title: Subgroup detection in genotype data using invariant coordinate selection.
abstract: BACKGROUND
  The current gold standard in dimension reduction methods for high-throughput genotype data is the Principle Component Analysis (PCA). The presence of PCA is so dominant, that other methods usually cannot be found in the analyst's toolbox and hence are only rarely applied.
  
  
  RESULTS
  We present a modern dimension reduction method called 'Invariant Coordinate Selection' (ICS) and its application to high-throughput genotype data. The more commonly known Independent Component Analysis (ICA) is in this framework just a special case of ICS. We use ICS on both, a simulated and a real dataset to demonstrate first some deficiencies of PCA and how ICS is capable to recover the correct subgroups within the simulated data. Second, we apply the ICS method on a chicken dataset and also detect there two subgroups. These subgroups are then further investigated with respect to their genotype to provide further evidence of the biological relevance of the detected subgroup division. Further, we compare the performance of ICS also to five other popular dimension reduction methods.
  
  
  CONCLUSIONS
  The ICS method was able to detect subgroups in data where the PCA fails to detect anything. Hence, we promote the application of ICS to high-throughput genotype data in addition to the established PCA. Especially in statistical programming environments like e.g. R, its application does not add any computational burden to the analysis pipeline.
authors.affiliation: Natural Resources Institute Finland (LUKE), Myllytie 1, Jokioinen, Finland. daniel.fischer@luke.fi.
authors.forename: Daniel
authors.identifier: http://orcid.org/0000-0002-7513-683X
authors.initials: D
authors.lastname: Fischer
authors.affiliation: Natural Resources Institute Finland (LUKE), Myllytie 1, Jokioinen, Finland.
authors.forename: Mervi
authors.initials: M
authors.lastname: Honkatukia
authors.affiliation: Natural Resources Institute Finland (LUKE), Myllytie 1, Jokioinen, Finland.
authors.forename: Maria
authors.initials: M
authors.lastname: Tuiskula-Haavisto
authors.affiliation: Department of Mathematics and Statistics, University of Turku, Turku, Finland.|University of Tampere, School of Health Sciences, Medisiinarinkatu 3, Tampere, 33014, Finland.
authors.forename: Klaus
authors.initials: K
authors.lastname: Nordhausen
authors.affiliation: Lohmann Tierzucht GmbH, Am Seedeich 9-11, Cuxhaven, 27454, Germany.
authors.forename: David
authors.initials: D
authors.lastname: Cavero
authors.affiliation: Lohmann Tierzucht GmbH, Am Seedeich 9-11, Cuxhaven, 27454, Germany.
authors.forename: Rudolf
authors.initials: R
authors.lastname: Preisinger
authors.affiliation: Natural Resources Institute Finland (LUKE), Myllytie 1, Jokioinen, Finland.
authors.forename: Johanna
authors.initials: J
authors.lastname: Vilkki
mesh_terms: D000465:Algorithms; D000818:Animals; D002645:Chickens / Q000235:genetics; D016000:Cluster Analysis; D005838:Genotype; D025341:Principal Component Analysis
keywords: Classification; Dimension reduction; Genotype data; ICS; PCA