RESEARCH ARTICLE


A Grid Algorithm for High Throughput Fitting of Dose-Response Curve Data



Yuhong Wang*, Ajit Jadhav, Noel Southal, Ruili Huang, Dac-Trung Nguyen
National Institutes of Health, NIH Chemical Genomics Center, 9800 Medical Center Drive, Rockville, MD 20850, USA


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© Wang et al.; Licensee Bentham Open.

open-access license: This is an open access article licensed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/) which permits unrestricted, non-commercial use, distribution and reproduction in any medium, provided the work is properly cited.

* Address correspondence to this author at the National Institutes of Health, NIH Chemical Genomics Center, 9800 Medical Center Drive, Rockville, MD 20850, USA; Tel: 215-358-0186; Fax: 301-217-5728; E-mail: wangyuh@mail.nih.gov


Abstract

We describe a novel algorithm, Grid algorithm, and the corresponding computer program for high throughput fitting of dose-response curves that are described by the four-parameter symmetric logistic dose-response model. The Grid algorithm searches through all points in a grid of four dimensions (parameters) and finds the optimum one that corresponds to the best fit. Using simulated dose-response curves, we examined the Grid program’s performance in reproducing the actual values that were used to generate the simulated data and compared it with the DRC package for the language and environment R and the XLfit add-in for Microsoft Excel. The Grid program was robust and consistently recovered the actual values for both complete and partial curves with or without noise. Both DRC and XLfit performed well on data without noise, but they were sensitive to and their performance degraded rapidly with increasing noise. The Grid program is automated and scalable to millions of dose-response curves, and it is able to process 100,000 dose-response curves from high throughput screening experiment per CPU hour. The Grid program has the potential of greatly increasing the productivity of large-scale dose-response data analysis and early drug discovery processes, and it is also applicable to many other curve fitting problems in chemical, biological, and medical sciences.

Keywords: Curve fitting, Hill equation, Grid algorithm, Dose-response curve, High throughput screening..