Byung Soo Kim

Motivation: It is a common practice in cancer microarray experiments that a normal tissue is collected from the same individual from whom the tumor tissue was taken. The indirect design is usually adopted for the experiment that uses a common reference RNA hybridized both to normal and tumor tissues. However, it is often the case that the test material is not large enough for the experimenter to extract enough RNA to conduct the microarray experiment. Hence, collecting ncases does not necessarily end up with a matched pair sample of size n. Instead we usually have a matched pair sample of size n₁, and two independent samples of sizes n₂ and n₃, respectively, for ‘reference versus normal tissue only’ and ‘reference versus tumor tissue only’ hybridizations (n = n₁ + n₂ + n₃). Standard statistical methods need to be modified and new statistical procedures are developed for analyzing this mixed dataset. Results: We propose a new test statistic, t₃, as a means of combining all the information in the mixed dataset for detecting differentially expressed (DE) genes between normal and tumor tissues. We employed the extended receiver operating characteristic approach to the mixed dataset. We devised a measure of disagreement between a RT–PCR experiment and a microarray experiment. Hotelling's T² statistic is employed to detect a set of DE genes and its prediction rate is compared with the prediction rate of a univariate procedure. We observe that Hotelling's T² statistic detects DE genes more efficiently than a univariate procedure and that further research is warranted on the formal test procedure using Hotelling's T² statistic. Contact:bskim@yonsei.ac.kr

The cDNA microarray has become a useful tool for observing the expression of thousands of genes simultaneously. However, obtaining good quality microarray data is not easy due to the inherent noise at various stages of the experiment. Therefore, it is essential to understand the source of the variation in the microarray experiment and its size as an initial step of the data analyses. The total RNA extracted from HT-1080 fibrosarcoma and normal rat tissues were hybridized to the cDNA microarrays with 0.5 K human and 5 K rat genes, respectively. A homotypic reaction and dye swap experiments were used to identify the sources of the variation. The relative fluorescent intensities of the microarray, if unnormalized, have a large variation, particularly in the lower intensity region. The distribution of the log intensity ratios also exhibit some departure from a band around zero, which is the distribution pattern expected when the majority of genes in the microarray are not regulated. Normalization of the log ratios is usually required as a means of preprocessing the data. We claim that a within-print tip group, an intensity-dependent normalization through a loess fit adjustment will be useful for this purpose, particularly in the initial stages of the microarray experiment. For proper data analysis, an understanding the source of the variation and preprocessing of data with a suitable normalization method will be important. It is important to have an interactive cooperation between a researcher and a statistician from the early stages of the study design and to the final stages of data analysis.

The comet assay is a sensitive and rapid method for detecting DNA damage and repair of damage in individual cells. It has been widely used in genetic toxicology, environmental biomonitoring, molecular and human epidemiology and clinical investigations, since it was first introduced by Östling and Johanson in 1984 and independently modified by Singh et al. and Olive et al. There are still several issues that have to be resolved before the comet assay is accepted as a standard assay for detecting DNA damage/repair in a single cell. One of the major issues is the proper quantification of DNA repair kinetics. This article develops a new quantitative measure of the DNA repair kinetics which is represented in the dose–time–response surface. For measuring the DNA repair kinetics, we propose to use the second derivative, 2D, of the dose–time–response surface. This approach enables us to represent with a single number the DNA repair activity of cells exposed to ionizing radiation, by combining all the information in the experiment. The computation procedure includes the application of linear regression. In our application to the assessment of radiation sensitivity of patients we considered for the response four DNA damage parameters, i.e. the tail moment, the tail length, the tail DNA and the tail inertia for constructing the dose–time–response surface. Based on the data from 25 patients we observed that the second derivatives based on the tail moment and the tail DNA showed high correlation and that the tail inertia might express a somewhat different aspect of the DNA damage/repair. Copyright © 2003 John Wiley & Sons, Ltd.

Since its introduction by Östling and Johanson [1984; Biochem Biophys Res Commun 123:291–298] and independent modifications by Singh et al. [1990; Exp Cell Res 175:184–191] and Olive et al. [1988; Radiat Res 112:86–94], the comet assay has been widely used in genetic toxicology, environmental biomonitoring, molecular and human epidemiology, and clinical investigations. There are still several issues to be resolved before the comet assay is accepted as a standard assay for detecting DNA damage and repair in a single cell. One of the major issues is the proper quantification of DNA damage/repair. The aim of this article is to develop a new quantitative measure of DNA damage/repair which is represented in the dose–time‐response surface. We propose to use the second derivative (2D) of the dose–time‐response surface for measuring DNA repair activity. This approach enables us to represent the DNA repair activity of cells exposed to a DNA‐damaging agent with a single number by combining all the information of a dose–time‐response experiment. The computation procedure includes the application of linear regression. An SAS/AF‐based program, “Comet Assay,” was developed for this computation and is freely available on the Internet. We considered the response of each of four DNA damage parameters: tail moment, tail length, tail DNA, and tail inertia for constructing the dose–time‐response surface. Using data from 25 patients, we observed that 2Ds based on tail moment and tail DNA were highly correlated and that tail inertia might provide information on a somewhat different aspect of DNA damage/repair. Environ. Mol. Mutagen. 40:50–56, 2002.

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.