The ability to quantify somatic mutations in vivo provides a new sourc
e of toxicological information that is relevant to the assessment of c
ancer risk. The major experimental factors that influence the mutant f
requency are age, time after treatment, treatment protocol, and tissue
analyzed. In untreated mice, the mutant frequency increases very rapi
dly with age from conception to birth, more slowly from birth to adult
hood, and very slowly thereafter. All somatic tissues studied so far i
n adults have similar mutant frequencies, The time after treatment (ex
pression time) is the most important experimental variable. The minimu
m time for expression varies from one tissue to another. To be valid,
comparisons between tissues and treatments must be made after complete
expression of the mutations. Unfortunately, the minimum expression ti
me has not been characterized in most tissues. Since carcinogens are t
issue specific, and many chemicals are distributed in the body in comp
lex patterns, it is to be expected that there will be differences in t
he frequency of mutation induced in different tissues, As yet this has
not been extensively studied. Since the mutations detected by the tra
nsgenic assays are neutral, the mutants should accumulate as the integ
ral of the mutation rate. Hence chronic treatment protocols should be
more effective than acute and subacute protocols whenever they permit
substantially larger doses to be delivered. Such protocols are more re
levant to human exposure and are preferable for dose extrapolations. T
he importance of transcription in determining mutation rates is not ye
t known, but it is noteworthy that the transgenes are not transcribed
whereas the loci involved in carcinogenesis are. The mutation spectrum
is important for quantitative risk estimation. Risk estimation must a
lso take into account the spectrum of mutations that are involved in t
he carcinogenic process in the tissue and the spectrum of mutations th
at are detectable by the assay. New assays are being used to quantify
mutations in vivo in order to understand the carcinogenic process, to
search for the environmental factors involved in human cancer, and to
evaluate the carcinogenic hazard qualitatively.