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Single Nucleotide Polymorphism Clustering in Systemic Autoimmune Diseases

Martínez-Bueno, Manuel
Bossini-Castillo, Lara
Carmona, F. David
Wojcik, Jérôme
Martín, Javier
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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.
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Research groups Computer Vision and Multimedia Laboratory
Stochastic Information Processing Group
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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

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Deposited on : 2019-06-19

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