Biostat 581. Statistical Genetics Seminar. http://courses.washington.edu/b581/

Spring 2019 Topic: Epigenetic analyses

Instructor: Ellen Wijsman, wijsman@uw.edu

Note on attendance for registered students: Please let Ellen know if you will be missing one of the meetings due to illness or other excusable absence.

I haven't gotten all the information up yet from our organizational meeting. I am still working on it. The key information for the next couple of weeks is up, and partial information for the rest of the quarter.

A paper to refer to throughout the quarter: Teschendorff & Relton (2018) "Statistical and integrative system-level analysis of DNA methylation data", Nature Reviews Genetics 19(3):129-147, doi: 10.1038/nrg.2017.86, https://www.ncbi.nlm.nih.gov/pubmed/29129922
Each week everyone should try to read the noted relevant parts that parallel the paper of the week. (Presenters of the week are not responsible for presenting from this paper - it is for everyone's benefit to help understand the topic).

Another paper that might be of interest to define/describe epigenetics:
Jablonka and Raz (2009) "Transgenerational epigenetic inheritance: prevalence, mechanisms, and implications for the study of heredity and evolution" The Quarterly Review of Biology 84(2):131-176. https://www.ncbi.nlm.nih.gov/pubmed/19606595

Schedule:

April 2. Scheduling day.

April 9. Overview: what is epigenetics?
Teschendorff 2018 paper, p 129-130 (first section)
Moore et al (2013) "DNA methylation and its basic function", Neuropsychopharmacology Reviews 38:23-38, doi: 10.1038/npp.2012.112 (main paper: a good starting point). https://www.ncbi.nlm.nih.gov/pubmed/22781841
Bock (2012) "Analysing and interpreting DNA methylation data", Nature Reviews Genetics 13:705-719, doi: 10.1038/nrg3273, (A second paper, more for some of the chemistry; use if needed). https://www.ncbi.nlm.nih.gov/pubmed/22986265

Presenters:Adrian, Esther, Edward

April 16. Deconvolution methods part 1, mixed samples.
Teschendorff 2018 paper, p 130-133
Houseman et al (2012) "DNA methylation arrays as surrogate measures of cell mixture distribution", BMC Bioinformatics 13:86. https://www.ncbi.nlm.nih.gov/pubmed/22568884

Presenters:Pearl, Amarise

April 23. Deconvolution methods part 2, correcting for heterogeneity in gene expression.
Teschendorff 2018 paper, p 130-133
Leek and Storey (2007) "Capturing heterogeneity in gene expression studies by surrogate variable analysis" PLoS Genetics 3:1724-1735 https://www.ncbi.nlm.nih.gov/pubmed/17907809

Presenters: Charles

April 30. Feature Selection part 1, bump hunting.
Teschendorff 2018 paper, p 135-138
Jaffe et al. (2012) "Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies" International Journal of Epidemiology 41(1):200-209. https://www.ncbi.nlm.nih.gov/pubmed/22422453

Presenters: Hanley, Maria

May 7. Feature Selection part 2, differential variability
Teschendorff 2018 paper, p 135-138
Jaffe et al.(2012) "Significance analysis and statistical dissection of variably methylated regions". Biostatistics 13(1):166-178. https://www.ncbi.nlm.nih.gov/pubmed/21685414

Presenters:Anna

May 14. An application:
Bailey et al 2016 "Genomic analyses identify molecular subtypes ofpancreatic cancer" Nature 531:47-51+. https://www.ncbi.nlm.nih.gov/pubmed/26909576

Presenters: Alan, Priyanka

May 21. Research talk: "Mutation rate estimation from 3-way IBD"

Presenter: Xiowen

May 28. Research talk: "Controlling for population structure in genetic association studies in admixed populations".

Presenter: Kelsey

June 4. Research talk: "Evolution of germline mutation rate in great apes"

Presenter: Michael