Working Hypotheses

This section frames your project’s guiding testable ideas. Each hypothesis should be clearly stated and falsifiable, grounded in prior knowledge or theory. Consider how each might be tested, refined, or rejected as evidence accumulates.

Primary Hypothesis

• What is your main mechanistic or predictive claim?
  • Example: "Variants in chromatin remodeling genes reduce penetrance in known monogenic disorders."
  • Example: "Pathway-level differential activity in WNT signaling distinguishes disease subtypes."

Alternative Hypotheses

• What competing or secondary explanations are plausible?
  • Example: "Noncoding regulatory variation explains observed expression shifts."
  • Example: "Technical artifact or population structure, not true biological signal, drives association."

Falsifiability Criteria

• What type of result would falsify each hypothesis?
  • Example: Lack of enrichment in expected gene sets under multiple models.
  • Example: No signal in matched control datasets or independent validation cohort.
  • Example: Failure to reproduce pathway signal across multiple quantification methods.