STA520 — Molecular Epidemiology

Interactive study reference and exam-prep tracker

Welcome

This app covers the nine lectures of STA520: from the biology (DNA, RNA, proteins, mutations) through genetic association (GWAS) and causal inference (Mendelian randomization) to high-dimensional omics, proteomics and polygenic risk scores. One clinical example runs through the whole course: the LDLR–PCSK9–LDL cholesterol pathway.

Weeks 1–2: Biology and genetics

Weeks 2–3: GWAS and MR

Week 4: Omics and proteomics

Week 5: Two-sample MR and PRS

How to study with it

  1. Read a lecture. Every topic section has a status control under its heading: Not reviewed / Reviewed / Confident. Click as you go.
  2. Answer the quizzes inside each lecture and the why-questions and spaced review at the bottom.
  3. Start the Exam practice page with the instructor’s 11 Lecture 7 example questions, then practise calculations: drills that generate new numbers every time (Benjamini–Hochberg, Bonferroni, Hardy–Weinberg, OR from β, Wald ratio, IVW, F-statistic, allele alignment, PRS, log₂FC, quantile normalization, moderated t) plus 34 written exam-style questions with model answers.
  4. Go through Martin’s key concepts: 20 short modules for GWAS, MR and proteomics, one per concept on the list, then the seminar questions with concept-level model answers.
  5. Prepare for the computer exercises with Computer exercises: concepts: QC, PLINK output, clumping, allele alignment and MR interpretation on made-up data.
  6. Practise the professor’s word list with the flashcards: write a sentence with each word, then compare.
  7. Check the dashboard to see what is left: exam topics in priority order (🎯 🎓 🔑 🗣️ 📌), then topics with unclear status.
  8. Look up terms in the glossary or use search (top right). Searching “PCSK9” finds it in Lectures 1, 2, 3, 6 and 8.

Exam flags

What is known about the exam: the written exam covers Lecture 7 (🎯) and the words and concepts on the professor’s list for Lectures 1–3 (🎓). For GWAS, MR and proteomics, Martin’s key-concepts list (2 October) names 20 concepts (🔑). GWAS and MR are also examined at the seminar (🗣️), and seminar content can also come on the written exam (corrected 2 October; an earlier version of this app said it would not). Do not focus on specific medicines, mutations or the running examples.

Badge Meaning
🎯 Instructor-flagged EXAM The slide carried the literal “EXAM” marker from the instructor (Lecture 7 only). Highest priority.
📌 Likely exam-relevant (AI-inferred) Inferred from definitions, formulas and worked examples. Not confirmed by the instructor.
🎓 On the professor’s list The section covers words or concepts on the professor’s exam list for Lectures 1–3 (lecture notes, 29 September). Practise them with the flashcards. On the written exam.
🎓 On the professor’s list (use uncertain) On the professor’s list, under “uncertain about use” (checking HWE, checking SNP–phenotype association).
❔ Exam status unclear GWAS/MR/PRS theory that is neither on Martin’s key-concepts list nor part of the computer exercises and seminar questions (for example covariates, Bradford Hill, polygenic risk scores, protein MR). Not confirmed either way.
🔑 Martin’s key concepts The section covers one of the 20 concepts on Martin’s key-concepts list for GWAS, MR and proteomics (2 October). Each has its own short module on Martin’s key concepts. Exam-relevant.
🗣️ Seminar topic (can also come on the exam) Covered by computer exercises 1–2 and the seminar questions. Examined at the seminar, and seminar content can also come on the written exam.
Example, not exam focus The course’s running examples (PCSK9, LDLR, specific medicines and mutations). The lecturer said not to learn them specifically.

How to read the diagrams

Arrows mean different things in different diagrams, so every flow diagram in the app starts its caption with its kind:

Caption starts with An arrow means Example
Biological process One step that happens in the cell or body; the text on the arrow names the step Gene → mRNA → protein (8.1)
Causal diagram “Directly affects”. A line without arrowheads is correlation (for example LD), not cause. Red dashed lines are paths that must be absent The three MR assumptions (6.5)
Workflow “Then”: the next step of an analysis or lab procedure. Not causal The GWAS and MR pipelines (Computer exercises)
Lecture map How the lecture’s problems lead into each other. Not causal The three themes of Lecture 7 (7.1)

A biological process is often also a causal chain (changing an earlier step changes the later ones), but the diagrams that test or assume causality, as in Mendelian randomization, are the ones labelled causal diagram.

ImportantInstructor’s example exam questions included

The 11 questions from “Lecture 7 - questions.pdf” are on the Exam practice page, with model answers written for this app. The computer exercise instructions are still missing; see About the content.

Code blocks marked Run Code are interactive: R runs in your browser, no installation needed. The first run on a page takes a few seconds while R loads.