Developmental toxicity experiments are designed to assess potential adverse
effects of drugs and other exposures on developing fetuses from pregnant d
ams. Extrapolation to humans is a very difficult problem. An important issu
e here is whether risk assessment should be based on the fetus or the litte
r level. In this paper, fetus and litter-based risks that properly account
for cluster size are defined and compared for the beta-binomial model and a
conditional model for clustered binary data. It is shown how the hierarchi
cal structure of non-viable implants and viable but malformed offspring can
be incorporated. Risks based on a joint model for death/resorption and mal
formation are contrasted with risks based on an adverse event defined as ei
ther death/resorption or malformation. The estimation of safe exposure leve
ls for all risk types is discussed and it is shown how estimation of the cl
uster size distribution affects variance estimation. The methods are applie
d to data collected under the National Toxicology Program and in large samp
le simulations.