Single Nucleotide Polymorphism Clustering in Systemic Autoimmune Diseases

Charlon, Thomas; Martínez-Bueno, Manuel; Bossini-Castillo, Lara; Carmona, F. David; Di Cara, Alessandro; Wojcik, Jérôme; Voloshynovskyy, Svyatoslav; Martín, Javier; Alarcón-Riquelme, Marta E.

doi:10.1371/journal.pone.0160270

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Title		Single Nucleotide Polymorphism Clustering in Systemic Autoimmune Diseases
Authors		Charlon, Thomas Martínez-Bueno, Manuel Bossini-Castillo, Lara Carmona, F. David Di Cara, Alessandro Wojcik, Jérôme Voloshynovskyy, Svyatoslav Martín, Javier Alarcón-Riquelme, Marta E. show all authors [1 - 9]
Published in		PloS one. 2016, vol. 11, no. 8, e0160270
Abstract		Systemic Autoimmune Diseases, a group of chronic inflammatory conditions, have variable symptoms and difficult diagnosis. In order to reclassify them based on genetic markers rather than clinical criteria, we performed clustering of Single Nucleotide Polymorphisms. However naive approaches tend to group patients primarily by their geographic origin. To reduce this “ancestry signal”, we developed SNPClust, a method to select large sources of ancestry-independent genetic variations from all variations detected by Principal Component Analysis. Applied to a Systemic Lupus Erythematosus case control dataset, SNPClust successfully reduced the ancestry signal. Results were compared with association studies between the cases and controls without or with reference population stratification correction methods. SNPClust amplified the disease discriminating signal and the ratio of significant associations outside the HLA locus was greater compared to population stratification correction methods. SNPClust will enable the use of ancestry-independent genetic information in the reclassification of Systemic Autoimmune Diseases. SNPClust is available as an R package and demonstrated on the public Human Genome Diversity Project dataset at https://github.com/ThomasChln/snpclust.
Identifiers		DOI: 10.1371/journal.pone.0160270
Full text		Article (Published version) (1.2 MB) - Free access Other version: http://dx.plos.org/10.1371/journal.pone.0160270
Structures		Faculté des sciences / Département d'informatique Centres et instituts / Centre universitaire d'informatique
Research groups		Computer Vision and Multimedia Laboratory Stochastic Information Processing Group
Citation (ISO format)		CHARLON, Thomas et al. Single Nucleotide Polymorphism Clustering in Systemic Autoimmune Diseases. In: PLOS ONE, 2016, vol. 11, n° 8, p. e0160270. doi: 10.1371/journal.pone.0160270 https://archive-ouverte.unige.ch/unige:119707