Quality Control of Quantitative High Throughput Screening Data.

Keith R Shockley,Soumendra N Lahiri,Shyamal D Peddada,Shuva Gupta,Shawn F Harris

doi:10.3389/fgene.2019.00387

Abstract

Quantitative high throughput screening (qHTS) experiments can generate 1000s of concentration-response profiles to screen compounds for potentially adverse effects. However, potency estimates for a single compound can vary considerably in study designs incorporating multiple concentration-response profiles for each compound. We introduce an automated quality control procedure based on analysis of variance (ANOVA) to identify and filter out compounds with multiple cluster response patterns and improve potency estimation in qHTS assays. Our approach, called Cluster Analysis by Subgroups using ANOVA (CASANOVA), clusters compound-specific response patterns into statistically supported subgroups. Applying CASANOVA to 43 publicly available qHTS data sets, we found that only about 20% of compounds with response values outside of the noise band have single cluster responses. The error rates for incorrectly separating true clusters and incorrectly clumping disparate clusters were both less than 5% in extensive simulation studies. Simulation studies also showed that the bias and variance of concentration at half-maximal response (AC50) estimates were usually within 10-fold when using a weighted average approach for potency estimation. In short, CASANOVA effectively sorts out compounds with “inconsistent” response patterns and produces trustworthy AC50 values.

Highlights

In 1978 the National Toxicology Program (NTP) was established to evaluate the toxicity and carcinogenicity of environmental chemicals
Concentration-response repeats having all responses across the concentration range located entirely within the noise band are removed, where the noise band is defined as ± 3 standard deviations (σ) of the response at the lowest where μ is the overall mean and ijk represents random error for concentration bin i, repeat j and observation k
CASANOVA was applied to publicly available Tox21 Phase II data related to stress response, nuclear receptor signaling and cell viability in order to assess the consistency of intrachemical response patterns within and between assays

Summary

Introduction

In 1978 the National Toxicology Program (NTP) was established to evaluate the toxicity and carcinogenicity of environmental chemicals. During the previous decade the NTP and other agencies, including the U.S Environmental Protection Agency (EPA), the National Center for Advancing Translational Sciences (NCATS), and the U.S Food and Drug Administration (FDA), established quantitative high throughput screening (qHTS) assays simultaneously screen 1000s of compounds and prioritize chemicals for further testing (Tice et al, 2013). The goal of these qHTS assays was to achieve the speed of evaluating

Methods

Results

Conclusion