Increasing the Content of High-Content Screening: An Overview.
Target-based high-throughput screening (HTS) has recently been critiqued for its relatively poor yield compared to phenotypic screening approaches. One type of phenotypic screening, image-based high-content screening (HCS), has been seen as particularly promising. In this article, we assess whether HCS is as high content as it can be. We analyze HCS publications and find that although the number of HCS experiments published each year continues to grow steadily, the information content lags behind. We find that a majority of high-content screens published so far (60-80%) made use of only one or two image-based features measured from each sample and disregarded the distribution of those features among each cell population. We discuss several potential explanations, focusing on the hypothesis that data analysis traditions are to blame. This includes practical problems related to managing large and multidimensional HCS data sets as well as the adoption of assay quality statistics from HTS to HCS. Both may have led to the simplification or systematic rejection of assays carrying complex and valuable phenotypic information. We predict that advanced data analysis methods that enable full multiparametric data to be harvested for entire cell populations will enable HCS to finally reach its potential.
Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Shantanu
S
Singh
Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA anne@broadinstitute.org auguste@broadinstitute.org.
Anne E
AE
Carpenter
Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA École Normale Supérieure, 45, Rue d'Ulm, 75005 Paris.
Auguste
A
Genovesio
D001681:Biological Assay; D002626:Chemistry, Pharmaceutical / Q000379:methods; D055808:Drug Discovery; D057166:High-Throughput Screening Assays / Q000379:methods*; D015999:Multivariate Analysis; D016011:Normal Distribution; D010641:Phenotype; D060388:Support Vector Machine
Cell-based assays; high-content screening; image analysis; phenotypic drug discovery; statistical analyses