Journal Club

Publishing a research article in a peer-reviewed journal is one of the primary mechanisms by which statistical methods and scientific results are communicated. Learning to navigate the format and writing style of research articles is a worthwhile skill to develop, but it takes practice. Practicing and developing this skill will be a big focus of this course.

Approximately once per week, our class time will serve as a “Journal Club.” During class time, a small group of students will present a short summary of the article and then lead a class-wide discussion on key takeaways, limitations, questions, etc. (Sign up here.) Everyone else will prepare for class that day by reading the assigned article(s) and taking note of any key points, insights, or questions to prepare for the in-class discussion. These Journal Clubs will serve as a primary resource for learning about statistical methods used in the field of statistical genetics.

General Instructions

To prepare for Journal Club discussions, please do the following:

  • Discussion leaders:
    1. Start reading the article early
    2. Meet with Kelsey to discuss the article (preferably the week before your presentation)
    3. Prepare a 20–30 minute presentation summarizing the key points of the article
      • Use the guiding questions from the UW Stat Gen Seminar or the How to Read an Article blog post to help structure your summary!
      • The format of the presentation is up to you. Use slides, prepare a handout, write on the board, etc.
      • Remember: you do not need to talk about every aspect of the article! Focus on what you think are the most important takeaways, the most interesting methods or results, etc.
    4. Prepare at least 15 minutes of small group and/or full class discussion
      • This can be integrated throughout your presentation, or set aside to the end.
      • Ideas for discussion: anything you found particularly interesting, connections you noticed between the paper and things we’ve covered in class (or other classes you’ve taken), potential limitations of the approach the authors took, parts of the paper you found confusing, etc.
      • I also encourage you to review the relevant Slido page, where other members of the class will be submitting their questions about the article. You might choose to center at least part of the discussion time around any common questions that appear here.
    5. Share all presentation materials with Kelsey before class so she can post them on the course website.
  • Everyone else:
    1. Read the article, using the tips we discussed during Journal Club 1
    2. Prepare a list of key takeaways, limitations, questions, etc. (about the paper content and the writing style/structure) to share during class.
    3. Submit at least one of these questions to the relevant Slido page before class. While you’re there, read the other questions that have been submitted and upvote any that resonate with you.

Journal Club 1: January 28

Discussion Leader: Kelsey

Paper: link

Butler, R., & Nisan, M. (1986). Effects of No Feedback, Task-Related Comments, and Grades on Intrinsic Motivation and Performance. Journal of Educational Psychology, 78(3), 210–216.

We’ll start things off with a “practice” Journal Club that Kelsey will lead. To further ease our transition into the difficult task of reading scientific articles, our first article will cover a topic with which you are all intimately acquainted: grading.

To prepare for class, please do the following:

  1. Read the following resources on how to read a scientific article:
  2. Read Butler and Nisan, practicing at least some of the tips you learned from Step #1.
    • NOTE: This will take awhile! As many of the resources above mention, reading an article typically involves multiple read throughs. Make sure you budget your time accordingly.
  3. Prepare a list of key takeaways, limitations, questions, etc. (about the paper content and the writing style/structure) to share during our next class.

Journal Club 2: February 4

Discussion Leaders: see here

Paper: link

Burton, P. R., Clayton, D. G., Cardon, L. R., Craddock, N., Deloukas, P., Duncanson, A., Kwiatkowski, D. P., McCarthy, M. I., Ouwehand, W. H., Samani, N. J., Todd, J. A., Donnelly, P., Barrett, J. C., Davison, D., Easton, D., Evans, D., Leung, H.-T., Marchini, J. L., Morris, A. P., et al. (2007). Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature, 447(7145), 661–678.

Our next paper is one of the earliest published examples of a genome-wide association study. This is a long one! Start early. It also uses quite a few methods that you may not have seen before. Remember – the goal is not to understand every detail. Focus on the big picture, and bring any questions you have to our class discussion!

See Section 1, above, for instructions. Here’s the Slido page for today: Journal Club 2 Slido.

Journal Club 3: February 11

Discussion Leaders: see here

Paper: link

Pulit, S. L., With, S. A. J., & Bakker, P. I. W. (2017). Resetting the bar: Statistical significance in whole-genome sequencing-based association studies of global populations. Genetic Epidemiology, 41(2), 145–151. https://doi.org/10.1002/gepi.22032

Journal Club 3 Slido: link

Journal Club 4: February 18

Important

This discussion has been rescheduled to Thursday, February 20.

Discussion Leaders: see here

Reading 1: link

Mathieson I., & Scally A. (2020). What is ancestry? PLoS Genetics, 16(3). https://doi.org/10.1371/journal.pgen.1008624

Reading 2: link – just read the Summary chapter!

National Academies of Sciences, Engineering, and Medicine. 2023. Using Population Descriptors in Genetics and Genomics Research: A New Framework for an Evolving Field. Washington, DC: The National Academies Press. https://doi.org/10.17226/26902.

Journal Club 4 Slido: link

Journal Club 5: February 25

Discussion Leaders: see here

Paper: link

Novembre, J., Johnson, T., Bryc, K., Kutalik, Z., Boyko, A. R., Auton, A., Indap, A., King, K. S., Bergmann, S., Nelson, M. R., Stephens, M., & Bustamante, C. D. (2008). Genes mirror geography within Europe. Nature, 456(7218), 98–101. https://doi.org/10.1038/nature07331

Journal Club 5 Slido: link

Journal Club 6: March 4

Discussion Leaders: see here

Paper: link

Bryc, K., Durand, E. Y., Macpherson, J. M., Reich, D., & Mountain, J. L. (2015). The genetic ancestry of African Americans, Latinos, and European Americans across the United States. American Journal of Human Genetics, 96(1), 37–53. https://doi.org/10.1016/j.ajhg.2014.11.010

Journal Club 6 Slido: link

Journal Club 7: March 27

Discussion Leaders: see here

Paper: link

Price, A. L., Zaitlen, N. A., Reich, D., & Patterson, N. (2010). New approaches to population stratification in genome-wide association studies. Nature Reviews. Genetics, 11(7), 459–463. https://doi.org/10.1038/nrg2813

Journal Club 7 Slido: link