High Throughput Screening — Methods, Statistics & Reproducible Workflows

Overview & scope

High throughput screening (HTS) at ChemDiv integrates automated liquid handling, multiplexed detection and robust analytics to test libraries ranging from focused collections (1k–10k) to large screening campaigns (100k+ wells). HTS supports biochemical target-based assays, cell-based phenotypic assays and high-content imaging. This document focuses on reproducible methods and quantitative acceptance criteria that enable translation from primary screen to validated leads.

Assay validation: Z′ factor, signal window (SW), and CV

Quantitative acceptance criteria are non-negotiable for reproducible HTS. Below are the formulas and interpretation used across ChemDiv screening operations.

Z′ factor

Define μ_p, σ_p as mean and SD of positive control wells; μ_n, σ_n for negative controls. The Z′ factor is computed as:

Z' = 1 - (3 * (σp + σn)) / |μp - μn|

Interpretation: Z' ≥ 0.5 considered excellent; 0 ≤ Z' < 0.5 acceptable with caution for complex phenotypic assays; Z' < 0 unacceptable. ChemDiv enforces plate-level Z′ thresholds prior to data release.

Signal window (SW) and coefficient of variation (CV)

Signal window SW = (μ_p − μ_n)/σ_n. Monitor CV = σ/μ for technical replicates — target CV < 10% for biochemical assays, allow higher CV for cell-based assays but track and document biological variability.

Normalization: B-score (median polish), Z-score, LOESS

Spatial biases (row/column) and skewed plate distributions require robust normalization. The B-score algorithm — median polish on rows and columns followed by scaling by MAD — is our default for plates with additive spatial effects. Use Z-score only for near-Gaussian plates without positional bias. LOESS or 2D surface fitting is appropriate for continuous gradients.

B-score pseudocode

Input: plate matrix P (r rows × c columns)
1. overall = median(P)
2. for iter until convergence:
     row_effect[i] = median(P[i,] - col_effect - overall)
     subtract row_effect from P
     col_effect[j] = median(P[,j] - row_effect - overall)
     subtract col_effect from P
3. residuals = P - (overall + row_effect + col_effect)
4. B-score = residuals / MAD(residuals)
      

MAD = median absolute deviation; robust medians reduce influence of hits on plate correction. On pilot datasets we compare normalization outputs (B-score vs LOESS vs robust Z) and select the method minimizing false positives on spiked controls. See independent comparisons in the literature for observed variance between methods.

Hit calling: thresholds, replicates, and FDR control

After robust normalization, hits are identified by standardized residual thresholds, replicate concordance and orthogonal confirmation. For standardized residuals (B-score normalized), a typical primary threshold T = ±3 (MAD units) is used; choose k (3–5) based on pilot error rates. However, statistical multiple testing and experimental replication matter — apply Benjamini–Hochberg FDR control where p-values are computed, and always confirm hits in independent replicates and orthogonal assays.

Recommended replicate workflow

1. Primary single-concentration run → retain top X% (e.g., 1–2%).
2. Retest retained set in duplicates/triplicates at the same concentration.
3. Progress replicated hits to 8–12 point dose–response (4PL/5PL fits).
4. Perform orthogonal counterscreens (different detection, label-free) to exclude artifacts.

Dose–response modelling: 4PL and 5PL implementations

Estimating potency requires reliable curve-fitting. Use nonlinear regression to fit the four-parameter logistic (4PL) or five-parameter logistic (5PL) when asymmetry is present.

4PL (four-parameter logistic) equation

Y = Bottom + (Top - Bottom) / (1 + 10^((LogIC50 - X) * HillSlope))

where X is log10(concentration), Top/Bottom are asymptotes, HillSlope defines steepness and LogIC50 is log10(IC₅₀). Fit by weighted nonlinear least squares when variance is heteroscedastic. Report 95% confidence intervals for IC₅₀ and Hill slope. Use R (drc), Python (lmfit/scipy), or GraphPad Prism for production fitting.

Plate artifacts, edge effects and mitigation strategies

Common artifacts include evaporation-driven edge effects, dispensing bias, and temperature gradients. Diagnostics include per-plate heatmaps, spatial autocorrelation metrics (e.g., Moran's I) and temporal drift analysis. Mitigation: humidity control, plate seals, randomized compound placement, multiple distributed controls and robust spatial normalization (B-score or LOESS).

• Detection interference: autofluorescent or quenching compounds — use orthogonal readouts.
• Aggregators: include detergent in counterscreens (e.g., 0.01% Triton X-100) to identify colloidal aggregators.

Library curation: PAINS, reactive groups and aggregators

Apply automated substructure filters (PAINS) and additional cheminformatics rules to flag reactive groups (Michael acceptors, isothiocyanates), metals and likely aggregators. Baell & Holloway PAINS filters are a starting point — combine automated filtering with manual expert curation to avoid discarding novel chemotypes. Implement aggregator detection assays (detergent counterscreens) and redox cycling checks where appropriate.

1. Automated PAINS filtering (flag, do not automatically discard without review).
2. Flag molecules with reactive warheads for chemist review.
3. Use cheminformatics descriptors (cLogP, aromaticity) to predict aggregation propensity.
4. Confirm in orthogonal, label-free assays before advancing.

Reproducible HTS pipeline & QC checklist

Standardized pipelines and provenance tracking are essential. A recommended experimental pipeline:

1. Assay definition and selection of primary readout (prefer homogeneous assays for throughput).
2. Pilot plates (8–24 plates) to determine Z′, SW, CV and spatial bias.
3. Normalization method selection and validation on pilot data.
4. Primary screen (single-concentration) with distributed controls.
5. Retest & dose–response for hits; orthogonal counterscreens to exclude artifacts.
6. Deliverables: raw plate files (with timestamps), normalized matrices, hit lists with curve fits (IC₅₀ ± 95% CI), PAINS/ADME flags and prioritization rationale.

Implementation: software stack, provenance & reproducibility

Recommended components:

• LIMS and plate mapping — barcode-driven tracking of plates, reagents and batches.
• Instrument orchestration — scheduling and device integration (liquid handlers, stackers, readers) with job recovery routines.
• Data warehouse — raw plate files, normalized matrices, curve fits, and audit logs stored with checksums for provenance.
• Analytics — containerized R/Python notebooks implementing B-score, LOESS, 4PL/5PL fits (drc, lmfit), automated QC dashboards and report generation.
• Reproducibility controls — store pilot data, normalization parameters, random seeds and transformation logs; versioned analytics containers (Docker) and notebooks (Git).

ChemDiv emphasizes reproducible pipelines: every HTS engagement includes a reproducibility package with pilot data, normalization scripts and stepwise processing logs.

References & further reading

1. Zhang JH, Chung TDY, Oldenburg KR. A Simple Statistical Parameter for Use in Evaluation and Validation of High Throughput Screening Assays. J Biomol Screen. 1999. (Z′ factor)
2. Brideau C, et al. Improved statistical methods for hit selection in high-throughput screening. J Biomol Screen. 2003. (B-score / median polish)
3. Baell JB, Holloway GA. New substructure filters for removal of pan assay interference compounds (PAINS). J Med Chem. 2010.
4. Mpindi JP, et al. Impact of normalization methods on high-throughput screening. BMC Genomics / PMC. 2015.
5. Macarron R, et al. Impact of high-throughput screening in biomedical research. Nat Rev Drug Discov. 2011.

For implementation examples and reproducible code, contact ChemDiv or request our technical appendix that includes R and Python scripts for B-score and 4PL fitting.