BiasCorrector: Fast and accurate correction of all types of experimental biases in quantitative DNA methylation data derived by different technologies

Kapsner L, Zavgorodnij MG, Majorova SP, Hotz-Wagenblatt A, Kolychev OV, Lebedev IN, Hoheisel JD, Hartmann A, Bauer A, Mate S, Prokosch HU, Haller F, Moskalev E (2021)

Publication Type: Journal article

Publication year: 2021

Journal

DOI: 10.1002/ijc.33681

Abstract

Quantification of DNA methylation in neoplastic cells is crucial both from mechanistic and diagnostic perspectives. However, such measurements are prone to different experimental biases. Polymerase chain reaction (PCR) bias results in an unequal recovery of methylated and unmethylated alleles at the sample preparation step. Post-PCR biases get introduced additionally by the readout processes. Correcting the biases is more practicable than optimising experimental conditions, as demonstrated previously. However, utilisation of our earlier developed algorithm strongly necessitates automation. Here, we present two R packages: rBiasCorrection, the core algorithms to correct biases; and BiasCorrector, its web-based graphical user interface frontend. The software detects and analyses experimental biases in calibration DNA samples at a single base resolution by using cubic polynomial and hyperbolic regression. The correction coefficients from the best regression type are employed to compensate for the bias. Three common technologies—bisulphite pyrosequencing, next-generation sequencing and oligonucleotide microarrays—were used to comprehensively test BiasCorrector. We demonstrate the accuracy of BiasCorrector's performance and reveal technology-specific PCR- and post-PCR biases. BiasCorrector effectively eliminates biases regardless of their nature, locus, the number of interrogated methylation sites and the detection method, thus representing a user-friendly tool for producing accurate epigenetic results.

Authors with CRIS profile

Involved external institutions

Deutsches Krebsforschungszentrum (DKFZ) Germany (DE) Zhukovsky – Gagarin Air Force Academy Russian Federation (RU) Voronezh State Technical University (VSTU) / Воронежский государственный технический университет (ВГТУ) Russian Federation (RU) Voronezh State University / Воронежский государственный университет Russian Federation (RU) Tomsk National Research Medical Center of the Russian Academy of Sciences Russian Federation (RU)

How to cite

APA:

Kapsner, L., Zavgorodnij, M.G., Majorova, S.P., Hotz-Wagenblatt, A., Kolychev, O.V., Lebedev, I.N.,... Moskalev, E. (2021). BiasCorrector: Fast and accurate correction of all types of experimental biases in quantitative DNA methylation data derived by different technologies. International Journal of Cancer. https://doi.org/10.1002/ijc.33681

MLA:

Kapsner, Lorenz, et al. "BiasCorrector: Fast and accurate correction of all types of experimental biases in quantitative DNA methylation data derived by different technologies." International Journal of Cancer (2021).

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