About the content
Sources, schedule, exam flags, and what is missing
Where the content comes from
The app is built from a study guide (sta520-study-app-guide_1.md) synthesized from the course’s lecture slides (PDF/PPTX), expanded with textbook-level background explanations. The background prose is written independently from general molecular biology, genetics and biostatistics knowledge. It is not copied from the assigned textbook (Principles of Genetics and Molecular Epidemiology, Gomez-Verjan & Rivero-Segura, eds., Springer 2022).
The quizzes, drills, R exercises, figures, written model answers and the illustrative MR numbers in Lecture 6 were added for this app.
Added later (Lecture 9): the Lecture 9 slides plus the course’s reading material: the PRS tutorial (Choi et al. 2020), the GWAS paper (Uffelmann et al. 2021) and chapter 12 of the course book (the “Polygenic Risk Scores” section, pp. 138–139). They are cited where they add to the slides, and each such passage is labelled with its source. The book is summarized and cited, not reproduced. Björnson et al. (2023, European Heart Journal), the UK Biobank study of remnant cholesterol, LDL and CHD, is extra material (not required reading); Section 9.14 is a worked reading of it and carries no exam flag.
Added later: “Lecture 7 - questions.pdf”, the instructor’s example exercises and possible exam questions. Its 11 questions are on the Exam practice page. The questions are the instructor’s; the model answers are written for this app and are not an official answer key. The survival result by cluster (M1 shorter survival, log-rank P = 0.029) in Lecture 7 comes from this document.
Added 2 October: “Martins part key_concepts.docx”, a list of 20 key concepts for GWAS, MR and proteomics, now on Martin’s key concepts with one module per concept; “Lecture Seminar (1).pdf”, the lecturer’s seminar questions, now on Seminar questions with model answers written for this app; and the Lecture 8 reading material, Kirsher et al. (2025, Communications Chemistry), a comparison of eight plasma proteomics platforms, worked through in Section 8.13. The PRS tutorial uploaded again as “lecture 9” reading is the same file as the Choi et al. (2020) tutorial already used in Lecture 9.
How to read the exam flags
The 🎓, ❔, 🗣️ and “example” labels were added on 29 September from the lecturer’s guidance, recorded in the lecture notes: a list of words and concepts from Lectures 1–3 (partial; the full list will be uploaded), “GWAS” and “Mendelian randomization” as seminar content, and “don’t focus on a specific medicine or mutation”. Which sections count as seminar was decided from what computer exercises 1–2 actually do. Where the professor’s list and the seminar mapping overlap (e.g. allele frequency, dbSNP), the professor’s list wins.
Updated 2 October. Seminar content can also come on the written exam, so 🗣️ topics now count as exam-relevant. The 🔑 label was added for sections that cover Martin’s key concepts; it replaced ❔ or 🗣️ on those sections (🎓 was kept where it applied). Order of priority on the dashboard: 🎯, 🎓, 🔑, 🗣️, 📌, then ❔.
| Badge | Meaning |
|---|---|
| 🎯 Instructor-flagged EXAM | The slide carried the literal text “EXAM” from the instructor. Lecture 7 only. The course’s reading guide confirms: “The slides with information that we will be testing on the exam are marked with a small text ‘EXAM.’” |
| 📌 Likely exam-relevant (AI-inferred) | An inference from what the slides present as a definition, formula, worked numerical example or something repeated across lectures. 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. |
| (no badge) | Background or context. Still course content. |
Course schedule (official rough plan)
STA520 Molecular Epidemiology, 4 credits, Sahlgrenska Academy, University of Gothenburg, autumn 2026 (31 Aug – 2 Oct), taught in English.
| Week | Day 1 | Day 2 |
|---|---|---|
| 1 | Intro to the biological language of molecular epidemiology; biological macromolecules (proteins, DNA, lipids) | DNA–RNA–Protein |
| 2 | Genetic variation and protein function | From SNP to GWAS |
| 3 | From GWAS to Mendelian randomisation | Computer exercise intro |
| 4 | High-dimensional data (gene expression, GO, clusters), proteomics | Study design, bias and interpretation; computer exercise discussion |
| 5 | Integrating molecular data | Workshop/Seminar |
“Lecture 3_genetics.pdf” was actually presented at the start of the Lecture 4 session, as a recap (“the same lecture notes as posted for lecture 3”). In this app, Lecture 3 merges “Lecture 3_recap and mutations.pdf” and “Lecture 3_genetics.pdf” by content. The genetics fundamentals (Mendel, LD, SNP arrays, HWE; Sections 3.6–3.9) were therefore taught in the Lecture 4 session, just before “Lecture 4 from SNP to GWAS.pdf”. This matters if an exam question refers to material “from lecture 4”.
Source files per lecture
| Lecture | Slide file(s) |
|---|---|
| 1 | Lecture 1A An introduction to the biological language of molecular epidemiology.pptx; Lecture 1_part2_ProteinsAndDNA.pdf |
| 2 | Lecture 2_DNA_RNA_protein.pdf |
| 3 | Lecture 3_recap and mutations.pdf; Lecture 3_genetics.pdf |
| 4 | Lecture 4 from SNP to GWAS.pdf |
| 5 | Lecture 5 GWAS and computer exercise 1.pdf |
| 6 | Lecture 6 from GWAS to MR.pdf |
| 7 | Lecture 7 part 1 PRELIMINARY.pdf |
| 8 | Lecture 8 proteomics.pdf |
| 9 | Lecture 9 PRS and 2sample MR.pdf. Reading material: “Tutorial a guide to performing polygenic risk score analyses.pdf” (Choi et al. 2020); “Genome- wide association studies.pdf” (Uffelmann et al. 2021); course book ch. 12. Extra material: “Triglyceride-rich lipoprotein remnants,.pdf” (Björnson et al. 2023) |
What is missing
These exist in the course but were not available when the study guide was written, so nothing here is built from them:
- The full siNET article (Arvidsson et al., Modern Pathology 2018): more methodological detail for Lecture 7.
- Solutions to
Computer exercise1.docxandComputer exercise 2.docx. These are deliberately not included: the Computer exercises: concepts page teaches the ideas behind them on made-up and simulated data, without code or results for the course data. - Raw exercise data:
Lecture4_ex1.csv,jointGwasMc_LDL.txt,simulated_LDL.pheno,all_hg38_subset.*,CAD_Summary_filtered.txt. - “STA520 Literature list.pdf” and “STA520 Syllabus.pdf” returned no extractable text (probably scanned), so only “STA520 Course Syllabus.docx” was used for the course context.
- The assigned textbook was deliberately not reproduced (copyright).
- Two uploads of “Lecture 3_recap and mutations.pdf” existed; only one was read. No personal comments or annotations were found in any slide PDF.
- Sessions from week 4 day 2 onward (“Study design, bias and interpretation”, “Integrating molecular data”, the seminar) have no slides in the guide yet.
If any of these become available, they can be added as new sections or questions.
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