Clustering of hepatotoxins based on mechanism of toxicity using gene expression profiles.

Microarray technology, which allows one to quantitate the expression of thousands of genes simultaneously, has begun to have a major impact on many different areas of drug discovery and development. The question remains of whether microarray analysis and gene expression signature profiles can be applied to the field of toxicology. To date, there are very few published studies showing the use of microarrays in toxicology and important questions remain regarding the predictability and accuracy of applying gene expression profiles to toxicology. To begin to address these questions, we have treated rats with 15 different known hepatotoxins, including allyl alcohol, amiodarone, Aroclor 1254, arsenic, carbamazepine, carbon tetrachloride, diethylnitrosamine, dimethylformamide, diquat, etoposide, indomethacin, methapyrilene, methotrexate, monocrotaline, and 3-methylcholanthrene. These agents cause a variety of hepatocellular injuries including necrosis, DNA damage, cirrhosis, hypertrophy, and hepatic carcinoma. Gene expression analysis was done on RNA from the livers of treated rats and was compared against vehicle-treated controls. The gene expression results were clustered and compared to the histopathology findings and clinical chemistry values. Our results show strong correlation between the histopathology, clinical chemistry, and gene expression profiles induced by the agents. In addition, genes were identified whose regulation correlated strongly with effects on clinical chemistry parameters. Overall, the results suggest that microarray assays may prove to be a highly sensitive technique for safety screening of drug candidates and for the classification of environmental toxins.

Evaluation of the extent of nonlinearity in reportable range studies.

OBJECTIVES: To extend the polynomial method for evaluating linearity in 2 ways. First, we developed a screen to ascertain whether the data were precise enough to permit a reliable evaluation of linearity and therefore eliminate findings of linearity due to low statistical power. Second, we assessed whether the degree of nonlinearity detected by the polynomial method was clinically relevant using a statistically rigorous method. METHODS: Because we assessed linearity relative to a clinically determined level of importance instead of the default value of zero, we used sampling theory based on the noncentral chi(2) distribution. Using statistical power calculations, we incorporated a screen for imprecision that guarantees that the probability of correctly identifying nonlinear methods is at least 80%. RESULTS: With the described methods, we achieved a sensitivity of at least 80% and a specificity of at least 95%. When the data were too imprecise to achieve a sensitivity of 80%, no determination of linearity was made. This procedure mimics the practice in manual inspection of flagging data that appear imprecise by visual inspection and halting the evaluation. CONCLUSIONS: Formal statistical tests for precision and amount of nonlinearity are advantageous because they allow us to quantify and limit classification errors. By formalizing these various aspects of linearity assessment, we maintain some of the complex features of manual methods while making the linearity assessment feasible to apply to a high volume of assessments and removing the between-analyst variability.

Privileged molecules for protein binding identified from NMR-based screening.

A statistical analysis of NMR-derived binding data on 11 protein targets was performed to identify molecular motifs that are preferred for protein binding. The analysis indicates that compounds which contain a biphenyl substructure preferentially bind to a wide range of proteins and that high levels of specificity (>250-fold) can be achieved even for these small molecules. These results suggest that high-throughput screening libraries that are enriched with biphenyl-containing compounds can be expected to have increased chances of yielding high-affinity ligands for proteins, and they suggest that the biphenyl can be utilized as a template for the discovery and design of therapeutics with high affinity and specificity for a broad range of protein targets.

A method for proficiency testing of small peer groups in the College of American Pathologists Coagulation Surveys.

OBJECTIVE: To develop a grading scheme for the proficiency testing of small peer groups of fewer than 10 members for the prothrombin time (PT) and activated partial thromboplastin time (APTT). METHODS: A modified target value for small peer groups was derived based on the assumption that measurement variability in the PT and APTT is more greatly influenced by variations in reagents than in instruments. Criteria for grading were established by statistical simulation to achieve misclassification errors of less than 5% for both incorrectly passing and failing participants. College of American Pathologists Coagulation Survey data were analyzed to determine the number of additional laboratories graded using the proposed scheme, as well as the failure rates among participants in the small peer groups. RESULTS: The modified target value for small peer groups is a weighted average between the mean of the peer group and the mean of all participants using the same reagent (reagent group). Peer groups with as few as 4 members can be graded provided that specific criteria are satisfied: there must be at least 5 peer groups for the same reagent, at least 3 of these 5 peer groups must have more than 3 members, and the coefficient of variation for the reagent group must be less than 10%. This proposed grading scheme decreased the number of ungraded laboratories by 44% to 46% for the PT and 42% to 55% for the APTT. The percentage of failing grades among participants in the small peer groups ranged from 1.3% to 4.1% for the PT and 1.4% to 7.2% for the APTT. These failure rates were 2.8- to 13.0-fold higher than the failure rates in large peer groups (P < or = .05). CONCLUSIONS: The proposed small peer group grading scheme can improve the effectiveness of College of American Pathologists proficiency testing for the PT and APTT and may also be generally applicable to other test methods and analytes.

The accuracy of laboratory measurements in clinical chemistry: a study of 11 routine chemistry analytes in the College of American Pathologists Chemistry Survey with fresh frozen serum, definitive methods, and reference methods.

CONTEXT: Better procedures are needed whereby national proficiency testing survey providers can assess and improve the accuracy of laboratory measurements in clinical chemistry. SETTING: The 1994 College of American Pathologists Comprehensive Chemistry Survey. DESIGN: This study of matrix effects and the accuracy of laboratory measurements for 11 analytes linked the logistics of the Survey to definitive methods at the National Institutes of Standards and Technology, reference methods at the Centers for Disease Control and Prevention, proficiency testing materials, and a fresh frozen serum sample. The data were analyzed with a statistical model of laboratory measurements. RESULTS: (1) Matrix biases affected the results reported from 69% of the 644 peer group/survey specimen pairs evaluated. (2) Because of matrix biases, the reference value was the correct target value only 32% of the time; thus, the traceability established by definitive method and reference method value assignments on Chemistry Survey specimens did not assure accuracy on patient samples. (3) In contrast to matrix biases, the error caused by random matrix effects with proficiency testing samples was about the same as that caused by random specimen effects with fresh frozen serum, and both were less than within-run random analytic error. (4) Calibration biases occurred in 73% of the 180 peer groups evaluated, and, after matrix biases were removed, the total variance of interlaboratory measurements was due to peer group calibration bias (48%), within-peer-group random calibration error (31 %), within-run random error (14%), and random specimen effects (7%). CONCLUSIONS: An opportunity exists to improve method calibration accuracy in clinical chemistry. With improved design, national proficiency testing surveys can monitor and help reduce method calibration error by converting reported survey results to a true accuracy base that predicts accuracy on patient samples. For medical purposes, the correct target values on artificial (matrix-modified) chemistry materials are reference values adjusted for the matrix bias of each peer group. Matrix biases estimated by the use of fresh frozen serum can be used as factors to transfer the accuracy of definitive methods from artificial reference materials to patient samples.