What is causation in genetic studies?

1. What is causation in genetic studies? Grier P Page Section on Statistical Genetics Department of Biostatistics University of Alabama at Birmingham

2. Genes for over 1300 Mendelian traits have been identified. Few genes for complex traits have been reproducibly identified (less than 40). The problem

3. The causes of the difficulty in identifying genes for complex traits are several. Phenotypes are complex and diseases may not be true biological phenomena. Replcation may not be in the exact phenotype. Sample sizes are often small Analytical methods are inadequate (assumptions, multiple testing), multiple alleles in same gene Biases Lack of standards of what constitutes causation for complex diseases and quantitative traits. Why are there such difficulties?

4. Koch’s Causation Hypotheses • (1) the parasite occurs in every case of the disease in question and under circumstances that can account for the pathological changes and the clinical course of the disease; • (2) the parasite occurs in no other disease as a fortuitous and nonpathogenic parasite; • (3) after being fully isolated from the body and repeatedly grown in pure culture, the parasite can induce the disease again

5. Bradford Hill’s Criteria • 1. Strength of association • 2. Consistency and unbiasedness of association • 3. Specificity of the association • 4. Temporality • 5. Biological gradient • 6. Biological plausibility • 7. Coherence with previous knowledge • 8. Experimental evidence • 9. Reasoning by analogy.

6. 1. Production: causes are conditions that play an essential part in producing the occurrence of disease. 2. Necessary: a necessary cause is a condition without which the effect cannot occur. 3. Sufficient: when the cause is present, the effect must occur. 4. Probabilistic: a probabilistic cause increases the probability of its effect occurring. 5. Counterfactual: a counterfactual cause makes a difference in the outcome when it is present verses when it is absent. What types of causation are there?

7. What types of causation are appropriate for complex genetics studies? • Mendelian traits, we usually talk about “sufficient causes,” • complex diseases, we are referring to “probabilistic causes,” which increase the probability of a disease occurring. • For quantitative traits, the concept of “counterfactual cause” is appropriate. • It is not clear what is sufficient evidence to establish any of these levels of causation between a polymorphism and a disease or trait.

8. 1. The polymorphism is actually causative for the disease or trait. 2. The association is a false positive due to random chance. 3. The polymorphism is in disequilibrium with the true causative allele. 4. The polymorphism is associated because of some systematic bias in the biology, study, samples, or analysis. Need to deal with 2-4 so that 1 becomes all that is left What are causes of association?

9. Recommendations I • Have crystal clear phenotype • Have clear analysis plan (know assumptions), don’t change in mid stream. • Design all study well (sample size, controls) • Both positive and negative studies • Have quality assurance and control procedures (data entry, sample tracking). • Control technical sources of error • Adjust for multiple testing (FDR or FWER). • Not just for markers, but models, covariates, multiple traits.

10. Recommendations II • Adjust for multiple testing (FDR or FWER). • Not just for markers, but models, covariates, multiple traits. • Reduction of association due to disequilibrium • Type most variation within a region • Controlling biological biases • Controlling for admixture, ancestry • Selection of controls • Selective censoring • Share all data

11. When should a reported causative allele be reported? • No result is ever 100% final, thus there needs to be room to report high confidence results, but enumerate issues that were not yet removed. • As Sherlock Holmes said, ‘ When you have eliminated all which are impossible, then whatever remains, however improbably, must be the truth. • An investigator needs to do a serious job of removing possible biases and is ready to move on to another part of the genome or move onto biological validation.