Quantitative genetics: applications of association mapping
Nora will first demonstrate an example of GWAS using easyGWAS (link below). That will give you an idea of what the data and results look like for a reasonably simple GWAS. One limitation of easyGWAS, so far as I can see, is that it does require you to have a fully sequenced genome. It doesn't appear that it can handle "random" RAD-seq or GBS SNPs.
Then Nora will lead you in a discussion of the papers below. Please read them carefully and come prepared to discuss them. The notes provide a guide for discussing the paper. They should help you focus on the most important parts of the papers.
Discussion guide PDF
Barrett, J. C., J. Buxbaum, D. Cutler, M. Daly, B. Devlin, J. Gratten, M. E. Hurles, J. A. Kosmicki, E. S. Lander, D. G. MacArthur, B. M. Neale, K. Roeder, P. M. Visscher and N. R. Wray. 2017. New mutations, old statistical challenges. bioRxiv link
Stessman, H. A. F., B. Xiong, B. P. Coe, T. Wang, K. Hoekzema, M. Fenckova, M. Kvarnung, J. Gerdts, S. Trinh, N. Cosemans, L. Vives, J. Lin, T. N. Turner, G. Santen, C. Ruivenkamp, M. Kriek, A. van Haeringen, E. Aten, K. Friend, J. Liebelt, C. Barnett, E. Haan, M. Shaw, J. Gecz, B.-M. Anderlid, A. Nordgren, A. Lindstrand, C. Schwartz, R. F. Kooy, G. Vandeweyer, C. Helsmoortel, C. Romano, A. Alberti, M. Vinci, E. Avola, S. Giusto, E. Courchesne, T. Pramparo, K. Pierce, S. Nalabolu, D. G. Amaral, I. E. Scheffer, M. B. Delatycki, P. J. Lockhart, F. Hormozdiari, B. Harich, A. Castells-Nobau, K. Xia, H. Peeters, M. Nordenskjold, A. Schenck, R. A. Bernier and E. E. Eichler. 2017. Targeted sequencing identifies 91 neurodevelopmental-disorder risk genes with autism and developmental-disability biases. Nature Genetics 49:515-526. linkReturn to lecture schedule