Prediction of chemical carcinogenicity in rodents from in vitro genetic toxicity assays.

Four widely used in vitro assays for genetic toxicity were evaluated for their ability to predict the carcinogenicity of selected chemicals in rodents. These assays were mutagenesis in Salmonella and mouse lymphoma cells and chromosome aberrations and sister chromatid exchanges in Chinese hamster ovary cells. Seventy-three chemicals recently tested in 2-year carcinogenicity studies conducted by the National Cancer Institute and the National Toxicology Program were used in this evaluation. Test results from the four in vitro assays did not show significant differences in individual concordance with the rodent carcinogenicity results; the concordance of each assay was approximately 60 percent. Within the limits of this study there was no evidence of complementarity among the four assays, and no battery of tests constructed from these assays improved substantially on the overall performance of the Salmonella assay. The in vitro assays which represented a range of three cell types and four end points did show substantial agreement among themselves, indicating that chemicals positive in one in vitro assay tended to be positive in the other in vitro assays.

Statistical studies in genetic toxicology: a perspective from the U.S. National Toxicology Program.

This paper surveys recent, as yet unpublished, statistical studies arising from research in genetic toxicology within the U.S. National Toxicology Program (NTP). These studies all involve analyses of data from Ames Salmonella/microsome mutagenicity tests, but the statistical methodologies are broadly applicable. Three issues are addressed: First, what is a tenable sampling model for Ames test data, and how does one best test the adequacy of the Poisson sampling assumption? Second, given that nonmonotone dose-response curves are fairly common in the Salmonella assay, what new statistical techniques or modifications of existing ones seem appropriate to accommodate to this reality? Finally, an intriguing question: How can the extensive NTP Ames test data base be used to assess the characteristics of any mutagen-nonmutagen decision rule? The last issue is illustrated with the commonly used "two-times background" rule.

Predicting carcinogenicity by using batteries of dependent short-term tests.

Among the various methods for predicting carcinogenicity from a battery of short-term tests (STTs), the carcinogenicity prediction and battery selection (CPBS) procedure is the most prominent. A major assumption of CPBS is that the STTs used in the prediction are conditionally independent. Results of recent National Toxicology Program studies of four commonly used in vitro STTs contradict this assumption, thereby necessitating modification of CPBS to accommodate dependencies. This is accomplished via log-linear modeling, which then also yields an important dividend: standard errors for the predicted probabilities of carcinogenicity.

Some comments on potency measures in mutagenicity research.

In this article, the measurement of the potency of a chemical or mixture from its dose response in a particular assay is addressed. Attention is focused on data from the Ames Salmonella assay. Three measures of potency are explored and shown to be highly correlated. The presentation then discusses specific areas of research that might benefit from a study of potency.

Prediction of rodent carcinogenicity utilizing a battery of in vitro and in vivo genotoxicity tests.

The primary purpose of this study is to investigate the degree to which we can improve the prediction of rodent carcinogenicity (CA) by combining results from an in vitro and two in vivo genotoxicity tests. We used the Ames Salmonella assay (SAL) for the in vitro test and the micronucleus assay (MNC) and chromosome aberration assay (ABS) in mouse bone marrow cells for the two in vivo tests. We collected complete assay data for 82 chemicals (55 carcinogens and 27 noncarcinogens) from the NTP data base and the IARC monograph series. Our results indicate that: (1) only SAL affects the predictivity of CA, (2) MNC has a strong association with ABS, and (3) SAL predicts ABS. It has been known for some time that once the SAL assay result is available for prediction, other in vitro mutation tests provide little additional information for predicting CA. Our study indicates that the same conclusion holds for CA, SAL, MNC, and ABS.

Predicting rodent carcinogenicity using potency measures of the in vitro sister chromatid exchange and chromosome aberration assays.

In vitro sister chromatid exchange (SCE) and chromosome aberration (ABS) tests have been extensively used to identify potential rodent carcinogens. A number of measures of potency were developed to describe in vitro SCE and ABS test results: the dose needed to induce a unit increase over the control; the lowest effective dose; the slope of the ordinary linear regression; the maximum observed slope; and the maximum fold increase over background. The ability of these potency measures to predict the qualitative and quantitative carcinogenicity of chemicals was compared to the predictivity of the qualitative in vitro responses. The results of the analyses showed that the quantitative measures of the SCE or ABS responses only minimally increased the predictivity of carcinogenesis when compared to the predictivity using the qualitative responses.

Evaluation of four in vitro genetic toxicity tests for predicting rodent carcinogenicity: confirmation of earlier results with 41 additional chemicals.

The effectiveness of four in vitro short-term tests (STT) for genetic toxicity, induction of mutations in Salmonella (SAL) and mouse lymphoma L5178Y cells (MLA), and induction of sister chromatid exchanges (SCE) and chromosome aberrations (ABS) in Chinese hamster ovary cells that are used for predicting rodent carcinogenicity were examined. The in vitro results were compared with the results from 41 rodent carcinogenicity studies performed by the National Toxicology Program. The predictive values of, and interrelationships among, the STT for these 41 chemicals were similar to those previously reported for 73 chemicals and confirm those earlier results [Tennant RW, Margolin BH, Shelby MD, Zeiger E, Haseman JK, Spalding J, Caspary W, Resnick M, Stasiewicz S, Anderson B, Minor R (1987): Science 236:933-941]. Because of this similarity among the two datasets, the chemicals were combined into a single dataset of 114. The results with 114 chemicals show that SAL had the lowest sensitivity (.48) and the highest specificity (.91), whereas MLA had the highest sensitivity (.72) and the lowest specificity (.40). The concordances of the test results with rodent carcinogenicity were .66, .61, .59, and .59, for SAL, ABS, SCE, and MLA, respectively. Salmonella was the most predictive for carcinogenicity; 89% of the chemicals mutagenic in SAL were carcinogenic in rodents, however a negative result in any or all of the STT was not indicative of noncarcinogenicity. The STT results reported here show good agreement with the potential electrophilicity of the chemicals, and the majority of carcinogens that are undetected by the STT do not have an electrophilic structure. There was no complementarity among the tests and no combination of the four tests was more effective than any single test for predicting carcinogenicity.

Report and summary of the major conclusions from statistics in genotoxicity testing working group from the International Workshop on Genotoxicity Test Procedures (IWGTP), March 1999.

A working group of five statisticians experienced in the use of statistical methods in mutagenicity reviewed aspects of the statistical analysis of genotoxicity test procedures. Issues discussed included methods for integrating biological importance and statistical significance, the relationship of the experimental unit to the experimental design, and the impact of new developments in statistics and computing. Three major recommendations were made relating to the need for: (1) the effective use of statistical advice in designing interlaboratory and intralaboratory investigations; (2) the development of appropriate experimental designs for new assays; and (3) education and training in the use of statistical methodology in mutagenicity testing. Environ. Mol. Mutagen. 35:260-263, 2000 Published 2000 Wiley-Liss, Inc.

Predicting rodent carcinogenicity from mutagenic potency measured in the Ames Salmonella assay.

Many in vitro tests have been developed to identify chemicals that can damage cellular DNA or cause mutations, and secondarily to identify potential carcinogens. The test receiving by far the most use and attention has been the Salmonella (SAL) mutagenesis test developed by Ames and colleagues [(1973): Proc Natl Acad Sci USA 70:2281-2285; (1975): Mutat Res 31:347-364], because of its initial promise of high qualitative (YES/NO) predictivity for cancer in rodents and, by extension, in humans. In addition to the initial reports of high qualitative predictivity, there was also an early report by Meselson and Russell [in Hiatt HH et al (1977): "Origins of Human Cancer, Book C: Human Risk Assessment," pp 1473-1481] of a quantitative relationship between mutagenic potency measured in SAL and carcinogenic potency measured in rodents, for a small number of chemicals. However, other reports using larger numbers of chemicals have found only very weak correlations. The primary purpose of this study was to determine whether mutagenic potency, as measured in a number of different ways, could be used to improve predictivity of carcinogenicity, either qualitatively or quantitatively. To this end, eight measures of SAL mutagenic potency were used. This study firmly establishes that the predictive relationship between mutagenic potency in SAL and rodent carcinogenicity is, at best, weak. When predicting qualitative carcinogenicity, only qualitative mutagenicity is useful; none of the quantitative measures of potency considered improves the carcinogenicity prediction. In fact, when qualitative mutagenicity is forced out of the model, the quantitative measures are still not predictive of carcinogenicity. When predicting quantitative carcinogenicity, several possible methods were considered for summarizing potency over all experiments; however, in all cases, the relationship between mutagenic potency predictors and quantitative carcinogenicity is very weak.

Study design and sample sizes for a lacI transgenic mouse mutation assay.

Design features that adjust and account for excess variation in a transgenic mouse mutation assay based on a lacI target transgene from E. coli are considered. These features include proper identification of plate, packaging reaction, and animal identifier codes throughout the experimental and analysis phases of the study, "blocking" of exposed and unexposed animals when preparing and plating multiple packaging reactions from the same genomic DNA sample, separating sectored mutant plaques and complete mutant plaques before performing any quantitative analyses, and testing for sources of excess variation attributable to features of the experimental protocol--such as plate-to-plate (within packaging reactions), packaging reaction-to-packaging reaction (within animals), and animal-to-animal (within study). Control and ethylnitrosourea-treated animal data are presented from a fully designed study in the lacI assay. The study design incorporates many of these experimental principles. Statistical methods to identify excess variability are noted, and the designed study data are used to illustrate the types of variability encountered in practice. A standard statistical test for two-sample testing is highlighted, from which recommendations are made for sample size selection in future studies.

Sources of variability in data from a lacI transgenic mouse mutation assay.

Experimental features of a transgenic mouse mutation assay based on a lacI target transgene from Escherichia coli are considered in detail. Sources of variability in the experimental protocol that can affect the statistical nature of the observations are examined with the goal of identifying sources of excess variation in the observed mutant fractions. The sources include plate-to-plate (within packages), package-to-package (within animals), and animal-to-animal (within study) variability. Data from two laboratories are evaluated, using various statistical methods to identify excess variability. Results suggest only scattered patterns of excess variability, except possibly in those cases where genomic DNA from test animals is stored for extended periods (e.g., > 90 days) after isolation from tissues. Further study is encouraged to examine the validity and implications of this time/storage-related effect.

Cigarette smoking and sperm density: a meta-analysis.

OBJECTIVE: To quantify, through meta-analysis techniques, the association between cigarette smoking and sperm density. METHODS: The logarithm of the ratio of mean sperm density for smokers to that for nonsmokers for the studies included in this meta-analysis was regressed against a constant, an indicator of study population source (infertility clinic patients or normal men), minimum number of cigarettes smoked per day among smokers (< 10, > or = 10), exclusion of azoospermic men (yes/no), number of semen specimens analyzed (one versus two), and blinding of laboratory personnel to the smoking status of the study participants (yes/no). Regression analyses were performed both unweighted and weighted inversely by study size. A qualitative and quantitative assessment of the relationship between the numbers of cigarettes smoked per day and sperm density was performed. RESULTS: Results of the meta-analysis indicate that smokers' sperm density is on average 13% to 17% (95% confidence interval = 8.0, 21.5) lower than that of nonsmokers. No other factors besides cigarette smoking were found to be independent predictors of sperm density. No clear dose-response relationships between the numbers of cigarettes smoked per day and sperm density emerged. Research conducted by the authors supports the findings of the meta-analysis. CONCLUSION: Cigarette smoking is associated with lowered sperm density. The inconsistency in the literature with regard to this conclusion appears to be the result of small sample sizes in most studies.

Quantitative methods for assessing a synergistic or potentiated genotoxic response.

The problem of assessing chemical interactions in studies of genotoxicity is discussed. Attention is focused on assessing possible synergism or potentiation when the observed genotoxic response is binary (yes-no). Different forms of enhancement are distinguished based upon different assumptions on the genotoxic activity of the experimental treatments. A generalized linear statistical model is considered that links the probability of the binary response to the doses, and data-analytic strategies are described for detecting synergy and potentiation in factorially designed experiments. This approach is illustrated with a series of analyses of various genotoxicity data-sets.

Statistical methods for the Ames Salmonella assay: a review.

The Ames Salmonella assay remains the most widely used in vitro genotoxicity assay. Several statistical methods have been proposed for its analysis [B.H. Margolin, N. Kaplan, E. Zeiger, Statistical analysis of the Ames Salmonella/microsome test, Proc. Natl. Acad. Sci., 78 (1981) 3779-3783; L.E. Myers, N.H. Saxton, L.I. Southerland, T.J. Wolff, Regression analysis of Ames test data, Environ. Mol. Mutagen., 3 (1981) 575-586; A.G. Stead, V. Hasselblad, J.P. Creason, L. Claxton, Modelling the Ames test, Mutation Res., 85 (1981) 13-27; L. Bernstein, J. Kaldor, J. McCaan, M.C. Pike, An empirical approach to the statistical analysis of mutagenesis data from the Salmonella test, Mutation Res., 97 (1982) 267-281; N.E. Breslow, Extra-Poisson variation in log-linear models, Appl. Stat., 33 (1984) 38-44; J. Wahrendorf, G.A.T. Mahon, M. Schumacher, A nonparametric approach to the statistical analysis of mutagenicity data, Mutation Res., 147 (1985) 5-13; D.G. Simpson, B.H. Margolin, Recursive nonparametric testing for dose-response relationships subject to downturns at high doses, Biometrika, 73 (1986) 589-596; D.G. Simpson, B.H. Margolin, Nonparametric testing for dose-response curves subject to downturns: Asymptotic power considerations, Annals Stat., 18 (1990) 373-390.]. In this paper we review recent literature to see what statistical methods are in fact employed for the analysis of the Ames assay. We then note that these methods can be classified into a common category in the framework of Haynes and Eckardt's mutation induction kinetics model [R.H. Haynes, F. Eckardt, Mathematical analysis of mutation induction kinetics, in: F.J. de Serres, A. Hollaender (Eds. ), Chemical Mutagens, Principles and Methods for Their Detection, Vol. 6, Plenum, New York, 1980, pp. 271-307]. The value in knowing this is that most methods of analysis considered here will likely exhibit common statistical behavior. These analyses are computationally intensive, e.g., [B.H. Margolin, N. Kaplan, E. Zeiger, Statistical analysis of the Ames Salmonella/microsome test, Proc. Nat. Acad. Sci., 78 (1981) 3779-3783], hence the ready availability of computer programs is essential if biologists are to use these methods. We briefly review two statistical software programs that are available in the public domain, and describe in detail a third program, Salm, [B.H. Margolin, N. Kaplan, E. Zeiger, Statistical analysis of the Ames Salmonella/microsome test, Proc. Nat. Acad. Sci., 78 (1981) 3779-3783; B.H. Margolin, B.S. Kim, K. Risko, The Ames Salmonella/microsome assay: Issues of inference and validation, J. Amer. Stat. Assoc., 84 (1989) 651-661]. The Salm program is obtainable through the file transfer protocol (ftp) or using a WWW browser. Finally, we discuss two statistical consequences of naively applying the two-fold rule, a method of analysis employed by a number of researchers.

Effects of the hepatic S9 fraction from aroclor-1254-treated rats on the mutagenicity of benzo[alpha]pyrene and 2-aminoanthracene in the Salmonella/microsome assay.

The mutagenicity of benzo[alpha]pyrene and 2-aminoanthracene for Salmonella typhimurium TA98 in the plate-incorporation test was studied using liver S9 from untreated and aroclor-1254-treated rats. The induction of liver S9 protein, arylhydrocarbon hydroxylase (AHH), and cytochrome P448/450 was followed with time. There was no change in protein concentrations with induction; AHH and cytochrome levels were increased at 1, 3, 5 and 7 days post Aroclor treatment. Benzo[alpha]pyrene mutagenicity was enhanced with Aroclor treatment while 2-aminoanthracene mutagenicity was depressed. The benzo[alpha]pyrene mutagenicity showed a positive correlation with the levels of AHH and cytochrome on the plate; 2-aminoanthracene showed a negative correlation with activity in induced samples.

A statistical analysis for the mouse lymphoma cell forward mutation assay.

This paper illustrates the usefulness of solvent control trials and presents a statistical analysis for mouse L5178Y lymphoma data. Examination of solvent control trials establishes that the natural logarithm of mutant frequency is approximately normally distributed and that both the mean and variance of mutant frequency vary by trial. There is little evidence of downturns at higher doses in the dose-response curves studied; therefore, a trend test is proposed for the detection of an increasing dose-response curve. A Monte Carlo investigation confirms that the proposed trend test is better able to detect an increasing dose-response than 4 alternate methods of analysis.

Sources of variability in Ames Salmonella typhimurium tester strains: analysis of the International Collaborative Study on 'genetic drift'.

Data from 38 laboratories using 5 strains of Salmonella typhimurium (TA98, TA100, TA1535, TA1537, and TA1538) were analyzed to determine sources and magnitudes of test data variability. Each laboratory tested the mutagenicity of 4-nitroquinoline-N-oxide by the same protocol, using both its in-house cultures and a set of reference cultures provided to all laboratories. It was found that neither plate-to-plate nor day-to-day variability within a laboratory differed substantially between the in-house and reference cultures for any strain; this indicated no difference in the laboratories' handling of the two cultures. Not surprisingly, on average, plate-to-plate variability was substantially smaller than day-to-day variability within a laboratory, which, in turn, was substantially smaller than inter-laboratory variability. The solvent DMSO was found to have a small (6-7%) but statistically significant depressive effect on the spontaneous mutant frequency for the two plasmid-containing strains, TA98 and TA100, but not for the other three strains. When the mean value and variance of all laboratories for the in-house culture were compared with the corresponding reference culture values for each dose and strain, no major differences were seen. Any increase in mean or variance in the distribution of laboratory means in one of the two cultures could be ascribed largely to a small number of laboratories. Laboratories that reported 'high' or 'low' levels of spontaneous or induced revertants per plate tended to deviate in the same direction for most strains and for both in-house and reference cultures. If 'genetic drift' contributed to the inter-laboratory variability in this collaborative study, it was a minor component that went undetected in our analyses.

Contributions to the design and statistical analysis of in vivo SCE experiments.

Two issues that arise in the design and statistical analysis of in vivo SCE and similar experiments are considered. First, with regard to analysis, the merits of various methods of data transformation are explored in depth. The conclusion drawn is that common transformations of the type studied here seemingly offer little advantage in the assessment of whether a test agent induces SCE in a dose-related manner. Second, a proposal is made for a method to determine, subject to budgetary constraints, the desired numbers of animals/dose group and cells scored/animal. The approach advocated also lends itself to discussions weighing the gains and losses from possible reductions in the number of animals below the 'desired' levels.

Statistical modeling and analyses of a base-specific Salmonella mutagenicity assay.

Statistical features of a base-specific Salmonella mutagenicity assay are considered in detail, following up on a previous report comparing responses of base-specific Salmonella (Ames II) strains with those of traditional tester strains. In addition to using different Salmonella strains, the new procedure also differs in that it is performed as a microwell fluctuation test, as opposed to the standard plate or preincubation test. This report describes the statistical modeling of data obtained from the use of these new strains in the microwell test procedure. We emphasize how to assess any significant interactions between replicate cultures and exposure doses, and how to identify a significant increase in the mutagenic response to a series of concentrations of a test substance.