Human Genetics: Linkage analysis and disease genetics

Short Course, 10-15 August 2015

Organized by Profs. Liping Wei, Peking University, and Jurg Ott, Institute of Psychology CAS, a short course on Genetic Linkage and Association Analysis will be held at Peking University in Beijing, China, 10-15 August 2015. 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), Andrew DeWan (Yale University), and Jurg Ott (Institute of Psychology CAS & Rockefeller University). The final two days are on autism genetics and will be covered by Stephan Sanders (UCSF). Supported by the School of Life Sciences at Peking University and research grant number 31470070 from NSFC (JO). This course is restricted to members and affiliates of Peking University.

Detailed information and application instructions may be obtained from Meng Wang (Peking U, Beijing; logistics) or Chao Chen (participants from IPCAS, Beijing; course materials).

Most 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 easy and automated although downloading the various portions of the system may take some time. Also, please download the LINKAGE programs. Some of the exercises make use of the Handbook of Human Genetic Linkage (Terwilliger & Ott 1994), which is now available as a pdf file. Course participants are encouraged to read the beginning sections of this book before coming to the course.

Monday 10 August 2015

Morning

01 Lecture: Introduction to Linkage Analysis (J. Ott)
02 Exercise: Introduction to LINKAGE software: File format, MAKEPED, PREPLINK, LCP; basic 2-point analysis (M. Devoto)

Afternoon

03 Lecture: Disease gene models in linkage analysis (M. Devoto)
04 Exercise: Analysis using LINKAGE programs: autosomal and X-linked modes of inheritance, reduced penetrance (M. Devoto)

Tuesday 11 August 2015

Morning

05 Lecture: Linkage analysis under heterogeneity (J. Ott)
06 Exercise:
HOMOG program (J. Ott)

Afternoon

07 Lecture: Allele sharing (nonparametric) methods for qualitative traits for sib-pairs and extended families (A. Dewan)
08 Exercise:
GENEHUNTER (A. Dewan)

Wednesday 12 August 2015

Morning

09 Exercise: Linkage analysis using Merlin (M. Devoto)
10 Lecture: Introduction and overview to association studies (J. Ott)

Afternoon

11 Exercise: Introduction to GWAS (M. Devoto)
12 Exercise: Interpreting GWAS results (M. Devoto)

13 Exercise: Controlling for population stratification using MDS (M. Devoto)

Thursday 13 August 2015

Morning

14 Lecture: Recent experience with linkage analysis using sequence variants in families (J. Ott)
15 Lecture: High-throughput sequencing: Methods and study design (A. DeWan)
16 Demonstration (if time permits): Sequence data alignment and variant calling (A. DeWan)

Afternoon

17 Lecture: Rare variant analysis: Introduction and methods I (A. DeWan)
18 Exercise:
SKAT and Burden tests (A. DeWan)

Friday 14 August 2015 -- Autism

Morning

19 Lecture: Heritability of ASD (S. Sanders)
20 Lecture: Copy number variation in ASD (S. Sanders)
21 Exercise: Detection of copy number variation in ASD (S. Sanders)

Afternoon

22 Lecture: Single nucleotide variation in ASD (S. Sanders)
23 Exercise: Detection of de novo single nucleotide variation in ASD (S. Sanders)

Saturday 15 August 2015 -- Autism

Morning

24 Lecture: Indel detection in ASD (S. Sanders)
25 Exercise:
Detection of de novo indels in ASD (S. Sanders)

Afternoon

26 Lecture: Progessing from genes to systems in ASD (S. Sanders)
27 Exercise: Systems analysis in ASD (S. Sanders)