Imperfect gold standard gene sets yield inaccurate evaluation of causal gene identification methods.
Commun Biol
; 7(1): 873, 2024 Jul 17.
Article
in En
| MEDLINE
| ID: mdl-39020054
ABSTRACT
Causal gene discovery methods are often evaluated using reference sets of causal genes, which are treated as gold standards (GS) for the purposes of evaluation. However, evaluation methods typically treat genes not in the GS positive set as known negatives rather than unknowns. This leads to inaccurate estimates of sensitivity, specificity, and AUC. Labeling biases in GS gene sets can also lead to inaccurate ordering of alternative causal gene discovery methods. We argue that the evaluation of causal gene discovery methods should rely on statistical techniques like those used for variant discovery rather than on comparison with GS gene sets.
Full text:
1
Database:
MEDLINE
Main subject:
Reference Standards
Limits:
Humans
Language:
En
Journal:
Commun Biol
Year:
2024
Type:
Article
Affiliation country:
United States