Development of a microarray platform for FFPET profiling: application to the classification of human tumors.

BACKGROUND: mRNA profiling has become an important tool for developing and validating prognostic assays predictive of disease treatment response and outcome. Archives of annotated formalin-fixed paraffin-embedded tissues (FFPET) are available as a potential source for retrospective studies. Methods are needed to profile these FFPET samples that are linked to clinical outcomes to generate hypotheses that could lead to classifiers for clinical applications. METHODS: We developed a two-color microarray-based profiling platform by optimizing target amplification, experimental design, quality control, and microarray content and applied it to the profiling of FFPET samples. We profiled a set of 50 fresh frozen (FF) breast cancer samples and assigned class labels according to the signature and method by van 't Veer et al 1 and then profiled 50 matched FFPET samples to test how well the FFPET data predicted the class labels. We also compared the sorting power of classifiers derived from FFPET sample data with classifiers derived from data from matched FF samples. RESULTS: When a classifier developed with matched FF samples was applied to FFPET data to assign samples to either "good" or "poor" outcome class labels, the classifier was able to assign the FFPET samples to the correct class label with an average error rate = 12% to 16%, respectively, with an Odds Ratio = 36.4 to 60.4, respectively. A classifier derived from FFPET data was able to predict the class label in FFPET samples (leave-one-out cross validation) with an error rate of approximately 14% (p-value = 3.7 x 10(-7)). When applied to the matched FF samples, the FFPET-derived classifier was able to assign FF samples to the correct class labels with 96% accuracy. The single misclassification was attributed to poor sample quality, as measured by qPCR on total RNA, which emphasizes the need for sample quality control before profiling. CONCLUSION: We have optimized a platform for expression analyses and have shown that our profiling platform is able to accurately sort FFPET samples into class labels derived from FF classifiers. Furthermore, using this platform, a classifier derived from FFPET samples can reliably provide the same sorting power as a classifier derived from matched FF samples. We anticipate that these techniques could be used to generate hypotheses from archives of FFPET samples, and thus may lead to prognostic and predictive classifiers that could be used, for example, to segregate patients for clinical trial enrollment or to guide patient treatment.

Two-year results of a feasibility study on antireflux transoral incisionless fundoplication using EsophyX.

BACKGROUND: A feasibility study (n = 19) evaluated the safety and initial efficacy of transoral incisionless fundoplication (TIF) for the treatment of gastroesophageal disease (GERD). The results at 1 year (n = 17) indicated that TIF was safe and had a significant effect on reducing GERD symptoms, proton pump inhibitor (PPI) usage, acid exposure, and small hiatal hernia. This study was designed to evaluate the long-term safety and durability of TIF. METHODS: Fourteen patients (50% female; median age, 34 years) completed the 2-year follow-up assessment tests. Three patients were excluded from the study after 1 year because two of them underwent retreatment and one was lost to follow-up. RESULTS: At 2 years, no adverse events related to TIF were reported. A >or=50% improvement in GERD-HRQL scores compared with those at baseline on PPIs was sustained by 64% of patients. TIF was effective in eliminating heartburn in 93% of patients and daily PPI therapy in 71% of patients. Significantly (p < 0.05) more patients were able to consume reflux-causing foods and maintain lifestyle activities without GERD symptoms compared with baseline on PPIs. Fundoplications were durable and maintained their geometric dimensions. TIF was effective in eliminating hiatal hernia in 60% of patients and esophagitis in 55% of patients. Global assessment of all outcomes in each patient revealed that 79% of patients experienced complete cure (29%) or remission (50%) of GERD at 2 years after TIF. CONCLUSION: The results at 2 years supported the long-term safety and durability of TIF and its sustained effect on the elimination of heartburn, esophagitis,

Reagent preparation and storage for amplification of microarray hybridization targets with a fully automated system.

The advent of automated systems for gene expression profiling has accentuated the need for the development of convenient and cost-effective methods for reagent preparation. We have developed a method for the preparation and storage of pre-aliquoted cocktail plates that contain all reagents required for amplification of nucleic acid by reverse transcription and in vitro transcription reactions. Plates can be stored at -80 degrees C for at least 1 month and kept in a hotel at 4 degrees C for at least 24 h prior to use. Microarray data quality generated from these pre-aliquoted reagent plates is not statistically different between cRNA amplified with stored cocktails and cRNA amplified with freshly prepared cocktails. Deployment of pre-aliquoted, stored cocktail plates in a fully automated system not only increases the throughput of amplifying cRNA targets from thousands of RNA samples, but could also considerably reduce reagent costs and potentially improve process robustness.