Short Course on Analysis of Association and Sequencing Data in Human Genetics, Shanghai, June 17-21, 2013

A short course will be held at Fudan University in Shanghai, China, 17-21 June 2013 (Hosts: Prof. Jurg Ott, IPCAS Beijing, and Prof. David Saffen, Department of Cellular and Genetic Medicine, Fudan University). Course participants are expected to bring their own laptops to carry out hands-on exercises. The course program is similar to the one at our previous Beijing course but additional material like sequencing and SNP imputation will be covered (see below). Instructors will be Marcella Devoto (University of Pennsylvania, Philadelphia), Suzanne Leal (Baylor College of Medicine & Rockefeller University), Yin Yao (National Institutes of Health, Washington DC), and Jurg Ott (Institute of Psychology CAS & Rockefeller University).

Detailed information and application instructions may be obtained from Lily Chen (Fudan U, Shanghai) or Chao Chen (IPCAS, Beijing). The course fee of CNY 5000 RMB (US$ 900) will cover lectures and handouts but not transportation or accommodation.

Some computer exercises will be done in Linux (not Windows). Course participants are expected to install Ubuntu Linux on their laptops well in advance of the course. If you follow instructions, installation is very easy and automated although downloading the various portions of the system may take some time.

Monday 17 June 2013

Morning

Welcome (J. Ott)
01 Lecture: Introduction and overview to association studies (J. Ott)
02 Exercise: Data quality control and data cleaning (Y. Yao)

Afternoon

03 Lecture: Association analysis – Genetic models, logistic regression, covariates (J. Ott)
04 Exercise: Association analysis including logistic regression and covariates (M. Devoto)

Tuesday 18 June 2013

Morning

05 Lecture: Controlling for multiple testing, permutation and false discovery rate (FDR) (J. Ott)
06 Exercise: UCSC Genome Browser, HapMap and Haploview (M. Devoto)

Afternoon

07 Exercise: Controlling for population stratification using MDS (M. Devoto)
08 Exercise: More genome-wide association analysis (Y. Yao)

Wednesday 19 June 2013

Morning

09 Lecture: Multi-locus analysis, GxG interactions, homozygosity mapping (J. Ott)
10 Exercise: SumStat and ScanStat programs, testing for gene interactions (J. Ott)
11 Lecture: Pedigree-based analysis to detect genetic risk factors (Y. Yao)

Afternoon

Free for sight-seeing on your own initiative

Thursday 20 June 2013

Morning

12 Lecture: Quality control for rare variant data obtained from next generation sequencing (S. Leal)
13 Lecture: Complex trait rare variant association analysis (S. Leal)
14 Exercise: Analysis of rare variants (S. Leal)

Afternoon

15 Lecture: Principles of genetic imputation (M. Devoto)
16 Exercise: Imputation and analysis of imputed data (M. Devoto)

Friday 21 June 2013

Morning

17 Exercise: Power analysis for common variants using Quanto and PGA (M. Devoto)
18 Exercise: Power analysis for rare variant data (S. Leal)
Remaining work not finished on previous days

Afternoon

Discussion, analyzing participants’ data, wrap-up