title: RAD-ADAPT: Software for modelling clonogenic assay data in radiation biology.
abstract: We present a comprehensive software program, RAD-ADAPT, for the quantitative analysis of clonogenic assays in radiation biology. Two commonly used models for clonogenic assay analysis, the linear-quadratic model and single-hit multi-target model, are included in the software. RAD-ADAPT uses maximum likelihood estimation method to obtain parameter estimates with the assumption that cell colony count data follow a Poisson distribution. The program has an intuitive interface, generates model prediction plots, tabulates model parameter estimates, and allows automatic statistical comparison of parameters between different groups. The RAD-ADAPT interface is written using the statistical software R and the underlying computations are accomplished by the ADAPT software system for pharmacokinetic/pharmacodynamic systems analysis. The use of RAD-ADAPT is demonstrated using an example that examines the impact of pharmacologic ATM and ATR kinase inhibition on human lung cancer cell line A549 after ionizing radiation.
authors.affiliation: Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, 90089, USA.
authors.forename: Yaping
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Departments of Radiation Oncology and Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA; School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China.
authors.forename: Kaiqiang
authors.initials: K
authors.lastname: Hu
authors.affiliation: Cancer Therapeutics Program, University of Pittsburgh Cancer Institute, Pittsburgh, PA, 15213, USA; Department of Pharmaceutical Sciences, University of Pittsburgh School of Pharmacy, Pittsburgh, PA, 15213, USA; Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA.
authors.forename: Jan H
authors.initials: JH
authors.lastname: Beumer
authors.affiliation: Departments of Radiation Oncology and Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA.
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Bakkenist
authors.affiliation: Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, 90089, USA. Electronic address: dargenio@usc.edu.
authors.forename: David Z
authors.initials: DZ
authors.lastname: D'Argenio
mesh_terms: D000072283:A549 Cells; D064007:Ataxia Telangiectasia Mutated Proteins / Q000037:antagonists & inhibitors; D002470:Cell Survival; D003114:Colony-Forming Units Assay / Q000379:methods* / Q000706:statistics & numerical data; D006801:Humans; D016013:Likelihood Functions; D008954:Models, Biological; D009369:Neoplasms / Q000188:drug therapy / Q000532:radiotherapy; D011839:Radiation, Ionizing; D011853:Radiobiology; D012984:Software
chemical_list: C576324:ATM protein, human; D064007:Ataxia Telangiectasia Mutated Proteins
keywords: Clonogenic assays; Clonogenic survival curves; Linear quadratic model; Radiation biology; Single-hit multi-target model