¶ Welch - The Great Hall ¶ Monday through Friday, May 22-26, 2003 General Information A..."

New page

__ NOTITLE __

Advanced Gene Mapping Course
The Rockefeller University, New York
¶ Welch - The Great Hall
¶ Monday through Friday, May 22-26, 2003

General Information
An Advanced Gene Mapping course will be held in New York from Monday through Friday, May 22-26, 2003. 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 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; transcriptome-wide association studies (TWAS); analysis of RNA-Seq data; eQTL mapping; elucidating pleiotropy; functional prediction and variant annotation; estimation of polygenic risk scores; Mendelian randomization; mediation analysis; LDclumping 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, GCTA, REGENIE will be implemented to analyze population- and family data by applying GLMM and LMM. PLINK will be used to perform data quality control and association analysis controlling for population admixture and substructures using principal component analysis (PCA) and multidimensional scaling (MDS). REGENIE, VAT, and PSEQ will be used to perform data quality control of sequence data and to perform rare variant aggregate association analysis. Gene x gene and gene x environmental interactions will be tested using PLINK and CASSI. Mediation analysis will be performed using Multiphen and R to aid in distinguishing between biological, mediated, and spurious pleiotropy. To make inferences on causality, Mendelian randomization will be performed using MRbase. MR-JTI will be used to perform TWAS analysis. Estimation of polygenic risk scores will be performed using LDpred2. SuSiE will be used for fine mapping to aid in the detection of causal susceptibility variants. To perform analytical and empirical power analysis for single and rare variant aggregate tests, a variety of tools 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) and Gao Wang (Columbia University). TBN (HRP Consulting Group) will lecture on ethics and the regulation of human subject research. A special guest lecture will be given by Jurg Ott (The Rockefeller University).

Additional Information
The maximum number of participants for this course is 34.

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 submit a copy of your CV with your application as well as a letter describing your expertise/experience in detail, e.g., research and training in statistical genetics or related fields. We may contact you personally to discuss your application. If you do not have experience using Unix/LINUX it is highly beneficial to obtain this knowledge before the start of the course.

For additional information contact the course organizer [mailto:suzannemleal@gmail.com?subject=Rockefeller%20Advanced%20Gene%20Mapping%20Course%202023 Suzanne Leal]:

email: [mailto:suzannemleal@gmail.com suzannemleal@gmail.com] or [mailto:sml3@cumc.columbia.edu sml3@cumc.columbia.edu]

@@ Line 16: / Line 16: @@
 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) and Gao Wang (Columbia University). TBN (HRP Consulting Group) will lecture on ethics and the regulation of human subject research. A special guest lecture will be given by Jurg Ott (The Rockefeller University).
-==Course Materials==
+==Additional Information==
-* [https://statgen.us/files/2023/05/Lecture_booklet.pdf Lecture Slides]
+The maximum number of participants for this course is 34.
-* [https://statgen.us/files/2023/05/Exercise_booklet_AGMC_May_23.pdf Exercises]

@@ Line 16: / Line 16: @@
 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) and Gao Wang (Columbia University). TBN (HRP Consulting Group) will lecture on ethics and the regulation of human subject research. A special guest lecture will be given by Jurg Ott (The Rockefeller University).
-==Additional Information==
+==Course Materials==
-The maximum number of participants for this course is 34.
+* [https://statgen.us/files/2023/05/Lecture_booklet.pdf Lecture Slides]
+* [https://statgen.us/files/2023/05/Exercise_booklet_AGMC_May_23.pdf Exercises]
-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.
-−
-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 submit a copy of your CV with your application as well as a letter describing your expertise/experience in detail, e.g., research and training in statistical genetics or related fields. We may contact you personally to discuss your application. If you do not have experience using Unix/LINUX it is highly beneficial to obtain this knowledge before the start of the course.
-−
-The course is supported by generous funding from the National Human Genome Research Institute.
-−
-For additional information contact the course organizer [mailto:suzannemleal@gmail.com?subject=Rockefeller%20Advanced%20Gene%20Mapping%20Course%202023 Suzanne Leal]:
-−
-email: [mailto:suzannemleal@gmail.com suzannemleal@gmail.com] or [mailto:sml3@cumc.columbia.edu sml3@cumc.columbia.edu]
-−
-Application Deadline: March 31, 2023
-−
-−
-−
-[https://statgen.us/files/2023/05/adv_gene_mapping_schedule_May_2023.pdf Click here for course schedule]
-−
-[https://statgen.us/files/2023/05/Application%20Advanced%20Gene%20Mapping%20Course%20%20May%202023%e2%80%93%20New%20York.html Click here for the application form]
-−
-[https://statgen.us/files/2023/05/Rockefeller_advanced_course_flyer_May_23.pdf Click here for the course flyer (please post and distribute)]

@@ Line 26: / Line 26: @@
 Knowledge genetic association analysis, genetic epidemiology, and/or statistical genetics are screening criteria for the selection of participants. Please submit a copy of your CV with your application as well as a letter describing your expertise/experience in detail, e.g., research and training in statistical genetics or related fields. We may contact you personally to discuss your application. If you do not have experience using Unix/LINUX it is highly beneficial to obtain this knowledge before the start of the course.
 For additional information contact the course organizer [mailto:suzannemleal@gmail.com?subject=Rockefeller%20Advanced%20Gene%20Mapping%20Course%202023 Suzanne Leal]:
@@ Line 39: / Line 41: @@
 [https://statgen.us/files/2023/05/Application%20Advanced%20Gene%20Mapping%20Course%20%20May%202023%e2%80%93%20New%20York.html Click here for the application form]
-[https://statgen.us/files/2023/05/Rockefeller_advanced_course_flyer_May_23.pdf Click here for course flyer (please post and distribute)]
+[https://statgen.us/files/2023/05/Rockefeller_advanced_course_flyer_May_23.pdf Click here for the course flyer (please post and distribute)]

@@ Line 4: / Line 4: @@
 The Rockefeller University, New York<br />
 Welch - The Great Hall<br />
-Monday through Friday, May 22-26, 2003
+Monday through Friday, May 22-26, 2023
 ==General Information==

← Older revision		Revision as of 18:41, 13 January 2023
Line 32:		Line 32:

	Application Deadline: March 31, 2023		Application Deadline: March 31, 2023
		+
		+
		+
		+	[https://statgen.us/files/2023/05/adv_gene_mapping_schedule_May_2023.pdf Click here for course schedule]
		+
		+	[https://statgen.us/files/2023/05/Application%20Advanced%20Gene%20Mapping%20Course%20%20May%202023%e2%80%93%20New%20York.html Click here for the application form]
		+
		+	[https://statgen.us/files/2023/05/Rockefeller_advanced_course_flyer_May_23.pdf Click here for course flyer (please post and distribute)]

← Older revision		Revision as of 15:57, 13 January 2023
Line 30:		Line 30:

	email: [mailto:suzannemleal@gmail.com suzannemleal@gmail.com] or [mailto:sml3@cumc.columbia.edu sml3@cumc.columbia.edu]		email: [mailto:suzannemleal@gmail.com suzannemleal@gmail.com] or [mailto:sml3@cumc.columbia.edu sml3@cumc.columbia.edu]
		+
		+	Application Deadline: March 31, 2023

@@ Line 1: / Line 1: @@
-__ NOTITLE __
+__NOTITLE__
 ==Advanced Gene Mapping Course==
@@ Line 9: / Line 9: @@
 An Advanced Gene Mapping course will be held in New York from Monday through Friday, May 22-26, 2003. 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 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; transcriptome-wide association studies (TWAS); analysis of RNA-Seq data; eQTL mapping; elucidating pleiotropy; functional prediction and variant annotation; estimation of polygenic risk scores; Mendelian randomization; mediation analysis; LDclumping 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, GCTA, REGENIE will be implemented to analyze population- and family data by applying GLMM and LMM. PLINK will be used to perform data quality control and association analysis controlling for population admixture and substructures using principal component analysis (PCA) and multidimensional scaling (MDS). REGENIE, VAT, and PSEQ will be used to perform data quality control of sequence data and to perform rare variant aggregate association analysis. Gene x gene and gene x environmental interactions will be tested using PLINK and CASSI. Mediation analysis will be performed using Multiphen and R to aid in distinguishing between biological, mediated, and spurious pleiotropy. To make inferences on causality, Mendelian randomization will be performed using MRbase. MR-JTI will be used to perform TWAS analysis. Estimation of polygenic risk scores will be performed using LDpred2. SuSiE will be used for fine mapping to aid in the detection of causal susceptibility variants. To perform analytical and empirical power analysis for single and rare variant aggregate tests, a variety of tools 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.
@@ Line 17: / Line 17: @@
 ==Additional Information==
 The maximum number of participants for this course is 34.
 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.
@@ Line 25: / Line 25: @@
 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 submit a copy of your CV with your application as well as a letter describing your expertise/experience in detail, e.g., research and training in statistical genetics or related fields. We may contact you personally to discuss your application. If you do not have experience using Unix/LINUX it is highly beneficial to obtain this knowledge before the start of the course.
+Knowledge genetic association analysis, genetic epidemiology, and/or statistical genetics are screening criteria for the selection of participants. Please submit a copy of your CV with your application as well as a letter describing your expertise/experience in detail, e.g., research and training in statistical genetics or related fields. We may contact you personally to discuss your application. If you do not have experience using Unix/LINUX it is highly beneficial to obtain this knowledge before the start of the course.
 For additional information contact the course organizer [mailto:suzannemleal@gmail.com?subject=Rockefeller%20Advanced%20Gene%20Mapping%20Course%202023 Suzanne Leal]:
 email: [mailto:suzannemleal@gmail.com suzannemleal@gmail.com] or [mailto:sml3@cumc.columbia.edu sml3@cumc.columbia.edu]

Advgenemap2023 - Revision history

Serveradmin: Undo revision 1462 by Serveradmin (talk)

Serveradmin at 14:41, 4 June 2023

Serveradmin: /* Additional Information */

Serveradmin: /* Advanced Gene Mapping Course */

Serveradmin: /* Additional Information */

Serveradmin: /* Additional Information */

Serveradmin: /* Additional Information */

Serveradmin at 17:44, 6 December 2022

Serveradmin at 17:43, 6 December 2022

Serveradmin: Created page with "__ NOTITLE __﻿ Advanced Gene Mapping Course The Rockefeller University, New York ¶ Welch - The Great Hall ¶ Monday through Friday, May 22-26, 2003 General Information A..."

Serveradmin: Created page with " NOTITLE Advanced Gene Mapping Course The Rockefeller University, New York ¶ Welch - The Great Hall ¶ Monday through Friday, May 22-26, 2003 General Information A..."