Why Gene Studies Use Such Tiny P-Values
Experimental Design domain · Lesson 8 of 20 · Biomedical Innovations (BI)
Today's goal: Students will explain why testing many hypotheses at once inflates false positives, and apply a Bonferroni-style correction to reach the genome-wide significance threshold p < 5 x 10^-8.
This is a model of the work you should turn in. Use it to check your own: match the structure and the level of detail, do not copy it. Your wording should be your own.
Genome-wide significance sort (p < 5 x 10^-8 is the bar; instructor practice values):
- SNP near IRF6: p = 2 x 10^-9. CLEARS the bar (2 x 10^-9 is smaller than 5 x 10^-8).
- SNP on chromosome 16: p = 1 x 10^-8. CLEARS the bar (1 x 10^-8 is smaller than 5 x 10^-8).
- SNP on chromosome 8: p = 3 x 10^-6. DOES NOT CLEAR (3 x 10^-6 is larger than 5 x 10^-8).
- SNP near an unknown gene: p = 0.0004. DOES NOT CLEAR (far larger than the bar).
Best follow-up for the cleared hits: independent replication in a second, separate cohort of patients, because a single scan can produce a hit by luck and only a repeat in fresh data earns the field's trust.
This model shows the level of evidence and organization needed to complete: A four-SNP sort against the 5 x 10^-8 bar with a replication recommendation.
- Name the variables and include units.
- Enter observations without changing the raw values.
- Check labels, calculations, and patterns before interpreting the data.
Keep the structure. Replace the question, facts, measurements, and evidence. Then recheck units, vocabulary, and whether the conclusion goes beyond the evidence.
Also due today: Show the Bonferroni step, 0.05 / 1,000,000 = 5 x 10^-8, so students see where the bar comes from.
The finished product above did not appear all at once. Here is the path from the question to the turned-in work, so you can follow the same steps.
- 1Start from today's question: What happens when thousands of sensors each can false-alarm?
- 2Work the Model and the Explore questions to reason it out before writing anything.
- 3Pull the specific evidence the product needs from the reading and any database you used.
- 4Write it up in the required format: Decide for four scanned SNPs whether each clears (p < 5 x 10^-8) with one sentence per call (IRF6: p = 2 x 10^-9; 8: p = 3 x 10^-6; unknown gene: p = 0.0004; chromosome 16: p = 1 x 10^-8), then name the single study that would make a cleared hit more trustworthy.
- 5Check it against the rubric, then submit.
| Criterion | Proficient | Developing | Beginning |
|---|---|---|---|
| Complete | Every required part of the artifact is present and filled in. | Most parts are present, but one is missing or left blank. | Several parts are missing. |
| Accurate | The science and data are correct and match the evidence. | Mostly correct, with a small factual slip. | Key science or data is wrong. |
| Scientific reasoning (CER) | States a claim, backs it with specific evidence, and explains the reasoning. | Has a claim and evidence, but the reasoning is thin or missing. | Gives an answer with no evidence or reasoning. |
| Professional communication | Clear, organized, and labeled the way a clinician or scientist would write it. | Readable but disorganized or missing labels. | Hard to follow. |
| Submitted | Turned in through the route named under Submit here and confirmed. | Turned in, but in the wrong place or unconfirmed. | Not turned in. |
- CompleteProficient: Nothing is left blank: the model fills every part of "Decide for four scanned SNPs whether each clears genome-wide significance (p < 5 x 10^-8) with one sentence per call (IRF6: p = 2 x 10^-9; chromosome 8: p = 3 x 10^-6; unknown gene: p = 0.0004; chromosome 16: p = 1 x 10^-8), then name the single study that would make a cleared hit more trustworthy.".
- AccurateProficient: Every number and claim matches the case evidence.
- Scientific reasoning (CER)Proficient: It names a claim, cites the specific evidence, and explains the reasoning, not just the answer.
- Professional communicationProficient: It is organized and labeled like a real chart note.
- SubmittedProficient: It would be attached to your class form or handed in, and confirmed.
One exam-style question that uses exactly what you practiced today. Try it before you reveal the answer, then read why each choice is right or wrong.
Tap an answer to see the full explanation. Nothing is recorded or graded.
It builds this reusable test skill: Applying the genome-wide significance threshold and the Bonferroni rationale.
- Name the concept or data pattern being tested.
- Cross out choices that violate that rule or the evidence.
- Justify the best remaining choice before checking the answer.