title: reGenotyper: Detecting mislabeled samples in genetic data.
abstract: 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.
authors.affiliation: Groningen Bioinformatics Centre, University of Groningen, Groningen, The Netherlands.
authors.forename: Konrad
authors.identifier: http://orcid.org/0000-0001-7426-0516
authors.initials: K
authors.lastname: Zych
authors.affiliation: Laboratory of Nematology, Wageningen University, Wageningen, The Netherlands.
authors.forename: Basten L
authors.initials: BL
authors.lastname: Snoek
authors.affiliation: Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom.
authors.forename: Mark
authors.initials: M
authors.lastname: Elvin
authors.affiliation: Laboratory of Nematology, Wageningen University, Wageningen, The Netherlands.
authors.forename: Miriam
authors.initials: M
authors.lastname: Rodriguez
authors.affiliation: Genomics Coordination Center, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
authors.forename: K Joeri
authors.identifier: http://orcid.org/0000-0002-0934-8375
authors.initials: KJ
authors.lastname: Van der Velde
authors.affiliation: Groningen Bioinformatics Centre, University of Groningen, Groningen, The Netherlands.
authors.forename: Danny
authors.initials: D
authors.lastname: Arends
authors.affiliation: Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America.|Partners Center for Personalized Genetic Medicine, Boston, Massachusetts, United States of America.|Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America.
authors.forename: Harm-Jan
authors.identifier: http://orcid.org/0000-0001-7038-567X
authors.initials: HJ
authors.lastname: Westra
authors.affiliation: Genomics Coordination Center, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
authors.forename: Morris A
authors.initials: MA
authors.lastname: Swertz
authors.affiliation: Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom.
authors.forename: Gino
authors.identifier: http://orcid.org/0000-0003-1016-348X
authors.initials: G
authors.lastname: Poulin
authors.affiliation: Laboratory of Nematology, Wageningen University, Wageningen, The Netherlands.
authors.forename: Jan E
authors.initials: JE
authors.lastname: Kammenga
authors.affiliation: Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom.
authors.forename: Rainer
authors.identifier: http://orcid.org/0000-0001-7173-0922
authors.initials: R
authors.lastname: Breitling
authors.affiliation: Groningen Bioinformatics Centre, University of Groningen, Groningen, The Netherlands.
authors.forename: Ritsert C
authors.identifier: http://orcid.org/0000-0003-2977-9110
authors.initials: RC
authors.lastname: Jansen
authors.affiliation: Groningen Bioinformatics Centre, University of Groningen, Groningen, The Netherlands.|University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands.
authors.forename: Yang
authors.initials: Y
authors.lastname: Li
mesh_terms: D000465:Algorithms; D000818:Animals; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D020869:Gene Expression Profiling / Q000379:methods*; D023281:Genomics / Q000379:methods; D005838:Genotype; D006801:Humans; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci / Q000235:genetics*; D015203:Reproducibility of Results