Project Title: Using Published Summary Data to Assess Causal Relationships between Sleep Habits and the Risk of Lung Cancer
BASIS Advisor: Dr. Ryan Grove
Internship Location: GW Columbian College of Arts & Sciences
Onsite Mentor: Dr. Hua Liang
In 2017, the International Agency for Research on Cancer declared “shift work leading to a disruption of circadian rhythm” as likely carcinogenic to humans. Disrupted sleep and exposure to light at night are among several hypothetical mechanisms that might link circadian rhythm disruption to cancer. It is not clear whether certain sleep habits can directly affect the risk of lung cancer (LC). Using publicly available summarized results from large scale genome-wide association studies (GWAS) on four sleep traits, including two chronotype-related traits (one with 2 levels, the other with 5 levels), sleep duration (hours of sleep), and insomnia (defined as never/rarely vs. frequent insomnia symptoms), and summarized results from a lung cancer GWAS, we will conduct Mendelian Randomization (MR) analyses in R to evaluate the potential causal effect from each considered sleep trait on the development of LC and summarize results in a research report. Each MR analysis uses selected genetic markers (i.e., single nucleotide polymorphisms (SNPs)) as proxies for the sleep trait to assess its direct effect on LC.
My Posts
Final Blog
May 29, 2020
Hello everyone, Here is the link to my final presentation: https://www.youtube.com/watch?v=GNyjeVXn9yo. Thanks for keeping up with my blog. This was a great experience!
Week 9-10: Wrapping up Deliverable
May 25, 2020
Hello everyone, These past few weeks have been spent writing up my research report and presentation. It has been great reflecting on this research experience. This week, I’ll make some final edits to my report and finish putting together my presentation! Look out for that blog post. Thanks for reading!
Week 8: Paper and Presentation Preparation Begins
May 08, 2020
Hello everyone, As mentioned in my Week 7 blog, work on my project is essentially done. Now, we turn to the next phase which is creating a research report. The structure of the paper will be as follows: Abstract – consisting of background information relevant to the topic, a description of our methods, summary of […]
Week 7: Plots
May 08, 2020
Hi everyone, Last week, all of the analysis was finished. As summarized in my week 6 blog, we discovered that there is a strong causal relationship between frequency of insomnia symptoms and the risk of lung cancer. This week, I created some plots to help visualize all three of the exposure/outcome combinations (chronotype, sleep duration, […]
Week 6: Analysis
Apr 24, 2020
Hi everyone, This week, I completed most of my analysis. My goal was to determine if there was any significant causal effect between sleep traits (chronotype, insomnia, sleep duration) and lung cancer development. This was done in R using the package “TwoSampleMR.” Because the procedure is fairly similar for each of the three sleep traits, […]
Week 5
Apr 24, 2020
Hello everyone, Sorry for not posting last week. My college replaced their traditional Campus Preview Weekend with weeks of zoom meetings, the bulk of which took place last week. Unfortunately, I was unable to get much done in terms of my project, but look out for my week 6 blog which makes up for this […]
Week 4: Understanding How to Use “TwoSampleMR”
Apr 10, 2020
Hello everyone, Last week, I was able to gather all of the data needed for analysis. This week, I studied the documentation for TwoSampleMR and practiced using Mendelian Randomization to assess the relationship between body mass index (BMI) and Coronary Heart Disease (CHD). The guide I followed for this can be found here. To do […]
Week 3: Obtaining Data and Importing
Apr 03, 2020
Hello everyone! Things have been a bit slower this week as I adapt to remote work, but luckily I’ve still been able to make some progress. As mentioned in last weeks blog, obtaining the lung cancer data was not as easy as anticipated. Fortunately, my advisor was able to gain access this week, so I […]
Week 2: Searching for Data
Mar 27, 2020
Hello everyone and welcome back to my blog! This week, I searched for the public summary data necessary to carry out the analysis part of my project. There are multiple sets of data to extract, so it is important to understand what is needed and why. As explained in my introduction blog, the idea behind […]
Week 1: Preparation
Mar 13, 2020
Welcome back to my blog! It’s been many months since I last touched statistics, so this week was all about review and preparation. Monday and Tuesday were spent skimming through the AP Statistics curriculum using The Practice of Statistics, with emphasis on conducting significance tests and creating confidence intervals. For the remainder of the week, […]
Introduction to Mendelian Randomization
Feb 27, 2020
Hello everyone, My project will use Mendelian Randomization and R to assess whether a relationship exists between sleep habits (chronotype, duration, etc.) and lung cancer. In 2019, California signed a state law that would delay school start times past 8:30 A.M with the intention of improving teenagers’ health. Though the impact of the law is […]