Analytical validation of the Oncotype DX prostate cancer assay - a clinical RT-PCR assay optimized for prostate needle biopsies.

BACKGROUND: The Oncotype DX Prostate Cancer Assay is a multi-gene RT-PCR expression assay that was developed for use with fixed paraffin-embedded (FPE) diagnostic prostate needle biopsies containing as little as 1 mm of prostate tumor in the greatest dimension. The assay measures expression of 12 cancer-related genes representing four biological pathways and 5 reference genes which are algorithmically combined to calculate the Genomic Prostate Score (GPS). This biopsy-based assay has been analytically and subsequently clinically validated as a predictor of aggressive prostate cancer. The aim of this study was to validate the analytical performance of the Oncotype DX Prostate Cancer Assay using predefined acceptance criteria. RESULTS: The lowest quartile of RNA yields from prostate needle biopsies (six 5 µm sections) was between 19 and 34 ng. Analytical validation of the process requiring as little as 5 ng of RNA met all pre-defined acceptance criteria. Amplification efficiencies, analytical sensitivity, and accuracy of gene assays were measured by serially diluting an RNA sample and analyzing features of the linear regression between RNA expression measured by the crossing point (Cp) versus the log2 of the RNA input per PCR assay well. Gene assays were shown to accurately measure expression over a wide range of inputs (from as low as 0.005 ng to 320 ng). Analytical accuracy was excellent with average biases at qPCR inputs representative of patient samples <9.7% across all assays while amplification efficiencies were within ±6% of the median. Assessments of reproducibility and precision were performed by testing 10 prostate cancer RNA samples over multiple instruments, reagent lots, operators, days (precision), and RNA input levels (reproducibility) using appropriately parameterized linear mixed models. The standard deviations for analytical precision and reproducibility were 1.86 and 2.11 GPS units (100-unit scale) respectively. CONCLUSIONS: The Oncotype DX Prostate Cancer Assay, a clinical RT-PCR assay specifically designed for use with prostate needle biopsies, has been analytically validated using very limited RNA inputs. The assay requirements and analytical performance will provide physicians with test results from a robust and reliable assay which will enable improved treatment decisions for men diagnosed with early-stage prostate cancer.

Diagnostic imaging rates for head injury in the ED and states' medical malpractice tort reforms.

OBJECTIVE: Physicians' fears of being sued may lead to defensive medical practices, such as ordering nonindicated medical imaging. We investigated the association between states' medical malpractice tort reforms and neurologic imaging rates for patients seen in the emergency department with mild head trauma. METHODS: We assessed neurologic imaging among a national sample of 8588 women residing in 10 US states evaluated in an emergency setting for head injury between January 1, 1992, and December 31, 2001. We assessed the odds of imaging as it varied by the enactment of medical liability reform laws. RESULTS: The medical liability reform laws were significantly associated with the likelihood of imaging. States with laws that limited monetary damages (odds ratio [OR], 0.63; 95% confidence interval [CI], 0.40-0.99), mandated periodic award payments (OR, 0.64; 95% CI, 0.43-0.97), or specified collateral source offset rules (OR, 0.62; 95% CI, 0.40-0.96) had an approximately 40% lower odds of imaging, whereas states that had laws that limited attorney's contingency fees had significantly higher odds of imaging (OR, 1.5; 95% CI, 0.99-2.4), compared to states without these laws. When we used a summation of the number of laws in place, the greater the number of laws, the lower the odds of imaging. In the multivariate analysis, after adjusting for individual and community factors, the total number of laws remained significantly associated with the odds of imaging, and the effect of the individual laws was attenuated, but not eliminated. CONCLUSION: The tort reforms we examined were associated with the propensity to obtain neurologic imaging. If these results are confirmed in larger studies, tort reform might mitigate defensive medical practices.

Screening mammography in the American elderly.

BACKGROUND: Substantial differences exist in estimates of the proportion of elderly women who undergo screening mammography and the impact of race and ethnicity on mammography usage. METHODS: A representative 5% sample of elderly women living in 11 Surveillance, Epidemiology, and End Results areas from 1991 to 2001 was constructed using Medicare data. Biennial rates of screening mammography (at least one mammogram within each 2-year period) were calculated for overlapping 2-year periods, adjusting to a 2000-2001 age and race distribution. Multivariate repeated-measures logistic regression was used to examine predictors of screening usage. RESULTS: The sample included 146,669 women. Between 1991 and 2001 the age- and race-adjusted proportion of women aged 65 years and older who underwent at least biennial screening mammography increased from 35.8% to 47.9%. Mammography screening increased for all racial and ethnic groups, but remained significantly higher for non-Hispanic white women as compared with all other groups. The biennial screening rate in 2000-2001 was 50.6% for non-Hispanic white, 40.5% for African-American, 34.7% for Asian-American, 36.3% for Hispanic, and 12.5% for Native-American women. After controlling for age, site, physician access, comorbidities, education, and income, African Americans (odds ratio [OR] = 0.80, 95% confidence interval [CI] = 0.78-0.83), Asian Americans (OR=0.53, CI = 0.51-0.55), Hispanics (OR = 0.70, CI = 0.67-0.74), and Native Americans (OR=0.37, CI=0.29-0.46) were still all less likely than non-Hispanic white women to undergo screening. CONCLUSIONS: Elderly women undergo significantly less mammography screening than is suggested by self-reported surveys. All groups of non-white women undergo less screening than do white women. The magnitude of the difference in screening rates comparing Asian-American and Hispanic women with white women is especially large; however, other studies have questioned the sensitivity of Medicare data for identifying people of Asian and Hispanic ethnicity. For African-American women, the magnitude of the gap is smaller, but it is of concern that the gap in screening as compared with white women has grown over time.

Generalized additive models with interval-censored data and time-varying covariates: application to human immunodeficiency virus infection in hemophiliacs.

We describe a method for extending smooth nonparametric modeling methods to time-to-event data where the event may be known only to lie within a window of time. Maximum penalized likelihood is used to fit a discrete proportional hazards model that also models the baseline hazard, and left-truncation and time-varying covariates are accommodated. The implementation follows generalized additive modeling conventions, allowing both parametric and smooth terms and specifying the amount of smoothness in terms of the effective degrees of freedom. We illustrate the method on a well-known interval-censored data set on time of human immunodeficiency virus infection in a multicenter study of hemophiliacs. The ability to examine time-varying covariates, not available with previous methods, allows detection and modeling of nonproportional hazards and use of a time-varying covariate that fits the data better and is more plausible than a fixed alternative.