reGenotyper: Detecting mislabeled samples in genetic data

Zych, Konrad; Snoek, Basten L.; Elvin, Mark; Rodriguez, Miriam; Velde, K.J. Van Der; Arends, Danny; Westra, Harm-Jan; Swertz, Morris A.; Poulin, Gino; Kammenga, Jan E.; Breitling, Rainer; Jansen, Ritsert C.; Li, Yang; Rutherford, Suzannah


In high-throughput molecular profiling studies, genotype labels can be wrongly assigned at various experimental steps; the resulting mislabeled samples seriously reduce the power to detect the genetic basis of phenotypic variation. We have developed an approach to detect potential mislabeling, recover the ideal genotype and identify best-matched labels for mislabeled samples. On average, we identified 4% of samples as mislabeled in eight published datasets, highlighting the necessity of applying a data cleaning step before standard data analysis.