title: Analysis of variability in high throughput screening data: applications to melanoma cell lines and drug responses.
abstract: High-throughput screening (HTS) strategies and protocols have undergone significant development in the last decade. It is now possible to screen hundreds of thousands of compounds, each exploring multiple biological phenotypes and parameters, against various cell lines or model systems in a single setting. However, given the vast amount of data such studies generate, the fact that they use multiple reagents, and are often technician-intensive, questions have been raised about the variability, reliability and reproducibility of HTS results. Assessments of the impact of the multiple factors in HTS studies could arguably lead to more compelling insights into the robustness of the results of a particular screen, as well as the overall quality of the study. We leveraged classical, yet highly flexible, analysis of variance (ANOVA)-based linear models to explore how different factors contribute to the variation observed in a screening study of four different melanoma cell lines and 120 drugs over nine dosages studied in two independent academic laboratories. We find that factors such as plate effects, appropriate dosing ranges, and to a lesser extent, the laboratory performing the screen, are significant predictors of variation in drug responses across the cell lines. Further, we show that when sources of variation are quantified and controlled for, they contextualize claims of inconsistencies and reveal the overall quality of the HTS studies performed at each participating laboratory. In the context of the broader screening study, we show that our analysis can also elucidate the robust effects of drugs, even those within specific cell lines.
authors.affiliation: J. Craig Venter Institute, La Jolla, CA, USA.|University of California, San Diego, CA, USA.
authors.forename: Kuan-Fu
authors.initials: KF
authors.lastname: Ding
authors.affiliation: Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.
authors.forename: Darren
authors.initials: D
authors.lastname: Finlay
authors.affiliation: The Translational Genomics Research Institute, Phoenix, AZ, USA.
authors.forename: Hongwei
authors.initials: H
authors.lastname: Yin
authors.affiliation: The Translational Genomics Research Institute, Phoenix, AZ, USA.
authors.forename: William P D
authors.initials: WPD
authors.lastname: Hendricks
authors.affiliation: The Translational Genomics Research Institute, Phoenix, AZ, USA.
authors.forename: Chris
authors.initials: C
authors.lastname: Sereduk
authors.affiliation: The Translational Genomics Research Institute, Phoenix, AZ, USA.
authors.forename: Jeffrey
authors.initials: J
authors.lastname: Kiefer
authors.affiliation: The Translational Genomics Research Institute, Phoenix, AZ, USA.
authors.forename: Aleksandar
authors.initials: A
authors.lastname: Sekulic
authors.affiliation: Yale University, New Haven, CT, USA.
authors.forename: Patricia M
authors.initials: PM
authors.lastname: LoRusso
authors.affiliation: Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.
authors.forename: Kristiina
authors.initials: K
authors.lastname: Vuori
authors.affiliation: The Translational Genomics Research Institute, Phoenix, AZ, USA.
authors.forename: Jeffrey M
authors.initials: JM
authors.lastname: Trent
authors.affiliation: J. Craig Venter Institute, La Jolla, CA, USA.|University of California, San Diego, CA, USA.|The Translational Genomics Research Institute, Phoenix, AZ, USA.
authors.forename: Nicholas J
authors.initials: NJ
authors.lastname: Schork
mesh_terms: D000704:Analysis of Variance; D000969:Antinematodal Agents / Q000494:pharmacology* / Q000627:therapeutic use; D045744:Cell Line, Tumor; D055808:Drug Discovery / Q000379:methods*; D057166:High-Throughput Screening Assays / Q000379:methods*; D006801:Humans; D008545:Melanoma / Q000188:drug therapy*; D015203:Reproducibility of Results
chemical_list: D000969:Antinematodal Agents
keywords: computational modeling; drug screens; high-throughput screening; melanoma; variability