The genetic interpretation of area under the ROC curve in genomic profiling.
paper
Cited
Public
- Authors
- Wray, Naomi R; Yang, Jian; Goddard, Michael E; Visscher, Peter M
- Year
- 2010
- Journal
- PLoS genetics
- PMID
- 20195508
- DOI
- 10.1371/journal.pgen.1000864
- PMCID
- PMC2829056
Genome-wide association studies in human populations have facilitated the creation of genomic profiles which combine the effects of many associated genetic variants to predict risk of disease. The area under the receiver operator characteristic (ROC) curve is a well established measure for determining the efficacy of tests in correctly classifying diseased and non-diseased individuals. We use quantitative genetics theory to provide insight into the genetic interpretation of the area under the ROC curve (AUC) when the test classifier is a predictor of genetic risk. Even when the proportion of genetic variance explained by the test is 100%, there is a maximum value for AUC that depends on the genetic epidemiology of the disease, i.e. either the sibling recurrence risk or heritability and disease prevalence. We derive an equation relating maximum AUC to heritability and disease prevalence. The expression can be reversed to calculate the proportion of genetic variance explained given AUC, disease prevalence, and heritability. We use published estimates of disease prevalence and sibling recurrence risk for 17 complex genetic diseases to calculate the proportion of genetic variance that a test must explain to achieve AUC = 0.75; this varied from 0.10 to 0.74. We provide a genetic interpretation of AUC for use with predictors of genetic risk based on genomic profiles. We provide a strategy to estimate proportion of genetic variance explained on the liability scale from estimates of AUC, disease prevalence, and heritability (or sibling recurrence risk) available as an online calculator.
The dependence of maximum AUC (AUCmax) from a genomic profile on heritability and disese prevalence.(A,B) Probability of disease versus genetic liability. (C,D) ROC curve [46].
Relationship between maximum AUC (AUCmax) from a genomic profile and heritability on the liability scale .For different disease prevalences (AβD) from simulation (dashed line) and from equation 3 (solid line).
The relationship between maximum AUC (AUCmax) from a genomic profile and heritability on the liability scale (dashed line) or heritability on the observed scale (solid line), for disease prevalences in order from top left, K = 0.001, 0.01, 0.1, 0.3.
β Prev
21β40 of 40
| Name | Type |
|---|---|
| A local | phenotype |
| Adad local | phenotype |
| advanced AMD local | phenotype |
| affected | phenotype |
| age-related macular degeneration | phenotype |
| AMD | phenotype |
| AMD cases local | cohort |
| Amend local | phenotype |
| Amum local | phenotype |
| auc | drug |
| AUCmax local | drug |
| AUCmax local | phenotype |
| bipolar disorder | phenotype |
| bladder cancer | phenotype |
| breast cancer | phenotype |
| broad sense heritability local | drug |
| cardiovascular events | phenotype |
| Caucasian genome local | cohort |
| CFH | gene |
| complex genetic disease local | phenotype |
| complex genetic diseases local | phenotype |
| controls | cohort |
| copy number variants | variant |
| coronary artery disease | phenotype |
| Crohn's disease | phenotype |
| de novo variant | variant |
| disease | phenotype |
| Disease_K0.01 local | phenotype |
| Disease_K0.5 local | phenotype |
| disease prevalence | phenotype |
| disease status | phenotype |
| family history positive | phenotype |
| G01 local | phenotype |
| general population | cohort |
| genetic liability | phenotype |
| genetic risk local | drug |
| genetic variants | cohort |
| genomic profile local | drug |
| Genomic profile local | drug |
| genomic profiles local | drug |
| genomic variance local | phenotype |
| heritability | phenotype |
| Heritability of liability local | phenotype |
| individuals with known disease status local | cohort |
| Janssens et al study local | cohort |
| liability | phenotype |
| Lifetime morbidity risk local | phenotype |
| Mendelian genetic disease local | phenotype |
| methylation status variants local | variant |
| monozygotic twin recurrence risk local | phenotype |
| non-heritable genetic variants local | variant |
| nuclear families local | cohort |
| P01 local | phenotype |
| p-factor | phenotype |
| phenotype | phenotype |
| prevalence local | phenotype |
| prostate cancer | phenotype |
| rare disease | phenotype |
| rheumatoid arthritis | phenotype |
| risk allele | cohort |
| rs1061170 local | variant |
| schizophrenia | phenotype |
| Scholl et al study local | cohort |
| Seddon et al twin study local | cohort |
| Shared genetic risk factors local | phenotype |
| sibling risk ratio local | phenotype |
| siblings | cohort |
| single nucleotide polymorphisms | variant |
| SLE | phenotype |
| test classifier local | drug |
| trait | phenotype |
| Twin cohort | cohort |
| type 1 diabetes | phenotype |
| type 2 diabetes | phenotype |
| unique environmental influences | phenotype |
| variant | cohort |
| Ξ»MZ local | phenotype |
| Ξ»S local | phenotype |
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