CFAssay: statistical analysis of the colony formation assay

Abstract

BackgroundColony formation assay is the gold standard to determine cell reproductive death after treatment with ionizing radiation, applied for different cell lines or in combination with other treatment modalities. Associated linear-quadratic cell survival curves can be calculated with different methods. For easy code exchange and methodological standardisation among collaborating laboratories a software package CFAssay for R (R Core Team, R: A Language and Environment for Statistical Computing, 2014) was established to perform thorough statistical analysis of linear-quadratic cell survival curves after treatment with ionizing radiation and of two-way designs of experiments with chemical treatments only.MethodsCFAssay offers maximum likelihood and related methods by default and the least squares or weighted least squares method can be optionally chosen. A test for comparision of cell survival curves and an ANOVA test for experimental two-way designs are provided.ResultsFor the two presented examples estimated parameters do not differ much between maximum-likelihood and least squares. However the dispersion parameter of the quasi-likelihood method is much more sensitive for statistical variation in the data than the multiple R2 coefficient of determination from the least squares method.ConclusionThe dispersion parameter for goodness of fit and different plot functions in CFAssay help to evaluate experimental data quality. As open source software interlaboratory code sharing between users is facilitated.AvailabilityThe package is available at http://www.bioconductor.org/packages/release/bioc/html/CFAssay.html.

Retracted Article: CircBANP acts as a sponge of let-7a to promote gastric cancer progression via the FZD5/Wnt/β-catenin pathway

“…A standard colony formation assay was carried out to assess cell survival based on the ability of single cells to grow into colonies, as described previously with modication. 17 In brief, transfected cells (500 per well) were seeded in the 6-well plates in growth media. 14 days later, colonies were stained with 0.1% crystal violet and colonies containing more than 50 cells were counted.…”

High mobility group box transcription factor 1 (HBP1) from Lampetra japonica affects cell cycle regulation

“…The systemic or granulosa-specific, but not oocyte-specific, ablation of HBP1 promotes follicle growth and oocyte production and is associated with reduced apoptotic signals in mouse granulosa cells (Dong et al, 2016). Moreover, in the hbp1- to grow into colonies, which is the gold standard for determining cell reproductive death after drug treatment (Braselmann, Michna, Heß, & Unger, 2015). In this study, L-HBP1 overexpression in Raji cells inhibited colony formation, indicating that L-HBP1 could affect cell cluster formation.…”

“…The results showed that the overexpression of L‐HBP1 inhibited cell proliferation and decreased cell counts of Raji cells. In vitro colony formation assays are based on the ability of single cells to grow into colonies, which is the gold standard for determining cell reproductive death after drug treatment (Braselmann, Michna, Heß, & Unger, ). In this study, L‐HBP1 overexpression in Raji cells inhibited colony formation, indicating that L‐HBP1 could affect cell cluster formation.…”

Epicatechin as a promising agent to countermeasure radiation exposure by mitigating mitochondrial damage in human fibroblasts and mouse hematopoietic cells

“…All experiments were repeated $3 times using independent samples. For colony assay, statistical analysis was performed using the CFAssay for R package (R Foundation for Statistical Computing, Vienna, Austria) (30). A 1-way ANOVA, followed by the Dunnett's test was used to detect significant differences between the means of $3 independent groups.…”